Relationship between protein structure and geometrical constraints

Protein Science

Volumn 5, Issue 11, 1996, Pages 2217-2225

  Lund, Ole ^a   Hansen, Jan ^a   Brunak, Søren ^a   Bohr, Jakob ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

chirality; distance geometry; protein folding; protein structure

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CHIRALITY; NUCLEAR MAGNETIC RESONANCE; PREDICTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; STRUCTURE ACTIVITY RELATION;

EID: 0029846867     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560051108     Document Type: Article

References (48)

1. Aszódi A, Gradwell MJ, Taylor WR. 1995. Global fold determination from a small number of distance restraints. J Mol Biol 251:308-326.
2. Aszódi A, Gradwell MJ, Taylor WR. 1996. Protein fold determination using a small number of distance restraints. In: Bohr H, Brunak S, eds. Protein folds. Boca Raton, Florida: CRC Press. pp 85-97.
3. Bernstein FC, Koetzle TF, Williams GJB, Meyer EF Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. 1977. The Protein Data Bank: A computer-based archival file for macromolecular structures. J Mol Biol 112:535-542.
4. Bohr J, Bohr H, Brunak S, Cotterill R, Fredholm H, Lautrup B, Petersen S. 1993. Protein structures from distance inequalities. J Mol Biol 231:861-869.
5. Bohr H, Bohr J, Brunak S, Cotterill RMC, Fredholm H, Lautrup B. Petersen SB. 1990. A novel approach to prediction of the 3-dimensional structures of protein backbones by neural networks. FEBS Lett 261:43-46.
6. Bohr H, Bohr J, Brunak S, Cotterill RMC, Lautrup B, Nørskov L, Olsen OH, Petersen SB. 1988. Protein secondary structure and homology by neural networks. The α-helices in rhodopsin. FEBS Lett 241:223-228.
7. Braun W. 1983. Representation of short and long-range handedness in protein structures by signed distance maps. J Mol Biol 163:613-621.
8. Brown JR, Hartley BS. 1966. Location of disulphide bridges by diagonal paper electrophoresis. The disulphide bridges of bovine chymotrypsinogen A. Biochem J 101:214-228.
9. Brünger AT, Nilges M. 1993. Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMR-spectroscopy. Q Rev Biophys 26:49-125.
10. Chou P, Fasman G. 1978. Prediction of the secondary structure of proteins from their amino acid sequence. Adv Enzymol Relat Areas Mol Biol 47:45-48.
11. Crippen G, Havel T 1988. Distance geometry and molecular conformation. New York: Wiley.
12. Elofsson A, Le Grand SM, Eisenberg D. 1995. Local moves: An efficient algorithm for simulation of protein folding. Proteins Struct Funct Genet 23:73-82.
13. Flöckner H, Braxenthaler M, Lackner P, Jaritz M, Ortner M, Sippl MJ. 1995. Progress in fold recognition. Proteins Struct Funct Genet 23:376-386.
14. Gunn JR, Monge A, Friesner RA, Marshall CH. 1994. Hierarchical algorithm for computer modeling of protein tertiary structure: Folding of myoglobin to 6.2 Å resolution. J Phys Chem 98:702-711.
15. Hänggi G, Braun W. 1994. Pattern recognition and self-correcting distance geometry calculations applied to myohemerythrin. FEBS Lett 344:147-153.
16. Havel TF, Snow ME. 1991. A new method for building protein conformations from sequence alignments with homologues of known structure. J Mol Biol 217:1-7.
17. Herzyk P, Hubbard RE. 1993. A reduced representation of proteins for use in restraint satisfaction calculations. Proteins Struct Funct Genet 17:310-324.
18. Holbrook SR, Muskal SM, Kim SH. 1990. Predicting surface exposure of amino acids from protein sequence. Protein Eng 3:659-665.
19. Holley LH, Karplus M. 1989. Protein secondary structure prediction with a neural network. Proc Natl Acad Sci USA 86:152-156.
20. Hubbard T 1994. Use of β-strand interaction pseudo-potentials in protein structure prediction and modelling. In: Lathrop RH, ed Proceedings of the Biotechnology Computing Track, Protein Structure Prediction MiniTrack of the 27th HICSS. IEEE Computer Society Press. pp 336-354.
21. Jin L, Cohen FE, Wells JA. 1994. Structure from function: Screning structural models with functional data. Proc Natl Acad Sci USA 91:113-117.
22. Kabsch W, Sander C. 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637.
23. Kikuchi T, Nemethy G, Scheraga HA. 1988. Prediction of the packing arrangement of strands in β-sheets in globular proteins. J Protein Chem 7:473-490.
24. Krogh A, Riis SK. 1996. Prediction of beta sheets in proteins. In: Tourelzky DS, Mozer MC, Hasselmo ME, eds. Advances in Neural Information Processing Systems 8. MIT press.
