Crossref journal-article
Wiley
Biopolymers (311)
Abstract

AbstractThe central ingredient of any structure modeling tool is a molecular model or force field that accounts for proper geometry and energy calculation. For protein and peptide modeling based on entire amino acids as building blocks, we describe a peptide force field in which each amino acid is represented by a single point in space, taken at the position of the α‐carbon atom. Apart from the positional coordinates, these units carry the two torsional angles φ and Ψ as additional degrees of freedom to account for the orientations of the peptide links. While some of the energy terms are analogous to expressions in atomic force fields, the presence of the angular variables leads to fundamental differences with new features and additional terms with no atomic counterparts.The force field reproduces secondary structure elements with very good accuracy. Globular parts of tertiary packing stay near the experimental structures with a rms deviation in C‐α positions of 0.1–0.3 nm and about 25° in φ and Ψ depending on the size of the structure. A tendency for larger discrepancies is observed in exposed loops or terminal segments the conformations of which may be strongly influenced by neighboring domains.Finally, a scope of possible applications is presented. They range from modeling activities, such as model building by homology, to coarse scanning of conformation space in conformation analysis and structure determination. An extension to a dynamics model would offer the possibility to eliminate the less interesting high‐frequency modes that in all‐atom force‐field dynamics absorb most of the computational effort.

Authors 1
  1. Paul R. Gerber (first)
References 63 Referenced 56
  1. {'key': 'e_1_2_1_2_2', 'first-page': '535', 'volume': '112', 'author': 'Bernstein F. C.', 'year': '1977', 'journal-title': 'J. Biol. Chem'} / J. Biol. Chem by Bernstein F. C. (1977)
  2. 10.1007/978-1-4612-6137-7
  3. {'key': 'e_1_2_1_4_2', 'volume-title': 'Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences, Methods in Enzymology', 'author': 'Doolittle R. F.', 'year': '1990'} / Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences, Methods in Enzymology by Doolittle R. F. (1990)
  4. {'key': 'e_1_2_1_5_2', 'first-page': '487', 'volume': '173', 'author': 'Taylor W. R.', 'year': '1984', 'journal-title': 'J. Biol. Chem.'} / J. Biol. Chem. by Taylor W. R. (1984)
  5. 10.1038/347631a0
  6. {'key': 'e_1_2_1_7_2', 'volume-title': 'Computer Simulations of Biomolecular Systems', 'author': 'van Gunsteren W. F.', 'year': '1989'} / Computer Simulations of Biomolecular Systems by van Gunsteren W. F. (1989)
  7. 10.1126/science.250.4984.1121
  8. 10.1098/rstb.1989.0059
  9. 10.1038/253694a0
  10. {'key': 'e_1_2_1_11_2', 'first-page': '59', 'volume': '104', 'author': 'Levitt M.', 'year': '1976', 'journal-title': 'J. Biol. Chem.'} / J. Biol. Chem. by Levitt M. (1976)
  11. 10.1002/bip.360211002
  12. 10.1111/j.1399-3011.1984.tb00955.x
  13. {'key': 'e_1_2_1_14_2', 'first-page': '783', 'volume': '210', 'author': 'Summers N.', 'year': '1989', 'journal-title': 'J. Biol. Chem.'} / J. Biol. Chem. by Summers N. (1989)
  14. {'key': 'e_1_2_1_15_2', 'first-page': '373', 'volume': '217', 'author': 'Lee C.', 'year': '1991', 'journal-title': 'J. Biol. Chem.'} / J. Biol. Chem. by Lee C. (1991)
  15. {'key': 'e_1_2_1_16_2', 'first-page': '183', 'volume': '218', 'author': 'Holm L.', 'year': '1991', 'journal-title': 'J. Biol. Chem.'} / J. Biol. Chem. by Holm L. (1991)
