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  • Polymer and Materials Science  (6,071)
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  • 101
    Electronic Resource
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    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 1261-1270 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A variety of solution conditions are known to induce collapse of linear DNA into a compact configuration without dramatic change of local structure. When visualized, these compact forms frequently have a toroidal appearance. We ask whether the molecular basis of the toroidal shape can be a stable curvature of isolated rodlike DNA segments. Application of the classical Euler-Lagrange theory for the buckling of elastic rods provides us with an affirmative answer. Specifically, we see that, in principle, sufficient addition of inert polymer to DNA solutions can induce buckling of DNA segments. However, no attempt is made to quantitate the Euler-Lagrange condition for sufficiency in terms of added polymer concentration. We find also that complete neutralization of the phosphate charge is more than sufficient to induce buckling of DNA segments of length comparable to a Kuhn segment. The quantitative argument involves comparison of buckling forces provided by polyelectrolyte theory with the Euler-Lagrange criterion. Knowledge of the ionic-strength dependence of DNA bending stiffness (persistence length) is not required.
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  • 102
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    Biopolymers 20 (1981), S. 621-624 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 103
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    Biopolymers 20 (1981) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 104
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    Biopolymers 20 (1981), S. 629-632 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 105
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The protein actinoxanthin (molecular weight 10,300) crystallizes in space group P212121, with cell dimensions a = 30.9 Å, b = 48.8 Å, c = 64.1 Å, and z = 4. The three-dimensional structure of actinoxanthin at 4-Å resolution was determined by x-ray methods on the basis of experimental data from the native protein and five isomorphous derivatives. At the stage of solving the phase problem, the heavy atoms in the derivatives were located using direct methods. The actinoxanthin molecule can be described as an oblate ellipsoid with approximate dimensions 20 × 30 × 40 Å and consists of two different sizes of folded units separated by a well-defined cleft. The larger unit, including the N- and C-terminals of the protein chain, is characterized by a significant content of β-sheet structure. The smaller unit, containing two deca- and hexapeptide cycles closed by disulfide bonds, has a mainly irregular structure.
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  • 106
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    Biopolymers 20 (1981), S. 753-763 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A Monte Carlo method is presented to calculate equilibria for the binding of ligands to one-dimensional heteropolymers. Equivalency with other methods suitable for particular cases was verified (i.e., matrix and combinatorial methods). The principal interest of this Monte Carlo method is in its facility for adaptation to any physically conceivable binding model and that it gives access to the parameters accounting for partial binding to each different type of site. General properties of binding isotherms with excluded-site effects and relations between partial binding ratios and partial free site ratios are discussed. An effective calculation is presented for illustration of the method.
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  • 107
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    Biopolymers 20 (1981), S. 1565-1573 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The vacuum-ultraviolet circular dichroism (VUCD) of chondroitin and chontroitin-6-sulfate has been measured to 160 nm for films and to 170 nm for D2O solutions. The pD-dependent dichroic behavior of these glycosaminoglycans in D2O is similar above 200 nm and is in agreement with previous studies. Near 190 nm, the CD band sign is also dependent on pD. VUCD spectra were recorded for films and solutions of poly(L-arginine). In trifluoroethanol the polypeptide is α-helical, while in D2O it exists as a random coil. The well-characterized coil-helix transition of poly(L-arginine) during complexation with chondroitin-6-sulfate was observed by VUCD, including the previously inaccessible entire π → π* band. By construction of difference spectra it was also possible to monitor the VUCD of the polysaccharide component during complexation.
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  • 108
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    Biopolymers 20 (1981), S. 1589-1603 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Investigations of DNA using CD spectroscopy show that the P-form is available in a wide variety of methanol-ethanol mixtures when the water content is low. Increasing the temperature or the ethanol content of a 95% methanol solution causes DNA to undergo a cooperative transition to the P-form. However, this transition cannot be reversed on cooling, or on adding methanol. Thus P-form DNA appears to be stable at high methanol concentrations, but it is usually not observed because the DNA is trapped by a kinetic barrier. P-form DNA will instantaneously assume the native B-form on addition of water, confirming earlier reports that P-form DNA is not strand separated [E. Kay (1976) Biochemistry 15, 5241]. CD spectra extended to 190 nm show that there is no base-base interaction in the P-form. However, the P-form is extremely stable to heat denaturation in solvents which promote hydrogen bonding between the base pairs. A number of models that can account for the properties of P-form DNA are discussed.
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  • 109
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    Biopolymers 20 (1981), S. 1651-1669 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Approximate methods are developed and evaluated for treating the rate of binding ligands that cover several contiguous sites to a homogeneous one-dimensional lattice, which represents a nucleic acid or other linear biopolymer. The model requires as input only the number of lattice sites necessary for binding, the total number (possibly infinite) of lattice sites, and elementary rate constants for the cooperative and noncooperative association and dissociation of the ligand on the lattice. The computational methods employed are an extension of the triplet closure approximation from the helix-coil (single-site ligand) problem to the large ligand binding problem. It is found that consideration of clusters of n + 2 lattice sites, where each ligand covers n sites, gives a surprisingly accurate description of the kinetics. The approximation is implemented by an extension of the matrix-iteration approach proposed by Craig and Crothers. The effects of the finite lattice length, as well as the capability to treat ligand motion along the lattice, are incorporated. When all symmetries are taken into consideration, the time required for the matrix iteration calculation rises only linearly with the ligand length n and is considerably less than that of the Monte Carlo method, which is used as a standard for comparison.
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  • 110
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Improved chemical synthesis of bovine pancreatic ribonuclease (RNase) A was achieved by applying a new deprotecting procedure with trifluoromethanesulfonic acid-thioanisole in combination with a modified air-oxidation procedure with glutathione for the disulfide formation. After purifications by affinity chromatography, followed by ion-exchange chromatography, a protein with the full enzymatic activity was obtained and subsequently crystallized from aqueous ethanol according to Kunitz. A totally synthetic enzyme with full RNase A activity was thus obtained in a crystalline form for the first time.
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  • 111
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    Biopolymers 20 (1981), S. 1901-1912 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: After a brief review of the genesis of cyclic peptide research, some current areas of interest in this field are examined. The final section of this manuscript considers some possible future directions of research with cyclic peptides.
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  • 112
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    Biopolymers 20 (1981), S. 1949-1958 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Important aspects in detailed nmr analyses of the conformations of linear peptides are discussed using enkephalin and the α-mating factor of Saccharomyces cerevisiae as examples. The cationic, dipolar, and anionic forms in dimethyl sulfoxide solution may be identified by ir analyses. Because of the electrostatic interaction between the N- and C-terminal groups, the dipolar form of enkephalin takes the folded conformation, as well as extended conformation(s), in dimethyl sulfoxide solution. Such conformational equilibrium is responsible for anomalous temperature dependences and solvent-composition dependences of the amide and Cα proton chemical shifts. Active analogs, enkephalinamide and enkephalinol, take extended conformation(s) in solution. These opioid peptides probably take a specific active conformation upon binding with a receptor. For the α-mating factor and active peptide analogs in aqueous solution, a folded conformation with two βturn structures is responsible for the biological activity.
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  • 113
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    Biopolymers 20 (1981), S. 1989-1999 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The comparative study of proteins which differ in primary structure by point mutations permits one to use thermodynamic experiments to obtain information about the role of specific amino acids in determining protein structure and stability. We have now determined the thermodynamic changes induced in six mutants of T4 lysozyme and have compared the results with the wildtype enzyme. Our work is in collaboration with B. Matthews and his colleagues, who have determined the crystal structure of T4 lysozyme and have obtained difference Fourier maps for four of the mutants. The ultimate aim is to correlate changes in protein stability with changes in the detailed structure of the protein. This paper discusses the thermodynamic results obtained from the mutants studied. All the mutants have a lower Tm than the wild-type enzyme and changes in the enthalpy of denaturation are sometimes extraordinarily large. Changes in ΔH of denaturation are usually accompanied by compensating changes in ΔS. The general question of protein stability and the manner in which it varies with temperature and mutations is discussed.
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  • 114
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    Biopolymers 20 (1981) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 115
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Two series of peptides containing L-phenylalanine, Nps-(L-Phe-L-Phe-Gly)n-OEt (n = 1-6) and Nps-(L-Phe-L-Leu-Gly)n-OEt (n = 1-7), were prepared by the fragment-condensation method using the tripeptide N-hydroxysuccinimide esters. Conformational characterization of these peptides in the solid state was performed by ir spectroscopy and x-ray powder diffraction measurement. The peptides Nps-(L-Phe-L-Phe-Gly)n-OEt take the β-structure, but the pentadecapeptide and higher peptides of Nps-(L-Phe-L-Leu-Gly)n-OEt form the α-helix, although the lower homologs take the β-structure.
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  • 116
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    Biopolymers 20 (1981), S. 2281-2283 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No. Abstract.
