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  • Articles  (183)
  • Computational Chemistry and Molecular Modeling  (134)
  • Binding Sites  (49)
  • 1995-1999
  • 1990-1994  (183)
  • 1950-1954
  • 1915-1919
  • 1990  (183)
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  • Articles  (183)
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  • 1995-1999
  • 1990-1994  (183)
  • 1950-1954
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  • 101
    Electronic Resource
    Electronic Resource
    Evaluation of a finite multipole expansion technique for the computation of electrostatic potentials of dibenzo-p-dioxins and related systems (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 112-120 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The electrostatic potential V(r) that the nuclei and electrons of a molecule create in the surrounding space is well established as a guide in the study of molecular reactivity, and particularly, of biological recognition processes. Its rigorous computation is, however, very demanding of computer time for large molecules, such as those of interest in recognition interactions. We have accordingly investigated the use of an approximate finite multicenter multipole expansion technique to determine its applicability for producing reliable electrostatic potentials of dibenzo-p-dioxins and related molecules, with significantly reduced amounts of computer time, at distances of interest in recognition studies. A comparative analysis of the potentials of three dibenzo-p-dioxins and a substituted naphthalene molecule computed using both the multipole expansion technique and Gaussian 82 at the STO-5G level has been carried out. Overall we find that regions of negative and positive V(r) at 1.75 Å above the molecular plane are very well reproduced by the multipole expansion technique, with up to a 20-fold improvement in computer time.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110114
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  • 102
    Electronic Resource
    Electronic Resource
    Ab initio study of substituent effect on the addition of hydrogen fluoride to fluoroethylenes (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 170-180 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An ab initio 3-21G study of the direct addition of HF to C2HnF(4-n), with n = 0 to 4, has been performed to investigate the effect of the substituent on the reaction. Geometry optimization of all charge-transfer complexes and transition states has been done. Standard analysis of activation energies of addition reactions, vibrational and thermodynamical analysis, as well as Morokuma energy decomposition, BSSE correction, PMO analysis, and Pauling bond orders were used to explain the results. A subset of the reactions, including that of C2H4 as reference one and the two most favorable cases, was also studied at the MP2/6-31G(d,p)//HF/6-31G(d,p) level. The barriers so obtained are in agreement with the indirectly found from experimental data. It was found that the effect of the substituent is not monotonic for the additions. Decomposition of the interaction energy is shown to be adequate to explain this nonmonotonic behavior. The implications for laser chemistry of the addition of hydrogen halides to fluorosubstituted olefins is briefly discussed.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110203
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  • 103
    Electronic Resource
    Electronic Resource
    Numerical solution of a partial differential equation system describing chemical kinetics and diffusion in a cell with the aid of compartmentalization (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 194-204 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: To build a kinetic model of a cell with diffusion one has to solve a coupled nonlinear partial differential equation system consisting of several hundred equations. (Several hundred chemical components undergoing several hundred reactions.) To solve this formidable mathematical problem the division of the model cell into compartments (most biochemical reactions take place in a certain part of the cell) was suggested.1 Solving the differential equation system in one compartment, the results can be used as input at other compartments until mutually consistent solutions are achieved.To test this suggestion 10 coupled chemical reactions with diffusion were investigated in a model that contains three compartments. The results in the case of pure diffusion are in excellent agreement with and without compartmentalization. After this the full problem was treated by compartmentalization using for the solution of the differential equation system a discretization of the concentrations as functions of space and time and the Newton-Raphson iterative procedure. The results obtained give reasonable space and time dependence for the concentrations of all 10 components.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110205
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  • 104
    Electronic Resource
    Electronic Resource
    Relaxed potential energy surfaces of N-linked oligosaccharides: The mannose-α(1 → 3)-mannose case (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 205-216 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We report calculations of potential energy surfaces where all the internal coordinates of the disaccharide Man-α(1 → 3)-Man-α-O-Me were relaxed and minimized through an extensive molecular mechanics scheme. Flexibility within the mannopyranose rings plays a crucial role. Introduction of the relaxed principle into the conformational description of the disaccharide does not greatly alter the overall shape of the low-energy domains but it reveals new local minima. However, its principle effect is the lowering of energy barriers in the potential energy surface. New conformational transitions about the glycosidic bonds appear, permiting pathways among the low energy sections. This occurs with only little variation of the classical 4C1 conformation of the mannopyranose residues. All the conformations observed in the solid state, along with those already predicted through the joint use of NMR and modeling techniques, fall into the populations of stable conformers calculated in the present work. Moreover, a satisfactory agreement is reached between previously observed NOE values, and the theoretical one, calculated from the averaging of more than 500 microstates. The present results reconciliate most of the apparently conflicting data previously reported; they provide strong support for the application of the concept of conformational averaging to solution behavior. Some limitations of the proposed methodology are also discussed.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110206
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  • 105
    Electronic Resource
    Electronic Resource
    Distance geometry and molecular conformation, by G. M. Crippen and T. F. Havel, Research Studies Press, Taunton, England, John Wiley and Sons, New York, 1988. pp. 541 + x pp. Price: $142.00 (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 265-266 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110212
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  • 106
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    Announcement (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 268-268 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110214
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  • 107
    Electronic Resource
    Electronic Resource
    Derivation of net atomic charges from molecular electrostatic potentials (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 297-310 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The dependence of net atomic charges, as derived from least-squares fitting to electrostatic potentials, on molecular orientation and potential site location is critically examined. A unique rotationally invariant algorithm, in which the charges may be constrained to reproduce the molecular dipole moment, is presented and the results for several basis sets compared to previous work. Significant improvements in dipole moments derived from the unconstrained charges are noted.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110304
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  • 108
    Electronic Resource
    Electronic Resource
    Theoretical study of the proton affinities of 2-, 3-, and 4-monosubstituted phenolate ions in the gas phase by means of MINDO/3, MNDO, and AM1 (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 269-290 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Proton affinities (PAs) of 2-, 3-, and 4-monosubstituted phenolates in the gas phase are calculated using the MINDO/3, MNDO, and AM1 methods. The following substituents are considered: H, F, Cl (only MNDO and AM1), CN, CH3, OH, NO2, OCH3, COOH, and NH2. The results are compared with experimental values (high-pressure mass spectroscopy) at 600 K. The MINDO/3 method overestimates the experimental PAs with a mean percentual error of ca. 4.3%. The MNDO results agree much better with the experimental values and are only ca. 1.3% too high. However, the best agreement is observed for the AM1 method, where the mean percentual error is only ca. 0.69% (in absolute value). The greatest disagreement is found for 2-hydroxyphenolate (ca. +2.0%) and 2-carboxyphenolate (ca. +2.7%). The PA of 2-nitrophenolate is underestimated by ca. 1.6%. Correlations between the calculated proton affinities on the one hand, charge densities on the acid H atom of the phenols, charges on the O atom in the phenolate ions, and substituent parameters on the other hand are studied. Particularly good linear relationships are found for the 3- and 4-monosubstituted compounds within the AM1 formlism. For the 2-substituted phenolates, only the AM1 method is satifactory. As a general conclusion, the AM1 method appears to be distinctly superior to MNDO for the calculation of PAs, and definitely superior to MINDO/3.
    Additional Material: 12 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110302
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  • 109
    Electronic Resource
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    Extended basis sets for the transition metals yttrium through cadmium (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 518-523 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Extended Slater basis sets were developed for the transition metals yttrium through cadmium. Gaussian expansions of these basis sets are extremely useful for ab initio methods which employ six Cartesian Gaussians for the description of the d orbitals. The s-type function generated from the symmetric combination of the x2, y2, and z2 Cartesian Gaussians is used to describe the 4s region, thereby reducing the overall number of functions for molecular calculations and reducing the redundancy in the basis set.
    Additional Material: 3 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110410
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  • 110
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    Reply to “Comments on a comparison of AM1 with the recently developed PM3 method” (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 543-544 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Additional Material: 1 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110414
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  • 111
    Electronic Resource
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    H/He Molecules in strong electric fields (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 548-559 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Floating spherical Gaussian orbitals are used within a split-shell description to calculate the properties of H, He, He+, H2, H+2, HeH+, and H+3 in a strong uniform electric field. Accurate polarizabilities including their field strength dependence are obtained with two basis functions at most. Critical field strengths for ionization and deprotonation are determined for different orientations of molecules. Electron tunneling is described within the time dependent approach using floating Gaussian orbitals also.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110503
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  • 112
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    A vibrational molecular force field of model compounds with biological interest. I. Harmonic dynamics of crystalline urea at 123 K (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 560-568 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Normal coordinate calculations have been performed for urea and deuterated urea in the crystalline state. We have used the modified Urey-Bradley-Shimanouchi intramolecular potential energy function and a rather sophisticated intermolecular energy function to reproduce I.R. and Raman frequencies with an average error of 2 cm-1. The general agreement between the calculation and experiment suggests that intermolecular interactions must be taken into account to determine reliable intramolecular parameters of the potential energy function, mainly the barrier to internal rotation around the C—N bond. The intermolecular energy function, which consists of the Buckingham function and an explicit harmonic function for hydrogen-bonding, then has the merit to reproduce quite well the observed frequencies of lattice vibrations.
    Additional Material: 11 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110504
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  • 113
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    Overestimation of the coupling component in the CP technique. Application of the indirect counterpoise correction to the H2O—HF hydrogen-bonded system (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 576-588 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An extension of the Indirect Counterpoise (ICP) method, proposed in previous work, has been applied to the H2O—HF hydrogen-bonded system. The new version, which introduces important numerical changes is called EICP (Extended Indirect Counterpoise method). In their framework, the nonnegligible overestimation of the Counterpoise correction (CP) of Boys and Bernardi in the coupling component (MIX) of the interaction energy, computed via the Kitaura and Morokuma method is studied. Several basis sets, BS, were used to describe the oxygen, fluorine and hydrogen atoms that constitute the complex. The EICP results leads to more coherent values with the uncorrected energy than with the CP correction, which seems to be significantly affected by the size and type of the basis set used (especially for minimal basis sets).
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110507
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  • 114
    Electronic Resource
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    On proper dissociation configurations of a molecule (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 629-635 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An analytical procedure is presented for the determination of the proper dissociation configurations of a molecule. We illustrate this procedure by determining the proper dissociation configurations of many electronic states of the first-row diatomic molecules and ozone. Finally, a few simple guidelines are provided to help in the identification of the important configurations needed for proper dissociation of a molecule.
    Additional Material: 2 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110511
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  • 115
    Electronic Resource
    Electronic Resource
    AM1 molecular orbital studies of the structures, conformations, protonation energies, and electronic properties of triazine dihydrofolate reductase inhibitors (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 644-653 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The structural, conformational, and electronic properties of three triazine antifolates were determined by AM1 molecular orbital calculations, and the results were compared with other theoretical studies and with X-ray crystallographic studies of these and similar triazines both in the crystalline state and as complexes bound to dihydrofolate reductase. Calculated protonation energies confirm crystal structure data indicating N-protonation analogous to that reported for MTX in similar environments. Overall, the calculated structural and conformational properties are in good agreement with X-ray crystallographic results for these and similar triazines as found in the crystalline state and in enzymebound ternary complexes. However, for one triazine AM1 predicts a conformation with the bulky aromatic substituent twisted about 60° away from coplanarity with the triazine ring, in contrast to the nearly coplanar conformation found in the crystalline state. Intermolecular interactions favoring the coplanar conformation may thus be operative in the crystalline environment. The unique conformational preferences and greater conformation flexibility of triazines in general and of this triazine in particular may provide a key to understanding their biological activity.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110513
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  • 116
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    A new method for the calculation of atomic and local hardness (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 694-699 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The relationships between atomic hardness, atomic electronegativity, and electronic energy are considered and emphasized. A new method for calculating atomic hardness is described. The concept of local hardness is quantified through the calculation of a new variable named alfahardness. Atomic hardness and alfahardness are used for the calculation of both the mean molecular and local properties. The results obtained are discussed and a comparison made with the analogous quantities presented by Pearson. An algorithm has been realized and transformed into a computer routine for use within a CAOS program.
