Protein Coadaptation and the Design of Novel Approaches to Identify Protein Protein Interactions

[EN] Proteins rarely function in isolation but they form part of complex networks of interactions with other proteins within or among cells. The importance of a particular protein for cell viability is directly dependent upon the number of interactions where it participates and the function it performs: the larger the number of interactions of a protein the greater its functional importance is for the cell. With the advent of genome sequencing and "omics'' technologies it became feasible conducting large-scale searches for protein interacting partners. Unfortunately, the accuracy of such analyses has been under-whelming owing to methodological limitations and to the inherent complexity of protein interactions. In addition to these experimental approaches, many computational methods have been developed to identify protein-protein interactions by assuming that interacting proteins coevolve resulting from the coadaptation dynamics between the amino acids of their interacting faces. We review the main technological advances made in the field of interactomics and discuss the feasibility of computational methods to identify protein-protein interactions based on the estimation of coevolution. As proof-of-concept, we present a classical case study: the interactions of cell surface proteins (receptors) and their ligands. Finally, we take this discussion one step forward to include interactions between organisms and species to understand the generation of biological complexity. Development of technologies for accurate detection of protein-protein interactions may shed light on processes that go from the fine-tuning of pathways and metabolic networks to the emergence of biological complexity. (C) 2011 IUBMB IUBMB Life, 63( 4): 264-271, 2011This work was supported by the Science foundation Ireland, under the Research Frontiers Program (RFP: 10/RFP/GEN2685) and a grant from Ministerio de Ciencia e Innovacion (BFU2009-12022) to M.A.F. J.P.L. is supported by the Principal Investigator Grant (07/IN.1/B913) and the Research Frontiers Program (08/RFP/NSC1617) from Science Foundation Ireland. The authors thank Prof. Herman Aberle, Dermot Harnett, and Ash Watson for their careful and critical reading of the manuscript.Fares Riaño, MA.; Ruíz González, MJ.; Labrador, JP. (2011). Protein Coadaptation and the Design of Novel Approaches to Identify Protein Protein Interactions. IUBMB Life. 63(4):264-271. https://doi.org/10.1002/iub.455264271634Albert, R., Jeong, H., & Barabási, A.-L. (2000). Error and attack tolerance of complex networks. Nature, 406(6794), 378-382. doi:10.1038/35019019Goh, C.-S., Milburn, D., & Gerstein, M. (2004). Conformational changes associated with protein–protein interactions. Current Opinion in Structural Biology, 14(1), 104-109. doi:10.1016/j.sbi.2004.01.005Edwards, A. M., Kus, B., Jansen, R., Greenbaum, D., Greenblatt, J., & Gerstein, M. (2002). 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