  16. Gerber P. R.&Muller K. to be published.
  17. 10.1002/bscb.19880970806
  18. {'key': 'e_1_2_1_19_2', 'first-page': '105', 'volume': '157', 'author': 'Kyte J.', 'year': '1982', 'journal-title': 'J. Biol. Chem.'} / J. Biol. Chem. by Kyte J. (1982)
  19. {'key': 'e_1_2_1_20_2', 'first-page': '867', 'volume': '168', 'author': 'Barlow D. J.', 'year': '1983', 'journal-title': 'J. Biol. Chem.'} / J. Biol. Chem. by Barlow D. J. (1983)
  20. 10.1093/protein/3.6.479
  21. 10.1038/316170a0
  22. {'key': 'e_1_2_1_23_2', 'first-page': '295', 'volume': '198', 'author': 'McGregor M. J.', 'year': '1987', 'journal-title': 'J. Biol. Chem.'} / J. Biol. Chem. by McGregor M. J. (1987)
  23. {'key': 'e_1_2_1_24_2', 'first-page': '97', 'volume': '147', 'author': 'Dijkstra B. W.', 'year': '1981', 'journal-title': 'J. Biol. Chem.'} / J. Biol. Chem. by Dijkstra B. W. (1981)
  24. 10.1038/290107a0
  25. 10.1016/S0021-9258(17)33415-4
  26. {'key': 'e_1_2_1_27_2', 'first-page': '175', 'volume': '170', 'author': 'Wistow G.', 'year': '1983', 'journal-title': 'J. Biol. Chem.'} / J. Biol. Chem. by Wistow G. (1983)
  27. 10.1111/j.1432-1033.1983.tb07429.x
  28. 10.1016/S0021-9258(19)42505-2
  29. 10.1107/S0108768183003262
  30. {'key': 'e_1_2_1_31_2', 'first-page': '737', 'volume': '152', 'author': 'Artymiuk P. J.', 'year': '1981', 'journal-title': 'J. Biol. Chem.'} / J. Biol. Chem. by Artymiuk P. J. (1981)
  31. {'key': 'e_1_2_1_32_2', 'first-page': '531', 'volume': '142', 'author': 'Phillips S. E. V.', 'year': '1980', 'journal-title': 'J. Biol. Chem.'} / J. Biol. Chem. by Phillips S. E. V. (1980)
  32. 10.1107/S010876738409930X
  33. {'key': 'e_1_2_1_34_2', 'first-page': '557', 'volume': '123', 'author': 'Ploegman J. H.', 'year': '1978', 'journal-title': 'J. Biol. Chem.'} / J. Biol. Chem. by Ploegman J. H. (1978)
  34. 10.1016/0006-291X(71)90823-0
  35. {'key': 'e_1_2_1_36_2', 'first-page': '497', 'volume': '170', 'author': 'Almassy R. J.', 'year': '1983', 'journal-title': 'J. Biol. Chem.'} / J. Biol. Chem. by Almassy R. J. (1983)
  36. {'key': 'e_1_2_1_37_2', 'first-page': '1071', 'volume': '203', 'author': 'Baker E. N.', 'year': '1988', 'journal-title': 'J. Biol. Chem.'} / J. Biol. Chem. by Baker E. N. (1988)
  37. 10.1111/j.1749-6632.1984.tb12314.x
  38. {'key': 'e_1_2_1_39_2', 'first-page': '627', 'volume': '186', 'author': 'Finzel B. C.', 'year': '1985', 'journal-title': 'J. Biol. Chem.'} / J. Biol. Chem. by Finzel B. C. (1985)
  39. {'key': 'e_1_2_1_40_2', 'first-page': '109', 'volume': '172', 'author': 'Higuchi Y.', 'year': '1984', 'journal-title': 'J. Biol. Chem.'} / J. Biol. Chem. by Higuchi Y. (1984)
  40. 10.1016/S0021-9258(19)41843-7
  41. 10.1016/S0021-9258(18)90651-4
  42. 10.1016/S0021-9258(20)65097-9
  43. 10.1111/j.1432-1033.1985.tb08762.x
  44. {'key': 'e_1_2_1_45_2', 'first-page': '339', 'volume': '121', 'author': 'Blake C. C. F.', 'year': '1978', 'journal-title': 'J. Biol. Chem.'} / J. Biol. Chem. by Blake C. C. F. (1978)