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  • 117
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    Biopolymers 20 (1981), S. 2285-2285 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 118
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    Biopolymers 20 (1981), S. 2323-2336 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present a model to describe the equilibrium binding properties for the attachment of multivalent ligands to mobile receptors in membranes. The interaction is assumed to be governed by two inherently different association constants. The first of these controls the initial attachment of a ligand to its first receptor, by adsorption from bulk solution, while the second governs subsequent receptor attachments to this initially bound ligand by rearrangement of membrane-bound species. Simple statistical mechanical expressions are used to estimate contributions to these association constants that are attributable to losses of translational and rotational degrees of freedom occurring upon binding. Suitable combinatorial expressions are combined with these association constants to derive the concentrations of bound species and the binding isotherms. Examination of these expressions leads to the conclusion that once initially bound, most multivalent ligands will be completely saturated by receptors and that partially bound species will be essentially nonexistent. This behavior is attributable to the generally high overall affinities of these ligands and to the mobility of the membrane-bound species. Some specific comments are made, in light of this theory, about the binding of cholera toxin to its membrane receptor, the ganglioside GM1.
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  • 119
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    Biopolymers 20 (1981), S. 1413-1419 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Chitosan flakes from shrimp shells and xerogels derived from branched 1-deoxyglycit-1-yl chitosan derivatives were examined by scanning electron microscopy; the former displayed relatively large, dome-shaped orifices and the latter were found to exhibit a wide variety of ultrastructures, ranging from smooth, nonporous to microporous and microfibrillar. Some correlation between the chemical structure of the side chains of the chitosan derivatives and their microarchitecture could be established.
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  • 120
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The host-guest technique has been applied to the determination of the helix-coil stability constants of two naturally occurring amino acids, L-alanine and L-leucine, in a nonaqueous solvent system. Random copolymers containing L-alanine and L-leucine, respectively, as guest residues and γ-benzyl-L-glutamate as the host residue were synthesized. The polymers were fractionated and characterized for their amino acid content, molecular weight, and helix-coil transition behavior in a dichloroacetic acid (DCA)-1,2-dichloroethane (DCE) mixture. Two types of helix-coil transitions were carried out on the copolymers: solvent-induced transitions in DCA-DCE mixtures at 25°C and thermally induced transitions in a 82:18 (wt %) DCA-DCE mixture. The thermally induced transitions were analyzed by statistical mechanical methods to determine the Zimm-Bragg parameters, σ and s, of the guest residues. The experimental data indicate that, in the nonaqueous solvent, the L-alanine residue stabilizes the α-helical conformation more than the L-leucine residue does. This is in contrast to their behavior in aqueous solution, where the reverse is true. The implications of this finding for the analysis of helical structures in globular proteins are discussed.
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  • 121
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The β-coil transition of poly(S-carboxymethyl-L-cysteine) (poly[Cys(CH2CO2H)]) and poly(S-carboxyethyl-L-cysteine) (poly[Cys((CH2)2CO2H)]) was followed by CD, potentiometric titration, and viscosity in the absence of added salt. These different properties give consistent results for poly[Cys((CH2)2CO2H)]. The CD spectra of poly[Cys(CH2CO2H)] change considerably with the degree of neutralization α even for a low-molecular-weight sample incapable of forming the β-structure. Because of the superposition of this additional effect, the dependence of CD on α is inconsistent with titration data for the case of poly[Cys(CH2CO2H)], particularly when the nπ transition is used to follow the β-coil transition. The change of CD inherent to the β-coil transition is characterized by an isodichroic point: 215 nm for poly[Cys((CH2)2CO2H)] and 218 nm for poly[Cys(CH2CO2H)]. A criterion supporting the stacking of the pleated sheet is suggested based on the isodichroic point.
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  • 122
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    Biopolymers 20 (1981), S. 1615-1623 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The nature of peptide bonds in poly(aspartic acid) prepared by debenzylation of poly(β-benzyl-L-aspartate) under various conditions has been studied by means of nmr spectroscopy. It was established that the majority of the polymers prepared, as well as the commercially obtained polymer, contained aspartic acid linked in both α- and β-peptide bonds. The purest polymer, having practically undetectable amounts of β-bond, was prepared by debenzylation by HBr in trifluoroacetic acid. It was established that the β-bonds are formed via succinimides.
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  • 123
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Proton magnetic resonance data have been obtained for 6-methyl-2′-deoxyuridine (dT*), its 3′- and 5′-monophosphates, and its 3′,5′-diphosphate, as well as for the corresponding thymine derivatives. The synthesis of the dideoxynucleoside monophosphates - d(TpT), d(T*pT), d(TpT*), and d(T*pT*) - was accomplished, and spectral data were obtained for these four dimers. The data show that the 6-methyluracil base prefers the syn conformation about the N-glycosyl bond at the monomer and dimer levels. The presence of the syn base leads to increases in the cis couplings of the sugar ring, J1′2″ and J2′3′, which indicate a trend towards eclipsing of the substituents on the C1′-C2′ and C2′-C3′ fragments. This trend is discussed in terms of changes in the pseudorotational parameters which describe the pucker of the ring. The syn base destabilizes the g+ conformer about the C4′-C5′ bond, leading to a preference for the t conformer in all dT* residues at the monomer and dimer levels. Preliminary work on the formation of cyclobutane-type photodimers in d(T*pT) and d(T*pT*) is discussed and presented as evidence for the capability of the syn 6-methyluracil base to form base-stacked complexes.
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  • 124
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    Biopolymers 20 (1981), S. 1727-1739 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A complete conformational analysis of B-type DNA was carried out in the independent two-dimensional surface of the hexa-dimensional conformational space of the helical structures. A theoretical double-helical model was derived by locating the deepest minimum of the conformational energy. It is similar to that obtained by x-ray refining methods; significant differences seem to be supported by relevant experimental data. Examination of the energy map allows a direct estimate of the flexibility limits of B-DNA, which are found to be consistent with a smoothly supercoiled DNA in chromatin. The structure of the hypothetical left-handed B-type DNA was predicted to be as stable as the standard right-handed model at high ionic strength. Left- and right-handed helices are, however, not interconvertible without separation of the strands, and mixing of opposite screw sense fragments is unlikely to give coaxial helices, which would prevent their packing in fibers.
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  • 125
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    Biopolymers 20 (1981), S. 1785-1791 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 1. The extent of racemization and the coupling yield in peptide synthesis were studied under high dilution conditions. The azide method yielded the best results. 2. Five linear penta-peptide precursors related to gramicidin S were subjected to cyclization in order to study how the difference in the sequence influences the yield and the ratio of cyclic dimer to monomer. The azide with the sequence of -L-Pro-L-Val-L-Orn(Z)-L-Leu-D-Phe- afforded diZ-gramicidin S in a high yield of 63%. 3. Alternaria mali toxin III, a cyclotetradepsipeptide phytotoxin, was synthesized. The activated linear tetradepsipeptide containing a D-Dap(Z) (N3-Z-D-2,3-diaminopropionic acid) residue at the N-terminus afforded the cyclic precursor (53%). The Dap residue in the precursor was converted into a ΔAla residue by Hofmann degradation to give the desired product.
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  • 126
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    Biopolymers 20 (1981), S. 1761-1784 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Striking advances have been made in the synthesis of biologically active peptides. The synthesis of fully active crystalline bovine ribonuclease A by Yajima and Fujii [(1981) Biopolymers 20, 1855-1863] represents an exciting milestone. The main factors contributing to this success include sequential coupling of many small segments and a sophisticated multistage protocol for the final acidolytic cleavage of all protecting groups. However, syntheses of large peptides and proteins and even of many medium-sized peptides continue to present formidable challenges. In peptide coupling the challenge is to join large peptide segments efficiently and in good yields. For solid-phase synthesis the challenge is application of polar supports and alternative Nα-protection. With protecting groups the challenge is to achieve quantitive cleavage at the end of synthesis. Concerning racemization the challenge is to develop sensitive and rapid procedures for measuring racemization during coupling. For purification the challenge is to improve the existing procedures and to search for novel alternative separation principles.
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  • 127
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Attachment of the side-chain carboxyl of the protected aspartic or glutamic acid ester to the resin support has been established for the solid-phase synthesis of the asparagine or glutamine peptide. After further elongation of the α-amino deprotected resin-bound peptide ester with protected peptide fragments and the final detachment from the resin support by ammonolysis, the larger peptides containing, or preferably C-terminated with, asparagine or glutamine could be obtained. Thus, the C-peptide of human proinsulin was prepared by coupling to the resin-bound dipeptide derivative, Leu-Glu(OCH2Ph®)·OtBu, with six fragments consecutively. It was obtained in an overall yield of 36% after detaching from the resin with alcoholic ammonia, followed by mild acidolysis, DEAE cellulose chromatography, and gel filtration. This procedure has now been applied to the synthesis of the C-terminal fragment of the insulin A chain ending in asparagine, and also to the synthesis of the threonine or serine peptide, where the anchorage to the resin was designed by the reaction of the sidechain hydroxyl with succinic anhydride in the presence of 4-dimethylaminopyridine to form the hemiester of succinic acid, which in turn was condensed to the aminomethyl resin by the DCC-HOBt procedure. Model experiments on the synthesis of the Z-Thr(CO-CH2CH2CONHCH2Ph®)·OtBu and Bpoc-Lys(Boc)-Thr(COCH2CH2CONHCH2Ph®)·OtBu, as well as their detachment from the resin by amminolysis or hydrazinolysis, have shown the potential for a milder process in the solid-phase synthesis of larger peptides.