    Additional Material: 5 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110604
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  • 117
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    Masthead (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990) 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110701
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  • 118
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    Adaptation of D2h ab initio computer code to higher-symmetry point groups (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 636-643 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The imposition of symmetry in electronic structure calculations can be plagued by artifactual symmetry-breaking in orbital or configuration amplitudes. While most ab initio computer code is well-developed to impose symmetry constraints in D2h and its subgroups, the problem is not nearly as tractable in higher-symmetry point groups. This article describes the successful modification of existing D2h ab initio computer code to handle symmetry constraints in higher-symmetry point groups. Prospects for the development of ab initio computer code that runs fully under any point group are also discussed.
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    URL: http://dx.doi.org/10.1002/jcc.540110512
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  • 119
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    Free energy calculation of a soft sphere solid using an adaptive, importance sampling Monte Carlo algorithm (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 511-517 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Using an adaptive, importance sampling Monte Carlo algorithm, the free energy and equation of state of a soft sphere solid are calculated. The Monte Carlo integration technique to be described is unlike standard methods in that it can evaluate directly the partition function and consequently the free energy of a solid. The results for a soft sphere solid are compared with data obtained from a thermodynamic integration method due to Hoover et al.7 The equation of state obtained from Monte Carlo integration is in agreement with Hoover's method while the free energy calculations compare favorably only at densities greater than that of the freezing transition.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110409
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  • 120
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    Masthead (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990) 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110501
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  • 121
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    Molecular modeling studies of novel heteroarotinoids (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 531-540 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The molecular structure and conformational properties of structurally related oxo and thio heteroarotinoids have been calculated by employing AM1 molecular orbital and both MM2P and Chem-X “optimize” molecular mechanics methods, and the results have been compared with crystal structure data. For the cis and trans oxo heteroarotinoids, MM2P gives values of the bridge torsion angles φ1 and φ2 in closest agreement with the crystal structure, and all three computational methods yield values of φ1 and φ2 within about 10° of that found in the crystal structures. All three computational methods locate a minimum-energy conformation for the trans isomer corresponding to the two bridged aryl rings being mutually perpendicular, in agreement with the crystal structure and similar to that found for the structurally analogous trans-stilbene. The calculated heteroring geometries also reproduce the twist-sofa conformation observed for the crystal structure. Calculated conformational energies versus φ1 and φ2 indicate broad energy wells about the minimum-energy conformation with barriers to rotation at the planar and perpendicular conformations, and with higher barriers found for the more sterically congested cis isomer. The corresponding cis and trans thio heteroarotinoids exhibit conformational properties similar to their oxo analogues. Both AM1 and MM2P fare poorly in reproducing the crystal structure values of the sulfur-containing bond lengths and bond angles. The C-S bonds found in these thio heteroarotinoids may possess more double-bond character than accounted for in the calculations. Also, the results suggest that the MM2P sulfur-related force-field parameters adopted for these calculations may require further refinement.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110412
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  • 122
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    Mechanistic aspects of biological redox reactions involving NADH 2: A combined semiempirical and ab initio study of hydride-ion transfer between the NADH analogue, 1-methyl-dihydronicotinamide, and folate and dihydrofolate analogue substrates of dihydrofolate reductase (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 791-804 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: As part of a study of factors controlling biological redox reactions of nicotinamide cofactors [nicotinamide adenine dinucleotide (phosphate) NAD(P)H], we have investigated the effect on a model reaction of the conformational state (cis or trans) of the carboxamide side chain, using quantum chemical methods. The reaction is that for the enzyme dihydrofolate reductase between the NADPH analogue, 1-methyl-dihydronicotinamide, and the protonated forms of the folate and dihydrofolate substrate analogues, pyrazine and dihydropyrazine. Some calculations on pterin and dihydropterin substrate analogues were also carried out in order to gauge the effects of inter-ring coupling. The influence of carboxamide side-chain conformation of nicotinamide on the energetics of the hydride-ion transfer, and on the structures of the transition states and stable intermolecular-interaction complexes, are examined as a function of the orientation of approach of the reactants. These approach geometries include those corresponding to the observed binding of cofactor and either substrate or inhibitor in the enzyme active site. Reactant, product, reactants-complex, and transition-state geometries were optimized at the semiempirical AM1 level, while ab initio SCF/STO-3G and SCF/3-21G single-point calculations were carried out at the AM1 optimized geometries for all species, as well as full geometry optimizations for isolated reactants and products. The results show that reactants-complex and transition-state energies are lower for the trans conformer of dihydronicotinamide than for the cis conformer, due to more favorable H-bonding or electrostatic interactions with the protonated substrate. Also, consideration of the structural parameters, including reaction coordinate bond lengths, ring geometries, and charge distributions, indicate that the trans transition states are more product-like than those for the cis. For the (trans) approaches corresponding to the enzymic orientation for substrate, the intermolecular interaction for the folate reaction lacks the stabilizing influence of the formal H-bond which is present for the dihydrofolate reaction, and consequently the reactants-complex and transition state are less stable.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110703
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    MM2 study of 20-hydroxy-4,7,13,16-tetraoxa-1,10-diazabicyclo [8,8,3] heneicosane and its formation controlled by hydrogen bonding (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 837-847 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A van der Waals-type parameter set has been developed for hydrogen bonding in the MM2(85) force field to reproduce the structures and binding energies of complexes (H2O)2, (CH3OH)2, H3N … H2O, H3N … HOCH3, (CH3)3N … H2O, and HCONH2 … H2O reported in the literature. The MM2(85) force field modified in this way was then applied to the title compound to explain its unexpected stability, unusual properties of its hydroxyl group, and solvent effect on the reaction mechanism in the condensation of Kryptofix 22 ® with epichlorohydrine.
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    URL: http://dx.doi.org/10.1002/jcc.540110707
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    The theoretical reaction path for the cation radical vinylcyclobutane rearrangement: A concerted SR path (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 896-898 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio reaction path calculations for the cation radical vinylcyclobutane rearrangement at the MP2/ 6-31G*//3-21G level reveal a concerted, sr reaction path with an activation energy of 9.4 kcal/mol. The vinylcyclobutane cation radical itself, at both the MP2 and MP3 levels of theory has predominant olefin cation radical character but with modest stretching of one of the adjacent ring carbon - carbon bonds.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110710
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    On the use of AM1 and MNDO wave functions to compute accurate electrostatic charges (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 909-923 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new strategy to evaluate accurate electrostatic charges from semiempirical wave functions is reported. The rigorous quantum mechanical molecular electrostatic potentials computed from both MNDO and AM1 wave functions are fitted to the point-charge molecular electrostatic potential to obtain the electrostatic charges. The reliability of this strategy is tested by comparing the semiempirical electrostatic charges for 21 molecules with the semiempirical Mulliken charges and with the ab initio STO-3G and 6-31G* electrostatic charges. The ability of the dipoles derived from the semiempirical electrostatic and Mulliken charges as well as from the SCF charge distributions to reproduce the ab initio 6-31G* electrostatic dipoles and the gas phase experimental values is determined. The statistical analysis clearly point out the goodness of the semiempirical electrostatic charges, specially when the MNDO method is used. The excellent relationships found between the MNDO and 6-31G* electrostatic charges permit to define a scaling factor which allows to accurately reproduce the 6-31G* electrostatic charge distribution as well as the experimental dipoles from the semiempirical electrostatic charges.
    Additional Material: 5 Ill.
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    Different approaches to conformational analysis: A comparison of completeness, efficiency, and reliability based on the study of a nine-membered lactam (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1021-1028 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Different methods such as molecular dynamics, systematic, or stochastic search and a special “generic shape” algorithm have been employed in the conformational analysis of a nine-membered lactam. Furthermore, crystal data were used to generate conformations of the compound under consideration. The various methods are compared in terms of their efficiency and completeness in the search for conformations with an energy content of up to 60 kJ/mol above the global minimum. Additionally, the generated conformations have been optimized by different techniques, molecular mechanics and quantum chemical calculations, to compare the number of existing local minima and their relative energies and geometries.
    Additional Material: 8 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540110904
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    An ab initio method for approximation of the frozen molecular fragment (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1072-1075 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An ab initio method for calculation on many-electron molecular systems with the approximation of the inactive part of a molecule by frozen molecular fragment is presented. In the following method the SCF calculations are performed in two series. First the molecular orbitals resulting from the first SCF calculation (modest basis set) are localized. In the second SCF run, the basis set is extended for the active part of the molecule, while molecular orbitals of the inactive part, selected from the localized set, are kept frozen. The results are in good agreement with the extended basis set calculation.
    Additional Material: 8 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540110909
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    Four-Index transformation on distributed-memory parallel computers (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1151-1159 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Because it has O(N5) operations, a low computation to data transfer ratio, and is a compact piece of code, the four-index transformation is a good test case for parallel algorithm development of electronic structure calculations. We present an algorithm primarily designed for distributed-memory machines. Unlike the previous algorithm of Whiteside et al., ours is not designed with a particular architecture in mind. It is a general algorithm in the sense that not only can it be used on some common architectures but it can utilize some of the advantages inherent in each. In addition, we present formulas predicting that there would be a twofold decrease in communication time if our algorithm was used instead of that of Whiteside et al., on a square array of processors and up to an N-fold decrease if the two algorithms were implemented on a hypercube.
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    URL: http://dx.doi.org/10.1002/jcc.540111006
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    Construction and molecular modeling of phospholipid surfaces (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1181-1186 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A protocol is given for the construction of phospholipid surfaces that possess variable head groups and thus variable net charge. Ab initio quantum mechanical calculations are performed to establish the necessary force field (AMBER) parameters. The charge distribution is defined by an electrostatic potential method consistent with the ab initio wave function. As a model calculation, a monolayer surface with head groups of phosphatidylserine and phosphatidylcholine derived from the crystal structure of 1,2-dilauroyl-DL-phosphatidylethanolamine (DLPE) is placed in a water bath with two Ca(II) ions present. The resultant surface is energy-optimized followed by 64 ps of molecular dynamics integration. Evaluation of calcium ion coordination environments, characterization of the P-N dipole inclination with respect ot the plane of the monolayer, and calculation of molecular surface area is performed and compared with experimental data.
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    Announcement (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1247-1247 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540111016
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    An improved empirical force field for saturated hydrocarbons (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1125-1138 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new molecular mechanics force field for alkanes is presented. The force field aims to eliminate some identified failures of the well-known MM2 force field. The new energy function gives an improved prediction of the rotational barriers of highly congested molecules, a better calculation of short nonbonded contacts, and the correct reproduction of bond elongation in small torsion angles. The calculation of sublimation enthalpies is also improved. The standard deviation of the formation enthalpies for a set of 54 compounds is 0.63 kcal/mol; this compares with the reported value of 0.42 calculated with MM2 and MM3 for different sets. The force field parameters were obtained using a least squares method.
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    Theoretical studies on the intramolecular cyclization of alkyl halide anions (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1119-1124 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The intramolecular cyclization reactions of alkyl fluoride and chloride anions1 were investigated theoretically using the AM1 method. Formation of five-membered ring was the most reactive and that of three-membered ring was the least reactive process in both series. For the fluoride series the reactivity order of n = 5 〉 6 〉 7 〉 4 〉 3 was dictated by the enthalpy (ΔH≠) effect while for the chloride series the entropy (ΔS≠) effect was found to play somewhat greater role due to the much better leaving ability of the chloride anion leading to the reactivity order of n = 5 〉 6 〉 4 〉 7 〉 3. For both series, BEP principle held and the degree of bond formation was greater with the fluoride series owing to the poor electron acceptor ability of the cleaving bond.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540111002
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    The bond order - bond length relationship (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1160-1163 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The difference in length between two bond orders was reported by Pauling to be essentially the same, regardless of the atoms that make up the bond. To a first approximation these differences hold not only for bond orders 1, 2 and 3 but also for six membered aromatic rings containing all carbon, carbon-nitrogen, nitrogen-nitrogen, carbon-phosphorous, carbon-arsenic, and carbon-antimony bonds. An equation was developed (based upon these differences) that relates bond order and bond length. The output of this equation was compared with those of Gordy and Pauling. Our equation as well as the Gordy equation (with revised constants) return a bond length of 1.4 Å for bond order 1.67 which is consistent with theory. (This bond order was not used in developing either the equation or the revised Gordy constants.)