  45. 10.1107/S0567740882006153
  46. {'key': 'e_1_2_1_47_2', 'first-page': '661', 'volume': '167', 'author': 'Furey W.', 'year': '1983', 'journal-title': 'J. Biol. Chem.'} / J. Biol. Chem. by Furey W. (1983)
  47. {'key': 'e_1_2_1_48_2', 'first-page': '697', 'volume': '131', 'author': 'Mitsui Y.', 'year': '1979', 'journal-title': 'J. Biol. Chem.'} / J. Biol. Chem. by Mitsui Y. (1979)
  48. {'key': 'e_1_2_1_49_2', 'first-page': '735', 'volume': '177', 'author': 'Jones T. A.', 'year': '1984', 'journal-title': 'J. Biol. Chem.'} / J. Biol. Chem. by Jones T. A. (1984)
  49. {'key': 'e_1_2_1_50_2', 'first-page': '299', 'volume': '163', 'author': 'James M. N. G.', 'year': '1983', 'journal-title': 'J. Biol. Chem'} / J. Biol. Chem by James M. N. G. (1983)
  50. 10.1038/newbio233015a0 / Nature New Biol. by Mathews F. S. (1971)
  51. 10.1107/S0108767388000303
  52. 10.1016/0022-2836(77)90031-6
  53. {'key': 'e_1_2_1_54_2', 'first-page': '623', 'volume': '160', 'author': 'Holmes M. A.', 'year': '1982', 'journal-title': 'J. Biol. Chem.'} / J. Biol. Chem. by Holmes M. A. (1982)
  54. 10.1016/S0021-9258(18)33497-5
  55. 10.1098/rstb.1988.0058
  56. {'key': 'e_1_2_1_57_2', 'first-page': '367', 'volume': '168', 'author': 'Rees D. C.', 'year': '1983', 'journal-title': 'J. Biol. Chem.'} / J. Biol. Chem. by Rees D. C. (1983)
  57. 10.1016/S0021-9258(19)84751-8
  58. {'key': 'e_1_2_1_59_2', 'volume-title': 'Methods and Applications in Crystallographic Computing', 'author': 'Takano T.', 'year': '1984'} / Methods and Applications in Crystallographic Computing by Takano T. (1984)
  59. {'key': 'e_1_2_1_60_2', 'first-page': '301', 'volume': '180', 'author': 'Wlodawer A.', 'year': '1984', 'journal-title': 'J. Biol. Chem.'} / J. Biol. Chem. by Wlodawer A. (1984)
  60. {'key': 'e_1_2_1_61_2', 'first-page': '615', 'volume': '138', 'author': 'Watenpaugh K. D.', 'year': '1980', 'journal-title': 'J. Biol. Chem.'} / J. Biol. Chem. by Watenpaugh K. D. (1980)
  61. 10.1093/protein/2.6.407
  62. 10.1021/bi00408a010
  63. 10.1073/pnas.82.6.1604
Dates
Type When
Created 20 years, 8 months ago (Dec. 29, 2004, 10 p.m.)
Deposited 1 year, 10 months ago (Oct. 23, 2023, 3:33 p.m.)
Indexed 1 year, 5 months ago (March 11, 2024, 7:07 p.m.)
Issued 33 years ago (Aug. 1, 1992)
Published 33 years ago (Aug. 1, 1992)
Published Online 21 years, 6 months ago (Feb. 1, 2004)
Published Print 33 years ago (Aug. 1, 1992)
Funders 0

None

@article{Gerber_1992, title={Peptide mechanics: A force field for peptides and proteins working with entire residues as smallest units}, volume={32}, ISSN={1097-0282}, url={http://dx.doi.org/10.1002/bip.360320811}, DOI={10.1002/bip.360320811}, number={8}, journal={Biopolymers}, publisher={Wiley}, author={Gerber, Paul R.}, year={1992}, month=aug, pages={1003–1017} }