JBiSE  Vol.7 No.1 , January 2014
Predicting residue contacts for protein-protein interactions by integration of multiple information
ABSTRACT
Detailed knowledge of interfacial region between interacting proteins is not only helpful in annotating function for proteins, but also very important for structure-based drug design and disease treatment. However, this is one of the most difficult tasks and current methods are constrained by some factors. In this study, we developed a new method to predict residue-residue contacts of two interacting protein domains by integrating information about evolutionary couplings andamino acid pairwise contact potentials, as well as domain-domain interaction interfaces. The experimental results showed that our proposed method outperformed the previous method with the same datasets. Moreover, the method promises an improvement in the source of template-based protein docking.

Cite this paper
Kien T. Le, T. , Hirose, O. , Tran, V. , Saethang, T. , T. Nguyen, L. , Dang, X. , Ngo, D. , Kubo, M. , Yamada, Y. and Satou, K. (2014) Predicting residue contacts for protein-protein interactions by integration of multiple information. Journal of Biomedical Science and Engineering, 7, 28-37. doi: 10.4236/jbise.2014.71005.
References
[1]   Chen, C.-T., Peng, H.-P., Jian, J.-W., Tsai, K.-C., Chang, J.-Y., Yang, E.-W., Chen, J.-B., Ho, S.-Y., Hsu, W.-L. and Yang, A.-S. (2012) Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces. PloS ONE, 7, e37706. http://dx.doi.org/10.1371/journal.pone.0037706

[2]   Jordan, A.R., El-Manzalawy, Y., Dobbs, D. and Honavar, V. (2012) Predicting protein-protein interface residues using local surface structural similarity. BMC Bioinformatics, 13, 41. http://dx.doi.org/10.1186/1471-2105-13-41

[3]   Bradford, J.R. and Westhead, D.R. (2005) Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics, 21, 1487-1494. http://dx.doi.org/10.1093/bioinformatics/bti242

[4]   Zhou, H.X. and Shan, Y. (2001) Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins, 44, 336-343. http://dx.doi.org/10.1002/prot.1099

[5]   Burgoyne, N.J. and Jackson, R.M. (2006) Predicting protein interaction sites: Binding hot-spots in protein-protein and protein-ligand interfaces. Bioinformatics, 22, 1335-1342. http://dx.doi.org/10.1093/bioinformatics/btl079

[6]   Friedrich, T., Pils, B., Dandekar, T. and Muller, T. (2006) Modelling interaction sites in protein domains with interaction profile hidden Markov models. Bioinformatics, 22, 2851-2857. http://dx.doi.org/10.1093/bioinformatics/btl486

[7]   Ofran, Y. and Rost, B. (2003) Predicted protein-protein interaction sites from local sequence information. FEBS Letters, 544, 236-239. http://dx.doi.org/10.1016/S0014-5793(03)00456-3

[8]   Zhou, H.-X. and Qin, S. (2007) Interaction-site prediction for protein complexes: A critical assessment. Bioinformatics, 23, 2203-2209. http://dx.doi.org/10.1093/bioinformatics/btm323

[9]   Ritchie, D.W. (2008) Recent progress and future directions in protein-protein docking. Current Protein and Peptide Science, 9, 1-15. http://dx.doi.org/10.2174/138920308783565741

[10]   Li, B. and Kihara, D. (2012) Protein docking prediction using predicted protein-protein interface. BMC Bioinformatics, 13, 7. http://dx.doi.org/10.1186/1471-2105-13-7

[11]   Thattai, M., Burak, Y. and Shraiman, B.I. (2007) The origins of specificity in polyketide synthase protein interactions. PLoS Computational Biology, 3, 1827-1835. http://dx.doi.org/10.1371/journal.pcbi.0030186

[12]   Burger, L. and Van Nimwegen, E. (2008) Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method. Molecular Systems Biology, 4, 1-14. http://dx.doi.org/10.1038/msb4100203

[13]   White, R.A., Szurmant, H., Hoch, J.A. and Hwa, T. (2007) Features of protein-protein interactions in two-component signaling deduced from genomic libraries. Methods in Enzymology, 422, 75-101. http://dx.doi.org/10.1016/S0076-6879(06)22004-4

