Ab initio construction of polypeptide fragments: Efficient generation of accurate, representative ensembles

Proteins: Structure, Function and Genetics

Volumn 51, Issue 1, 2003, Pages 41-55

  DePristo, Mark A ^a   De Bakker, Paul I W ^a   Lovell, Simon C ^a   Blundell, Tom L ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Anchor geometry; Conformational sampling; Conformational search algorithms; Decoy sets; Discrete state sets; Loop modeling

Indexed keywords

PEPTIDE FRAGMENT; POLYPEPTIDE;

AB INITIO CALCULATION; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; GEOMETRY; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; STEREOCHEMISTRY;

ALGORITHMS; AMINO ACID SEQUENCE; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PEPTIDE FRAGMENTS; PROTEIN CONFORMATION; PROTEINS; REPRODUCIBILITY OF RESULTS;

EID: 0037375742     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10285     Document Type: Article

References (56)

1. Holm L, Sander C. Database algorithm for generating protein backbone and side-chain co-ordinates from a C alpha trace application to model building and detection of co-ordinate errors. J Mol Biol 1991;218:183-194.
2. Jones T, Thirup S. Using known substructures in protein model building and crystallography. EMBO J 1986;5:819-922.
3. Read RJ, Moult J. Fitting electron density by systematic search. Acta Crystallogr Sect A 1992;48:104-113.
4. Sippl MJ. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol 1990;213:859-883.
5. Harbury PB, Plecs JJ, Tidor B, Alber T, Kim PS. High-resolution protein design with backbone freedom. Science 1998;282:1462-1467.
6. Park B, Levitt M. Energy functions that discriminate X-ray and near native folds from well-constructed decoys. J Mol Biol 1996;258:367-392.
7. Moult J. Comparison of database potentials and molecular mechanics force fields. Curr Opin Struct Biol 1997;7:194-199.
8. Samudrala R, Levitt M. Decoys "R" Us: a database of incorrect conformations to improve protein structure prediction. Protein Sci 2000;9:1399-1401.
9. Sippl MJ, Hendlich M, Lackner P. Assembly of polypeptide and protein back-bone conformations from low energy ensembles of short fragments: development of strategies and construction of models for myoglobin, lysozyme, and thymosin beta 4. Protein Sci 1992;1:625-640.
10. Simons KT, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997;268:209-225.
11. Engh RA, Huber R. Accurate bond and angle parameters for X-ray protein-structure refinement. Acta Crystallogr Sect A 1991;47:392-400.
12. Ramachandran G, Sasisekharan V. Conformation of polypeptides and proteins. Adv Protein Chem 1968;28:283-437.
13. van Vlijmen H, Karplus M. PDB-based protein loop prediction: parameters for selection and methods for optimization. J Mol Biol 1997;267:975-1001.
14. Bystroff C, Thorsson V, Baker D. HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins. J Mol Biol 2000;301:173-190.
15. Deane CM, Blundell TL. CODA: a combined algorithm for predicting the structurally variable regions of protein models. Protein Sci 2001;10:599-612.
16. Wojcik J, Mornon JP, Chomilier J. New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification. J Mol Biol 1999;289:1469-1490.
17. Fidelis K, Stern PS, Bacon D, Moult J. Comparison of systematic search and database methods for constructing segments of protein structure. Protein Eng 1994;7:953-960.
18. Moult J, James MN. An algorithm for determining the conformation of polypeptide segments in proteins by systematic search. Proteins 1986;1:146-163.
19. Bruccoleri RE, Karplus M. Prediction of the folding of short polypeptide segments by uniform conformational sampling. Biopolymers 1987;26:137-168.
20. Deane CM, Blundell TL. A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins. Proteins 2000;40:135-144.
21. Cornell W, Cieplak P, Bayly C, Gould I, Merz KJ, Ferguson D, Spellmeyer D, Fox T, Caldwell J, Kollman P. A second generation force field for the simulation of proteins and nucleic acids. J Am Chem Soc 1995;117:5179-5197.
22. MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 1998;102:3586-3616.
23. Samudrala R, Moult J. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 1998;275:893-914.
24. Bruccoleri RE, Karplus M. Conformational sampling using high-temperature molecular-dynamics. Biopolymers 1990;29:1847-1862.