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    An algorithm for the simultaneous superposition of a structural series (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1187-1192 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A procedure is delineated for finding the optimal superposition of a series of chemical structures. Quaternions are used to represent the absolute orientation of the structures-rotations of the structures need never be carried out explicitly. The Rational Function Optimization method is used to minimize a simultaneous superposition residual similar to the one given by Gerber and Müller. The robustness of the method is illustrated by comparing a series of conformations of a polyene carotenoid.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540111011
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    Evidence of changes in protease sensitivity and subunit exchange rate on DNA binding by C/EBP (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-08-17
    Description: The transcription factor C/EBP uses a bipartite structural motif to bind DNA. Two protein chains dimerize through a set of amphipathic alpha helices termed the leucine zipper. Highly basic polypeptide regions emerge from the zipper to form a linked set of DNA contact surfaces. In the recently proposed a "scissors grip" model, the paired set of basic regions begin DNA contact at a central point and track in opposite directions along the major groove, forming a molecular clamp around DNA. This model predicts that C/EBP must undertake significant changes in protein conformation as it binds and releases DNA. The basic region of ligand-free C/EBP is highly sensitive to protease digestion. Pronounced resistance to proteolysis occurred when C/EBP associated with its specific DNA substrate. Sequencing of discrete proteolytic fragments showed that prominent sites for proteolysis occur at two junction points predicted by the "scissors grip" model. One junction corresponds to the cleft where the basic regions emerge from the leucine zipper. The other corresponds to a localized nonhelical segment that has been hypothesized to contain an N-cap and facilitate the sharp angulation necessary for the basic region to track continuously in the major groove of DNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shuman, J D -- Vinson, C R -- McKnight, S L -- New York, N.Y. -- Science. 1990 Aug 17;249(4970):771-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Research Laboratories, Department of Embryology, Baltimore, MD 21210.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2202050" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; CCAAT-Enhancer-Binding Proteins ; Chromatography, High Pressure Liquid ; DNA/*metabolism ; DNA-Binding Proteins/metabolism ; Kinetics ; Leucine ; Macromolecular Substances ; Models, Molecular ; Molecular Sequence Data ; Nuclear Proteins/*metabolism ; Peptide Fragments/metabolism ; Peptide Hydrolases/*metabolism ; Protein Conformation ; Transcription Factors/*metabolism ; Trypsin/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Site-specific cleavage of a yeast chromosome by oligonucleotide-directed triple-helix formation (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-07-06
    Description: Oligonucleotides equipped with EDTA-Fe can bind specifically to duplex DNA by triple-helix formation and produce double-strand cleavage at binding sites greater than 12 base pairs in size. To demonstrate that oligonucleotide-directed triple-helix formation is a viable chemical approach for the site-specific cleavage of large genomic DNA, an oligonucleotide with EDTA-Fe at the 5' and 3' ends was targeted to a 20-base pair sequence in the 340-kilobase pair chromosome III of Saccharomyces cerevisiae. Double-strand cleavage products of the correct size and location were observed, indicating that the oligonucleotide bound and cleaved the target site among almost 14 megabase pairs of DNA. Because oligonucleotide-directed triple-helix formation has the potential to be a general solution for DNA recognition, this result has implications for physical mapping of chromosomes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Strobel, S A -- Dervan, P B -- GM 42966/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1990 Jul 6;249(4964):73-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Arnold and Mabel Beckman Laboratories of Chemical Synthesis, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2195655" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Chromosomes, Fungal/*metabolism ; DNA, Fungal/*genetics/metabolism ; Densitometry ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Nucleic Acid Conformation ; Nucleic Acid Hybridization ; Oligonucleotides/*genetics/metabolism ; Saccharomyces cerevisiae/*genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    No specific recognition of leader peptide by SecB, a chaperone involved in protein export (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-05-18
    Description: Most proteins destined for export from Escherichia coli are made as precursors containing amino-terminal leader sequences that are essential for export and that are removed during the process. The initial step in export of a subset of proteins, which includes maltose-binding protein, is binding of the precursor by the molecular chaperone SecB. This work shows directly that SecB binds with high affinity to unfolded maltose-binding protein but does not specifically recognize and bind the leader. Rather, the leader modulates folding to expose elements in the remainder of the polypeptide that are recognized by SecB.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Randall, L L -- Topping, T B -- Hardy, S J -- GM 29798/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1990 May 18;248(4957):860-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biochemistry/Biophysics Program, Washington State University, Pullman 99164-4660.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2188362" target="_blank"〉PubMed〈/a〉
    Keywords: *ATP-Binding Cassette Transporters ; Bacterial Proteins/*metabolism ; Binding Sites ; Biological Transport ; Carrier Proteins/*metabolism ; Cytosol/metabolism ; Escherichia coli/*metabolism ; *Escherichia coli Proteins ; Maltose-Binding Proteins ; Molecular Weight ; *Monosaccharide Transport Proteins ; Protein Conformation ; Protein Precursors/*metabolism ; Protein Sorting Signals/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    GT-1 binding site confers light responsive expression in transgenic tobacco (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-04-27
    Description: Light-dependent expression of rbcS, the gene encoding the small subunit of ribulose-1,5-bisphosphate carboxylase, which is the key enzyme involved in carbon fixation in higher plants, is regulated at the transcriptional level. Sequence analysis of the gene has uncovered a conserved GT motif in the -150 to -100 region of many rbcS promoters. This motif serves as the binding site of a nuclear factor, designated GT-1. Analysis of site-specific mutants of pea rbcS-3A promoter demonstrated that GT-1 binding in vitro is correlated with light-responsive expression of the rbcS promoter in transgenic plants. However, it is not known whether factors other than GT-1 might also be required for activation of transcription by light. A synthetic tetramer of box II (TGTGTGGTTAATATG), the GT-1 binding site located between -152 to -138 of the rbcS-3A promoter, inserted upstream of a truncated cauliflower mosaic virus 35S promoter is sufficient to confer expression in leaves of transgenic tobacco. This expression occurs principally in chloroplast-containing cells, is induced by light, and is correlated with the ability of box II to bind GT-1 in vitro. The data show that the binding site for GT-1 is likely to be a part of the molecular light switch for rbcS activation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lam, E -- Chua, N H -- New York, N.Y. -- Science. 1990 Apr 27;248(4954):471-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY 10021.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2330508" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Chloramphenicol O-Acetyltransferase/genetics ; Cloning, Molecular ; DNA-Binding Proteins/*metabolism ; Gene Expression Regulation/*physiology ; Genetic Vectors ; *Light ; Molecular Sequence Data ; Mutation ; Nuclear Proteins/*metabolism ; Plant Proteins/*metabolism ; *Plants, Toxic ; Promoter Regions, Genetic/genetics ; Ribulose-Bisphosphate Carboxylase/*genetics ; Tobacco/enzymology/*genetics ; Transcription, Genetic/radiation effects ; Transformation, Genetic
    Print ISSN: 0036-8075
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    A potent GAL4 derivative activates transcription at a distance in vitro (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-02-09
    Description: Transcription of a typical eukaryotic gene by RNA polymerase II is activated by proteins bound to sites found near the beginning of the gene as well as to sites, called enhancers, located a great distance from the gene. According to one view, the primary difference between an activator that can work at a large distance and one that cannot is that the former bears a particularly strong activating region; the stronger the activating region, the more readily the activator interacts with its target bound near the transcriptional start site, with the intervening DNA looping out to accommodate the reaction. One alternative view is that the effect of proteins bound to enhancers might require some special aspect of cellular or chromosome structure. Consistent with the first view, an activator bearing an unusually potent activating region can stimulate transcription of a mammalian gene in a HeLa nuclear extract when bound as far as 1.3 kilobase pairs upstream or 320 base pairs downstream of the transcriptional start site.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carey, M -- Leatherwood, J -- Ptashne, M -- New York, N.Y. -- Science. 1990 Feb 9;247(4943):710-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, MA 02138.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2405489" target="_blank"〉PubMed〈/a〉
    Keywords: Activating Transcription Factors ; Binding Sites ; Blood Proteins/pharmacology ; Cloning, Molecular ; DNA/metabolism ; DNA-Binding Proteins ; Fungal Proteins/metabolism/*pharmacology ; HeLa Cells ; Phosphoproteins/pharmacology ; Promoter Regions, Genetic ; RNA Polymerase II/metabolism ; Recombinant Fusion Proteins/pharmacology ; *Saccharomyces cerevisiae Proteins ; Templates, Genetic ; Trans-Activators/pharmacology ; Transcription Factors/pharmacology ; Transcription, Genetic/*drug effects
    Print ISSN: 0036-8075
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    Autophosphorylation of protein kinase C at three separated regions of its primary sequence (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-07-27
    Description: The major autophosphorylation sites of the rat beta II isozyme of protein kinase C were identified. The modified threonine and serine residues were found in the amino-terminal peptide, the carboxyl-terminal tail, and the hinge region between the regulatory lipid-binding domain and the catalytic kinase domain. Because this autophosphorylation follows an intrapeptide mechanism, extraordinary flexibility of the protein is necessary to phosphorylate the three regions. Comparison of the sequences surrounding the modified residues showed no obvious recognition motif nor any similarity to substrate phosphorylation sites, suggesting that proximity to the active site may be the primary criterion for their phosphorylation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Flint, A J -- Paladini, R D -- Koshland, D E Jr -- DK09765/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1990 Jul 27;249(4967):408-11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Biology, University of California, Berkeley 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2377895" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Brain/enzymology ; Cloning, Molecular ; Isoenzymes/genetics/*metabolism ; Molecular Sequence Data ; Peptide Fragments/isolation & purification/metabolism ; Phosphorylation ; Protein Conformation ; Protein Kinase C/genetics/*metabolism ; Rats ; Recombinant Proteins/metabolism ; Signal Transduction ; Trypsin
    Print ISSN: 0036-8075
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    The energetic basis of specificity in the Eco RI endonuclease--DNA interaction (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-11-09
    Description: High sequence selectivity in DNA-protein interactions was analyzed by measuring discrimination by Eco RI endonuclease between the recognition site GAATTC and systematically altered DNA sites. Base analogue substitutions that preserve the sequence-dependent conformational motif of the GAATTC site permit deletion of single sites of protein-base contact at a cost of +1 to +2 kcal/mol. However, the introduction of any one incorrect natural base pair costs +6 to +13 kcal/mol in transition state interaction energy, the resultant of the following interdependent factors: deletion of one or two hydrogen bonds between the protein and a purine base; unfavourable steric apposition between a group on the protein and an incorrectly placed functional group on a base; disruption of a pyrimidine contact with the protein; loss of some crucial interactions between protein and DNA phosphates; and an increased energetic cost of attaining the required DNA conformation in the transition state complex. Eco RI endonuclease thus achieves stringent discrimination by both "direct readout" (protein-base contracts) and "indirect readout" (protein-phosphate contacts and DNA conformation) of the DNA sequence.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lesser, D R -- Kurpiewski, M R -- Jen-Jacobson, L -- GM-29207/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1990 Nov 9;250(4982):776-86.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, University of Pittsburgh, PA 15260.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2237428" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Binding Sites ; DNA/chemistry/genetics/*metabolism ; Deoxyribonuclease EcoRI/chemistry/*metabolism ; Energy Transfer ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phosphates/metabolism ; Substrate Specificity
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  • 142
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    Design of DNA-binding peptides based on the leucine zipper motif (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-08-17