25. Leonard CK, Spellman MW, Riddle L, Harris RJ, Thomas JN, Gregory TJ. 1990. Assignment of intrachain disulfide bonds and characterization of potential glycosylation sites of the type I recombinant human immunodeficiency virus envelope glycoprotein (gp120) expressed in Chinese hamster ovary cells. J Biol Chem 265:10373-10382.
26. Levitt M. 1976. A simplified representation of protein conformations for rapid simulation of protein folding. J Mol Biol 104:59-107.
27. Monge A, Friesner RA, Honig B. 1994. An algorithm to generate low-resolution protein tertiary structures from knowledge of secondary structure. Proc Natl Acad Sci USA 91:5027-5029.
28. Moore JP, Sattentau QJ, Wyatt R, Sodroski J. 1993a. Probing the structure of the human immunodeficiency virus surface glycoprotein gp120 with a panel of monoclonal antibodies. J Virol 65:469-484.
29. Moore JP, Thali M, Jameson BA, Viganaux F, Lewis GK, Poon SW, Charles M, Fung MS, Sun B, Druda PJ, Åkerblom L, Wahren B, Ho DD, Sattentau QJ, Sodroski J. 1993b. Immunochemical analysis of the gp120 surface glycoprotein of human immunodeficiency virus type 1: Probing the structure of the C4 and V4 domains and the interaction of the C4 domain with the V3 loop. J Virol 67:4785-4796.
30. Mumenthaler C, Braun W. 1995. Prediction of the helix packing of globular proteins by self-correcting distance geometry. Protein Sci 4:863-871.
31. Nishikawa K, Ooi T. 1980. Prediction of the surface-interior diagram of globular proteins by an empirical method. Int J Pept Protein Res 16:19-32.
32. Pastore A, Atkinson RA, Saudek V, Williams RJ. 1991. Topological mirror images in protein structure computation: An underestimated problem. Proteins Struct Funct Genet 10:22-32.
33. Qian N, Sejnowski TJ. 1988. Predicting the secondary structure of globular proteins using neural network models. J Mol Biol 202:865-884.
34. Reczko M, Bohr H. 1994. Recurrent neural networks for protein distance matrix prediction. In: Bohr H, Brunak S, eds. Protein structure by distance analysis. Amsterdam: IOS Press. pp 87-97.
35. Rost B, Sander C. 1993. Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol 232:584-599.
36. Rost B, Sander C. 1994. Conservation and prediction of solvent accessibility in protein families. Proteins Struct Funct Genet 20:216-226.
37. Salamov AA, Solovyev W. 1995 Prediction of protein secondary structure by combining nearest-neighbor algorithms and multiple sequence alignments. J Mol Biol 247:11-15.
38. Seitoh S, Nakai T, Nishikawa K. 1993. A geometrical constraint approach for reproducing the native backbone conformation of a protein. Proteins Struct Funct Genet 15:191-204.
39. Slidel TWF, Thornton JM. 1996. Chirality in protein structure. In: Bohr H, Brunak S. eds. Protein folds. Boca Raton, Florida: CRC Press. pp 253-264.
40. Smith-Brown MJ, Kominos D, Levy RM. 1993. Global folding of proteins using a limited number of distance constraints. Protein Eng 6:605-614.
41. Srinivasan R, Rose GD. 1995. LINUS: A hierarchic procedure to predict the fold of a protein. Proteins Struct Funct Genet 22:81-99.
42. Wako H, Blundell TL. 1994a. Use of amino acid environment-dependent substitution tables and conformational propensities in structure prediction from aligned sequences of homologous proteins. I Solvent accessibility classes. J Mol Biol 238:682-692.
43. Wako H, Blundell TL. 1994b. Use of amino acid environment-dependent substitution tables and conformational propensities in structure prediction from aligned sequences of homologous proteins. II. Secondary structures. J Mol Biol 238:693-708.
44. Wako H, Kubota Y. 1991 Distance-constraint approach to higher-order structures of globular proteins with empirically determined distances between ammo acid residues. J Protein Chem 10:233-243.
45. Wako H, Scheraga HA. 1982a. Distance-constraint approach to protein folding. I. Statistical analysis of protein conformations in terms of distances between residues. J Protein Chem 1:5-45.
46. Wako H, Scheraga HA. 1982b Distance-constraint approach to protein folding. II. Prediction of the three-dimensional structure of bovine pancreatic trypsin inhibitor. J Protein Chem 1:85-117.
47. Wuthrich K, Spitzfaden C, Memmert K, Widmer H, Wider G. 1991. Protein secondary structure determination by NMR. Application with recombinant human cyclophilin. FEBS Lett 285:237-247.
48. Yčas M. 1990 Computing tertiary structures of proteins. J Protein Chem 9:177-200.