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  • 1
    Electronic Resource
    Electronic Resource
    A proposal of standard conventions and nomenclature for the description of polypeptide conformations (1966)
    New York : Wiley-Blackwell
    Biopolymers 4 (1966), S. 1149-1150 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1966.360041010
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  • 2
    Electronic Resource
    Electronic Resource
    Spatial configurations of polynucleotide chains. I. Steric interactions in polyribonucleotides: A virtual bond modelFrom the thesis submitted by Wilma K. Olson in fulfillment of the requirements for the degree of Doctor of Philosophy, Stanford University, 1971. (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1-23 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A simplified scheme for treating the spatial configurations of polynucleotide chains is developed using the rotational isomeric state approximation and statistical methods applicable to linear systems of interacting subunits. As a consequence of geometric constraints imposed by the skeletal structure and of the severity of certain steric interactions, it is possible to represent the repeat unit comprising six skeletal bonds by two virtual bonds of fixed length. The configuration of the polynucleotide chain as a whole may be conveniently described by an alternating succession of these two virtual bonds. Moreover, analysis of steric interactions suggests that bond rotations governing the mutual orientation of a given pair of successive virtual bonds should be sensibly independent of the rotations affecting the mutual orientation of other pairs. The statistical mechanical treatment of configuration-dependent properties is much simplified in consequence of this mutual independence. Mean-square dimensions calculated by giving equal weights to all sterically allowed conformations are much smaller than values determined by Felsenfeld and co-workers. The calculated dimensions are markedly increased, however, by placing certain arbitrary restrictions on the rotations about selected pairs of skeletal bonds. It is thus demonstrated that steric interactions alone are insufficient to account for the spatial characteristics of polynucleotide chains. The dimensions are also found to be sensitive to the conformation of the ribose ring of each nucleotide unit, but, insofar as the influences of steric interactions are concerned, the dimensions do not depend on the heterocyclic base attached to the ribose ring.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1972.360110102
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  • 3
    Electronic Resource
    Electronic Resource
    Kinetic analysis of the reversible folding reactions of small proteins: Application to the folding of lysozyme and cytochrome c (1977)
    New York : Wiley-Blackwell
    Biopolymers 16 (1977), S. 731-747 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A general kinetic analysis for unimolecular three-species models is presented. Criteria are established for each model in order to allow selection among alternative models on the basis of their amplitude behavior. These criteria are applied to the previously reported kinetic data for the folding transitions of lysozyme and cytochrome c in guanidine hydrochloride. The degree of success in applying these criteria is found to depend on the extent to which the apparent rate constants, λ1 and λ2, approach each other in certain conditions. Ikai and Tanford have presented a similar kinetic analysis, although these authors considered only the case where no intermediate kinetic species was populated initially. For one protein system, namely, ribonuclease A (RNase A), at least one stable intermediate exists after unfolding outside of the equilibrium transition zone. The criteria developed by Ikai and Tanford cannot be applied to RNase A kinetics and, therefore, a more general analysis is presented. Previously published studies of the reversible folding kinetics of lysozyme and cytochrome c are reexamined using the current amplitude analysis, and it is found that both of these folding transitions can be described by the three-species model, \documentclass{article}\pagestyle{empty}\begin{document}$$ U_{1} \rightleftharpoons U \rightleftharpoons N $$\end{document} used previously to describe the folding kinetics of RNase A (U1 and U2 are two forms of unfolded enzyme and N is the native species). These results suggest that this three-species model may provide a fairly general description of the reversible folding kinetics of small proteins. As an outgrowth of the current analysis, several suggestions for experimental design in studying protein folding will be presented and discussed.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1977.360160404
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  • 4
    Electronic Resource
    Electronic Resource