    Description: A class of transcriptional regulator proteins bind to DNA at dyad-symmetric sites through a motif consisting of (i) a "leucine zipper" sequence that associates into noncovalent, parallel, alpha-helical dimers and (ii) a covalently connected basic region necessary for binding DNA. The basic regions are predicted to be disordered in the absence of DNA and to form alpha helices when bound to DNA. These helices bind in the major groove forming multiple hydrogen-bonded and van der Waals contacts with the nucleotide bases. To test this model, two peptides were designed that were identical to natural leucine zipper proteins only at positions hypothesized to be critical for dimerization and DNA recognition. The peptides form dimers that bind specifically to DNA with their basic regions in alpha-helical conformations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉O'Neil, K T -- Hoess, R H -- DeGrado, W F -- New York, N.Y. -- Science. 1990 Aug 17;249(4970):774-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Central Research and Development Department, E.I. du Pont de Nemours & Co., Wilmington, DE 19880-0328.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2389143" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Binding Sites ; Chemistry, Physical ; Circular Dichroism ; Computer Simulation ; DNA/*metabolism ; DNA-Binding Proteins/*metabolism ; Hydrogen Bonding ; *Leucine ; Macromolecular Substances ; Models, Molecular ; Molecular Sequence Data ; Physicochemical Phenomena ; Protein Conformation
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  • 143
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    DNA looping and unlooping by AraC protein (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-10-26
    Description: Expression of the L-arabinose BAD operon in Escherichia coli is regulated by AraC protein which acts both positively in the presence of arabinose to induce transcription and negatively in the absence of arabinose to repress transcription. The repression of the araBAD promoter is mediated by DNA looping between AraC protein bound at two sites near the promoter separated by 210 base pairs, araI and araO2. In vivo and in vitro experiments presented here show that an AraC dimer, with binding to half of araI and to araO2, maintains the repressed state of the operon. The addition of arabinose, which induces the operon, breaks the loop, and shifts the interactions from the distal araO2 site to the previously unoccupied half of the araI site. The conversion between the two states does not require additional binding of AraC protein and appears to be driven largely by properties of the protein rather than being specified by the slightly different DNA sequences of the binding sites. Slight reorientation of the subunits of AraC could specify looping or unlooping by the protein. Such a mechanism could account for regulation of DNA looping in other systems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lobell, R B -- Schleif, R F -- GM18277/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1990 Oct 26;250(4980):528-32.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate Department of Biochemistry, Brandeis University, Waltham, MA 02254.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2237403" target="_blank"〉PubMed〈/a〉
    Keywords: AraC Transcription Factor ; Arabinose/genetics/pharmacology ; *Bacterial Proteins ; Binding Sites ; *DNA, Bacterial/genetics/metabolism ; DNA, Superhelical/metabolism ; Escherichia coli/*genetics ; Escherichia coli Proteins ; Fucose/pharmacology ; Gene Expression Regulation, Bacterial/*drug effects ; Guanine/metabolism ; Macromolecular Substances ; Methylation ; Mutation ; Nucleic Acid Conformation/*drug effects ; Operon ; Protein Conformation/drug effects ; Repressor Proteins/metabolism/*pharmacology ; *Transcription Factors
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  • 144
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    An insertion in the human thyrotropin receptor critical for high affinity hormone binding (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-09-21
    Description: Thyrotropin (TSH), luteinizing hormone (LH), and chorionic gonadotropin (CG) are structurally related glycoprotein hormones, which bind to receptors that share a high degree of sequence similarity. However, comparison of the primary amino acid sequences of the TSH and LH-CG receptors reveals two unique insertions of 8 and 50 amino acids in the extracellular domain of the TSH receptor. The functional significance of these insertions were determined by site-directed mutagenesis. Deletion of the 50-amino acid tract (residues 317 to 366) had no effect on TSH binding or on TSH and thyroid-stimulating immunoglobulin (TSI) biological activities. In contrast, either deletion or substitution of the eight-amino acid region (residues 38 to 45) abolished these activities. This eight-amino acid tract near the amino terminus of the TSH receptor appears to be an important site of interaction for both TSH and TSI.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wadsworth, H L -- Chazenbalk, G D -- Nagayama, Y -- Russo, D -- Rapoport, B -- DK-19289/DK/NIDDK NIH HHS/ -- DK-36182/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1990 Sep 21;249(4975):1423-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine, Veterans Administration Medical Center, San Francisco, CA 94121.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2169649" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; Cell Line ; Chromosome Deletion ; Clone Cells ; Cyclic AMP/metabolism ; Humans ; Molecular Sequence Data ; Mutation ; Oligonucleotide Probes ; Receptors, Thyrotropin/*genetics/metabolism ; Thyrotropin/*metabolism/pharmacology ; Transfection
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  • 145
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    Involvement of the silencer and UAS binding protein RAP1 in regulation of telomere length (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-10-26
    Description: The yeast protein RAP1, initially described as a transcriptional regulator, binds in vitro to sequences found in a number of seemingly unrelated genomic loci. These include the silencers at the transcriptionally repressed mating-type genes, the promoters of many genes important for cell growth, and the poly[(cytosine)1-3 adenine] [poly(C1-3A)] repeats of telomeres. Because RAP1 binds in vitro to the poly(C1-3A) repeats of telomeres, it has been suggested that RAP1 may be involved in telomere function in vivo. In order to test this hypothesis, the telomere tract lengths of yeast strains that contained conditionally lethal (ts) rap1 mutations were analyzed. Several rap1ts alleles reduced telomere length in a temperature-dependent manner. In addition, plasmids that contain small, synthetic telomeres with intact or mutant RAP1 binding sites were tested for their ability to function as substrates for poly(C1-3A) addition in vivo. Mutations in the RAP1 binding sites reduced the efficiency of the addition reaction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lustig, A J -- Kurtz, S -- Shore, D -- GM 40094/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1990 Oct 26;250(4980):549-53.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Memorial Sloan-Kettering Cancer Center, New York, NY 10021.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2237406" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Chromosomes, Fungal/metabolism/*ultrastructure ; DNA-Binding Proteins/metabolism ; Fungal Proteins/genetics/*metabolism ; *Genes, Fungal ; *Genes, Mating Type, Fungal ; Molecular Sequence Data ; Mutation ; Plasmids ; Poly A/metabolism ; Poly C/metabolism ; Repetitive Sequences, Nucleic Acid ; Saccharomyces cerevisiae/*genetics ; Temperature ; *Transcription Factors ; Transformation, Genetic
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  • 146
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    Three-dimensional structure of cellobiohydrolase II from Trichoderma reesei (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-07-27
    Description: The enzymatic degradation of cellulose is an important process, both ecologically and commercially. The three-dimensional structure of a cellulase, the enzymatic core of CBHII from the fungus Trichoderma reesei reveals an alpha-beta protein with a fold similar to but different from the widely occurring barrel topology first observed in triose phosphate isomerase. The active site of CBHII is located at the carboxyl-terminal end of a parallel beta barrel, in an enclosed tunnel through which the cellulose threads. Two aspartic acid residues, located in the center of the tunnel are the probable catalytic residues.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rouvinen, J -- Bergfors, T -- Teeri, T -- Knowles, J K -- Jones, T A -- New York, N.Y. -- Science. 1990 Jul 27;249(4967):380-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, BMC, Uppsala, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2377893" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Cellulose/metabolism ; Cellulose 1,4-beta-Cellobiosidase ; Chemistry, Physical ; Crystallization ; Crystallography ; *Glycoside Hydrolases/metabolism ; Glycosylation ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Mitosporic Fungi/*enzymology ; Molecular Sequence Data ; Molecular Structure ; Physicochemical Phenomena ; Protein Conformation ; Trichoderma/*enzymology
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  • 147
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    Regulation of an enzyme by phosphorylation at the active site (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-08-31
    Description: The isocitrate dehydrogenase of Escherichia coli is an example of a ubiquitous class of enzymes that are regulated by covalent modification. In the three-dimensional structure of the enzyme-substrate complex, isocitrate forms a hydrogen bond with Ser113, the site of regulatory phosphorylation. The structures of Asp113 and Glu113 mutants, which mimic the inactivation of the enzyme by phosphorylation, show minimal conformational changes from wild type, as in the phosphorylated enzyme. Calculations based on observed structures suggest that the change in electrostatic potential when a negative charge is introduced either by phosporylation or site-directed mutagenesis is sufficient to inactivate the enzyme. Thus, direct interaction at a ligand binding site is an alternative mechanism to induced conformational changes from an allosteric site in the regulation of protein activity by phosphorylation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hurley, J H -- Dean, A M -- Sohl, J L -- Koshland, D E Jr -- Stroud, R M -- GM 24485/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1990 Aug 31;249(4972):1012-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2204109" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Escherichia coli/*enzymology/genetics ; Homeostasis ; Isocitrate Dehydrogenase/genetics/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Phosphorylation ; Protein Conformation
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  • 148
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    Conserved residues make similar contacts in two repressor-operator complexes (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-03-09
    Description: Comparison of a lambda repressor-operator complex and a 434 repressor-operator complex reveals that three conserved residues in the helix-turn-helix (HTH) region make similar contacts in each of the crystallographically determined structures. These conserved residues and their interactions with phosphodiester oxygens help establish a frame of reference within which other HTH residues make contacts that are critical for site-specific recognition. Such "positioning contacts" may be important conserved features within families of HTH proteins. In contrast, the structural comparisons appear to rule out any simple "recognition code" at the level of detailed side chain-base pair interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pabo, C O -- Aggarwal, A K -- Jordan, S R -- Beamer, L J -- Obeysekare, U R -- Harrison, S C -- GM 29109/GM/NIGMS NIH HHS/ -- GM 31471/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1990 Mar 9;247(4947):1210-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2315694" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Asparagine ; Base Composition ; Base Sequence ; Binding Sites ; *DNA-Binding Proteins ; Glutamine ; Hydrogen Bonding ; Molecular Sequence Data ; Molecular Structure ; *Operator Regions, Genetic ; Protein Conformation ; Repressor Proteins/*metabolism ; Transcription Factors/*metabolism ; Viral Proteins ; Viral Regulatory and Accessory Proteins
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  • 149
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    Molecular cloning and expression of a complementary DNA for inositol 1,4,5-trisphosphate 3-kinase (1990)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1990-04-06
    Description: A complementary DNA (cDNA) clone that encodes inositol 1,4,5-trisphosphate 3-kinase was isolated from a rat brain cDNA expression library with the use of monoclonal antibodies. This clone had an open reading frame that would direct the synthesis of a protein consisting of 449 amino acids and with a molecular mass of 49,853 daltons. The putative protein revealed a potential calmodulin-binding site and six regions with amino acid compositions (PEST regions) common to proteins that are susceptible to calpain. Expression of the cDNA in COS cells resulted in an approximately 150-fold increase in inositol 1,4,5-trisphosphate 3-kinase activity of these cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Choi, K Y -- Kim, H K -- Lee, S Y -- Moon, K H -- Sim, S S -- Kim, J W -- Chung, H K -- Rhee, S G -- New York, N.Y. -- Science. 1990 Apr 6;248(4951):64-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2157285" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Brain/enzymology ; Calcium/metabolism ; Calmodulin/metabolism ; Calpain/antagonists & inhibitors/pharmacology ; Cell Line ; *Cloning, Molecular ; Codon ; DNA/*genetics ; *Gene Expression ; Molecular Sequence Data ; Molecular Weight ; Phosphotransferases/*genetics/metabolism ; *Phosphotransferases (Alcohol Group Acceptor) ; Plasmids ; Rats ; Transfection
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    The structure of a complex of recombinant hirudin and human alpha-thrombin (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-07-20
    Description: The crystallographic structure of a recombinant hirudin-thrombin complex has been solved at 2.3 angstrom (A) resolution. Hirudin consists of an NH2-terminal globular domain and a long (39 A) COOH-terminal extended domain. Residues Ile1 to Tyr3 of hirudin form a parallel beta-strand with Ser214 to Glu217 of thrombin with the nitrogen atom of Ile1 making a hydrogen bond with Ser195 O gamma atom of the catalytic site, but the specificity pocket of thrombin is not involved in the interaction. The COOH-terminal segment makes numerous electrostatic interactions with an anion-binding exosite of thrombin, whereas the last five residues are in a helical loop that forms many hydrophobic contacts. In all, 27 of the 65 residues of hirudin have contacts less than 4.0 A with thrombin (10 ion pairs and 23 hydrogen bonds). Such abundant interactions may account for the high affinity and specificity of hirudin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rydel, T J -- Ravichandran, K G -- Tulinsky, A -- Bode, W -- Huber, R -- Roitsch, C -- Fenton, J W 2nd -- HL13160/HL/NHLBI NIH HHS/ -- HL43229/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1990 Jul 20;249(4966):277-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Michigan State University, East Lansing 48824.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2374926" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Hirudins/*metabolism ; Humans ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Conformation ; Recombinant Proteins/metabolism ; Thrombin/*metabolism ; X-Ray Diffraction
