DOI: 10.1002/bip.360030205. Theoretical determination of sterically allowed conformations of a polypeptide chain by a computer method

Theoretical determination of sterically allowed conformations of a polypeptide chain by a computer method

10.1002/bip.360030205

Crossref journal-article

Wiley

Biopolymers (311)

Abstract

AbstractA mathematical method has been developed, together with a digital computer program for its evaluation, for the determination of possible conformations of a polypeptide chain for any given amino acid sequence. Allowed conformations were required to satisfy predetermined criteria regarding the locations of potential energy minima for rotation around single bonds, steric restrictions arising from van der Waals contacts between atoms, and the formation of a closed polypeptide loop by means of a peptide linkage or a disulfide bridge. Requirements for specific noncovalent interactions can also be considered. Various assumptions regarding the selection of the minima for rotational potentials and of the van der Waals contact distances are discussed. According to the assumptions adopted in the paper, 21 conformations are allowed for a glycine residue which is part of a dipeptide. These conformations are assumed to lie at minima of the rotational potential function, and satisfy simultaneously the steric requirements. Dipeptides containing alanine or other residues are restricted to 7 such conformations. As an example of the applicability of the method, the computation was performed for the smallest loop containing a disulfide bridge in the ribonuclease molecule, i.e., the cyclic octapeptide formed by residues 65 to 72. Only 15 allowed conformations were found for the loop as a whole. Parameters characterizing these allowed conformations are tabulated. Approximate calculations indicate the importance of steric restrictions and of the presence of side chains in reducing the conformational freedom of this peptide. Further potentialities of the method are discussed.

Bibliography

NÃ©methy, G., & Scheraga, H. A. (1965). Theoretical determination of sterically allowed conformations of a polypeptide chain by a computer method. Biopolymers, 3(2), 155â184. Portico.

Authors 2

George Némethy (first)
Harold A. Scheraga (additional)

References 36 Referenced 141

{'key': 'e_1_2_1_2_2', 'first-page': '478', 'volume-title': 'The Proteins', 'author': 'Scheraga H. A.', 'year': '1963'} / The Proteins by Scheraga H. A. (1963)
Poland D. C. andScheraga H. A. Biopolymers (paper II) in press.
{'key': 'e_1_2_1_4_2', 'first-page': '230', 'volume': '29', 'author': 'Schellman J. A.', 'year': '1955', 'journal-title': 'Compt. Rend. Trav. Lab. Carlsberg, Ser. Chim.'} / Compt. Rend. Trav. Lab. Carlsberg, Ser. Chim. by Schellman J. A. (1955)
10.1073/pnas.51.5.839
{'key': 'e_1_2_1_6_2', 'first-page': '1', 'volume-title': 'The Proteins', 'author': 'Schellman J. A.', 'year': '1964'} / The Proteins by Schellman J. A. (1964)
{'key': 'e_1_2_1_7_2', 'first-page': '39', 'volume-title': 'Collagen', 'author': 'Sasisekharan V.', 'year': '1962'} / Collagen by Sasisekharan V. (1962)
10.1016/S0022-2836(63)80023-6
10.1007/BF03046447 / Proc. Indian Acad. Sci. by Ramakrishnan C. (1964)
10.1073/pnas.44.2.211
10.1002/9780470143483.ch9
{'key': 'e_1_2_1_12_2', 'first-page': '70ff', 'volume-title': 'Configurational Statistics of Polymeric Chains', 'author': 'Volkenstein M. V.', 'year': '1963'} / Configurational Statistics of Polymeric Chains by Volkenstein M. V. (1963)
{'key': 'e_1_2_1_13_2', 'first-page': '1', 'volume': '23', 'author': 'Mizushima S.‐I.', 'year': '1961', 'journal-title': 'Adv. Enzymol.'} / Adv. Enzymol. by Mizushima S.‐I. (1961)
Scott R. A. andH. A.Scheraga J. Chem. Phys. in press.
10.1073/pnas.37.11.729
Scott R. A. personal communication.
10.1063/1.1742845
{'key': 'e_1_2_1_18_2', 'first-page': '135', 'volume-title': 'The Nature of the Chemical Bond', 'author': 'Pauling L.', 'year': '1960'} / The Nature of the Chemical Bond by Pauling L. (1960)
{'key': 'e_1_2_1_18_3', 'first-page': '260', 'volume-title': 'The Nature of the Chemical Bond', 'year': '1960'} / The Nature of the Chemical Bond (1960)
{'key': 'e_1_2_1_18_4', 'first-page': '281', 'volume-title': 'The Nature of the Chemical Bond', 'year': '1960'} / The Nature of the Chemical Bond (1960)
{'key': 'e_1_2_1_18_5', 'first-page': '114', 'volume-title': 'The Nature of the Chemical Bond', 'year': '1960'} / The Nature of the Chemical Bond (1960)
Ramachandran G. N. personal communication.
Leach S. J. G.Némethy andH. A.Scheraga work in progress.
10.1063/1.1730021
10.1103/PhysRev.39.746
10.1021/ja01162a002
10.1016/S0021-9258(19)67917-2
10.1016/S0021-9258(19)67918-4
10.1016/S0021-9258(19)73946-5
10.1016/S0021-9258(19)73947-7
10.1016/S0021-9258(19)83984-4
Poland D. C. andH. A.Scheraga Biopolymers(paper VIII) in press.
{'key': 'e_1_2_1_30_2', 'first-page': '399ff', 'volume-title': 'Principles of Polymer Chemistry', 'author': 'Flory P. J.', 'year': '1953'} / Principles of Polymer Chemistry by Flory P. J. (1953)
10.1021/ja00881a009
{'key': 'e_1_2_1_32_2', 'first-page': '216', 'volume': '15', 'author': 'Kendrew J. C.', 'year': '1962', 'journal-title': 'Brookhaven Symp. Biol.'} / Brookhaven Symp. Biol. by Kendrew J. C. (1962)
Scott R. A. andH. A.Scheraga work in progress.
{'key': 'e_1_2_1_34_2', 'first-page': '1383', 'volume': '1', 'author': 'de Santis P.', 'year': '1963', 'journal-title': 'J. Polymer Sci.'} / J. Polymer Sci. by de Santis P. (1963)

Dates

Type	When
Created	20 years, 8 months ago (Dec. 30, 2004, 10:22 p.m.)
Deposited	1 year, 9 months ago (Nov. 12, 2023, 8:42 a.m.)
Indexed	24 minutes ago (Sept. 3, 2025, 4:41 a.m.)
Issued	60 years, 5 months ago (April 1, 1965)
Published	60 years, 5 months ago (April 1, 1965)
Published Online	21 years, 7 months ago (Feb. 1, 2004)
Published Print	60 years, 5 months ago (April 1, 1965)

Funders 0

None

BibTeX

@article{N_methy_1965, title={Theoretical determination of sterically allowed conformations of a polypeptide chain by a computer method}, volume={3}, ISSN={1097-0282}, url={http://dx.doi.org/10.1002/bip.360030205}, DOI={10.1002/bip.360030205}, number={2}, journal={Biopolymers}, publisher={Wiley}, author={Némethy, George and Scheraga, Harold A.}, year={1965}, month=apr, pages={155–184} }

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