Potential energy functions for threading

Current Opinion in Structural Biology

Volumn 6, Issue 2, 1996, Pages 210-216

  Jones, David T ^a   Thornton, Janet M ^b  

^a UNIVERSITY OF WARWICK   (United Kingdom)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR MODEL; MOLECULAR RECOGNITION; PREDICTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN TERTIARY STRUCTURE; REVIEW;

EID: 0029964055     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(96)80076-5     Document Type: Article

References (40)

1. Bowie JU, Lüthy R, Eisenberg D: A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991, 253:164-170.
2. Holm L, Sander C: Evaluation of protein models by atomic solvation preference. J Mol Biol 1992, 225:93-105.
3. Luthardt G, Frommel C: Local polarity analysis: a sensitive method that discriminates between native proteins and incorrectly folded models. Protein Eng 1994, 7:627-631.
4. Hendlich M, Lackner P, Weitckus S, Floeckner H, Froschauer R, Gottsbacher K, Casari G, Sippl MJ: Identification of native protein folds amongst a large number of incorrect models: the calculation of low energy conformations from potentials of mean force. J Mol Biol 1990, 216:167-180.
5. Jones DT, Taylor WR, Thornton JM: A new approach to protein fold recognition. Nature 1992, 358:86-89.
6. Sippl MJ, Weitckus S: Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations. Proteins 1992, 13:258-271.
7. Godzik A, Skolnick J: Sequence-structure matching in globular proteins: Application to supersecondary and tertiary structure determination. Proc Natl Acad Sci USA 1992, 89:12098-12102.
8. Maiorov VN, Crippen GM: Contact potential that recognizes the correct folding of globular proteins. J Mol Biol 1992, 227:876-888.
9. Bryant SH, Lawrence CE: An empirical energy function for threading protein-sequence through the folding motif. Proteins 1993, 16:92-112.
10. Ouzounis C, Sander C, Scharf M, Schneider R: Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles derived from three dimensional structures. J Mol Biol 1993, 232:805-825.
11. Abagyan R, Frishman D, Argos P: Recognition of distantly related proteins through energy calculations. Proteins 1994, 19:132-140.
12. Overington J, Donnelly D, Johnson MS, Šali A, Blundell TL: Environment-specific amino-acid substitution tables - tertiary templates and prediction of protein folds. Protein Sci 1992, 1:216-226.
13. Rost B, Sander C: Progress of 1D protein structure prediction at last Proteins 1995, 23:295-300.
14. Kocher JPA, Rooman MJ, Wodak SJ: Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J Mol Biol 1994, 235:1598-1613.
15. Nishikawa K, Matsuo Y: Development of pseudoenergy potentials for assessing protein 3-D-1-D compatibility and detecting weak homologies. Protein Eng 1994, 6:811-820.
16. Matuso Y, Nakamura H, Nishikawa K: Detection of protein 3D-1D compatability characterised by the evaluation of side-chain packing and electrostatic interactions. J Biochem (Tokyo) 1995, 118:137-148.
17. Thomas PD, Dill KA: Statistical potentials extracted from protein structures: what is wrong with them? J Mol Biol 1996, in press. Although this is a clear well written paper, which needed to be written, the results will not be surprising 10 those who have derived and used empirical potentials. The shortcomings, which have often been described before, are apparent within the formalism used to derive the potentials and are just elegantly illustrated by the lattice models.
18. Russell RB, Barton GJ: Structural features can be unconserved in proteins with similar folds - an analysis of sidechain to sidechain contacts, secondary structure and accessibility. J Mol Biol 1994, 244:332-350.
19. Huang ES, Subbiah S, Levitt M: Recognising native folds by the arrangement of hydrophobic and polar residues. J Mol Biol 1995, 252:709-720. A very simple fold-recognition potential is described with no concerns about sequence memory. The potentials pass the self-recognition test with remarkable success, but this method will be very sensitive to poorly packed structures.
20. Koehl P, Delarue M: Polar and non-polar atomic environments in the protein core: implications for folding and binding. Proteins 1994, 20:264-278. The authors introduce a new formalism for calculating the solvation contribution to the free energy of folding that is based on the area buried only by non-polar atoms on folding (NPCA). This is a carefully tested and well presented implementation of a reasonable (though not novel) idea.
21. Eisenberg D, McLachlan AD: Solvation energy in protein folding and binding. Nature 1986, 319:199-203.
22. Delarue M, Koehl P: Atomic environment energies in proteins defined from statistics of accessible and contact surface areas. J Mol Biol 1995, 249:675-690.
23. Novotny J, Bruccoleri R, Karplus M: An analysis of incorrectly folded protein models - implications for structure predictions. J Mol Biol 1984, 177:787-818.
24. Novotny J, Rashin AA, Bruccoleri R: Criteria that discriminate between native proteins and incorrectly folded models. Proteins 1988, 4:19-30.