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    A new redox cofactor in eukaryotic enzymes: 6-hydroxydopa at the active site of bovine serum amine oxidase (1990)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1990-05-25
    Description: An active site, cofactor-containing peptide has been obtained in high yield from bovine serum amine oxidase. Sequencing of this pentapeptide indicates: Leu-Asn-X-Asp-Tyr. Analysis of the peptide by mass spectrometry, ultraviolet-visible spectroscopy, and proton nuclear magnetic resonance leads to the identification of X as 6-hydroxydopa. This result indicates that, contrary to previous proposals, pyrroloquinoline quinone is not the active site cofactor in mammalian copper amine oxidases. Although 6-hydroxydopa has been implicated in neurotoxicity, the data presented suggest that this compound has a functional role at an enzyme active site.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Janes, S M -- Mu, D -- Wemmer, D -- Smith, A J -- Kaur, S -- Maltby, D -- Burlingame, A L -- Klinman, J P -- GM 39296/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1990 May 25;248(4958):981-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, Berkeley 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2111581" target="_blank"〉PubMed〈/a〉
    Keywords: *Amine Oxidase (Copper-Containing) ; Amino Acid Sequence ; Animals ; Binding Sites ; Cattle ; Copper ; Dihydroxyphenylalanine/*analogs & derivatives/metabolism ; Magnetic Resonance Spectroscopy ; Mass Spectrometry ; Molecular Sequence Data ; Oxidoreductases/metabolism ; Oxidoreductases Acting on CH-NH Group Donors/blood/*metabolism ; Peptide Fragments/analysis/chemical synthesis ; Quinones/metabolism ; Spectrophotometry, Ultraviolet
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  • 152
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    Zinc mediation of the binding of human growth hormone to the human prolactin receptor (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-12-21
    Description: Human growth hormone (hGH) elicits a diverse set of biological activities including lactation that derives from binding to the prolactin (PRL) receptor. The binding affinity of hGH for the extracellular binding domain of the hPRL receptor (hPRLbp) was increased about 8000-fold by addition of 50 micromolar ZnCl2. Zinc was not required for binding of hGH to the hGH binding protein (hGHbp) or for binding of hPRL to the hPRLbp. Other divalent metal ions (Ca2+, Mg2+, Cu2+, Mn2+, and Co2+) at physiological concentrations did not support such strong binding. Scatchard analysis indicated a stoichiometry of one Zn2+ per hGH.hPRLbp complex. Mutational analysis showed that a cluster of three residues (His18, His21, and Glu174) in hGH and His188 from the hPRLbp (conserved in all PRL receptors but not GH receptors) are probable Zn2+ ligands. This polypeptide hormone.receptor "zinc sandwich" provides a molecular mechanism to explain why nonprimate GHs are not lactogenic and offers a molecular link between zinc deficiency and its association with altered functions of hGH.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cunningham, B C -- Bass, S -- Fuh, G -- Wells, J A -- New York, N.Y. -- Science. 1990 Dec 21;250(4988):1709-12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Protein Engineering, Genentech, Inc., South San Francisco, CA 94080.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2270485" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Binding Sites ; Chlorides/*pharmacology ; Growth Hormone/*metabolism ; Humans ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Oligonucleotide Probes ; Plasmids ; Protein Conformation ; Receptors, Prolactin/drug effects/genetics/*metabolism ; Restriction Mapping ; Zinc/metabolism/*pharmacology ; *Zinc Compounds
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    Targeting the E1 replication protein to the papillomavirus origin of replication by complex formation with the E2 transactivator (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-12-21
    Description: The mechanism by which transcription factors stimulate DNA replication in eukaryotes is unknown. Bovine papillomavirus DNA synthesis requires the products of the viral E1 gene and the transcriptional activator protein encoded by the E2 gene. Experimental data showed that the 68-kilodalton (kD) E1 protein formed a complex with the 48-kD E2 transcription factor. This complex bound specifically to the viral origin of replication, which contains multiple binding sites for E2. Repressor proteins encoded by the E2 open reading frame failed to complex with E1 suggesting that the 162-amino acid region of E2 that participates in transactivation contained critical determinants for interaction with E1. The physical association between a replication protein and a transcription factor suggests that transcriptional activator proteins may function in targeting replication initiator proteins to their respective origins of replication.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mohr, I J -- Clark, R -- Sun, S -- Androphy, E J -- MacPherson, P -- Botchan, M R -- CA-30490/CA/NCI NIH HHS/ -- CA-42414/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1990 Dec 21;250(4988):1694-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkely 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2176744" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Bovine papillomavirus 1/*genetics ; Cell Line ; *DNA Replication ; DNA, Viral/biosynthesis/genetics ; DNA-Binding Proteins/*metabolism ; Genes, Viral ; Open Reading Frames ; Protein Binding ; Repressor Proteins/*metabolism ; Transcription Factors/*metabolism ; Viral Proteins/*metabolism
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  • 154
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    Sequence-specific DNA binding by a short peptide dimer (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-08-17
    Description: A recently described class of DNA binding proteins is characterized by the "bZIP" motif, which consists of a basic region that contacts DNA and an adjacent "leucine zipper" that mediates protein dimerization. A peptide model for the basic region of the yeast transcriptional activator GCN4 has been developed in which the leucine zipper has been replaced by a disulfide bond. The 34-residue peptide dimer, but not the reduced monomer, binds DNA with nanomolar affinity at 4 degrees C. DNA binding is sequence-specific as judged by deoxyribonuclease I footprinting. Circular dichroism spectroscopy suggests that the peptide adopts a helical structure when bound to DNA. These results demonstrate directly that the GCN4 basic region is sufficient for sequence-specific DNA binding and suggest that a major function of the GCN4 leucine zipper is simply to mediate protein dimerization. Our approach provides a strategy for the design of short sequence-specific DNA binding peptides.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Talanian, R V -- McKnight, C J -- Kim, P S -- GM13665/GM/NIGMS NIH HHS/ -- GM44162/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1990 Aug 17;249(4970):769-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Whitehead Institute for Biomedical Research, Nine Cambridge Center, MA 02142.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2389142" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Binding Sites ; Circular Dichroism ; DNA/*metabolism ; DNA-Binding Proteins/*metabolism ; Deoxyribonuclease I ; Disulfides ; Fungal Proteins/*metabolism ; Leucine ; Macromolecular Substances ; Molecular Sequence Data ; Peptides/*metabolism ; Protein Conformation ; *Protein Kinases ; *Saccharomyces cerevisiae Proteins ; Transcription Factors/*metabolism
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  • 155
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    The MerR metalloregulatory protein binds mercuric ion as a tricoordinate, metal-bridged dimer (1990)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1990-02-23
    Description: Bacterial MerR proteins are dimeric DNA-binding proteins that mediate the Hg(II)-dependent induction of mercury resistance operons. Site-directed mutagenesis of the Bacillus sp. RC607 MerR protein reveals that three of four Cys residues per monomer are required for Hg(II) binding at the single high-affinity binding site. Inactive mutant homodimers can exchange subunits to form heterodimers active for Hg(II) binding. Studies of a heterodimer retaining only three of eight cysteine residues per dimer reveal that Cys79 in one subunit and Cys114 and Cys123 in the second subunit are necessary and sufficient for high-affinity Hg(II) binding in an asymmetric, subunit bridging coordination complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Helmann, J D -- Ballard, B T -- Walsh, C T -- GM20011/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1990 Feb 23;247(4945):946-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2305262" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacillus/*analysis/genetics ; Bacterial Proteins/genetics/*metabolism ; Base Sequence ; Binding Sites ; Cations ; DNA-Binding Proteins/genetics/*metabolism ; Macromolecular Substances ; Mercury/*metabolism ; Molecular Sequence Data ; Mutation ; Structure-Activity Relationship
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  • 156
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    Dissociation of gp120 from HIV-1 virions induced by soluble CD4 (1990)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1990-11-23
    Description: The CD4 antigen is the high affinity cellular receptor for the human immunodeficiency virus type-1 (HIV-1). Binding of recombinant soluble CD4 (sCD4) or the purified V1 domain of sCD4 to the surface glycoprotein gp120 on virions resulted in rapid dissociation of gp120 from its complex with the transmembrane glycoprotein gp41. This may represent the initial stage in virus-cell and cell-cell fusion. Shedding of gp120 from virions induced by sCD4 may also contribute to the mechanism by which these soluble receptor molecules neutralize HIV-1.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moore, J P -- McKeating, J A -- Weiss, R A -- Sattentau, Q J -- New York, N.Y. -- Science. 1990 Nov 23;250(4984):1139-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Chester Beatty Laboratories, Institute of Cancer Research, London, United Kingdom.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2251501" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies, Monoclonal/pharmacology ; Antigens, CD4/immunology/*metabolism ; Binding Sites ; Binding, Competitive ; Cell Line ; Cricetinae ; HIV Envelope Protein gp120/*metabolism ; HIV Envelope Protein gp41/metabolism ; HIV-1/*metabolism ; Virion/*metabolism
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  • 157
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    NF's cancer connection (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-08-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roberts, L -- New York, N.Y. -- Science. 1990 Aug 17;249(4970):744.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2117777" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; GTPase-Activating Proteins ; Genes, ras ; Humans ; Neurofibromatosis 1/*genetics ; Proteins/genetics ; Sequence Homology, Nucleic Acid ; ras GTPase-Activating Proteins
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  • 158
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    Mechanism of insect resistance to the microbial insecticide Bacillus thuringiensis (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-01-05
    Description: Receptor binding studies show that resistance of a laboratory-selected Plodia interpunctella strain to a Bacillus thuringiensis insecticidal crystal protein (ICP) is correlated with a 50-fold reduction in affinity of the membrane receptor for this protein. The strain is sensitive to a second type of ICP that apparently recognizes a different receptor. Understanding the mechanism of resistance will provide strategies to prevent or delay resistance and hence prolong the usefulness of B. thuringiensis ICPs as environmentally safe insecticides.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Van Rie, J -- McGaughey, W H -- Johnson, D E -- Barnett, B D -- Van Mellaert, H -- New York, N.Y. -- Science. 1990 Jan 5;247(4938):72-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Plant Genetic Systems, Gent, Belgium.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2294593" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Bacillus thuringiensis ; *Bacterial Proteins/metabolism ; Bacterial Toxins/metabolism ; Binding Sites ; Cell Membrane/metabolism ; *Endotoxins ; Hemolysin Proteins ; Insecticide Resistance/*physiology ; *Lepidoptera ; Microvilli/metabolism ; *Moths ; *Pest Control, Biological ; Receptors, Drug/metabolism
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  • 159
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    Interfacial catalysis: the mechanism of phospholipase A2 (1990)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1990-12-14
    Description: A chemical description of the action of phospholipase A2 (PLA2) can now be inferred with confidence from three high-resolution x-ray crystal structures. The first is the structure of the PLA2 from the venom of the Chinese cobra (Naja naja atra) in a complex with a phosphonate transition-state analogue. This enzyme is typical of a large, well-studied homologous family of PLA2S. The second is a similar complex with the evolutionarily distant bee-venom PLA2. The third structure is the uninhibited PLA2 from Chinese cobra venom. Despite the different molecular architectures of the cobra and bee-venom PLA2s, the transition-state analogue interacts in a nearly identical way with the catalytic machinery of both enzymes. The disposition of the fatty-acid side chains suggests a common access route of the substrate from its position in the lipid aggregate to its productive interaction with the active site. Comparison of the cobra-venom complex with the uninhibited enzyme indicates that optimal binding and catalysis at the lipid-water interface is due to facilitated substrate diffusion from the interfacial binding surface to the catalytic site rather than an allosteric change in the enzyme's structure. However, a second bound calcium ion changes its position upon the binding of the transition-state analogue, suggesting a mechanism for augmenting the critical electrophile.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3443688/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3443688/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scott, D L -- White, S P -- Otwinowski, Z -- Yuan, W -- Gelb, M H -- Sigler, P B -- GM22324/GM/NIGMS NIH HHS/ -- HL36235/HL/NHLBI NIH HHS/ -- R01 HL036235/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1990 Dec 14;250(4987):1541-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2274785" target="_blank"〉PubMed〈/a〉
