Strain in protein structures as viewed through nonrotameric side chains: I. Their position and interaction

Proteins: Structure, Function and Genetics

Volumn 37, Issue 1, 1999, Pages 30-43

  Heringa, Jaap ^a,b   Argos, Patrick ^b  

^a NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

Protein folding; Protein stability; Protein tertiary structure; Rotamer; Side chain clusters

Indexed keywords

PROTEIN;

AMINO ACID COMPOSITION; AMINO TERMINAL SEQUENCE; ARTICLE; CRYSTALLOGRAPHY; POSITION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN TERTIARY STRUCTURE; TEMPERATURE;

AMINO ACIDS; BACTERIAL PROTEINS; CRYSTALLOGRAPHY, X-RAY; MOTION; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEINS; STRESS, MECHANICAL; TEMPERATURE;

EID: 0033213892     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19991001)37:1<30::AID-PROT4>3.0.CO;2-P     Document Type: Article

References (47)

1. Ramakrishnan C, Ramachandran GN. Stereochemical criteria for polypeptide and protein chain conformation. J Mol Biol 965;5:909-933.
2. Chandrasekharan R, Ramachandran GN. Studies on the conformation of amino acids. XI. Analysis of the observed side group conformations in proteins. Int J Protein Peptide Res 1970;2:223-233.
3. Janin J, Wodak S, Levitt M, Maigret B. Conformations of amino acid side-chains in proteins. J Mol Biol 1978;125:357-386.
4. Bhat TN, Sasisekharan V, Vijayan M. An analysis of side-chain conformation in proteins. Int. J Protein Peptide Res 1979;13:170-184.
5. Ghelin BR, Karplus M. Sidechain torsional potentials and motion of amino acids in proteins: bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci USA 1975;72:2002-2006.
6. Ghelin BR, Karplus M. Side-chain torsional potentials: effect of dipeptide, protein and solvent environment. Biochemistry 1979;18: 1256-1268.
7. Ponder JW, Richards FM. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J Mol Biol 1987;193:775-791.
8. Creamer TP, Rose GD. Side-chain entropy opposes α-helix formation but rationalizes experimentally determined helix-forming propensities. Proc Natl Acad Sci USA 1992;89:5937-5941.
9. Lee KH, Xie D, Amzel LM. Estimation of changes in side chain configurational entropy in binding and folding: general methods and application to helix formation. Proteins Struct Func Genet 1994;20:68-84.
10. Tufféry P, Etchebest C, Hazout S, Lavery RA. A new approach to the rapid determination of protein side chain conformations. J Biomol Struct Dyn 1991;8:1267-1289.
11. Wilson C, Gregoret LM, Agard DA. Modeling side-chain conformation for homologous proteins using an energy-based rotamer search. J Mol Biol 1993;229:996-1006.
12. Vasquez M. An evaluation of discrete and continuum search techniques for conformational analysis of side chains in proteins. Biopolymers 1995;36:53-70.
13. Dunbrack RL, Karplus M. Prediction of protein side-chain conformations from a backbone dependent rotamer library. J Mol Biol 1993;230:543-571.
14. Shenkin PS, Farid H, Fetrow JS. Prediction and evaluation of side-chain conformations for protein backbone structures. Protein Struct Func Genet 1996;26:323-352.
15. Tufféry P, Etchebest C, Hazout S. Prediction of protein side chain conformations: a study on the influence of backbone accuracy on conformation stability in the rotamer space. Protein Eng 1997;10: 361-372.
16. Lasters I, Demayer M, Desmet J. Enhanced dead-end elimination in the search for the global minimum energy conformation of a collection of protein side-chains. Protein Eng 1995;8:815-822.
17. Hwang JK, Liao WF. Side-chain prediction by neural networks and simulated annealing optimization. Protein Eng 1995;8:363-370.
18. Bower MJ, Cohen FE, Dunbrack RL. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. J Mol Biol 1997;267:1268-1282.
19. Leach RL, Lemon AP. Exploring the conformation space of protein side chains using dead-end elimination and the A* algorithm. Protein Struct Func Genet 1998;33:227-239.
20. Holm L, Sander C. Database algorithm for generating protein backbone and side-chain co-ordinates from Cα trace: application to model building and detection of co-ordinate errors. J Mol Biol 1991;218:183-194.
