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A Computational Model for Predicting Protein Interactions Based on Multidomain Collaboration
July-Aug. 2012 (vol. 9 no. 4)
pp. 1081-1090
Suk-Hoon Jung, Dept. of Inf. & Commun. Eng., Korea Adv. Inst. of Sci. & Technol., Daejeon, South Korea
Woo-Hyuk Jang, Dept. of Inf. & Commun. Eng., Korea Adv. Inst. of Sci. & Technol., Daejeon, South Korea
Dong-Soo Han, Dept. of Inf. & Commun. Eng., Korea Adv. Inst. of Sci. & Technol., Daejeon, South Korea
Recently, several domain-based computational models for predicting protein-protein interactions (PPIs) have been proposed. The conventional methods usually infer domain or domain combination (DC) interactions from already known interacting sets of proteins, and then predict PPIs using the information. However, the majority of these models often have limitations in providing detailed information on which domain pair (single domain interaction) or DC pair (multidomain interaction) will actually interact for the predicted protein interaction. Therefore, a more comprehensive and concrete computational model for the prediction of PPIs is needed. We developed a computational model to predict PPIs using the information of intraprotein domain cohesion and interprotein DC coupling interaction. A method of identifying the primary interacting DC pair was also incorporated into the model in order to infer actual participants in a predicted interaction. Our method made an apparent improvement in the PPI prediction accuracy, and the primary interacting DC pair identification was valid specifically in predicting multidomain protein interactions. In this paper, we demonstrate that 1) the intraprotein domain cohesion is meaningful in improving the accuracy of domain-based PPI prediction, 2) a prediction model incorporating the intradomain cohesion enables us to identify the primary interacting DC pair, and 3) a hybrid approach using the intra/interdomain interaction information can lead to a more accurate prediction.

[1] S.-K. Ng, Z. Zhang, and S.-H. Tan, "Integrative Approach for Computationally Inferring Protein Domain Interactions," Bioinformatics, vol. 19, no. 8, pp. 923-929, May 2003.
[2] L. Chen, L.-Y. Wu, Y. Wang, and X.-S. Zhang, "Inferring Protein Interactions from Experimental Data by Association Probabilistic Method," Proteins, vol. 62, no. 4, pp. 833-837, Mar. 2006.
[3] H. Fei-Hung and C. Hung-Wen, "Protein-Protein Interaction Prediction Based on Association Rules of Protein Functional Regions," Proc. Second Int'l Conf. Innovative Computing, Information and Control (ICICIC '07), 2007.
[4] E. Sprinzak and H. Margalit, "Correlated Sequence-signatures as Markers of Protein-Protein Interaction," J. Molecular Biology, vol. 311, no. 4, pp. 681-692, Aug. 2001.
[5] M. Deng, S. Mehta, F. Sun, and T. Chen, "Inferring Domain-Domain Interactions from Protein-Protein Interactions," Genome Research, vol. 12, no. 10, pp. 1540-1548, Oct. 2002.
[6] Y. Liu, N. Liu, and H. Zhao, "Inferring Protein-Protein Interactions through High-Throughput Interaction Data from Diverse Organisms," Bioinformatics, vol. 21, no. 15, pp. 3279-3285, Aug. 2005.
[7] R. Riley, C. Lee, C. Sabatti, and D. Eisenberg, "Inferring Protein Domain Interactions from Databases of Interacting Proteins," Genome Biology, vol. 6, no. 10, p. R89, 2005.
[8] S.L. Lo, C.Z. Cai, Y.Z. Chen, and M.C.M. Chung, "Effect of Training Datasets on Support Vector Machine Prediction of Protein-Protein Interactions," Proteomics, vol. 5, no. 4, pp. 876-884, Mar. 2005.
[9] S. Dohkan, A. Koike, and T. Takagi, "Improving the Performance of an SVM-Based Method for Predicting Protein-Protein Interactions," Silico Biology, vol. 6, no. 6, pp. 515-529, 2006.
[10] J.-M. Chia and P.R. Kolatkar, "Implications for Domain Fusion Protein-Protein Interactions Based on Structural Information," BMC Bioinformatics, vol. 5, article no. 161, Oct. 2004.