    Keywords: Bee Venoms/analysis ; Binding Sites ; Calcium/metabolism ; Catalysis ; Chemistry, Physical ; Cobra Venoms/analysis ; Models, Molecular ; Molecular Structure ; Organophosphonates/metabolism ; Phospholipases A/chemistry/*metabolism ; Phospholipases A2 ; Phospholipids/metabolism ; Physicochemical Phenomena ; Protein Conformation ; X-Ray Diffraction
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    Crystal structure of bee-venom phospholipase A2 in a complex with a transition-state analogue (1990)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1990-12-14
    Description: The 2.0 angstroms crystal structure of a complex containing bee-venom phospholipase A2 (PLA2) and a phosphonate transition-state analogue was solved by multiple isomorphous replacement. The electron-density map is sufficiently detailed to visualize the proximal sugars of the enzyme's N-linked carbohydrate and a single molecule of the transition-state analogue bound ot its active center. Although bee-venom PLA2 does not belong to the large homologous Class I/II family that encompasses most other well-studied PLA2s, there is segmental sequence similarity and conservation of many functional substructures. Comparison of the bee-venom enzyme with other phospholipase structures provides compelling evidence for a common catalytic mechanism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scott, D L -- Otwinowski, Z -- Gelb, M H -- Sigler, P B -- GM22324/GM/NIGMS NIH HHS/ -- HL36235/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1990 Dec 14;250(4987):1563-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2274788" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bee Venoms/*analysis ; Binding Sites ; Calcium/metabolism ; Carbohydrate Metabolism ; Catalysis ; Chemistry, Physical ; Crystallization ; Hydrogen Bonding ; Molecular Sequence Data ; Molecular Structure ; Phosphatidylethanolamines/*metabolism ; Phospholipases A/*chemistry/metabolism ; Phospholipases A2 ; Physicochemical Phenomena ; Protein Conformation
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    A T cell-specific transcriptional enhancer within the human T cell receptor delta locus (1990)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1990-03-09
    Description: The T cell antigen receptor (TCR) delta gene is located within the TCR alpha locus. A T cell-specific transcriptional enhancer, distinct from the TCR alpha enhancer, has been identified within the J delta 3-C delta intron of the human T cell receptor delta gene. This enhancer activates transcription from the V delta 1 and V delta 3 promoters as well as from heterologous promoters. Enhancer activity has been localized to a 250-bp region that contains multiple binding sites for nuclear proteins. Thus, transcriptional control of the TCR delta and TCR alpha genes is mediated by distinct regulatory elements.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Redondo, J M -- Hata, S -- Brocklehurst, C -- Krangel, M S -- R01-GM41052/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1990 Mar 9;247(4947):1225-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Tumor Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2156339" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Cell Line ; Chloramphenicol O-Acetyltransferase/genetics ; DNA Restriction Enzymes ; Deoxyribonuclease I ; Enhancer Elements, Genetic/*genetics ; Gene Rearrangement ; Gene Rearrangement, alpha-Chain T-Cell Antigen Receptor ; Humans ; Molecular Sequence Data ; Mutation ; Nuclear Proteins/metabolism ; Plasmids ; Promoter Regions, Genetic/genetics ; Receptors, Antigen, T-Cell/*genetics ; Repetitive Sequences, Nucleic Acid ; *Transcription, Genetic ; Transfection
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    Inhibition of factor VIIa-tissue factor coagulation activity by a hybrid protein (1990)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1990-06-25
    Description: Lipoprotein-associated coagulation inhibitor (LACI) appears to inhibit tissue factor (TF)-induced blood coagulation by forming a quaternary inhibitory complex containing factor Xa, LACI, factor VIIa, and TF. A genetically engineered hybrid protein consisting of the light chain of factor Xa and the first Kunitz-type inhibitor domain of LACI is shown to directly inhibit the activity of the factor VIIa-TF catalytic complex. Unlike inhibition of factor VIIa-TF activity by native LACI, inhibition by the hybrid protein is not dependent on factor Xa. In an assay of TF-induced coagulation, 50% TF inhibition occurs with hybrid protein at 35 nanograms per milliliter, whereas LACI at 2.5 micrograms per milliliter is required for an equivalent effect. gamma-Carboxylation of glutamic acid residues in the factor Xa light chain portion of the hybrid protein is required for inhibitory activity, indicating that the first Kunitz-type domain of LACI alone is not sufficient for inhibition of factor VIIa-TF.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Girard, T J -- MacPhail, L A -- Likert, K M -- Novotny, W F -- Miletich, J P -- Broze, G J Jr -- New York, N.Y. -- Science. 1990 Jun 15;248(4961):1421-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Hematology/Oncology, Jewish Hospital, Washington University Medical Center, St. Louis, MO 63110.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1972598" target="_blank"〉PubMed〈/a〉
    Keywords: 1-Carboxyglutamic Acid/metabolism ; Amino Acid Sequence ; Animals ; Binding Sites ; Calcium/metabolism ; Cell Line ; Cloning, Molecular ; Factor VII/antagonists & inhibitors/metabolism/*pharmacology ; Factor VIIa/*antagonists & inhibitors/metabolism ; Factor Xa/metabolism/*pharmacology ; Fibroblasts/metabolism ; Glutamates/metabolism ; Glutamic Acid ; Lipoproteins/metabolism/*pharmacology ; Mice ; Molecular Sequence Data ; Papillomaviridae ; Protease Inhibitors/*pharmacology ; Protein Sorting Signals ; Recombinant Fusion Proteins/*pharmacology ; Thromboplastin/antagonists & inhibitors/metabolism/*pharmacology ; Transfection
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    A novel nucleoprotein complex at a replication origin (1990)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1990-05-25
    Description: The viral protein p6, required for the protein-primed initiation of replication of Bacillus subtilis phage phi 29, forms a nucleoprotein complex at the viral replication origins that shows novel features. Deoxyribonuclease I and hydroxyl radical footprinting data, as well as the induction of positive supercoiling, support a model in which a DNA right-handed superhelix tightly wraps around a multimeric p6 core. The interaction occurs through the DNA minor groove. The activity of p6 not only requires the formation of the complex but also its correct positioning, indicating that the other proteins involved in the initiation of replication recognize, at a precise position, either the p6 core or the DNA conformational change induced by p6.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Serrano, M -- Salas, M -- Hermoso, J M -- 5 R01 GM 27242-10/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1990 May 25;248(4958):1012-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centro de Biologia Molecular (CSIC-UAM), Universidad Autonoma, Madrid, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2111580" target="_blank"〉PubMed〈/a〉
    Keywords: Bacillus subtilis ; Bacteriophages/*genetics ; Base Sequence ; Binding Sites ; *DNA Replication ; DNA, Superhelical/metabolism ; DNA-Binding Proteins/*ultrastructure ; Deoxyribonucleoproteins/*metabolism/ultrastructure ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oligonucleotides ; Viral Proteins/metabolism/ultrastructure ; Virus Replication
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  • 164
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    Crystal structure of cobra-venom phospholipase A2 in a complex with a transition-state analogue (1990)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1990-12-14
    Description: The crystal structure of a complex between a phosphonate transition-state analogue and the phospholipase A2 (PLA2) from Naja naja atra venom has been solved and refined to a resolution of 2.0 angstroms. The identical stereochemistry of the two complexes that comprise the crystal's asymmetric unit indicates both the manner in which the transition state is stabilized and how the hydrophobic fatty acyl chains of the substrate are accommodated by the enzyme during interfacial catalysis. The critical features that suggest the chemistry of binding and catalysis are the same as those seen in the crystal structure of a similar complex formed with the evolutionarily distant bee-venom PLA2.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉White, S P -- Scott, D L -- Otwinowski, Z -- Gelb, M H -- Sigler, P B -- GM22324/GM/NIGMS NIH HHS/ -- HL 36235/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1990 Dec 14;250(4987):1560-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2274787" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bee Venoms/analysis ; Binding Sites ; Calcium/metabolism ; Catalysis ; Chemistry, Physical ; Cobra Venoms/*analysis ; Crystallization ; Hydrogen Bonding ; Molecular Sequence Data ; Molecular Structure ; Phosphatidylethanolamines/*metabolism ; Phospholipases A/*chemistry/metabolism ; Phospholipases A2 ; Physicochemical Phenomena ; Protein Conformation
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  • 165
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    Calcium-induced peptide association to form an intact protein domain: 1H NMR structural evidence (1990)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1990-07-20
    Description: The 70-residue carboxyl-terminal domain of the muscle contractile protein troponin-C contains two helix-loop-helix calcium (Ca)-binding sites that are related to each other by approximate twofold rotational symmetry. Hydrophobic residues from the helices and a short three residue beta sheet at the interface of the two sites act to stabilize the protein domain in the presence of Ca. A synthetic 34-residue peptide representing one of these sites (site III) has been synthesized and studied by H-1 nuclear magnetic resonance (NMR) spectroscopy. In solution this peptide undergoes a Ca-induced conformational change to form the helix-loop-helix Ca-binding motif. Two-dimensional nuclear Overhauser effect spectra have provided evidence for the formation of a beta sheet and interactions between several hydrophobic residues from opposing helices as found in troponin-C. It is proposed that a symmetric two-site dimer similar in tertiary structure to the carboxyl-terminal domain of troponin-C forms from the assembly of two site III peptides in the Ca-bound form.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shaw, G S -- Hodges, R S -- Sykes, B D -- New York, N.Y. -- Science. 1990 Jul 20;249(4966):280-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Alberta, Edmonton, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2374927" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Calcium/*metabolism/pharmacology ; Hydrogen ; Magnetic Resonance Spectroscopy/methods ; Models, Molecular ; Molecular Sequence Data ; Peptides/chemical synthesis/*metabolism ; Protein Conformation ; Troponin/chemical synthesis/*metabolism ; Troponin C ; Turkeys
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    A 49-kilodalton phosphoprotein in the Drosophila photoreceptor is an arrestin homolog (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-04-27
    Description: The gene encoding the 49-kilodalton protein that undergoes light-induced phosphorylation in the Drosophila photoreceptor has been isolated and characterized. The encoded protein has 401 amino acid residues and a molecular mass of 44,972 daltons, and it shares approximately 42 percent amino acid sequence identity with arrestin (S-antigen), which has been proposed to quench the light-induced cascade of guanosine 3',5'-monophosphate hydrolysis in vertebrate photoreceptors. Unlike the 49-kilodalton protein, however, arrestin, which appears to bind to phosphorylated rhodopsin, has not itself been reported to undergo phosphorylation. In vitro, Ca2+ was the only agent found that would stimulate the phosphorylation of the 49-kilodalton protein. The phosphorylation of this arrestin-like protein in vivo may therefore be triggered by a Ca2+ signal that is likely to be regulated by light-activated phosphoinositide-specific phospholipase C.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yamada, T -- Takeuchi, Y -- Komori, N -- Kobayashi, H -- Sakai, Y -- Hotta, Y -- Matsumoto, H -- EY06595/EY/NEI NIH HHS/ -- New York, N.Y. -- Science. 1990 Apr 27;248(4954):483-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City 73190.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2158671" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; *Antigens ; Arrestin ; Binding Sites ; Calcium/pharmacology ; Cloning, Molecular ; Cyclic GMP/metabolism ; DNA/genetics ; Drosophila melanogaster/*genetics ; Enzyme Activation/drug effects ; *Eye Proteins ; Isoelectric Point ; Molecular Sequence Data ; Molecular Weight ; Mutation ; Phosphatidylinositol Diacylglycerol-Lyase ; *Phosphoproteins/genetics/metabolism ; Phosphoric Diester Hydrolases/metabolism ; Phosphorylation ; Photoreceptor Cells/*analysis ; Protein Biosynthesis ; Restriction Mapping ; Sequence Homology, Nucleic Acid
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  • 167
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    Molecular switch for signal transduction: structural differences between active and inactive forms of protooncogenic ras proteins (1990)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1990-02-23