21. Holm L, Sander C. Fast and simple Monte Carlo algorithm for side-chain optimization in proteins: application to model building by homology. Proteins Struct Func Genet 1992;14:213-223.
22. Abagyan R, Totrov M, Kuznetsov D. ICM - a new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation. J Comp Chem 1994;15:488-506.
23. Laughton CA. Prediction of protein side-chain conformations from local three-dimensional homology relationships. J Mol Biol 1994; 235:1088-1097.
24. Koehl P, Delarue M. A self-consistent field approach to simultaneous gap closure and side-chain positioning in homology modeling. Nature Struct Biol 1994;2:163-170.
25. Kono H, Doi J. A new method for side-chain conformation prediction using a Hopfield network and reproduced rotamers. J Comp Chem 1996;17:1667-1683.
26. Ogata K, Umeyama H. Prediction of protein side-chain conformations by principal component analysis for fixed main-chain atoms. Protein Eng 1997;10:353-359.
27. Lee C, Subbiah S. Prediction of side chain conformation by packing optimization. J Mol Biol 1991;26:137-168.
28. Schrauber H, Eisenhaber F, Argos P. Rotamers: to be or not to be? An analysis of amino acid side-chain conformations in globular proteins. J Mol Biol 1993;230:592-612.
29. Doig AJ, Sternberg MJE. Side-chain conformational entropy in protein folding. Protein Sci 1995;4:2247-2251.
30. Heringa J, Sommerfeldt H, Higgins D, Argos P. OBSTRUCT: a program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity. Comput Appl Biosci 1992;8:599-600.
31. Bernstein FC, Koetzle TF, Williams GJB, Meyer EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. Protein data bank: a computer based archival file for macromolecular structures. J Mol Biol 1977;112:535-542.
32. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
33. Levitt M. Conformational preferences of amino acids in globular proteins. Biochemistry 1978;17:4277-4285.
34. Argos P, Palau J. Amino acid distribution in protein secondary structures. Int J Peptide Protein Res 1982;19:380-393.
35. Stout GH, Jensen LH. X-ray structure determination: a practical guide. London: Macmillan Company; 1968. p 205-208.
36. Carugo O, Argos P. Correlation between side chain mobility and conformation in protein structures. Protein Eng 1997;10:777-787.
37. Trontud DEJ. Knowledge-based B-factor restraints for the refinement of proteins. Appl Crystallogr 1996;29:100-104.
38. Heringa J, Argos P. Side-chain clusters in protein structures and their role in protein folding. J Mol Biol 1991;220:151-171.
39. Nakai K, Kidera A, Kanehisa M. Cluster analysis of amino acid indices for prediction of protein structure and function. Protein Eng 1988;2:93-100.
40. Lovell SC, Word JM, Richardson JS, Richardson DC. Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering. Proc Natl Acad Sci USA 1999;96:400-405.
41. Heringa J, Argos P, Egmond MR, de Vlieg J. Increasing thermal stability of subtilisin from mutations suggested by strongly interacting side-chain clusters. Protein Eng 1995;8:21-30.
42. Wan WY, Milner-White EJ. A natural grouping of motif with an aspartate or asparagine residue forming two hydrogen bonds to residues ahead in sequence: their occurrence at alpha-helical N termini and in other situations. J Mol Biol 1999;286:1633-1649.
43. Wan WY, Milner-White EJ. A recurring two-hydrogen-bond motif incorporating a serine or threonine residue is found both at alpha-helical N termini and in other situations. J Mol Biol 1999;286:1651-1662.
44. Doig AJ, MacArthur MW, Stapley BJ, Thornton MJ. Structures of N-termini of helices in proteins. Protein Sci 1997;6:147-155.
45. Tanimura R, Kidera A, Nakamura H. Determinants of protein side-chain packing. Protein Sci 1994;3:2358-2365.
46. Sayle RA, Milner-White EJ. RasMol: biomolecular graphics for all. Trends Biochem Sci 1995;20:374-376.
47. Heringa J, Argos P. Strain in protein structures as viewed through nonrotameric side chains: II. Effects upon ligand binding. Proteins 1999;37:44-55.