25. Fiser A, Do RKG, Sali A. Modeling of loops in protein structures. Protein Sci 2000;9:1753-1773.
26. Abagyan R, Totrov M. Biased probability Monte-Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol 1994;235:983-1002.
27. Zhang HY, Lai LH, Wang LY, Han YZ, Tang YQ. A fast and efficient program for modeling protein loops. Biopolymers 1997;41:61-72.
28. Sibanda BL, Blundell TL, Thornton JM. Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering. J Mol Biol 1989;206:759-777.
29. Swindells MB, MacArthur MW, Thornton JM. Intrinsic phi, psi propensities of amino acids, derived from the coil regions of known structures. Nat Struct Biol 1995;2:596-603.
30. Kabsch W, Sander C. Identical pentapeptides with different backbones. Nature 1985;317:207.
31. Cohen BI, Presnell SR, Cohen FE. Origins of structural diversity within sequentially identical hexapeptides. Protein Sci 1993;2:2134-2145.
32. Sibanda BL, Thornton JM. Beta-hairpin families in globular proteins. Nature 1985;316:170-174.
33. Chothia C, Lesk AM, Tramontano A, Levitt M, Smith-Gill SJ, Air G, Sheriff S, Padlan EA, Davies D, Tulip WR, et al. Conformations of immunoglobulin hypervariable regions. Nature 1989;342:877- 883.
34. Holm L, Sander C. Evaluation of protein models by atomic solvation preference. J Mol Biol 1992;225:93-105.
35. Rojnuckarin A, Subramaniam S. Knowledge-based interaction potentials for proteins. Proteins 1999;36:54-67.
36. Novotny J, Bruccoleri R, Karplus M. An analysis of incorrectly folded protein models. Implications for structure predictions. J Mol Biol 1984;177:787-818.
37. Hinds DA, Levitt M. Exploring conformational space with a simple lattice model for protein structure. J Mol Biol 1994;243:668-682.
38. Wang Y, Zhang H, Li W, Scott RA. Discriminating compact nonnative structures from the native structure of globular proteins. Proc Natl Acad Sci USA 1995;92:709-13.
39. Monge A, Friesner RA, Honig B. An algorithm to generate low-resolution protein tertiary structures from knowledge of secondary structure. Proc Natl Acad Sci USA 1994;91:5027-5029.
40. Dominy BN, Brooks CL. Identifying native-like protein structures using physics-based potentials. J Comput Chem 2001;31:147-160.
41. de Bakker PIW, DePristo MA, Burke DF, Blundell TL. Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER forcefield with the generalized Born solvation model. Proteins 2003;51:21-40.
42. Lovell SC, Word JM, Richardson JS, Richardson DC. The penultimate rotamer library. Proteins 2000;40:389-408.
43. Hobohm U, Sander C. Enlarged representative set of protein structures. Protein Sci 1994;3:522-524.
44. Word JM, Lovell SC, LaBean TH, Taylor HC, Zalis ME, Presley BK, Richardson JS, Richardson DC. Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. J Mol Biol 1999;285:1711-1733.
45. Rooman MJ, Kocher JP, Wodak SJ. Prediction of protein backbone conformation based on seven structure assignments. Influence of local interactions. J Mol Biol 1991;221:961-979.
46. Park BH, Levitt M. The complexity and accuracy of discrete state models of protein structure. J Mol Biol 1995;249:493-507.
47. Laskowski RA, MacArthur WM, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystall 1993;26:283-291.
48. Berman H, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
49. Collura V, Higo J, Garnier J. Modeling of protein loops by simulated annealing. Protein Sci 1993;2:1502-1510.
50. Hooft RW, Vriend G, Sander C, Abola EE. Errors in protein structures. Nature 1996;381:272.
51. Go N, Scheraga HA. Ring closure and local conformational deformationals of chain molecules. Macromolecules 1970;3:178-187.
52. Wedemeyer W, Scheraga H. Exact analytical loop closure in proteins using polynomial equations. J Comput Chem 1999;20:819-844.
53. Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993;234:779- 815.
54. Blundell T, Carney D, Gardner S, Hayes F, Howlin B, Hubbard T, Overington J, Singh DA, Sibanda BL, Sutcliffe M. 18th. Sir Hans Krebs lecture. Knowledge-based protein modelling and design. Eur J Biochem 1988;172:513-520.
55. Burke DF, Deane CM. Improved protein loop prediction from sequence alone. Protein Eng 2001;14:473-478.
56. Rufino SD, Donate LE, Canard LHJ, Blundell TL. Predicting the conformational class of short and medium size loops connecting regular secondary structures: Application to comparative modelling. J Mol Biol 1997;267:352-367.