    Description: Ras proteins participate as a molecular switch in the early steps of the signal transduction pathway that is associated with cell growth and differentiation. When the protein is in its GTP complexed form it is active in signal transduction, whereas it is inactive in its GDP complexed form. A comparison of eight three-dimensional structures of ras proteins in four different crystal lattices, five with a nonhydrolyzable GTP analog and three with GDP, reveals that the "on" and "off" states of the switch are distinguished by conformational differences that span a length of more than 40 A, and are induced by the gamma-phosphate. The most significant differences are localized in two regions: residues 30 to 38 (the switch I region) in the second loop and residues 60 to 76 (the switch II region) consisting of the fourth loop and the short alpha-helix that follows the loop. Both regions are highly exposed and form a continuous strip on the molecular surface most likely to be the recognition sites for the effector and receptor molecule(or molecules). The conformational differences also provide a structural basis for understanding the biological and biochemical changes of the proteins due to oncogenic mutations, autophosphorylation, and GTP hydrolysis, and for understanding the interactions with other proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Milburn, M V -- Tong, L -- deVos, A M -- Brunger, A -- Yamaizumi, Z -- Nishimura, S -- Kim, S H -- CA45593/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1990 Feb 23;247(4945):939-45.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, Berkeley.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2406906" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallization ; Crystallography ; Guanosine Diphosphate/metabolism ; Guanosine Triphosphate/metabolism ; Humans ; Models, Molecular ; Molecular Structure ; Protein Conformation ; Proto-Oncogene Proteins/*metabolism ; Proto-Oncogene Proteins p21(ras) ; *Signal Transduction ; Structure-Activity Relationship
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    Structure of ribonuclease H phased at 2 A resolution by MAD analysis of the selenomethionyl protein (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-09-21
    Description: Ribonuclease H digests the RNA strand of duplex RNA.DNA hybrids into oligonucleotides. This activity is indispensable for retroviral infection and is involved in bacterial replication. The ribonuclease H from Escherichia coli is homologous with the retroviral proteins. The crystal structure of the E. coli enzyme reveals a distinctive alpha-beta tertiary fold. Analysis of the molecular model implicates a carboxyl triad in the catalytic mechanism and suggests a likely mode for the binding of RNA.DNA substrates. The structure was determined by the method of multiwavelength anomalous diffraction (MAD) with the use of synchrotron data from a crystal of the recombinant selenomethionyl protein.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, W -- Hendrickson, W A -- Crouch, R J -- Satow, Y -- GM 34102/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1990 Sep 21;249(4975):1398-405.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2169648" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Computer Graphics ; *Endoribonucleases/genetics ; Escherichia coli/enzymology ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Recombinant Proteins ; Ribonuclease H ; *Selenium ; *Selenomethionine ; Sequence Homology, Nucleic Acid ; X-Ray Diffraction/methods
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  • 169
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    Electrostatic and steric contributions to regulation at the active site of isocitrate dehydrogenase (1990)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1990-08-31
    Description: The isocitrate dehydrogenase of Escherichia coli is regulated by covalent modification at the active site rather than, as expected, at an allosteric site. As a means of evaluating the mechanism of regulation, the kinetics of the substrate, 2R,3S-isocitrate, and a substrate analog, 2R-malate, were compared for the native, phosphorylated, and mutant enzymes. Phosphorylation decreases activity by more than a factor of 10(6) for the true substrate, but causes minor changes in the activity of the substrate analog. The kinetic results indicate that electrostatic repulsion and steric hindrance between the phosphoryl moiety and the gamma carboxyl group of 2R,3S-isocitrate are the major causes of the inactivation, with a lesser contribution from the loss of a hydrogen bond.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dean, A M -- Koshland, D E Jr -- New York, N.Y. -- Science. 1990 Aug 31;249(4972):1044-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2204110" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Site ; Amino Acid Sequence ; Binding Sites ; Escherichia coli/*enzymology/genetics ; Isocitrate Dehydrogenase/genetics/*metabolism ; Models, Molecular ; Mutation ; Protein Conformation
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    Sequence-specific DNA binding by the c-Myc protein (1990)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1990-11-23
    Description: While it has been known for some time that the c-Myc protein binds to random DNA sequences, no sequence-specific binding activity has been detected. At its carboxyl terminus, c-Myc contains a basic--helix-loop-helix (bHLH) motif, which is important for dimerization and specific DNA binding, as demonstrated for other bHLH protein family members. Of those studied, most bHLH proteins bind to sites that contain a CA- -TG consensus. In this study, the technique of selected and amplified binding-sequence (SAAB) imprinting was used to identify a DNA sequence that was recognized by c-Myc. A purified carboxyl-terminal fragment of human c-Myc that contained the bHLH domain bound in vitro in a sequence-specific manner to the sequence, CACGTG. These results suggest that some of the biological functions of Myc family proteins are accomplished by sequence-specific DNA binding that is mediated by the carboxyl-terminal region of the protein.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Blackwell, T K -- Kretzner, L -- Blackwood, E M -- Eisenman, R N -- Weintraub, H -- R01 CA20525/CA/NCI NIH HHS/ -- T32 CA09437/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1990 Nov 23;250(4984):1149-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98104.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2251503" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; DNA/*metabolism ; Glutathione Transferase ; Leucine Zippers ; Macromolecular Substances ; Molecular Sequence Data ; Oligonucleotides/metabolism ; Polymerase Chain Reaction ; Protein Conformation ; Proto-Oncogene Proteins c-myc/*metabolism ; Recombinant Fusion Proteins/metabolism ; Templates, Genetic
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  • 171
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    Differences and similarities in DNA-binding preferences of MyoD and E2A protein complexes revealed by binding site selection (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-11-23
    Description: A technique was developed for studying protein-DNA recognition that can be applied to any purified protein, partially purified protein, or cloned gene. From oligonucleotides in which particular positions are of random sequence, that subset to which a given protein binds is amplified by the polymerase chain reaction and sequenced as a pool. These selected and amplified binding site (SAAB) "imprints" provide a characteristic set of preferred sequences for protein binding. With this technique, it was shown that homo- and heterooligomers of the helix-loop-helix proteins MyoD and E2A recognize a common consensus sequence, CA--TG, but otherwise bind to flanking and internal positions with different sequence preferences that suggest half-site recognition. These findings suggest that different combinations of dimeric proteins can have different binding sequence preferences.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Blackwell, T K -- Weintraub, H -- New York, N.Y. -- Science. 1990 Nov 23;250(4984):1104-10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Fred Hutchinson Cancer Research Center, Seattle, WA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2174572" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; DNA/*metabolism ; DNA-Binding Proteins/*metabolism ; Glutathione Transferase ; Macromolecular Substances ; Molecular Sequence Data ; Muscle Proteins/*metabolism ; MyoD Protein ; Oligonucleotides/metabolism ; Polymerase Chain Reaction ; Protein Conformation ; Recombinant Fusion Proteins/metabolism ; Repetitive Sequences, Nucleic Acid ; TCF Transcription Factors ; Templates, Genetic ; Transcription Factor 7-Like 1 Protein ; *Transcription Factors
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  • 172
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    Binding of the Wilms' tumor locus zinc finger protein to the EGR-1 consensus sequence (1990)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1990-11-30
    Description: The Wilms' tumor locus (WTL) at 11p13 contains a gene that encodes a zinc finger-containing protein that has characteristics of a DNA-binding protein. However, binding of this protein to DNA in a sequence-specific manner has not been demonstrated. A synthetic gene was constructed that contained the zinc finger region, and the protein was expressed in Escherichia coli. The recombinant protein was used to identify a specific DNA binding site from a pool of degenerate oligonucleotides. The binding sites obtained were similar to the sequence recognized by the early growth response-1 (EGR-1) gene product, a zinc finger-containing protein that is induced by mitogenic stimuli. A mutation in the zinc finger region of the protein originally identified in a Wilms' tumor patient abolished its DNA-binding activity. These results suggest that the WTL protein may act at the DNA binding site of a growth factor-inducible gene and that loss of DNA-binding activity contributes to the tumorigenic process.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rauscher, F J 3rd -- Morris, J F -- Tournay, O E -- Cook, D M -- Curran, T -- CA0917-15/CA/NCI NIH HHS/ -- CA10817/CA/NCI NIH HHS/ -- CA23413/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1990 Nov 30;250(4985):1259-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wistar Institute, Philadelphia, PA 19104.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2244209" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Binding Sites ; Binding, Competitive ; Chromosomes, Human, Pair 11 ; Consensus Sequence ; DNA/genetics/*metabolism ; DNA-Binding Proteins/genetics/*metabolism ; Early Growth Response Protein 1 ; Escherichia coli/genetics ; *Genes, Wilms Tumor ; Humans ; *Immediate-Early Proteins ; Molecular Sequence Data ; Mutation ; Oligonucleotides/metabolism ; Polymerase Chain Reaction ; Recombinant Proteins/metabolism ; Restriction Mapping ; Transcription Factors/genetics/*metabolism ; *Zinc Fingers/genetics
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    Design, activity, and 2.8 A crystal structure of a C2 symmetric inhibitor complexed to HIV-1 protease (1990)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1990-08-03
    Description: A two-fold (C2) symmetric inhibitor of the protease of human immunodeficiency virus type-1 (HIV-1) has been designed on the basis of the three-dimensional symmetry of the enzyme active site. The symmetric molecule inhibited both protease activity and acute HIV-1 infection in vitro, was at least 10,000-fold more potent against HIV-1 protease than against related enzymes, and appeared to be stable to degradative enzymes. The 2.8 angstrom crystal structure of the inhibitor-enzyme complex demonstrated that the inhibitor binds to the enzyme in a highly symmetric fashion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Erickson, J -- Neidhart, D J -- VanDrie, J -- Kempf, D J -- Wang, X C -- Norbeck, D W -- Plattner, J J -- Rittenhouse, J W -- Turon, M -- Wideburg, N -- AI 27220/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1990 Aug 3;249(4968):527-33.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Computer-Assisted Molecular Design, Abbott Laboratories, Abbott Park, IL 60064.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2200122" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Drug Design ; Endopeptidases/*metabolism ; Gene Products, pol/*metabolism ; HIV Protease ; HIV-1/*enzymology ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Protease Inhibitors/*pharmacology ; Protein Conformation ; Sugar Alcohols/*pharmacology ; Valine/*analogs & derivatives/pharmacology
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  • 174
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    Two distinct transcription factors that bind the immunoglobulin enhancer microE5/kappa 2 motif (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-01-26
    Description: Activity of the immunoglobulin heavy and kappa light chain gene enhancers depends on a complex interplay of ubiquitous and developmentally regulated proteins. Two complementary DNAs were isolated that encode proteins, denoted ITF-1 and ITF-2, that are expressed in a variety of cell types and bind the microE5/kappa 2 motif found in both heavy and kappa light chain enhancers. The complementary DNAs are the products of distinct genes, yet both ITF-1 and ITF-2 are structurally and functionally similar. The two proteins interact with one another through their putative helix-loop-helix motifs and each possesses a distinct domain that dictates transcription activation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Henthorn, P -- Kiledjian, M -- Kadesch, T -- New York, N.Y. -- Science. 1990 Jan 26;247(4941):467-70.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Philadelphia, PA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2105528" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; B-Lymphocytes/metabolism ; Base Sequence ; Binding Sites ; Cell Line ; Cloning, Molecular ; DNA/genetics/*metabolism ; *Enhancer Elements, Genetic ; *Genes, Immunoglobulin ; Humans ; Immunoglobulin kappa-Chains/genetics ; Immunoglobulin mu-Chains/genetics ; Macromolecular Substances ; Mice ; Molecular Sequence Data ; Plasmids ; Protein Conformation ; Saccharomyces cerevisiae/genetics ; Transcription Factors/*metabolism ; Transcription, Genetic ; Transfection ; Transformation, Genetic
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    Acetylcholine binding by a synthetic receptor: implications for biological recognition (1990)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1990-12-14
    Description: The neurotransmitter acetylcholine (ACh) is bound with 50-micromolar affinity by a completely synthetic receptor (host) comprising primarily aromatic rings. The host provided an overall hydrophobic binding site, but one that could recognize the positive charge of the quaternary ammonium group of ACh through a stabilizing interaction with the electron-rich pi systems of the aromatic rings (cation-pi interaction). Similar interactions may be involved in biological recognition of ACh and other choline derivatives.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dougherty, D A -- Stauffer, D A -- GM36356/GM/NIGMS NIH HHS/ -- GM43936/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1990 Dec 14;250(4987):1558-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Arnold and Mabel Beckman Laboratories of Chemical Synthesis, California Institute of Technology, Pasadena 91125.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2274786" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylcholine/*metabolism ; Affinity Labels ; Amino Acid Sequence ; Animals ; Binding Sites ; Cations ; Drosophila ; Electrochemistry ; Immunoglobulin Fab Fragments/metabolism ; *Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Phosphorylcholine/metabolism ; Quaternary Ammonium Compounds/*metabolism ; Receptors, Cholinergic/chemistry/*metabolism ; Thermodynamics ; Torpedo
