Co-evolution of proteins with their interaction partners1 Export

@article{citeulike:393118, abstract = {The divergent evolution of proteins in cellular signaling pathways requires ligands and their receptors to co-evolve, creating new pathways when a new receptor is activated by a new ligand. However, information about the evolution of binding specificity in ligand-receptor systems is difficult to glean from sequences alone. We have used phosphoglycerate kinase (PGK), an enzyme that forms its active site between its two domains, to develop a standard for measuring the co-evolution of interacting proteins. The N-terminal and C-terminal domains of PGK form the active site at their interface and are covalently linked. Therefore, they must have co-evolved to preserve enzyme function. By building two phylogenetic trees from multiple sequence alignments of each of the two domains of PGK, we have calculated a correlation coefficient for the two trees that quantifies the co-evolution of the two domains. The correlation coefficient for the trees of the two domains of PGK is 0.79, which establishes an upper bound for the co-evolution of a protein domain with its binding partner. The analysis is extended to ligands and their receptors, using the chemokines as a model. We show that the correlation between the chemokine ligand and receptor trees' distances is 0.57. The chemokine family of protein ligands and their G-protein coupled receptors have co-evolved so that each subgroup of chemokine ligands has a matching subgroup of chemokine receptors. The matching subfamilies of ligands and their receptors create a framework within which the ligands of orphan chemokine receptors can be more easily determined. This approach can be applied to a variety of ligand and receptor systems.}, address = {Program in Medical Information Sciences, University of California, San Francisco 94143, USA.}, author = {Goh, Chern-Sing and Bogan, Andrew A. and Joachimiak, Marcin and Walther, Dirk and Cohen, Fred E.}, citeulike-article-id = {393118}, citeulike-linkout-0 = {http://dx.doi.org/10.1006/jmbi.2000.3732}, citeulike-linkout-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0022-2836(00)93732-X}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/10860738}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=10860738}, citeulike-linkout-4 = {http://www.sciencedirect.com/science/article/B6WK7-45F51MG-HB/2/7be5709415cb1e2cc9962d8101820f62}, day = {02}, doi = {10.1006/jmbi.2000.3732}, issn = {00222836}, journal = {Journal of Molecular Biology}, month = {June}, number = {2}, pages = {283--293}, posted-at = {2005-11-15 06:18:00}, priority = {2}, title = {Co-evolution of proteins with their interaction partners1}, url = {http://dx.doi.org/10.1006/jmbi.2000.3732}, volume = {299}, year = {2000} }

TY - JOUR ID - citeulike:393118 L3 - citeulike-article-id:393118 N2 - The divergent evolution of proteins in cellular signaling pathways requires ligands and their receptors to co-evolve, creating new pathways when a new receptor is activated by a new ligand. However, information about the evolution of binding specificity in ligand-receptor systems is difficult to glean from sequences alone. We have used phosphoglycerate kinase (PGK), an enzyme that forms its active site between its two domains, to develop a standard for measuring the co-evolution of interacting proteins. The N-terminal and C-terminal domains of PGK form the active site at their interface and are covalently linked. Therefore, they must have co-evolved to preserve enzyme function. By building two phylogenetic trees from multiple sequence alignments of each of the two domains of PGK, we have calculated a correlation coefficient for the two trees that quantifies the co-evolution of the two domains. The correlation coefficient for the trees of the two domains of PGK is 0.79, which establishes an upper bound for the co-evolution of a protein domain with its binding partner. The analysis is extended to ligands and their receptors, using the chemokines as a model. We show that the correlation between the chemokine ligand and receptor trees’ distances is 0.57. The chemokine family of protein ligands and their G-protein coupled receptors have co-evolved so that each subgroup of chemokine ligands has a matching subgroup of chemokine receptors. The matching subfamilies of ligands and their receptors create a framework within which the ligands of orphan chemokine receptors can be more easily determined. This approach can be applied to a variety of ligand and receptor systems. IS - 2 JF - Journal of Molecular Biology SN - 00222836 AD - Program in Medical Information Sciences, University of California, San Francisco 94143, USA. EP - 293 TI - Co-evolution of proteins with their interaction partners1 VL - 299 SP - 283 AU - Goh, Chern-Sing AU - Bogan, Andrew AU - Joachimiak, Marcin AU - Walther, Dirk AU - Cohen, Fred PY - 2000/06/02/ UR - http://dx.doi.org/10.1006/jmbi.2000.3732 ER -