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  • 128
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    Biopolymers 20 (1981), S. 1913-1920 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: β-Turns are a common feature of cyclic peptides, but judging from recent x-ray and solution studies of cyclic hexapeptides it is not always possible to predict in advance the type of turn and the position of the turns in the sequence. Two or more backbone conformations containing β-turns may be of comparable energy and in rapid solvent- and temperature-dependent equilibrium in solution. The use of differential relaxation effects produced by a nitroxyl radical to locate β-turns with only minor perturbation of such equilibria is noted. Examination of the effect of a nitroxyl on the N-H resonances of the decapeptide hormone luteinizing hormone releasing hormone supports a dominant conformation with a β-turn at Gly6-Leu7. Although this turn is probably part of the biologically active conformation, it is not obvious in the more active [D-Ala6] analog.
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  • 129
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A quinoxaline antibiotic triostin A has a bicyclic octadepsipeptide structure. Proton and carbon-13 nmr spectra showed the presence of two symmetrical conformations favoring polar and nonpolar solvents, respectively. They interconvert slowly on the nmr time scale, and this slow interconversion is due to the cooperative effects of the presence of the quinoxaline ring and the N-methyl peptide bonds. Reversal of the chirality of the disulfide bond as the origin of the slow exchange was excluded by the presence of two conformers for S-benzyltriostin A. Conformer 2, which favors the polar solvent, can form hydrogen-bonded complexes with purine nucleoside derivatives in organic solvents, but conformer 1 does not. The binding sites were elucidated and a mode of interaction with DNA proposed.
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    Biopolymers 20 (1981), S. 2001-2010 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: There is a general parallelism in the strategy followed in the design of hormonal peptide analogs and protease inhibitors. However, in the latter, one more dimension has been added with the development of mechanism-based inhibitors, a dimension that is not yet available for hormonal peptides because of the lack of knowledge about receptor mechanisms. The recently advanced concepts of transition state and bi-product analogs have made possible the development of highly potent active-site directed reversible protease inhibitors of great therapeutic potential.
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  • 131
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    Biopolymers 20 (1981), S. 2021-2031 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Two-dimensional nmr techniques have been carried out for the peak assignment of the spectrum of a somatostatin analog. Two-dimensional J-resolved spectroscopy simplified the rather broad and complicated spectrum to show the center of chemical shifts of each resonance and gave information on the coupling profiles. Another technique, two-dimensional spin-echo correlated spectroscopy, revealed the connectivities between protons which are correlated by weak spin-spin couplings. The combination of the results of these two complementary techniques made it possible for us to assign almost all peaks of the spectrum of the 11-residue somatostatin analog.
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    Biopolymers 20 (1981), S. 2093-2120 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effect of excluded volume on the thermodynamic activity of globular macromolecules and macromolecular complexes in solution is studied in the hard-particle approximation. Activity coefficients are calculated as a function of the fraction of total volume occupied by macromolecules using relations obtained from scaled particle and lattice models. Significant and readily observable effects are predicted to occur as the fraction of volume occupied by globular macromolecules increases, including the following: (i) Compact quasi-spherical macromolecular conformations become increasingly energetically favored over extended anisometric conformations. (ii) Self- and heteroassociation processes are enhanced, particularly those leading to the formation of compact quasi-spherical aggregates. (iii) Depending upon the details of the reaction mechanism, the rate of an enzyme-catalyzed reaction may monotonically decrease, go through a maximum, or exhibit more complex behavior. A given degree of volume occupancy by larger macromolecules is predicted to have less effect on the structure and self-association of smaller macromolecules than the same degree of volume occupancy by smaller macromolecules has on the structure and self-association of larger macromolecules.
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    Biopolymers 20 (1981), S. 2143-2163 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Measurements have been made on the flow dichroism of T7 DNA as a function of NaCl concentration. In high salt, our results are compatible with an optical factor of -1.4 and a persistence length of 470 Å. The former is in agreement with expectations from the x-ray diffraction structure of fibrous B-DNA, and the latter is in the midrange of recent determinations. As salt concentration is decreased, the persistence length increases. The relation of our study to other recent investigations and with current theories of the electrostatic contribution to persistence length is discussed. We note that the separation of the electrostatic expansion factor into long- and short-range effects is somewhat arbitrary and might affect the interpretation of different experimental results in different ways. Finally, our hydrodynamic factors are consistent with a chain which is partially free-draining. This goes against the traditional interpretation but is in agreement with two recent observations.
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  • 134
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    Topics: Chemistry and Pharmacology
    Notes: The conformations of a pentapeptide L-His-L-Arg-L-Trp-Gly with weak adrenocorticotropin (ACTH) activity and its analogs, where each L-amino acid residue is substituted by D-residue, were investigated by means of proton and carbon-13 nmr spectroscopy on their DMSO-d6 solutions. The spectra indicated the presence of slowly exchangeable conformation isomers for D-Phe and D-Arg analogs, due to steric hindrance around the arginine residue. The activation energy of the hindered rotation of the arginine side chain was estimated to be more than 19 ∼ 20 kcal/mol. Spin-lattice relaxation times of carbon-13 nuclei also indicated slow segmental motion of the arginine side chain of the D analogs. An effect on proton chemical shifts by intermolecular electrostatic interaction between the arginine side chain and the C terminal carboxylic residue was observed. We did not observe, however, a direct correlation between pentapeptide activity and molecular conformation at this stage of the experiments.
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  • 135
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    Topics: Chemistry and Pharmacology
    Notes: Simultaneous curve fitting for the ionization parameters of oxidized and reduced horse heart cytochrome c in 0.15M KCl and 20°C yields values for the ionization constants (as pK′) and the heats of ionization (ΔHi) which can reconstruct either the potentiometric or thermal titration curves. Reduced cytochrome c requires 8 sets of groups, whereas oxidized cytochrome c requires 10 sets of groups. The additional groups in the oxidized preparation appear to involve the ferriheme (pK′, 9.25; ΔHi, 13.7 kcal/mol) and a tyrosine (pK′ ≃ 10.24) that is not present in the reduced form. The potentiometric and thermal difference curves (reduced - oxidized) involve the appearance of 17 kcal/mol centered at pH 9.7 and 5.8 kcal/mol centered at pH 4.9. The carboxyl groups in both species appear to be normal for the hydrogen-bonded form. Only one histidine has normal ionization properties (pK′, 6.7; ΔHi, 7.5 kcal/mol), as do 17 of the lysine residues (pK′, 10.8; ΔHi, 11.5 kcal/mol).
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  • 136
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    Biopolymers 20 (1981) 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 137
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    Biopolymers 20 (1981), S. 2369-2380 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Transient electric birefringence measurements of the rotational diffusion constant of five short restriction fragments of the plasmid pBR322 show that the hydrodynamic length is independent of sodium ion concentration in the range of 0.2 to 2.5 mM. The fragments are too stiff to be modeled as wormlike molecules. The rotational relaxation times of the fragments, which range from 64 to 124 base pairs, have been used to calculate the rise per base pair using six different theoretical expressions for the length dependence of the rotational diffusion coefficient of straight cylinder. The best estimate for the rise per base pair of Na-DNA in solution is 3.3 ± 0.1 Å.
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    Biopolymers 20 (1981) 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 139
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    Biopolymers 20 (1981), S. 2509-2531 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The thermodynamic parameters for the double-strand formation of the molecules rCAmG + rCUnG, m,n = 5-7, and dCAmG + dCTnG, m,n = 5,6, were measured from optical melting curves. Normal helices are formed when m = n. The deoxyoligomers are more stable than the ribo-oligomers, due to a more favorable enthalpy. Double helices with mismatched bases can be formed by mixing oligomers with m ≠ n. Such helices may form several possible structures. A structure with a dangling base is favored over a structure with a bulged base. The destabilization of the double strands by the formation of a bulged base was determined to be greater than 1.6 kcal/mol at 10°C. The extent of aggregation in the oligomer double strand rCA7G·rCU7G was determined using ultracentrifugation equilibrium. The possible effects of aggregation on the determination of the thermodynamic parameters for double-strand formation are discussed.