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    Structural motif of the GCN4 DNA binding domain characterized by affinity cleaving (1990)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1990-05-18
    Description: The NH2-terminal locations of a dimer containing the DNA binding domain of the yeast transcriptional activator GCN4 have been mapped on the binding sites 5'-CTGACTAAT-3' and 5'-ATGACTCTT-3'. Affinity cleaving was effected by synthetic GCN4 proteins with Fe.EDTA moieties at the NH2-terminus. Analysis of the DNA cleavage patterns for dimers of the Fe.EDTA-proteins corresponding to GCN4 residues 222 to 281 and 226 to 281 revealed that the NH2-termini were in the major groove nine to ten base pairs apart and were symmetrically displaced four to five base pairs from the central C of the recognition site. This result is consistent with the Y-shaped scissor grip-leucine zipper model recently proposed for a class of DNA binding proteins important in the regulation of gene expression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Oakley, M G -- Dervan, P B -- New York, N.Y. -- Science. 1990 May 18;248(4957):847-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2111578" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Binding Sites ; DNA/*metabolism ; *DNA-Binding Proteins ; Edetic Acid/metabolism ; Ferric Compounds/metabolism ; Fungal Proteins/*metabolism ; Leucine ; Macromolecular Substances ; Molecular Sequence Data ; Molecular Structure ; *Protein Kinases ; *Saccharomyces cerevisiae Proteins ; Transcription Factors/*metabolism
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    Derepression of ferritin messenger RNA translation by hemin in vitro (1990)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1990-01-05
    Description: Incubation of a 90-kilodalton ferritin repressor protein (FRP), either free or complexed with an L-ferritin transcript, with hemin or Co3+-protoporphyrin IX prevented subsequent repression of ferritin synthesis in a wheat germ extract. Neither FeCl3 in combinations with H2O2, nor Fe3+ or Fe2+ chelated with EDTA, nor Zn2+-protoporphyrin IX, nor protoporphyrin IX caused significant inactivation of FRP. FRP that had been inactivated by hemin remained chemically intact, as revealed by SDS-polyacrylamide gel electrophoresis. Inclusion of chelators of iron or free radical scavengers did not alter the inactivation produced by hemin. These and other results indicate that hemin derepresses ferritin synthesis in vitro.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lin, J J -- Daniels-McQueen, S -- Patino, M M -- Gaffield, L -- Walden, W E -- Thach, R E -- AI 20484/AI/NIAID NIH HHS/ -- RR 5369/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1990 Jan 5;247(4938):74-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Washington University, St. Louis, MO 63130.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2294594" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Binding, Competitive ; Electrophoresis, Polyacrylamide Gel ; Ferritins/biosynthesis/*genetics ; Free Radicals ; Heme/*analogs & derivatives ; Hemin/*pharmacology ; Iron Chelating Agents/pharmacology ; Protein Biosynthesis/*drug effects ; Protoporphyrins/metabolism ; RNA, Messenger/*genetics ; Repressor Proteins/*genetics/metabolism ; Transcription Factors/*genetics
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    A new member of the leucine zipper class of proteins that binds to the HLA DR alpha promoter (1990)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1990-03-30
    Description: Several mutants derived from transformed human B cell lines are defective in expressing major histocompatibility complex (MHC) class II genes. The failure to express a class II gene in at least one such mutant line has been mapped to the MHC class II X box, a conserved transcriptional element in the promoter region. A complementary DNA encoding a DNA-binding protein (human X box binding protein, hXBP-1) whose target is the human DR alpha X box and the 3' flanking region has now been cloned. This complementary DNA encoded a protein with structural similarities to the c-jun proto-oncogene product, and its target sequence was closely related to the palindromic target sequence of c-jun. Mutation of the hXBP-1 DNA target sequence decreased DR alpha promoter activity in vivo. These studies suggest that the hXBP-1 protein acts as a transcription factor in B cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liou, H C -- Boothby, M R -- Finn, P W -- Davidon, R -- Nabavi, N -- Zeleznik-Le, N J -- Ting, J P -- Glimcher, L H -- CA42771-01/CA/NCI NIH HHS/ -- GM36864/GM/NIGMS NIH HHS/ -- R01-CA48185/CA/NCI NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1990 Mar 30;247(4950):1581-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cancer Biology, Harvard School of Public Health, Boston, MA 02115.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2321018" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; B-Lymphocytes ; Base Sequence ; Binding Sites ; Cell Line, Transformed ; DNA/*genetics ; DNA-Binding Proteins/*genetics/metabolism ; HLA-DR Antigens/*genetics/metabolism ; Humans ; Leucine ; Molecular Sequence Data ; Mutation ; *Promoter Regions, Genetic ; Transcription Factors/*genetics/metabolism ; Transfection
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 179
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    A beta 3 integrin mutation abolishes ligand binding and alters divalent cation-dependent conformation (1990)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1990-08-24
    Description: The ligand-binding function of integrin adhesion receptors depends on divalent cations. A mutant alpha IIb beta 3 integrin (platelet gpIIb/IIIa) that lacks ligand recognition shows immunologic evidence of a perturbed interaction with divalent cations. This was found to be caused by a G----T mutation that resulted in an Asp119----Tyr119 substitution in the beta 3 subunit. This residue is proximal to bound ligand and is in a conserved region among integrins that are enriched in oxygenated residues. The spacing of these residues aligns with the calcium-binding residues in EF hand proteins, suggesting interaction with receptor-bound divalent cation as a mechanism of ligand binding common to all integrins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Loftus, J C -- O'Toole, T E -- Plow, E F -- Glass, A -- Frelinger, A L 3rd -- Ginsberg, M H -- AR 27214/AR/NIAMS NIH HHS/ -- HL 28235/HL/NHLBI NIH HHS/ -- HL 42977/HL/NHLBI NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1990 Aug 24;249(4971):915-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Committee on Vascular Biology, Research Institute of Scripps Clinic, La Jolla, CA 92037.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2392682" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Aspartic Acid ; Base Sequence ; Binding Sites ; Cell Line ; Integrins/*genetics/metabolism ; Ligands ; Macromolecular Substances ; Molecular Sequence Data ; *Mutation ; Oligonucleotide Probes ; Platelet Membrane Glycoproteins/*genetics/metabolism ; Polymerase Chain Reaction ; Protein Conformation ; Sequence Homology, Nucleic Acid ; Tyrosine
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 180
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    Inhibition of FKBP rotamase activity by immunosuppressant FK506: twisted amide surrogate (1990)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1990-05-18
    Description: The immunosuppressive agents cyclosporin A and FK506 inhibit the transcription of early T cell activation genes. The binding proteins for cyclosporin A and FK506, cyclophilin and FKBP, respectively, are peptidyl-prolyl-cis-trans isomerases, or rotamases. One proposed mechanism for rotamase catalysis by cyclophilin involves a tetrahedral adduct of an amide carbonyl and an enzyme-bound nucleophile. The potent FKBP rotamase inhibitor FK506 has a highly electrophilic carbonyl that is adjacent to an acyl-pipicolinyl (homoprolyl) amide bond. Such a functional group would be expected to form a stabilized, enzyme-bound tetrahedral adduct. Spectroscopic and chemical evidence reveals that the drug interacts noncovalently with its receptor, suggesting that the alpha-keto amid of FK506 serves as a surrogate for the twisted amide of a bound peptide substrate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rosen, M K -- Standaert, R F -- Galat, A -- Nakatsuka, M -- Schreiber, S L -- GM-38627/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1990 May 18;248(4957):863-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Harvard University, Cambridge, MA 02138.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1693013" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Isomerases/*antagonists & inhibitors ; Anti-Bacterial Agents/metabolism/*pharmacology ; Binding Sites ; Carrier Proteins/antagonists & inhibitors/metabolism ; Chemical Phenomena ; Chemistry ; Cloning, Molecular ; Cyclosporins/metabolism/pharmacology ; Escherichia coli/genetics ; Gene Expression ; *Immunosuppressive Agents ; Lymphocyte Activation ; Magnetic Resonance Spectroscopy ; Molecular Structure ; Peptidylprolyl Isomerase ; Recombinant Proteins ; T-Lymphocytes/immunology ; Tacrolimus
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 181
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    Anatomy of a conformational change: hinged "lid" motion of the triosephosphate isomerase loop (1990)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1990-09-21
    Description: Triosephosphate isomerase (TIM) is used as a model system for the study of how a localized conformational change in a protein structure is produced and related to enzyme reactivity. An 11-residue loop region moves more than 7 angstroms and closes over the active site when substrate binds. The loop acts like a "lid" in that it moves rigidly and is attached by two hinges to the remainder of the protein. The nature of the motion appears to be built into the loop by conserved residues; the hinge regions, in contrast, are not conserved. Results of molecular dynamics calculations confirm the structural analysis and suggest a possible ligand-induced mechanism for loop closure.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Joseph, D -- Petsko, G A -- Karplus, M -- New York, N.Y. -- Science. 1990 Sep 21;249(4975):1425-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2402636" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Carbohydrate Epimerases/*metabolism ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; *Protein Conformation ; Software ; Triose-Phosphate Isomerase/*metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 182
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    A bacterial enhancer functions to tether a transcriptional activator near a promoter (1990)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1990-04-27
    Description: The nitrogen regulatory protein NtrC of enteric bacteria activates transcription of the glnA gene by catalyzing isomerization of closed complexes between RNA polymerase and the glnA promoter to open complexes. NtrC binds to sites upstream of glnA that have properties of eukaryotic transcriptional enhancers. NtrC-binding sites were found to facilitate open complex formation when these sites and the glnA promoter were located on different rings of a singly linked catenane, but not when the two rings were decatenated. The results provide evidence that NtrC contacts RNA polymerase-promoter complexes in a process mediated by formation of a DNA loop. NtrC-binding sites serve to tether NtrC near the glnA promoter, thereby increasing the frequency of collisions between NtrC and polymerase-promoter complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wedel, A -- Weiss, D S -- Popham, D -- Droge, P -- Kustu, S -- GM 38361/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1990 Apr 27;248(4954):486-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Pathology, University of California, Berkeley 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1970441" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*metabolism ; Binding Sites ; DNA Transposable Elements ; DNA, Bacterial/metabolism ; DNA, Superhelical/metabolism ; DNA-Binding Proteins/*metabolism ; DNA-Directed RNA Polymerases/metabolism ; *Enhancer Elements, Genetic ; Glutamate-Ammonia Ligase/*genetics ; Nucleotidyltransferases/metabolism ; PII Nitrogen Regulatory Proteins ; Plasmids ; *Promoter Regions, Genetic ; Templates, Genetic ; *Trans-Activators ; *Transcription Factors ; *Transcription, Genetic ; Transposases
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Characterization of an extremely large, ligand-induced conformational change in plasminogen (1990)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1990-04-06
    Description: Native human plasminogen has a radius of gyration of 39 angstroms. Upon occupation of a weak lysine binding site, the radius of gyration increases to 56 angstroms, an extremely large ligand-induced conformational change. There are no intermediate conformational states between the closed and open form. The conformational chang is not accompanied by a change in secondary structure, hence the closed conformation is formed by interaction between domains that is abolished upon conversion to the open form. This reversible change in conformation, in which the shape of the protein changes from that best described by a prolate ellipsoid to a flexible structure best described by a Debye random coil, is physiologically relevant because a weak lysine binding site regulates the activation of plasminogen.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mangel, W F -- Lin, B H -- Ramakrishnan, V -- New York, N.Y. -- Science. 1990 Apr 6;248(4951):69-73.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biology Department, Brookhaven National Laboratory, Upton, NY 11973.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2108500" target="_blank"〉PubMed〈/a〉
    Keywords: Aminocaproic Acid/metabolism/pharmacology ; Binding Sites ; Chemistry, Physical ; Circular Dichroism ; Deuterium ; Humans ; Lysine/metabolism ; Neutrons ; Physicochemical Phenomena ; *Plasminogen/metabolism ; Plasminogen Activators/pharmacology ; Protein Conformation/drug effects ; Scattering, Radiation ; Urokinase-Type Plasminogen Activator/pharmacology ; Water
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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