    Nearest-neighbor and next-nearest-neighbor effects in the proton NMR spectra of the oligoribonucleotides ApGpX and CpApX (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 557-573 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The variable-temperature proton nmr spectra of the oligoribonucleotides in the series CpApX and the series ApGpX, X = A, G, C, U, together with the parent dimers CpA and ApG have been measured. A complete analysis of all the nonexchangeable base proton resonances and ribose H-1′ proton resonances was made. The presence of trends in the shielding abilities of the various bases at both the nearest-neighbor and next-nearest-neighbor positions were identified. The observed shieldings could be used to predict the chemical shifts of protons in related systems. Based on the empirical results from ribodinucleoside monophosphates, the temperature-dependent behavior of the J1′2′ coupling constants of the triribonucleotides suggested that the compounds in the CpApX series stacked from the 5′-end to the 3′-end, while those in the ApGpX series stacked from the 3′-end to the 5′-end.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360190309
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  • 5
    Electronic Resource
    Electronic Resource
    Monte Carlo approach to the analysis of the rotational diffusion of wormlike chains (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 1481-1502 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A Monte Carlo analysis is presented which establishes a relationship between the rotational diffusion coefficients and the flexibility (persistence length, P) of short, wormlike chains. The results of this analysis are presented in terms of experimentally observable quantities; namely, the rotational relaxation times for the field-free decay of optical anisotropy. The pertinent theoretical quantity is R, defined as the ratio of the longest rotational relaxation time of a wormlike chain to the transverse rotational relaxation time of a rigid cylinder having the same axial length (L) and segmental volume. R, so defined, is essentially independent of the axial ratio of the cylinder for any value of L/P within the range of validity of the present analysis (axial ratio 〉 20; 0.1 〈 L/P 〈 5). It is pointed out that P can be determined with reasonable accuracy even in the absence of a precise knowledge of the local hydrodynamic radius of the chain.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1981.360200709
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  • 6
    Electronic Resource
    Electronic Resource
    Investigation of the flexibility of DNA using transient electric birefringence (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 1503-1535 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In the preceding article, a Monte Carlo analysis was presented which provides a quantitative numerical relationship between the rotational diffusion coefficients, as measured by the decay of optical anisotropy following an electric field pulse, and the flexibility (persistence length) of short, wormlike chains. In the present article, the results of the foregoing analysis are applied to the observed rates of decay of birefringence for a series of sequenced DNA fragments ranging in size from 104 to 910 base pairs. Under the conditions used in this study, the DNA fragments exist as native, duplex molecules. Furthermore, conditions are defined in which the observed relaxation times are not dependent on DNA concentration, field strength, or the duration of the pulse. It is pointed out that the ionic atmosphere associated with a wormlike polyion does not exert any significant (direct) influence on the rotational diffusion of the polyion and, therefore, that the rotational relaxation times are a true measure of the configurations of the DNA molecules in solution. Moreover, excluded-volume effects are shown not to be significant for the moderately short molecules employed in this study. The major conclusion of this study is that there is no strong ionic strength dependence of the persistence length for ionic strengths above 1 mM and that the persistence length, under conditions where electrostatic contributions are negligible, is approximately 500 Å. For ionic strengths significantly lower than 1 mM, electrostatic contributions to the stiffness of DNA become significant.
    Additional Material: 17 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1981.360200710
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  • 7
    Electronic Resource
    Electronic Resource
    Analysis of the ring-closure probabilities of isotropic wormlike chains: Application to duplex DNA (1985)
    New York : Wiley-Blackwell
    Biopolymers 24 (1985), S. 1881-1897 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The configurational properties of an isotropically bendable wormlike chain have been investigated using a Monte Carlo approach. In particular, radial distributions for end-to-end separation, ring closure probabilities, and the angular correlation of the two ends of the chain have all been determined as a function of the contour length of the chain. The results of this analysis, when applied to the data of Shore et al. [(1981) Proc. Natl. Acad. Sci. USA 78, 4833-4837] for the length dependence of ring closure for doublehelical DNA, yields a value for the persistence length of DNA in remarkable agreement with earlier hydrodynamic studies.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360241004
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  • 8
    Electronic Resource
    Electronic Resource
