A Contact Energy Function Considering Residue Hydrophobic Environment and Its Application in Protein Fold Recognition

Overview

Journal Genomics Proteomics Bioinformatics

Specialty Biology

Date 2006 May 13

PMID 16689689

Citations 2

Authors

Mo Jie Duan

Yan Hong Zhou

Affiliations

Soon will be listed here.

Abstract

The three-dimensional (3D) structure prediction of proteins is an important task in bioinformatics. Finding energy functions that can better represent residue-residue and residue-solvent interactions is a crucial way to improve the prediction accuracy. The widely used contact energy functions mostly only consider the contact frequency between different types of residues; however, we find that the contact frequency also relates to the residue hydrophobic environment. Accordingly, we present an improved contact energy function to integrate the two factors, which can reflect the influence of hydrophobic interaction on the stabilization of protein 3D structure more effectively. Furthermore, a fold recognition (threading) approach based on this energy function is developed. The testing results obtained with 20 randomly selected proteins demonstrate that, compared with common contact energy functions, the proposed energy function can improve the accuracy of the fold template prediction from 20% to 50%, and can also improve the accuracy of the sequence-template alignment from 35% to 65%.

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References

Bowie J, Luthy R, Eisenberg D . A method to identify protein sequences that fold into a known three-dimensional structure. Science. 1991; 253(5016):164-70. DOI: 10.1126/science.1853201. View

Eisenberg D, McLachlan A . Solvation energy in protein folding and binding. Nature. 1986; 319(6050):199-203. DOI: 10.1038/319199a0. View

Berman H, Westbrook J, Feng Z, Gilliland G, Bhat T, Weissig H . The Protein Data Bank. Nucleic Acids Res. 1999; 28(1):235-42. PMC: 102472. DOI: 10.1093/nar/28.1.235. View

Khatun J, Khare S, Dokholyan N . Can contact potentials reliably predict stability of proteins?. J Mol Biol. 2004; 336(5):1223-38. DOI: 10.1016/j.jmb.2004.01.002. View

Dobson C . Protein folding and misfolding. Nature. 2003; 426(6968):884-90. DOI: 10.1038/nature02261. View

Godzik A, Kolinski A, Skolnick J . Topology fingerprint approach to the inverse protein folding problem. J Mol Biol. 1992; 227(1):227-38. DOI: 10.1016/0022-2836(92)90693-e. View

Baker D, Sali A . Protein structure prediction and structural genomics. Science. 2001; 294(5540):93-6. DOI: 10.1126/science.1065659. View

Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W . Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25(17):3389-402. PMC: 146917. DOI: 10.1093/nar/25.17.3389. View

Jones D, Taylor W, Thornton J . A new approach to protein fold recognition. Nature. 1992; 358(6381):86-9. DOI: 10.1038/358086a0. View

10.

Park J, Karplus K, Barrett C, Hughey R, Haussler D, Hubbard T . Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J Mol Biol. 1998; 284(4):1201-10. DOI: 10.1006/jmbi.1998.2221. View

11.

Vendruscolo M, Najmanovich R, Domany E . Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading?. Proteins. 2000; 38(2):134-48. DOI: 10.1002/(sici)1097-0134(20000201)38:2<134::aid-prot3>3.0.co;2-a. View

12.

Buchete N, Straub J, Thirumalai D . Development of novel statistical potentials for protein fold recognition. Curr Opin Struct Biol. 2004; 14(2):225-32. DOI: 10.1016/j.sbi.2004.03.002. View

13.

Lee B, Richards F . The interpretation of protein structures: estimation of static accessibility. J Mol Biol. 1971; 55(3):379-400. DOI: 10.1016/0022-2836(71)90324-x. View

14.

Jones D, Thornton J . Potential energy functions for threading. Curr Opin Struct Biol. 1996; 6(2):210-6. DOI: 10.1016/s0959-440x(96)80076-5. View

15.

Miyazawa S, Jernigan R . Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol. 1996; 256(3):623-44. DOI: 10.1006/jmbi.1996.0114. View

16.

BRYANT S, Altschul S . Statistics of sequence-structure threading. Curr Opin Struct Biol. 1995; 5(2):236-44. DOI: 10.1016/0959-440x(95)80082-4. View

17.

Bonneau R, Baker D . Ab initio protein structure prediction: progress and prospects. Annu Rev Biophys Biomol Struct. 2001; 30:173-89. DOI: 10.1146/annurev.biophys.30.1.173. View

18.

McGuffin L, Jones D . Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics. 2003; 19(7):874-81. DOI: 10.1093/bioinformatics/btg097. View

19.

Stuart A, Fiser A, Sanchez R, Melo F, Sali A . Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct. 2000; 29:291-325. DOI: 10.1146/annurev.biophys.29.1.291. View

20.

Russell R, Alber F, Aloy P, Davis F, Korkin D, Pichaud M . A structural perspective on protein-protein interactions. Curr Opin Struct Biol. 2004; 14(3):313-24. DOI: 10.1016/j.sbi.2004.04.006. View