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    Biopolymers 20 (1981), S. 2635-2648 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An azo pyrimidine nucleotide has been prepared and enzymatically attached to oligo(A) primers. The nucleotide's azo pyrimidine group has previously been shown to initiate polymerization of methacrylate esters designed to bind marker groups for visualization by microscopy. When attached to RNA molecules complementary to a chromosomal DNA segment, these nucleotides may allow localization of the DNA segment following in situ hybridization of the probe, methacrylate polymerization, and marker attachment. Since mRNA molecules of potential interest as probes bear a 3′-poly(A) tail, the modified nucleotides were added to oligo(A) primers as models. First, N4-ureidocytosine nucleotides were enzymatically added to ApApA, (Ap)9A, or [5′-32P]-(pA)10, using the modified cytidine 5′-diphosphate and “primer-dependent” polynucleotide phosphorylase (M. luteus). In the case of the ApApA-primed reaction, the N4-ureidocytosine nucleotides in the product polynucleotide were converted into azo nucleotides by oxidation with N-bromosuccinimide. The other two primers were employed to study the time course of polynucleotide formation and to verify that primer was indeed being utilized by the enzyme. The suitability of the modified nucleotide for in situ hybridization studies was examined. Poly(N4-ureidocytidylic acid) was prepared from poly(C) and semicarbazide by the bisulfite-catalyzed transamination reaction. It was found that 95% of the N4-ureidocytosine nucleotides in this polynucleotide survive the elevated temperatures typically required for DNA:DNA denaturation and RNA:DNA annealing. When poly(N4-ureidocytidylic acid) was mixed with poly(I) in buffered aqueous salt solutions, no evidence for hybridization was found, so binding of the probe RNA to the denatured chromosomal DNA molecule via the modified nucleotides is not expected. Upon oxidation of poly(N4-ureidocytidylic acid) with N-bromosuccinimide, the azo nucleotides were formed, as judged by the appearance of a characteristic peak at approximately 350 nm in the uv-absorption spectrum of the yellow-orange product, azoRNA. The azo nucleotides in azoRNA exhibited the expected acid lability, which is known to be accompanied by 1-glyceryl methacrylate polymerization in the case of the simple azo pyrimidine. Because 1-glyceryl metharcylate bears substituent glycol groups for attaching heavy atoms or fluorescent markers, it is possible that probe RNA molecules bearing azo nucleotides may be useful for localizing low-multiplicity genes along eukaryotic chromosomes.
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    Biopolymers 20 (1981), S. 2671-2690 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We show that the persistence length a of DNA, derived from total intensity laser light scattering of linear Col E1 DNA and corrected for excluded-volume effects, varies from about 68 nm in 0.005M NaCl to about 40 nm in 0.2M NaCl, leveling off to a constant value (about 27 nm) at high NaCl (1-4M) concentration. These observations do not agree with current views on the effect of electrostatic charge and ionic conditions on DNA dimensions. The apparent diffusion constant Dapp, determined from laser light scattering autocorrelation as a function of scattering vector q, at NaCl concentrations 0.005-4M, correctly yields the translational diffusion coefficient Dt at low values of q and scales with molecular dimensions rather than segment length at high values of q; thus, Dapp/Dt yields a universal curve when plotted against q2Rg2, where Rg is the radius of the gyration. The sedimentation coefficients s at 0.1 and 0.2M NaCl concentration closely agree with the well-tested empirical relations, and a combination of s, Dt, and the appropriate density increments yield correct molar masses over the whole salt concentration range. Approximate constancy of DtRg indicates limited draining in translational flow. We present some observations and thoughts on the regimes in which a dependence of the correlation decay times on q3 rather than q2 applies. We conclude that quasielastic laser light scattering discloses little information about dynamics of internal motion of DNA chains.
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  • 142
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    Biopolymers 22 (1983), S. xi 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 143
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    Biopolymers 22 (1983), S. 33-36 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Potential-energy calculations are reported on the interaction between two collagenlike triple-stranded poly(Gly-L-Pro-L-Pro) helices. Short helices can pack in a variety of orientations, but there is a unique parallel packing arrangement of the two helices for longer polypeptide chains.
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    Biopolymers 22 (1983), S. 43-47 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The lattice model of Flory has been extended in order to consider equilibrium between isotropic and nematic phases containing helix-coil type chains. Nearly complete exclusion of coil sequences from the lyotropic nematic phase produces an enhanced cooperativity in the helix-coil transition. In poor solvents this enhancement begins to occur at concentrations typical of some experiments.
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  • 145
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    Topics: Chemistry and Pharmacology
    Notes: The major unfolded form of ribonuclease A is known to show well-populated structural intermediates transiently during folding at 0°-10°C. We describe here how the exchange reaction between D2O and peptide NH protons can be used to trap folding intermediates. The protons protected from exchange during folding can be characterized by 1H-nmr after folding is complete. The feasibility of using 1H-nmr to resolve a set of protected peptide protons is demonstrated by using a specially prepared sample of ribonuclease S in D2O in which only the peptide protons of residues 7-14 are in the 1H-form. All eight of these protected peptide protons are H-bonded. Resonance assignments made on isolated peptides containing these residues have been used to identify the protected protons. Other sets of protected protons trapped in the 1H-form can also be isolated by differential exchange, using either ribonuclease A or S. Earlier model compound studies have indicated that H-bonded folding intermediates should be unstable in water unless stabilized by additional interactions. Nevertheless, peptides derived from ribonuclease A that contain residues 3-13 do show partial helix formation in water at low temperatures. We discuss the possibility that specific interactions between side chains can stabilize short α-helixes by nucleating the helix, and that specific interactions may also define the helix boundaries at early stages in folding.
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    Biopolymers 22 (1983), S. 93-99 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Denaturation profiles of 17 globular proteins were studied by the spectroscopic and chromatographic methods with high-data-point density. The denaturational transitions are broadly classified into three types according to their multiphasic characteristics. In general, more or less complex internal cooperative events seem to take place in the conformation transition of globular proteins.
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  • 147
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    Topics: Chemistry and Pharmacology
    Notes: We report on the effects that the presence of ethylene glycol or glycerol has on the oxygen affinity of hemoglobin. We attribute these effects to an altered equilibrium between T and R quaternary conformations of hemoglobin and separate them into bulk-electrostatic and non-bulk-electrostatic contributions to the standard free-energy difference between the R and T states.
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    Biopolymers 22 (1983), S. 139-145 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The 270-MHz proton-nmr spectra of short neurotoxins (erabutoxins from Laticauda semifasciata and cobrotoxin from Naja naja atra) and long neurotoxins (toxin B from Naja naja and α-bungarotoxin from Bungarus multicinctus) have been analyzed. The conformation of erabutoxin b in solution is largely consistent with the x-ray crystal analysis, although the environment of His-7 in solution is definitely different from that in the crystal. The pH-dependent transition has been found for toxin B, indicating that the conformation in neutral solution is different from that in the crystal as grown from acidic solution. The deuterium-exchange rates of the amide protons for the four neurotoxins have been measured. The order of structural rigidity is the same as the order of the irreversibility of neuromuscular block by neurotoxins.
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    Biopolymers 22 (1983), S. 163-169 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformational studies on poly(oxyethylene)-bound homo-, oligo-, guest-host, and sequential peptides synthesized according to the liquid-phase method were carried out by means of 1H-nmr spectroscopy. The solubilizing effect of the C-terminal polymeric support allowed a thorough investigation of the secondary structure in solution.
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    Biopolymers 22 (1983), S. 217-225 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A vibrational force field for the polypeptide chain has been developed for normal-mode analysis of such molecules. It can reproduce observed frequencies of known structures to within about 5 cm-1. We review the application of this technique to conformational problems in peptides (β-turns and their model compounds), polypeptides [the αII-helix and crystalline poly(glycine II)], and proteins (bacteriorhodopsin and glucagon).
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    Biopolymers 22 (1983), S. 247-253 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 1H-nmr studies of [pGlu6]SP6-11, [gpGlu6,mPhe7]SP6-11, and [pGlu6,N-CH3Phe7]SP6-11 in DMSO-d6 reveal characteristic chemical shifts, 3JNH-αCH, temperature dependence, as well as deuterium exchange half-times. Marked similarities are revealed for the two first analogs, whereas the N-methylated analog is clearly different. Possible conformations are considered.
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  • 152
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    Topics: Chemistry and Pharmacology
    Notes: The 36-amino acid avian pancreatic polypeptide has been studied by x-ray analysis at 0.98-Å resolution and refined using a restrained least-squares technique to an agreement factor of 15.6%. The polypeptide, which has a compact globular structure with a hydrophobic core, comprises a polyproline-like helix (residues 2-8) and an α-helix (residues 14-32). The molecule forms symmetrical dimers linked through zinc atoms in the crystal lattice. The high-resolution analysis defines sequence-dependent distortions in the α-helical parameters due to hydrogen bonding of water molecules and side chains. The thermal parameters indicate an increased flexibility of the main chain at the turn between the helices and in the C-terminal residues. For the first time, six-parameter anisotropic thermal ellipsoids have been refined for each atom; these define the directions of the molecular motions in the polypeptide, indicating concerted vibrations. The physiological roles of conformation, flexibility, and dynamics of this polypeptide hormone are discussed.
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  • 153
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    Topics: Chemistry and Pharmacology
    Notes: We have carried out a systematic analysis of the solid-state conformational preferences of a number of linear homo-oligoprolines (to the tetramer) by ir absorption and x-ray diffraction. The peptides present different chiral sequences (tacticities), various types (urethane and amide) of N-protecting groups, and free and blocked C-termini (which imply different capabilities of forming H-bonds). The following conclusions can be drawn: (i) values for the geometry of the prolyl residue and the peptide bond in the cis and in the trans conformations are proposed; (ii) in general the conformational angles ϕ and ψ in the linear homo-oligoprolines have values appropriate for the polyproline II structure (conformation F); (iii) the pyrrolidine ring shows various types of puckering with no apparent relation to the backbone conformation; (iv) Pro-Pro peptide bonds generally take the trans conformation, the few cases of cis conformation being formed by Pro residues of different chirality; (v) the single H-bond donor  -  OH, when present, is always bonded to H-acceptors, which can be either the urethane or the amide or the peptide carbonyl but never the carbonyl group of the  -  COOH moiety.