25. Wang Y, Zhang H, Li W, Scott RA: Discriminating compact normative structures from the native structure of globular proteins. Proc Natl Acad Sci USA 1995, 92:709-713.
26. 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.
27. Miyazawa S, Jernigan RL: Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 1985, 18:534-552.
28. Finkelstein AV, Badretdinov AY, Gutin AM: Why do protein architectures have Boltzmann-like statistics? Proteins 1995, 23:142-150. This paper offers support for the Boltzmann formalism in relating the frequency of occurrence of structural features in proteins and the related energy.
29. Flores TP, Orengo CA, Moss DS, Thornton JM: Comparison of conformational characteristics in structurally similar protein pairs. Protein Sci 1993, 2:1811-1826.
30. Orengo CA, Jones DT, Thornton JM: Protein superfamilies and domain superfolds. Nature 1994, 372:631-634.
31. Wright PE, Dyson HJ, Lerner RA: Conformation of peptide fragments of proteins in aqueous solution: implications for initiation of protein folding. Biochemistry 1988, 27:7167-7175.
32. Dyson HJ, Merutka G, Waltho JP, Lerner RA, Wright PE: Folding of peptide fragments comprising the complete sequence of proteins: models for initiation of protein folding. I. Myohemerythrin. J Mol Biol 1992, 226:795-817.
33. Dyson HJ, Sayre JR, Merutka G, Shin H-C, Lerner RA, Wright PE: Folding of peptide fragments comprising the complete sequence of proteins: models for initiation of protein folding. II. Plastocyanin. J Mol Biol 1992, 226:819-835.
34. Valey P, Gronenborn AM, Christensen H, Wingfield PT, Pain RH, Clore GM: Kinetics of folding of the all-β sheet protein interleukin-1β. Science 1993, 260:1110-1113.
35. Wetlaufer D: Nucleation, rapid folding, and globular interchain regions in proteins. Proc Natl Acad Sci USA 1973, 70:697-701.
36. Lemer CMR, Rooman MJ, Wodak SJ: Protein structure prediction by threading methods: evaluation of current techniques. Proteins 1995, 23:337-355. A very thorough summary of the threading results from the recently completed large-scale experiment to assess protein structure prediction methods, organized by John Moult and colleagues. Although a very encouraging degree of success in recognizing folds is reported, the quality of the sequence-structure alignments was generally found to be poor. It is suggested that this lack of alignment accuracy is due to the over-emphasis of solvation terms in current threading procedures.
37. Jones DT, Miller RT, Thornton JM: Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing. Proteins 1995, 23:387-397. Highly encouraging fold-recognition results are presented for a number of blind trials using a development of the original 'threading' method. Out of 11 folds that share either local or global structural similarity with previously known folds, seven are recognized correctly. Despite good recognition results, however, poor alignment quality is reported.
38. Flöckner H, Braxenthaler M, Lackner P, Jaritz M, Ortner M, Sippl MJ: Progress in fold recognition. Proteins 1995, 23:376-386. Again, very encouraging threading results are presented. Although the quality of alignments is, again, reported to be generally poor, in one case, a reasonable alignment was obtained between the replication-termination protein and histone H5, which both display the winged DNA-binding protein fold. The small size and high helix content of the domain in question may be the reason for the favourable alignment accuracy in this case.
39. Srinivasan R, Rose GD: Linus - a hierarchical procedure to predict the fold of a protein. Proteins 1995, 22:81-99. An interesting approach to predicting protein structure is presented, which attempts to encompass some of the current ideas on protein folding pathways. This paper has generated much controversy due to the rather over-enthusiastic reports on the work in various non-academic publications. Nevertheless, the accuracy of secondary and supersecondary structure prediction for the examples shown is very impressive. However, the method does not appear to work for αβ structures, which is probably due to the high emphasis on β-hairpin formation (and consequent high emphasis on antiparallel sheet formation). Only a few test cases are presented, and it is clear that a great deal of blind-testing will be required before the significance of the method can be properly assessed.
40. Pederson JT, Moult J: Ab initio structure prediction for small polypeptides and protein fragments using genetic algorithms. Proteins 1995, 23:454-460. This paper constitutes another interesting approach to predicting protein structure that is based on protein folding pathways. The method attempts to predict the regions of a protein that might achieve the greatest degree of local burial. These regions are treated as protein folding nucleation sites, and the subsequent folding process is simulated using a genetic algorithm. Some blind testing has been performed on a preliminary version of the method with somewhat mixed results.