[11] E.M. Marcotte, M. Pellegrini, H.L. Ng, D.W. Rice, T.O. Yeates, and D. Eisenberg, "Detecting Protein Function and Protein-Protein Interactions from Genome Sequences," Science, vol. 285, no. 5428, pp. 751-753, July 1999.
[12] K.S. Guimaraes, R. Jothi, E. Zotenko, and T.M. Przytycka, "Predicting Domain-Domain Interactions Using a Parsimony Approach," Genome Biology, vol. 7, no. 11, p. R104, 2006.
[13] H. Lee, M. Deng, F. Sun, and T. Chen, "An Integrated Approach to the Prediction of Domain-Domain Interactions," BMC Bioinformatics, vol. 7, article no. 269, 2006.
[14] K.S. Guimaraes and T.M. Przytycka, "Interrogating Domain-Domain Interactions with Parsimony Based Approaches," BMC Bioinformatics, vol. 9, article no. 171, 2008.
[15] B. Raghavachari, A. Tasneem, T.M. Przytycka, and R. Jothi, "Domine: A Database of Protein Domain Interactions," Nucleic Acids Research, vol. 36, no. database issue, pp. D656-D661, Jan. 2008.
[16] P. Bjorkholm and E.L.L. Sonnhammer, "Comparative Analysis and Unification of Domain-Domain Interaction Networks," Bioinformatics, vol. 25, no. 22, pp. 3020-3025, Nov. 2009.
[17] D.-S. Han, H.-S. Kim, W.-H. Jang, S.-D. Lee, and J.-K. Suh, "Prespi: A Domain Combination Based Prediction System for Protein-Protein Interaction," Nucleic Acids Research, vol. 32, no. 21, pp. 6312-6320, 2004.
[18] R.-S. Wang, Y. Wang, L.-Y. Wu, X.-S. Zhang, and L. Chen, "Analysis on Multi-Domain Cooperation for Predicting Protein-Protein Interactions," BMC Bioinformatics, vol. 8, article no. 391, 2007.
[19] D.-S. Han, H.-S. Kim, W.-H. Jang, S.-D. Lee, and J.K. Suh, "Prespi: Design and Implementation of Protein-protein Interaction Prediction Service System," Genome Informatics, vol. 15, no. 2, pp. 171-180, 2004.
[20] X.-M. Zhao, L. Chen, and K. Aihara, "A Discriminative Approach for Identifying Domain-Domain Interactions from Protein-Protein Interactions," Proteins, vol. 78, no. 5, pp. 1243-1253, Apr. 2010.
[21] X. Yang, R. Jiang, and M. Carlson, "A Family of Proteins Containing a Conserved Domain that Mediates Interaction with the Yeast Snf1 Protein Kinase Complex," EMBO J., vol. 13, no. 24, pp. 5878-5886, Dec. 1994.
[22] V.J. Bardwell and R. Treisman, "The Poz Domain: A Conserved Protein-Protein Interaction Motif," Genes Development, vol. 8, no. 14, pp. 1664-1677, July 1994.
[23] G. Apic, W. Huber, and S.A. Teichmann, "Multi-Domain Protein Families and Domain Pairs: Comparison with Known Structures and a Random Model of Domain Recombination," J. Structural Functional Genomics, vol. 4, nos. 2/3, pp. 67-78, 2003.
[24] S.H. Jung, H.-Y. Hur, D. Kim, and D.-S. Han, "Identification of Conserved Domain Combinations in S. cerevisiae Proteins," Proc. Seventh IEEE Int'l Conf. Bioinformatics and Bioeng. (BIBE '07), pp. 14-20, 2007.
[25] L. Salwinski, C.S. Miller, A.J. Smith, F.K. Pettit, J.U. Bowie, and D. Eisenberg, "The Database of Interacting Proteins: 2004 Update," Nucleic Acids Research, vol. 32, no. database issue, pp. D449-D451, Jan. 2004.