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  • 154
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    Biopolymers 22 (1983), S. 377-380 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Myelin basic protein isolated from bovine white matter is known to consist of a mixture of three or more “charge isomers”, which can be separated by cation-exchange chromatography. We are using 360-MHz 1H-nmr spectroscopy to establish the chemical and structural differences among them. Preliminary studies by difference spectroscopy between two of the isomers suggest (a) all aromatic residues, and probably their nearest-neighbors, are unchanged; (b) the less cationic isomer lacks one (or two) of its C-terminal Arg residues; and (c) a significant fraction of the two Met residues in the less cationic isomer is present as methionine sulfoxide.
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  • 155
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: A hydrophobic linear peptide has been synthesized and studied over a range of environments using several complementary spectroscopic approaches, including nmr, CD, and vibrational spectroscopies. The sequence of this model peptide, carbobenzoxy-L-Pro-D-Phe-D-Ala-L-Pro-NHCH3, was designed such that a small number of “folded” conformations, stabilized by intramolecular hydrogen bonding, would be accessible to it. Additionally, the extremely hydrophobic character of the peptide favors its interactions with hydrophobic regions of a membrane. The conformational impact of the membrane environment on the peptide, and the effect of the peptide on lipid organization have been explored both in micellar media and in vesicles. To facilitate nmr analysis, the peptide has been synthesized with one of the prolines perdeuterated. Results of these studies reveal that the peptide experiences a microenvironment of moderate polarity in micellar media and causes changes in lipid structure in a vesicle that are indicative of a hydrophobic peptide-lipid interaction.
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    Biopolymers 22 (1983), S. 425-440 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Most of a protein surface is potentially antigenic, consisting of numerous overlapping domains each complementary to antibody-combining sites. These domains may include peptide sequences that are demonstrably antigenic but only when antibodies from the appropriate host individuals and species are used. Methods for locating antigenic peptide sequences are described in which hydrophilic polyamide supports are used for peptide synthesis, then solid-phase radioimmunoassay with antisera and protein A. Most antigenic domains, however, comprise amino acid side chains contributed by two or more nearby polypeptide chains. Such domains can be identified by comparing the cross-reactivities of groups of very closely related proteins towards monoclonal antibodies raised to one of them. Such studies, using myoglobins, have identified a number of residues not previously shown to be antigenic and have provided a guide for the choice of synthetic peptides which are likely to carry several immunodominant side chains. One such peptide corresponding to residues (72-89) of beef myoglobin has been shown, using CD and antibodies to the parent protein, to have interesting conformational and antigenic properties. The peptide (25-55) is also antigenic.
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  • 157
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: A series of novel, functionalized catecholamines (congeners) has been synthesized in which, formalistically, the N-isopropyl group of isoproterenol has been extended by a linear alkyl chain of varying length, terminated by a carboxyl group. Model amide derivatives have also been prepared in order to optimize the biological activity of these derivatives and also to aid in the design of appropriate peptides for the synthesis of conjugates. As a result of these studies, a series of amino acid and monodisperse peptide carriers, containing p-aminophenylalanine as the point of attachment for the drug, was prepared, together with the corresponding conjugates. In vitro and in vivo evaluation of the congeners, model amides, and conjugates has demonstrated that the biological activity of these derivatives is extremely sensitive to structural modifications at a point far-removed from the pharmacophore, in both the congener amide and conjugate series. A number of the model amides and conjugates have proven to be highly active when tested in both in vitro and in vivo test systems. The implications of these results in terms of a novel structure-activity approach to drug design are discussed.
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  • 158
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    Biopolymers 22 (1983), S. 557-567 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Antineoplastic drugs such as daunomycin, adriamycin, methotrexate, 5-fluorouridine, cytosine arabinoside, and platinate were bound to antibodies directly or via a polymeric bridge. The drug antibody conjugates retained most of their drug and antibody activities when tested in vitro. Daunomycin-antibody conjugates were shown to penetrate tumor cells in the conjugated form. In animals, daunomycin-antibody conjugates were at least as effective chemotherapeutically as the corresponding free drugs and considerably less toxic. In some tumor systems, the daunomycin-antibody conjugates represented an improvement over the free drug. This improvement was restricted in some tumors to a particular injection route of the tumor and the treatment.
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  • 159
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We describe a synthetic method aimed at specifically coupling poly(ethylene oxide) (PEO) to proteins without altering their spectroscopic properties. To do so, we have first modified the alcohol end group of PEO to an acid end group (PEO-COOH). Coupling of PEO-COOH to Gly A1 methylsulfonylethyloxycarbonyl (Msc) protected insulin yielded NαB1,N∊B29-(PEO)2-insulin. Conversely, coupling of PEO-COOH to insulin whose Gly A1 and Lys B29 amino groups were protected with Msc yielded NαB1-PEO-insulin. The products were obtained in a spectroscopically pure form and characterized by uv and CD spectroscopy. Conformational and biological studies are in progress.
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  • 160
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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  • 161
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    Biopolymers 22 (1983), S. 633-641 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The crystal structure and conformation of the synthetic cyclic tetrapeptide, cyclo(L-Pro-Sar)2, was determined by x-ray analysis. The peptide crystallizes in the orthorhombic space group P212121 with cell parameters a = 9.277(1), b = 12.884(1), and c = 15.581(2) Å. The crystal structure was solved by the symbolic addition procedure for direct phase determination and least-squares refinement using 1796 reflections, which led to the final R value of 0.043. This structure provides the first example observed in a crystal of a cyclic tetrapeptide in which all four peptide units have been found in the cis conformation with ω angles deviating slightly by 2°-10° from the ideal value of 0°. It was also found that the two Pro Cα-CO single bonds assumed a trans′ (ψ = 159.6° and 158.4°) conformation. Adjoining average planes of the peptide groups fall at nearly right angles to each other. The pyrrolidine ring conformations of the two prolyl residues are in the envelope form, with Cγ carbon out of the least-squares planes for the remaining four atoms.
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  • 162
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Molecular-mechanics calculations have been carried out on the base-paired hexanucleoside pentaphosphates d(TATATA)2, d(ATATAT)2, d(A6)·d(T6), d(CGCGCG)2, d(GCGCGC)2, and d(C6)·d(G6) in both A- and B-DNA geometries. The calculated relative energies of these polymers are consistent with the relative stabilities of the polymers found experimentally. In particular, the results of our calculations support the observation that the homopolymer d(A)n·d(T)n is more stable in a B-DNA conformation, while the homopolymer d(G)n·d(C)n is more stable in an A-DNA conformation. The molecular interactions responsible for these differential stabilities include both inter- and intrastrand base stacking, as well as base-phosphate interactions. While definitive experiments on the heteropolymer stabilities have not yet been carried out, the results of our calculations also suggest a greater stability of the purine-3′,5′-pyrimidine sequence over the pyrimidine-3′,5′-purine sequence in both the A- and B-conformations. The reason for this greater stability lies in the importance of the inherent directionality (5′ → 3′ vs 3′ → 5′) of phosphate-base and base-base interactions. The largest conformation change observed on energy refinement is sugar repuckering, which occurs mainly on pyrimidine-attched sugars and only in the B-DNA geometry. We suggest a molecular mechanism, specifically, differential base-sugar steric interactions involving neighboring sugars, to explain why this repuckering occurs more with d(A6)·d(T6) than with other isomers.
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  • 163
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    Biopolymers 22 (1983), S. 879-893 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We examined three sonicated, specific-seqiemce polydeoxynucleotides in solution over a wide range of concentrations of several salts by 13P-nmr spectroscopy, and we found that the alternating copolymer poly(dAdT)·poly(dAdT) exhibits a dinucleotide repeat unit in all five salts and at all concentrations studied, as indicated by the presence of a doubled in its 31P-nmr spectra. The two components of the doublet show selective shift effects. The upfield component is assigned to dApdT in the gauche--gauche- conformation and shifts upfield in all four monovalent salts used, relative to a single-stranded oligonucleotide control. The downfield component is assigned to dTpdA in the trans-gauche- conformation and shifts downfield with increasing CsF concentration but remains essentially constant in LiCl, NaCl, and CsCl. These changes indicate a fast noncooperative transition for poly(dAdT)·poly-(dAdT) from a presumed right-handed dinucleotide-repeat B-form to another conformation with a dinucleotide-repeat structure, via a continuum of structures that may differ in the extent of the winding of the double helix. Ethanol causes the upfield component to collapse into the other component, indicating conversion to a structure with a mononucleotide repeat unit and a trans-gauche- conformation. Up to 1M Mg2+ appears to have no significant effect on the phosphodiester conformations of poly(dAdT)·poly(dAdT). By contrast, poly-(dGdC)·poly(dGdC) gives a slow cooperative transition from what is considered to be a right-handed regular B-form to a left-handed Z-form on increasing MgCl2 and NaCl concentrations, although we observed no changes in chemical shifts below the transition points. The homopolymer poly(dA)·poly(dT) exhibits no unusual shift effects or transitions upon the addition of salts when compared to the oligonucleotide control and is considered to be a regular B-form with a gauche--gauche- phosphodiester backbone conformation. These differences emphasize the distinct secondary structures of DNAs of different sequences and their selective responses to changes in solution conditions.