[14]   Weigt, M., White, R.A., Szurmant, H., Hoch, J.A. and Hwa, T. (2009) Identification of direct residue contacts in protein-protein interaction by message passing. PNAS, 106, 67-72. http://dx.doi.org/10.1073/pnas.0805923106

[15]   González, A.J., Liao, L. and Wu, C.H. (2013) Prediction of contact matrix for protein-protein interaction. Bioinformatics, 29, 1018-1025. http://dx.doi.org/10.1093/bioinformatics/btt076

[16]   Ghoorah, A.W., Devignes, M.-D., Smaïl-Tabbone, M. and Ritchie, D.W. (2011) Spatial clustering of protein binding sites for template based protein docking. Bioinformatics, 27, 2820-2827. http://dx.doi.org/10.1093/bioinformatics/btr493

[17]   Aloy, P., Ceulemans, H., Stark, A. and Russell, R.B. (2003) The relationship between sequence and interaction divergence in proteins. Journal of Molecular Biology, 332, 989-998. http://dx.doi.org/10.1016/j.jmb.2003.07.006

[18]   Keskin, O. and Nussinov, R. (2007) Similar binding sites and different partners: Implications to shared proteins in cellular pathways. Structure, 15, 341-354. http://dx.doi.org/10.1016/j.str.2007.01.007

[19]   Morcos, F., Pagnani, A., Lunt, B., Bertolino, A., Marks, D.S., Sander, C., Zecchina, R., Onuchic, J.N., Hwa, T. and Weigt, M. (2011) Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proceedings of the National Academy of Sciences of the United States of America, 108, E1293-E1301. http://dx.doi.org/10.1073/pnas.1111471108

[20]   Kawashima, S., Pokarowski, P., Pokarowska, M., Kolinski, A., Katayama, T. and Kanehisa, M. (2008) AAindex: Amino acid index database, progress report 2008. Nucleic Acids Research, 36, D202-D205. http://dx.doi.org/10.1093/nar/gkm998

[21]   Krogh, A., Brown, M., Mian, I.S., Jokander, K. and David, H. (1994) Hidden Markov Models in Computational Biology Applications to Protein Modeling. Journal of Molecular Biology, 235, 1501-1531. http://dx.doi.org/10.1006/jmbi.1994.1104

[22]   Eddy, S.R. (1998) Profile hidden Markov models. Bioinformatics Review, 14, 755-763.

[23]   González, A.J. and Liao, L. (2010) Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines. BMC Bioinformatics, 11, 537. http://dx.doi.org/10.1186/1471-2105-11-537

[24]   González, A.J. and Liao, L. (2009) Constrained fisher scores derived from interaction profile hidden Markov models improve protein to protein interaction. Proceedings of the First International Conference BICoB 2009, New Orleans, 8-10 April 2009, 236-247.

[25]   Hopf, T.A., Colwell, L.J., Sheridan, R., Rost, B., Sander, C. and Marks, D.S. (2012) Three-dimensional structures of membrane proteins from genomic sequencing. Cell, 149, 1607-1621. http://dx.doi.org/10.1016/j.cell.2012.04.012

[26]   Marks, D.S., Colwell, L.J., Sheridan, R., Hopf, A.T., Pagnani, A., Zecchina, R. and Sander, C. (2011) Protein 3D structure computed from evolutionary sequence variation. PloS ONE, 6, e28766. http://dx.doi.org/10.1371/journal.pone.0028766

[27]   Procaccini, A., Lunt, B., Szurmant, H., Hwa, T. and Weigt, M. (2011) Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: orphans and crosstalks. PloS ONE, 6, e19729. http://dx.doi.org/10.1371/journal.pone.0019729

[28]   Punta, M., Coggill, P.C., Eberhardt, R.Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J, Heger, A., Holm, L., Sonnhammer, E.L.L., Eddy, S.R., Bateman, A. and Finn, R.D. (2012) The Pfam protein families database. Nucleic Acids Research, 40, D290-D301. http://dx.doi.org/10.1093/nar/gkr1065

[29]   Stein, A., Russell, R.B. and Aloy, P. (2005) 3did: Interacting protein domains of known three-dimensional structure. Nucleic Acids Research, 33, D413-D417. http://dx.doi.org/10.1093/nar/gki037

 
 
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