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Analysis of proton chemical shifts in regular secondary structure of proteins (1994)

Ösapay, Klara ; Case, David A.

Springer

Journal of biomolecular NMR 4 (1994), S. 215-230

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ISSN: 1573-5001

Keywords: Chemical shift ; Secondary structure

Source: Springer Online Journal Archives 1860-2000

Topics: Biology , Chemistry and Pharmacology

Notes: Summary The contribution of peptide groups to Hα and Hβ proton chemical shifts can be modeled with empirical equations that represent magnetic anisotropy and electrostatic interactions [Ösapay, K. and Case, D.A. (1991) J. Am. Chem. Soc., 113, 9436–9444]. Using these, a model for the ‘random coil’ reference state can be generated by averaging a dipeptide over energetically allowed regions of torsion-angle space. Such calculations support the notion that the empirical constant used in earlier studies arises from neighboring peptide contributions in the reference state, and suggest that special values be used for glycine and proline residues, which differ significantly from other residues in their allowed ϕ,ψ-ranges. New constants for these residues are reported that provide significant improvements in predicted backbone shifts. To illustrate how secondary structure affects backbone chemical shifts we report calculations on oligopeptide models for helices, sheets and turns. In addition to suggesting a physical mechanism for the widely recognized average difference between α and β secondary structures, these models suggest several additional regularities that should be expected: (a) Hα protons at the edges of β-sheets will have a two-residue periodicity; (b) the Hα2 and Hα3 protons of glycine residues will exhibit different shifts, particularly in sheets; (c) Hβ protons will also be sensitive to local secondary structure, but in different directions and to a smaller extent than Hα protons; (d) Hα protons in turns will generally be shifted upfield, except those in position 3 of type I turns. Examples of observed shift patterns in several proteins illustrate the application of these ideas.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF00175249

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An all atom force field for simulations of proteins and nucleic acids (1986)

Weiner, Scott J. ; Kollman, Peter A. ; Nguyen, Dzung T. ; [et al.]

New York, NY [u.a.] : Wiley-Blackwell

Journal of Computational Chemistry 7 (1986), S. 230-252

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ISSN: 0192-8651

Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry

Source: Wiley InterScience Backfile Collection 1832-2000

Topics: Chemistry and Pharmacology , Computer Science

Notes: We present an all atom potential energy function for the simulation of proteins and nucleic acids. This work is an extension of the CH united atom function recently presented by S.J. Weiner et al. J. Amer. Chem. Soc., 106, 765 (1984). The parameters of our function are based on calculations on ethane, propane, n-butane, dimethyl ether, methyl ethyl ether, tetrahydrofuran, imidazole, indole, deoxyadenosine, base paired dinucleoside phosphates, adenine, guanine, uracil, cytosine, thymine, insulin, and myoglobin. We have also used these parameters to carry out the first general vibrational analysis of all five nucleic acid bases with a molecular mechanics potential approach.

Additional Material: 6 Ill.