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  • 164
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Seven dinucleoside monophosphates containing 2′-halogeno-2′-deoxypurine nucleoside residue, dAfl-U, dAcl-U, dAbr-U, dAio-U, dGfl-U, and dIfl-C, were chemically synthesized and investigated by 1H-nmr spectroscopy at 300 MHz. The sugar and backbone conformations of these compounds were analyzed by the spectral pattern of furanose proton resonances; and the extents of base-base interaction were estimated from chemical shifts and their temperature-dependent changes of base-proton resonances. It is found that the population of C3′-endo conformer and the extent of base-base interaction decrease as the electronegativity of 2′-substituent decreases in dAx-U (x = fl, cl, br, and io) series. The C3′-endo (3E) population and the base-base interaction in Nfl-U (N = A,G)-type dimers as well as dIfl-C are relatively higher than the corresponding natural ribo-dimers but can be recognized as grossly similar to the conformation of regular RNA dimers.
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  • 165
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    Biopolymers 22 (1983) 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 166
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    Biopolymers 22 (1983), S. 1267-1283 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We studied the Raman spectra of the zwitterionic glycylglycine crystal (GG) and its N-deuterated analog. A normal coordinate analysis on its α-crystalline form was performed and the effects of intra-and intermolecular couplings are discussed. A modified Urey-Bradley potential was used as a model of the intramolecular force field. Factor group splittings are described by the use of intermolecular potentials consisting of nonbonded atom-atom interactions and dipole-dipole interactions. Effects of hydrogen bonds on the vibrational frequencies of amino and carboxylate groups are also analyzed.
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  • 167
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    Topics: Chemistry and Pharmacology
    Notes: The ir absorption and CD conformational analyses of solutions of the protected 2-9 fragment of the peptaibol antibiotics emerimicins III and IV \documentclass{article}\pagestyle{empty}\begin{document}$ \rlap{--} (Aib_3 \rlap{--} )L - Val - Gly - L - Leu\rlap{--} (Aib_2 \rlap{--} ) $\end{document} and related short sequences are consistent with the presence of a right-handed α-helix for the octapeptide, while the tri-, tetra-, and pentapeptides adopt a 310-helix, either right- or left-handed, depending on the amino acid sequences. The structural preferences of solid-state \documentclass{article}\pagestyle{empty}\begin{document}$ Z\rlap{--} (Aib_3 \rlap{--} )L - Val - OMe $\end{document} and \documentclass{article}\pagestyle{empty}\begin{document}$ Z\rlap{--} (Aib_3 \rlap{--} )L - Val - Gly - OMe $\end{document} have been determined by x-ray diffraction. In accord with the solution data, incipient 310-helices, formed by two and three β-turns, have been found for the tetra- and pentapeptides, respectively. The tetrapeptide helix has the left-handed screw sense, while that of the pentapetide is right-handed, thus confirming the conclusions of the CD analysis of the solution.
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  • 168
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    Biopolymers 22 (1983), S. 1401-1407 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Isomeric oligopeptides composed of five methionyl residues and one glycyl residue or of five γ-methyl-L-glutamyl residues and one glycyl residue all exhibit marked differences in retention on normal-phase silica. When the glycyl residue is at internal positions of hexa or heptapeptides, the peptide elutes most rapidly form the μPorasil column. Comparison of the effect of positional isomerism on retention in short oligopeptides with the effect on retention of hexamers and heptamers suggests that a change in peptide conformation may be responsible for the change in oligopeptide mobility.
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  • 169
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    Biopolymers 22 (1983), S. 1319-1334 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The CD spectrum of an enzymatically derived sodium hyaluronate (NaHA) segment preparation with chain length 18 ± 3 disaccharide units [NaHAseg, ( NaGlcUA GlcNAc)15-20°. NaGlcUA, sodium D-glucuronate; GlcNAc, 2-acetamido-2-deoxy-D-glucose] in H2O was recorded to 180 nm using a computer-controlled vacuum-uv CD instrument. Near 190 nm the spectrum is of low intensity, similar to the sum of the free monosaccharide contributios, attributed to the π-π* transitions of the acetamido and carboxylate substituents. In contrast, much smaller oligosaccharides, also derived from high-molecular-weight NaHA by enzymatic digestions, show CD spectra in H2O with prominent bands centered near 190 nm. The oligosaccharide spectra can be matched as linear combinations of interior sugar residue (= NaHAseg) and end sugar residue CD contributions. End residues from oligosaccharides of the type (NaGlcUA-GlcNAc)n show a negative CD band near 190 nm. End residues from oligosaccharides of the reverse sequence (GlcNAc-NaGlcUA)n show a positive CD band near 190 nm. Averaging of the two end-residue spectral contributions yields an approximate match for the spectrum of NAHAseg below 200 nm. It is proposed that the low intensity CD of NaHA in the π-π* region is the result of large-magnitude, oppositely signed contributions, which can be visulized by studying oligosaccharides.
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    Biopolymers 22 (1983), S. 1383-1399 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of a crystalline cellulose II-hydrazine complex has been determined by x-ray diffraction methods as part of an investigation of cellulose-solvent interaction. The complex studied was that formed when Fortisan fibers were swollen in hydrazine and then vacuumdried. The unit cell is monoclinic with dimensions a = 9.37 Å, b = 19.88 Å, c = 10.39 Å, and γ = 120.0° and contains disaccharide segments of four chains, with one hydrazine per glucose residue. In view of the limited x-ray intensity data, the structure has been determined based on an approximate unit cell containing two chain segments, with a = 4.69 Å, using the linked-atom least-squares refinement procedures. The refined model contains antiparallel cellulose chains that are linked by both intermolecular hydrogen bonds and hydrogen-bonded hydrazine molecules. The parallel chains in the 020 planes are packed in register, leading to stacks of chains analogous to those in chitin. All the hydroxyl groups are satisfactorily hydrogen-bonded, and each hydrazine forms four donor and two acceptor hydrogen bonds, including an N—H…N bond between hydrazines. From this work it can be seen that the interaction of cellulose II with hydrazine involves scission of the intermolecular hydrogen bonds followed by disruption of the stacks of quarter-staggered chains. The latter effect is probably necessary for hydrazine to act as a cellulose solvent.
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    Biopolymers 22 (1983), S. 1445-1448 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    Biopolymers 22 (1983), S. 1489-1498 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Empirical force-field calculations and ir and 1H-nmr spectra indicate that five-membered (C5) and seven-membered (C7eq) hydrogen-bonded rings are the preferred conformations of acetyl-L-Phe p-acetyl and p-valeryl anilides in nonpolar media. The C5/C7eq ratio was found to be dependent on the dryness of the solute and the solvent. This fact and the results from conformational-energy calculations suggest that a molecule of water participates in the stabilization of the C7eq conformation.
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    Biopolymers 22 (1983), S. 333-339 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction of the amino terminal half-molecule of histone H4 with duplex DNA has been studied by fiber x-ray diffraction. Changes induced in the diffraction pattern of B-DNA by the presence of the bound peptide have been Fourier-analyzed and the results presented in terms of a deweighted radial projection of the electron density. We conclude that the peptide binds on the major groove side of the sugar-phosphate chain.
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    Biopolymers 22 (1983), S. 355-362 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Recent studies of the neurophysins and associated neuropeptide hormones have addressed both the biosynthetic pathways by which these noncovalent protein-peptide complexes are derived in neurosecretory neurons and the nature of the noncovalent interactions likely to occur during transport and storage in neurosecretory granules within the neurons. In vitro translation of hypothalamic mRNA and sequencing of cDNA obtained from this mRNA have yielded chemical evidence that each complex of hormone and major neurophysin is made through a common precursor molecule. The mature complexes obtained upon proteolytic processing of precursors exhibit interdependent hormone binding and self-association interactions. Photoaffinity labeling and quantitative affinity chromatography have helped detect and define the binding surfaces involved. Further study of the structural nature of these surfaces is being carried out using large neurophysin fragments obtained by limited tryptic proteolysis.
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    Biopolymers 22 (1983), S. 397-402 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Gramicidin A exists in distinctly different conformations in phospholipid vesicles and in organic solvents. These different folding motifs are also reflected in crystals of gramicidin formed in the presence and absence of lipid molecules.
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    Biopolymers 22 (1983), S. 409-414 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Macrocyclic molecules can serve as ion carriers when their polar groups form an inner cage to capture ions while their hydrophobic groups form an outer layer to dissolve the molecule in lipid membranes. A “template method” has been developed for high-yield synthesis of a whole variety of macrocyclic esters, amides, and other families which may show ionophoric properties. In order to select the more promising compounds for synthesis, energetic and conformational characteristics of such molecules have been calculated from empirical energy functions. Calculations are examined using known structures and are employed to predict the properties of molecules not yet synthesized.
