Abstract
Understanding the recognition mechanism of protein complexes is a challenging task in bioinformatics and computational biology. We have developed a novel energy based approach for identifying the binding site residues in protein–protein, protein-RNA and protein-DNA complexes. In protein-protein complexes, the residues and residue-pairs with charged and aromatic side chains are important for binding. These residues influence to form cation–π, electrostatic and aromatic interactions. In protein-RNA complexes, the positively charged, polar and aromatic residues are important for binding. These residues influence to form electrostatic, hydrogen bonding and stacking interactions. The positive charged and polar residues are preferred to bind with DNA in protein-DNA complexes. These results provide an overall view of binding in protein complexes. Our observations have been verified with the experimental binding specificity of protein-protein and protein-nucleic acid complexes and found good agreement with experiments.
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References
Berman, H., Henrick, K., Nakamura, H., Markley, J.L.: The Worldwide Protein Data Bank (wwPDB): Ensuring a Single. Uniform Archive of PDB Data. Nucleic Acids Res. 35(Database issue), D301–303 (2007)
Treger, M., Westhof, E.: Statistical Analysis of Atomic Contacts at RNA-protein Interfaces. J Mol. Recognit. 14, 199–214 (2001)
Jones, S., Daley, D.T., Luscombe, N.M., Berman, H.M., Thornton, J.M.: Protein-RNA Interactions: a Structural Analysis. Nucleic Acids Res. 29, 943–954 (2001)
Guharoy, M.: Chakrabarti Conservation and Relative Importance of Residues Across Protein-protein Interfaces. P. Proc. Natl. Acad. Sci. U.S.A. 102, 15447–15452 (2005)
Gromiha, M.M., Siebers, J.G., Selvaraj, S., Kono, H., Sarai, A.: Intermolecular and Intramolecular Readout Mechanisms in Protein-DNA Recognition. J. Mol. Biol. 337, 285–294 (2004)
Morozova, N., Allers, J., Myers, J., Shamoo, Y.: Protein-RNA Interactions: Exploring Binding Patterns with a Three-dimensional Superposition Analysis of High Resolution Structures. Bioinformatics 22, 2746–2752 (2006)
Shoemaker, B.A., Panchenko, A.R.: Deciphering Protein-protein Interactions. Part II. Computational methods to predict protein and domain interaction partners PLoS Comput. Biol. 3, 43 (2006)
Ellis, J.J., Broom, M., Jones, S.: Protein-RNA Interactions: Structural Analysis and Functional Classes. Proteins 66, 903–911 (2007)
Pan, Y., Tsai, C.J., Ma, B., Nussinov, R.: How Do Transcription Factors Select Specific Binding Sites in the Genome? Nat. Struct. Mol. Biol. 16, 1118–1120 (2009)
Gromiha, M.M., Yokota, K., Fukui, K.: Energy Based Approach for Understanding the Recognition Mechanism in Protein-protein Complexes. Mol. Biosyst. 5, 1779–1786 (2009)
Sikić, M., Tomić, S., Vlahovicek, K.: Prediction of Protein-protein Interaction Sites in Sequences and 3D Structures by Random Forests. PLoS Comput. Biol. 5, e1000278 (2009)
Koike, A., Takagi, T.: Prediction of Protein-protein Interaction Sites Using Support Vector Machines. Protein. Eng. Des. Sel. 17, 165–173 (2004)
Ofran, Y., Rost, B.: ISIS: Interaction Sites Identified From Sequence. Bioinformatics 23(2), e13-6 (2007)
Terribilini, M., Sander, J.D., Lee, J.H., Zaback, P., Jernigan, R.L., Honavar, V., Dobbs, D.: RNABindR: A Server for Analyzing and Predicting RNA-binding Sites in Proteins. Nucleic Acids Res. 35(Web Server issue), W578–W584 (2007)
Wang, L., Brown, S.J.: BindN: A web-based Tool for Efficient Prediction of DNA and RNA Binding Sites in Amino Acid Sequences. Nucleic. Acids Res. 34(Web Server issue), W243–W248 (2006)
Kumar, M., Gromiha, M.M., Raghava, G.P.: Prediction of RNA Binding Sites in a Protein Using SVM and PSSM Profile. Proteins 71, 189–194 (2008)
Ahmad, S., Gromiha, M.M., Sarai, A.: Analysis and Prediction of DNA-binding Proteins and Their Binding Residues Based on Composition, Sequence and Structural Information. Bioinformatics 20, 477–486 (2004)
Ofran, Y., Mysore, V., Rost, B.: Prediction of DNA-binding Residues from Sequence. Bioinformatics 53, i347–i353 (2007)
Gromiha, M.M., Yokota, K., Fukui, K.: Sequence and Structural Analysis of Binding Site Residues in Protein-protein Complexes. Int. J. Biol. Macromol. 46, 187–192 (2010)
Bahadur, R.P., Zacharias, M., Janin, J.: Dissecting Protein-RNA Recognition Sites. Nucleic Acids Res. 36, 2705–2716 (2008)
Xu, B., Yang, Y., Liang, H., Zhou, Y.: An All-atom Knowledge-based Energy Function for Protein-DNA Threading, Docking Decoy Discrimination, and Prediction of Transcription-Factor Binding Profiles. Proteins 76, 718–730 (2009)
Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz, K.M., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W., Kollman, P.A.: A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules. J. Amer. Chem. Soc. 117, 5179–5197 (1995)
Pichierri, F., Aida, M., Gromiha, M.M., Sarai, A.: Free-Energy Maps of Base−Amino Acid Interactions for DNA−Protein Recognition. J. Amer. Chem. Soc. 121, 6152–6157 (1999)
Gromiha, M.M., Yokota, K., Fukui, K.: Understanding the Recognition Mechanism in Protein-RNA Complexes Using Energy Based Approach. Curr. Protein Pept. Sci., (in press, 2010)
Kumar, M.D., Gromiha, M.M.: PINT: Protein-protein Interactions Thermodynamic Database. Nucleic Acids Res. 34, D195–D198 (2006)
Prabakaran, P., An, J., Gromiha, M.M., Selvaraj, S., Uedaira, H., Kono, H., Sarai, A.: Thermodynamic Database for Protein-nucleic Acid Interactions (ProNIT). Bioinformatics 17, 1027–1034 (2001)
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Gromiha, M.M., Selvaraj, S., Jayaram, B., Fukui, K. (2010). Identification and Analysis of Binding Site Residues in Protein Complexes: Energy Based Approach. In: Huang, DS., Zhao, Z., Bevilacqua, V., Figueroa, J.C. (eds) Advanced Intelligent Computing Theories and Applications. ICIC 2010. Lecture Notes in Computer Science, vol 6215. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-14922-1_78
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DOI: https://doi.org/10.1007/978-3-642-14922-1_78
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