[26] S. Kerrien, Y. Alam-Faruque, B. Aranda, I. Bancarz, A. Bridge, C. Derow, E. Dimmer, M. Feuermann, A. Friedrichsen, R. Huntley, C. Kohler, J. Khadake, C. Leroy, A. Liban, C. Lieftink, L. Montecchi-Palazzi, S. Orchard, J. Risse, K. Robbe, B. Roechert, D. Thorneycroft, Y. Zhang, R. Apweiler, and H. Hermjakob, "Intact-Open Source Resource for Molecular Interaction Data," Nucleic Acids Research, vol. 35, no. database issue, pp. D561-D565, Jan. 2007.
[27] A. Ceol, A.C. Aryamontri, L. Licata, D. Peluso, L. Briganti, L. Perfetto, L. Castagnoli, and G. Cesareni, "Mint, The Molecular Interaction Database: 2009 Update," Nucleic Acids Research, vol. 38, no. database issue, pp. D532-D539, Jan. 2010.
[28] R.D. Finn, J. Mistry, J. Tate, P. Coggill, A. Heger, J.E. Pollington, O.L. Gavin, P. Gunasekaran, G. Ceric, K. Forslund, L. Holm, E.L.L. Sonnhammer, S.R. Eddy, and A. Bateman, "The Pfam Protein Families Database," Nucleic Acids Research, vol. 38, no. database issue, pp. D211-D222, Jan. 2010.
[29] U. Consortium, "The Universal Protein Resource (uniprot) in 2010," Nucleic Acids Research, vol. 38, no. database issue, pp. D142-D148, Jan. 2010.
[30] H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne, "The Protein Data Bank," Nucleic Acids Research, vol. 28, no. 1, pp. 235-242, Jan. 2000.
[31] R.D. Finn, M. Marshall, and A. Bateman, "ipfam: Visualization of Protein-Protein Interactions in Pdb at Domain and Amino Acid Resolutions," Bioinformatics, vol. 21, no. 3, pp. 410-412, Feb. 2005.
[32] A.J. Enright, I. Iliopoulos, N.C. Kyrpides, and C.A. Ouzounis, "Protein Interaction Maps for Complete Genomes Based on Gene Fusion Events," Nature, vol. 402, no. 6757, pp. 86-90, Nov. 1999.
[33] G. Apic, J. Gough, and S.A. Teichmann, "Domain Combinations in Archaeal, Eubacterial and Eukaryotic Proteomes," J. Molecular Biology, vol. 310, no. 2, pp. 311-325, July 2001.
[34] E.V. Koonin, Y.I. Wolf, and G.P. Karev, "The Structure of the Protein Universe and Genome Evolution," Nature, vol. 420, no. 6912, pp. 218-223, Nov. 2002.
[35] H. Jeong, B. Tombor, R. Albert, Z.N. Oltvai, and A.L. Barabasi, "The Large-Scale Organization of Metabolic Networks," Nature, vol. 407, no. 6804, pp. 651-654, Oct. 2000.
[36] S. Bilke and C. Peterson, "Topological Properties of Citation and Metabolic Networks," Physical Rev. E, vol. 64, no. 3, p. 036106, Sept. 2001.
[37] C. Prieto and J.D.L. Rivas, "Apid: Agile Protein Interaction Dataanalyzer," Nucleic Acids Research, vol. 34, no. web server issue, pp. W298-W302, July 2006.
[38] Z. Itzhaki, E. Akiva, and H. Margalit, "Preferential Use of Protein Domain Pairs as Interaction Mediators: Order and Transitivity," Bioinformatics, vol. 26, no. 20, pp. 2564-2570, Oct. 2010.

Index Terms:
proteins,biology computing,groupware,multidomain interaction,multidomain collaboration,domain-based computational models,protein-protein interactions,PPI,domain combination,single domain interaction,Proteins,Couplings,Computational modeling,Predictive models,Equations,Accuracy,Databases,computational model.,Classification,protein interaction,domain interaction,multidomain collaboration
Suk-Hoon Jung, Woo-Hyuk Jang, Dong-Soo Han, "A Computational Model for Predicting Protein Interactions Based on Multidomain Collaboration," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 4, pp. 1081-1090, July-Aug. 2012, doi:10.1109/TCBB.2012.55
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