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    Biopolymers 22 (1983), S. 453-464 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: For a better understanding of the molecular nature of the antigen-specific T-cell recognition system, continuous T-cell lines specific to the synthetic polypeptide antigen poly(Tyr,Glu)-poly(DLAla)--poly(Lys) [(T,G)-A--L] were established from C3H.SW (high-responder) activated T-cells, cloned, and characterized. These lines and their derived clones are also constitutive secretors of antigen-specific T-cell replacing helper factors. The secreted T-cell helper factor was shown to possess MHC determinants as well as V-region determinants, or more specifically, idiotypic determinants that are cross-reactive with those expressed on (T,G)-A--L-specific antibodies of the same mouse strain. Using the fluorescence-activated cell sorter (FACS II) and individual C57BL/6 anti-idiotypic sera produced against (T,G)-A--L-specific antibodies of C3H.SW origin, we have demonstrated the expression of the cross-reactive idiotypic markers on the monoclonal helper T-cells. Attempts were made to purify the active fraction of the T-cell factors secreted by the (T,G)-A--L continuous helper lines. Gel analysis of the twice affinity-purified eluate of a (T,G)-A--L column revealed the existence of iodinated bands with molecular weight of 17,000 and 15,000, in addition to a diffuse band of high molecular weight. The specific helper activity of the factors was associated with a 65-75% ammonium sulfate precipitate. Gel electrophoresis of the latter fraction, as well as of an eluate of a (T,G)-A--L-Sepharose column indicated that a high-molecular-weight (〈 67,000) and a low-molecular-weight (15,000-17,000) fraction contained the biological activity of the factor. Similar results were obtained following chromatography of the factor on Sephadex G-100 columns. The two fractions were shown to be synthesized by the T-cell lines, as indicated by internal labeling experiments using 35S-methionine. Thus, it is suggested that a fraction of an apparent molecular weight of 15,000-17,000 preserves both the antigen specificity and the helper activity of the factor produced by the (T,G)-A--L-specific T-cell lines.
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    Biopolymers 22 (1983), S. 465-473 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Activation of mutant β-galactosidase by antibodies can be explained by a “selection” mechanism in which the antibody binds and stabilizes those mutants in a native-like conformation and by an “induction” mechanism where binding of the antibody itself induces a conformational change activating β-galactosidase. The “selection” hypothesis was tested by passing β-galactosidase through a column packed with monoclonal antibody-derivatized Sepharose. The antibody retains the active, in preference to the inactive, proteins. The “induction” mechanism was tested by mixing antibody-Sepharose with mutant β-galactosidase and measuring enzyme activity before mixing and that remaining in the supernatant. The activity of the antibody-Sepharose pellet exceeded the sum of the original activity plus supernatant activity. As a result of these experiments, both mechanisms are found to be operative.
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    Biopolymers 22 (1983), S. 507-515 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Eledoisin and ceruletide, two nonmammalian hormonelike peptides, have been explored for possible pharmaceutical application. At present, only a few of the potentialities of the two drugs have been exploited. Eledoisin is used in ophthalmology as a lachrymal secretagogue; ceruletide is applied in the radiological diagnosis of gallbladder, biliary system, and digestive tract disorders, in the study of exocrine pancreatic function, and in the treatment of postoperative paralytic ileus and intestinal hypotony and atony. Possible analgesic and antipsychotic applications of ceruletide are under study. Developments of synthetic and analytical methods for both peptides are briefly reviewed. Technical devices or alternative routes of administration are envisaged in order to enlarge both the present market and the field of application.
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    Biopolymers 22 (1983), S. 1869-1883 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: High-resolution 1H-nmr analyses are presented for partially modified retro-inverso derivatives of peptides with emphasis on enkephalins. Studies in DMSO-d6 reveal the unique as well as common characteristics of the non-amino acid residues incorporated into these modified peptides. The complete assignment of 1,1-diaminoalkyl and malonyl, as well as of amino acid, residues provides the basis for the exploration of the conformational features induced in peptides by such topochemical modifications.
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  • 181
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    Topics: Chemistry and Pharmacology
    Notes: The preceding paper develops the theory for the interpretation of fluorescence photobleaching recovery (FPR) measurements of multiple binding of a ligand to a multivalent substrate molecule. Based on a reasonable assumption about the mechanism of the photobleaching process, this analysis shows that the observed behavior of a multivalent system should be practically identical to that of a univalent binding system. This is in contrast to the expected and observed behavior of fluorescence correlation spectroscopy (FCS) measurments. Experimental FPR measurements of multivalent binding of ethidium bromide to DNA confirm these conclusions. The FCS and FPR measurements also reveal an apparently enhanced diffusion of ethidium at high DNA concentration. This enhancement might result from direct transfer of ethidium among DNA molecules.
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    Biopolymers 22 (1983), S. 2001-2016 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Tm values of 16 fully complementary RNA duplexes with repeating base sequence have been employed as the empirical basis for developing a reliable and practical method for computing apparent enthalpies (ΔHcalc) for their helix → coil transitions. The approach taken is the same as in the accompanying investigation of DNA duplexes, although some of the computational variables of the “best-fit” function are necessarily different due to the distinguishing structural properties of the RNA-type helix. An excellent linear correlation was thus obtained between experimental Tm and ΔHcalc values. An equally good fit was obtained between Tm and ΔHcalc for five unrelated (to the 16 RNAs) decaribonucleotide duplexes. The differences in computational variables between the best-fit methods for RNA and DNA duplexes are shown to be a reflection of differences in cation binding and the effective local dielectric. The greater Tm dependence on G·C content of RNA helices than of DNA helices is shown to be due to a greater latitude of stacking stabilities of complementary dinucleotide fragments containing A·T than A·U base pairs.
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    Biopolymers 22 (1983), S. 2045-2060 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A sharp feature is observed at about 600 MHz in the inelastic scattered light spectrum of fibers of calf thymus DNA. It broadens so as to be no longer distinctly resolved when the ordering of a fiber is disrupted by convection caused by laser heating. To within experimental uncertainties the frequency of this feature is wavevector independent. A possible origin of the feature lies in a defect resonance such as that associated with the chain terminus.
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  • 184
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    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The ir-spectra in the N—H stretching region of Piv-Pro-NHMe and Boc-Pro-NHMe have been studied in carbon tetrachloride and chloroform solutions over a wide range of concentrations. Based on the concentration dependence of the N—H stretching bands, it has been shown that the characteristic N—H stretching band due to the C7 intramolecular hydrogen bond is around 3335 cm-1. Intermolecular hydrogen bonding also occurs to a small extent in these peptides, giving rise to a slight concentration dependence of the N—H stretching bands. The band around 3335 cm-1 need not necessarily be due to C7 hydrogen bonds alone as proposed by Tsuboi et al. or to intermolecular hydrogen bonding alone as proposed by Maxfield et al.; this conclusion is supported by studies on Boc-Leu-NHMe, which undergoes only intermolecular hydrogen bonding. We have shown that Z-Aib-Aib-OMe and Z-Aib-Ala-OMe form C7 intramolecular hydrogen bonds in addition to C5 intramolecular hydrogen bonds. The present studies also show that all the peptides studied exist in more than one conformation in solution.
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  • 185
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    Biopolymers 22 (1983), S. 895-909 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Hydrogen exchange-rate probability density functions for lysozyme have been derived by numerical Laplace inversion with the computer program CONTIN. The resulting solution set includes a smooth bimodal solution in agreement with previous analytical results together with a smooth three-peak solution. Numerical analysis of lysozyme hydrogen-exchange data in glycerol/water cosolvent mixtures confirms the previous assignment of the slow-exchange peak to an exchange mechanism involving reversible unfolding. Physicochemical constrations that can reduce the size of the solution set are described. The results are compared with those obtained from previous analytical methods and the limitations of the discrete class and analytical appraches are discussed.
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  • 186
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    Biopolymers 22 (1983), S. 919-933 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We report the temperature dependence of the H2 and H8 purine ring proton resonances of oligoriboadenylates up to chain length 11, with or without a single guanosine residue at the 5′-end, second position, or 3′-end. The results suggest the following generalizations: (1) Stacking of the bases in a right-handed single-stranded helix is more extensive in the interior of the chain than at the chain ends. (2) The tendency of the terminal base to unstack is greater at the 5′-end than at the 3′-terminus. (3) G stacks more weakly than A, as evidenced by weak stacking of 3′-terminal G. Anomalies were also observed in the unstacking profile of G at the second position in the chain, indicating a conformational anomaly such as looping out of G, thereby allowing adjacent A's to stack together, or adoption by G of some other alternative structure. (4) The results imply that the environment at a given base is influenced by effects of longer range than nearest- or next-nearest-neighbor. Increasing ion condensation as chain length increases may be responsible for the slow approach of oligomer behavior to the properties of the high polymer.
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  • 187
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    Biopolymers 22 (1983) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 188
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    Biopolymers 22 (1983), S. 1097-1106 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A comparison of the condensation of T4 phage DNA by spermidine and Co(NH3)63+ at pH values between 5.1 and 10.2 has been made using quasielastic light scattering to determine translational diffusion coefficients and Stokes radii. Co(NH3)63+ is more effective than spermidine in causing condensation at all pH, indicating that the differences observed in previous work were not due to pH effects, as might have been inferred from recent theories of intermolecular forces. The DNA particles collapsed with Co(NH3)63+ are smaller than those obtained with spermidine. The hydrodynamic radius of spermide-collapsed structures decreases slightly with increasing pH, while the size of the Co(NH3)63+collapsed structures is almost independent of pH. These results confirm that there are specific ion effects in DNA condensation by oligocations, in addition to the dominant general polyelectrolyte effects.
