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  • 1
    Electronic Resource
    Electronic Resource
    Local interactions favor the native 8-residue disulfide loop in the oxidation of a fragment corresponding to the sequence Ser-50-Met-79 derived from bovine pancreatic ribonuclease A (1988)
    Springer
    The protein journal 7 (1988), S. 377-398 
    Details
    ISSN: 1573-4943
    Keywords: RNase A ; protein fragment ; disulfide-loop formation ; native-like conformation ; protein folding
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract A 30-residue peptide was obtained from ribonuclease A by chemical cleavage with cyanogen bromide, subsequent sulfitolysis with concomitant S-sulfonation, and finally enzymatic cleavage withStaphylococcus aureus protease. The peptide was converted to the free thiol form by reductive cleavage of the S-sulfo-protecting groups withd,l-dithiothreitol. This peptide consisted of residues 50–79 of the native sequence of ribonuclease A, with the exception that methionine-79 had been converted to homoserine. Included in this sequence are residues cysteine-65 and cysteine-72, which form a disulfide bond in the native enzyme, as well as cysteine-58. This molecule may form one of three possible intramolecular disulfide bonds upon thiol oxidation, viz. one loop of 15 and 2 of 8 residues each. These isomeric peptides were prepared by oxidation with cystamine, 2-aminoethanethiolation of residual thiols, and fractionation by reverse-phase high-performance liquid chromatography. Disulfide pairings were established by mapping the tryptic fragments and confirming their composition by amino acid analysis. After protracted incubation under oxidizing conditions at 25.0°C andp H 8.0, the 26-member ring incorporating the native disulfide bond between residues 65 and 72 is the dominant product. Assuming that equilibrium is established, we infer that local interactions in the sequence of ribonuclease A significantly stabilize the native 8-residue disulfide loop with respect to the non-native 8-residue loop (ΔG°=−1.1±0.1 kcal mole−1). The implications of this observation for the oxidative folding of the intact protein are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01024887
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  • 2
    Electronic Resource
    Electronic Resource
    Conformational analysis of proteins: Algorithms and data structures for array processing (1980)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 1 (1980), S. 46-58 
    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: Current efforts to determine the nature of the interactions that influence protein folding involve, among other things, minimization of an appropriate empirical conformational energy function (ECEPP, Emprical Conformational Energy Program for Peptides) to obtain the native structure. Because of the prohibitive cost of such a massive computational project, either on a conventional large-scale machine at a self-supporting installation or on a dedicated minicomputer, an alternative computer hardware system has been developed to aid in the conformational analysis of proteins. It consists of a Floating Point Systems AP-120B array processor and a Prime 350 minicomputer host. A version of ECEPP has been adapted to run on the AP-120B. The data structures and algorithms chosen for this version reflect the highly unusual parallel architecture of this machine. Benchmark comparisons with BPTI (Bovine Pancreatic Trypsin Inhibitor), a protein of 58 residues and a known structure, have been carried out on this system as well as on an IBM 370/168. They show a significant advantage in speed for the AP-120B/Prime 350 system as well as a substantially lower cost. An energy minimization of BPTI with 154 variable dihedral angles is reported, an effort heretofore prohibited by the computer costs involved.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540010106
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  • 3
    Electronic Resource
    Electronic Resource
    Revised algorithms for the build-up procedure for predicting protein conformations by energy minimization (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 826-834 
    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 build-up procedure for predicting low-energy conformations of polypeptides has been extended to cover the case of peptides in aqueous solutions. The revised procedure consists of five steps to be applied to each stage of the build-up. I. All low-energy minima of each of the two fragments to be joined are combined as starting points for energy minimization of the enlarged fragment, and those minima of the enlarged fragment within a certain upper bound of the lowest energy are retained. II. Whenever one of the combinations in Step I leads to an atomic overlap, the minimization is started again using a pseudoenergy function which remains finite everywhere and becomes equal to the standard energy function when no atoms overlap. III. The minima generated in Steps I and II are culled by ignoring side-chain conformations and retaining only those minima whose backbone conformations differ significantly. IV. The rotameric states of the side chains are optimized, by testing their energy of interaction with the rest of the molecule, and subjecting the whole molecule to a further round of energy minimization if the test indicates that this would reduce the energy. V. The energies of all minima are recomputed with inclusion of a term for solvation and with a smaller upper bound as the criterion for retention. The original build-up procedure consisted of Steps I and III only. Examples are presented showing the effectiveness of the new Steps II and IV in locating low-energy minima, and the problems that remain to be solved, chiefly concerning Step V, are discussed.
    Additional Material: 2 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080611
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  • 4
    Electronic Resource
    Electronic Resource
    Implementation of the ECEPP algorithm, the Monte Carlo minimization method, and the electrostatically driven Monte Carlo method on the Kendall square research KSR1 computer (1995)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 16 (1995), S. 1153-1163 
    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: In this article the adaptation of the Empirical Conformational Energy Program for Peptides (ECEPP/3) and two conformational search methods [viz., the Monte Carlo minimization (MCM) method and the electrostatically driven Monte Carlo (EDMC) method] to the Kendall Square Research KSR1 computer is described. The MCM and EDMC methods were developed to surmount the multiple-minima problem in protein folding. Parallelization of these codes led to substantial speedups (expressed as the ratio between the mean time per energy evaluation in one processor and the mean time per energy evaluation in a set of processors) over the serial versions of these codes. A comparison of the performance of these algorithms on the KSR1 and on the IBM ES9000 computers is presented. © 1995 by John Wiley & Sons, Inc.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540160909
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