    Spatial configuration of polynucleotide chains. II. Conformational energies and the average dimensions of polyribonucleotidesFrom the thesis submitted by Wilma K. Olson in fulfillment of the requirements for the degree of Doctor of Philosophy, Stanford University, 1971. (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 25-56 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformational energies are calculated for pairs of successive bond rotations within an internal residue of a polyribonucleotide chain. Contributions to these energies include bond torsional strain, van der Waals repulsions, London attractions, electrostatic interactions, and inductive interactions between nonbonded atoms in the nucleotide repeat unit. The average dimensions of unperturbed random-coil polyribonucleotide chains are then evaluated on the basis of energies thus estimated, using for this purpose the previously developed virtual bond treatment. The characteristic ratio \documentclass{article}\pagestyle{empty}\begin{document}$ C_\infty = \mathop {{\rm lim}}\limits_{n \to \infty } (\langle r^2 \rangle_0/nl^2) $\end{document} of the mean-square end-to-end distance calculated for polyribonucleotide chains in which all pentose rings are fixed in a C3′-endo conformation is ≈9; for chains consisting exclusively of C2′-endo units it is ≈25. These values are considerably greater than those obtained by giving equal weight to all conformations judged to be sterically allowed. Satisfactory agreement between the calculations here and experimental values from viscosity and light-scattering studies is achieved by treating the chain as a random copolymer of C3′-endo and C2′-endo conformational isomers. The critical dependence of the characteristic ratio on the rotation about bond C3′-O3′ in the C2′-endo chain, however, obscures the interpretation of chain dimensions. The chain is also treated in higher approximation as a sequence of independent repeat units, each of which consists of six chemical bonds. The characteristic ratio obtained in this manner is 6.5 for the C3′-endo chain and 18.5 for the C2′-endo chain. Finally, the effects of partially stacked conformations in polyribonucleotides are investigated using the virtual bond treatment. Chain dimensions are calculated for random coil poly rA chains in which stacking is introduced by both noncooperative and cooperative processes.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1972.360110103
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  • 9
    Electronic Resource
    Electronic Resource
    Spatial configurations of polynucleotide chains. III. PolydeoxyribonucleotidesFrom the thesis submitted by Wilma K. Olson in fulfillment of the requirements for the degree of Doctor of Philosophy, Stanford University, 1971. (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 57-66 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The virtual bond scheme set forth in preceding papers for treating the average properties of polyriboadenylic acid (poly rA) is here applied to the calculation of the unperturbed mean-square end-to-end distance of polydeoxyriboadenylic acid (poly dA). The modifications in structure and in charge distribution resulting from the replacement of the hydroxyl group at C2′ in the ribose residue by hydrogen in deoxyribose produce only minor modifications in the conformational energies associated with the poly dA chain as compared to those found for poly rA. The main difference is manifested in the energy associated with rotations about the C3′-O3′ bond of the deoxyribose residue in the C2′-endo conformation; accessible rotations are confined to the range between 0° and 30° relative to the trans conformation, whereas in the ribose unit the accessible regions comprise two ranges centered at approximately 35° and 85°. The characteristic ratio 〈r2〉0/nl2 calculated on the basis of the conformational energy estimates is ≈9 for the poly dA chain with all deoxyribose residues in the C3′-endo conformation and ≈21 with all residues in the C2′-endo form. Satisfactory agreement is achieved between the theoretical values and experimental results on apurinic acid by treating the poly dA chain as a random copolymer of C3′-endo and C2′-endo conformational isomers present in a ratio of ∼1 to 9.
    Additional Material: 5 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1972.360110104
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  • 10
    Electronic Resource
    Electronic Resource
    Cross-polarization/magic-angle spinning 13C-nmr of (1 → 6)-β-D-glucan (pustulan): Mechanism of gelation (1985)
    New York : Wiley-Blackwell
    Biopolymers 24 (1985), S. 2333-2343 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 13C-nmr has been employed to probe the molecular conformation and crystal structure of (1 → 6)-β-D-glucan (pustulan) in the solution, gel, and solid states. CP/MAS 13C-nmr spectra recorded for partially crystalline solid pustulan display a resonance near 82 ppm that is absent in solution spectra. The intensity and peak width of this resonance were found to depend on relative crystallinity as determined by x-ray diffraction. CP/MAS spectra of aqueous pustulan gels also exhibit the 82-ppm resonance, suggesting that the gelation mechanism may involve microcrystalline junction zones. Since the 82-ppm resonance is absent in the CP/MAS spectrum of the (1 → 6)-β-linked dimer gentiobiose, we tentatively conclude the crystal structure of this dimer does not adequately model the yet undetermined structure of pustulan.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360241211
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