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  • 189
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Cyclic tetradepsipeptides, AM-toxin I and II, are the host-specific phytotoxins of Alternaria mali. In order to elucidate conformation-toxicity relationships, we analyzed the 270-MHz proton nmr spectra of AM-toxins and hydrogenated analogs, (D-Ala2)AM-toxin I (toxic) and (L-Ala2)AM-toxin I (not toxic), in (C2H3)2SO. These cyclic tetradepsipeptides do not contain N-substituted amino acid residues, and all the peptide and ester groups have been found to be transoid. Two conformers with very unequal populations have been found for AM-toxin I and II; the Cβ=Cα—C=O conformations of the Dha2 residues are nonplanar S-trans in the major conformer and nonplanar S-cis in the minor conformer. Only one ring conformation has been found for each of (L-Ala2) and (D-Ala2)AM-toxin I. (L-Ala2)AM-toxin I takes a C4-type ring conformation; all the C=O groups and Cα-H bonds are oriented to the same side of the ring. (D-Ala2)AM-toxin I takes a new ring conformation; the side chain and C=O group of the L-Amp1 residue are oriented to the same side of the ring. This new conformation is also found for the major conformers of AM-toxin I and II and thus appears to be required for the toxicity. The ring conformations of Tyr(OCH3)1-bearing analog tetradepsipeptides have been found to be much the same as those of Amp1-bearing depsipeptides. Furthermore, on the basis of the two distinct conformations of (D-Ala2) and (L-Ala2)AM-toxin I, an empirical rule is proposed for the stable ring conformations of cyclic tetra-D,L-peptides, not containing N-substituted amino acid residues.
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  • 190
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The kinetics of helix formation were investigated using the temperature-jump technique for the following two molecules: dC-G-T-G-A-A-T-T-C-G-C-G, which forms a double helix containing a G·T base pair(the G·T 12-mer), and dC-G-C-A-G-A-A-T-T-C-G-C-G, which forms a double helix containing an extra adenine (the 13-mer). When data were analyzed in an all-or-none model, the activation energy for the helix association process was 22 ± 4 kcal/mol for the G·T 12-mer and 16 ± 7 kcal/mol for the 13-mer. The activation energy for the helix-dissociation process was 68 ± 2 kcal/mol for the G·T 12-mer and 74 ± 3 kcal/mol for the 13-mer. Rate constants for recombination were near 105s-1M-1 in the temperature range from 32 to 47°C; for the dissociation process, the rate constants varied from 1s-1 near 32°C to 130s-1 near 47°C. Possible effects of hairpin loops and fraying ends on the above data are discussed.
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  • 191
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    Biopolymers 22 (1983), S. 1285-1300 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Raman and ir spectra of the glycyl-L-proline (GP) dipeptide were recorded. A normal-coordinate treatment was performed on the basis of the experimental spectra, using a modified Urey-Bradley force field (MUBFF). Cyclic redundancies were eliminated, and those due to the ring methylene groups, particularly distorted in regard to the tetrahedral conformation, were treated. An assignment of the experimental frequencies is proposed on the basis of the normal treatment.
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  • 192
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Primary and tertiary amine-initiated polymerizations of L-alanine-N-carboxyanhydride (L-Ala-NCA) were conducted at 20 or 100°C in a variety of solvents. The 75.5-MHz 13C-nmr CP/MAS spectra of the resulting poly(L-alanines) revealed that all samples contain both α-helix and pleated-sheet structures. Depending on the reaction conditions the α-helix content varied between ca. 1 and 99%. Reprecipitation from aprotic nonsolvents does not change the α-helix/β-sheet ratio, indicating that this ratio is thermodynamically controlled. Since relatively large amounts of oligopeptides of degree of polymerization (DP) 4-6 can be extracted by means of acetic acid, it is concluded that (a) most poly(L-alanines) possess a bimodal molecular weight distribution, (b) the oligopeptide fraction with DP ≤ 11 is responsible for the β-sheet fraction of all samples, and (c) the two-stage crystal growth proposed by Komoto and Kawai is not correct. Solubilizing initiators such as poly(ethylene oxide) NH2 prevent the precipitation of oligoalanine and, thus, the formation of a β-sheet structure. 13C-nmr CP/MAS measurements also show that tri- and tetra-L-alanines form insoluble β-sheet structures.
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  • 193
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    Biopolymers 20 (1981), S. 1747-1750 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 194
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A strategy suitable for the synthesis of larger peptides is proposed. It involves the following four considerations: (1) all of the side-chain functional groups are protected by benzyl-type protective groups; (2) a water-soluble carbodiimide, 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide, is used for the fragment-condensation reactions together with 1-hydroxybenzotriazole as the additive; (3) all the protective groups are cleaved simultaneously by the HF method in the final stage of the synthesis; and (4) side products formed are detected and removed by an efficient high-performance liquid chromatography procedure. The usefulness of these procedures is demonstrated taking the synthesis of human parathyroid hormone [hPTH(1-84)] as an example.
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  • 195
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    Biopolymers 20 (1981), S. 1877-1899 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Several examples are cited to demonstrate how conformational-energy calculations provide information about the manner in which interatomic interactions influence the structure and stability of polypeptides and proteins, and of intermolecular complexes involving these same species. These include the screw senses of α-helical polyamino acids, helix-coil transition parameters, properties of β-bends, and the structures of gramicidin S and of synthetic poly-(tripeptide) models of collagen. In all of these calculations, the multiple-minimum problem has been surmounted. A description is provided as to how the multiple-minimum problem is being approached in calculations on globular proteins. These computational methods have also been applied to protein structure refinement and to the calculation of structures of homologous proteins and of enzyme-substrate complexes.
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  • 196
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    Biopolymers 20 (1981), S. 1921-1927 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The Dnp-pNA derivatives of more than 30 tetrapeptides were synthesized and subjected to CD measurements in MeOH. The CD spectra were analyzed on the basis of exciton chirality theory and were found to be useful for estimating β-turn preference of the parent tetrapeptides based on the following facts: (1) when a compound of the series takes the βturn conformation, a pair of strong CD bands with opposite sign are observed at 305 and 350 nm, and (2) when it is in a random or nonfolded conformation, no significant bands are observed at the wavelengths. The intensity of the 350-nm band reflects especially well the βturn preference. The CD spectra can be classified into two groups according to the sign of the band at 350 nm, and the groups seem to correspond to the type of βturn. By summarizing the results obtained, some generalizations concerning the sequence-conformation relationship are proposed.
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  • 197
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    Biopolymers 22 (1983), S. 2191-2206 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Cyclic octapeptides, cyclo(X-Pro)4, where X represents Phe, Leu, or Lys(Z), were synthesized and their conformations investigated. A C2-symmetric conformer containing two cis peptide bonds was found in all of these cyclic octapeptides. The numbers of available conformations due to the cis-trans isomerization of Pro peptide bonds depended on the nature of the solvent and X residue: they decreased in the following order: cyclo[Lys(Z)-Pro]4 〉 cyclo(Leu-Pro)4 〉 cyclo(Phe-Pro)4 in CDCl3. 13C spin-lattice relaxation times (T1) of these cyclic octapeptides were measured, and the contribution of segmental mobility to T1 was found to vary with the nature of the X residue.
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  • 198
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    Biopolymers 22 (1983), S. 2397-2409 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Densities of solutions of several α-amino acids and peptides in 3 and 6m aqueous urea solvents have been determined at 298.15 K. These data have been used to evaluate the infinite-dilution apparent molar volumes of the solutes and the volume changes due to transfer (Vtr0) of the α-amino acids and peptides at infinite dilution from water to aqueous urea solutions. The sign and magnitude of the Vtr0 values have been rationalized in the framework of Friedman's cosphere-overlap model. The Vtr0 values for the glycyl group (—CH2CONH—) and alkyl side chains have been estimated.
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  • 199
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    Biopolymers 22 (1983), S. 2459-2476 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformational-energy calculations of the zwitterionic forms of Trp, Gly-Trp, Pro-Trp, Phe-Trp, Trp-Gly, Trp-Phe, Trp-Trp, and Trp-Gly-Gly were done using an empirical energy program for peptides (ECEPP). The resulting low-energy conformations were analyzed for the presence of hydrogen bonds, the distances between carbonyl groups and the indole ring, the distances between the N-terminal amino group and the indole ring, the dihedral angle between the planes containing carbonyl groups and the indole ring, and for dipeptides with two aromatic side chains, the dihedral angle and distance between the planes of the aromatic rings. This information was correlated with literature data from x-ray crystallographic studies, fluorescence lifetime studies, and quantum-yield experiments; proposed models of intramolecular quenching are discussed in light of the peptide conformations.
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  • 200
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    Biopolymers 22 (1983), S. 2497-2500 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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