publication . Article . Preprint . Other literature type . 2019

Non-catalytic Binding Sites Induce Weaker Long-Range Evolutionary Rate Gradients than Catalytic Sites in Enzymes

Sharir-Ivry, Avital; Xia, Yu;
Open Access
  • Published: 19 Feb 2019 Journal: Journal of Molecular Biology, volume 431, pages 3,860-3,870 (issn: 0022-2836, Copyright policy)
  • Publisher: Elsevier BV
Abstract
<jats:title>Abstract</jats:title><jats:p>Enzymes exhibit a strong long-range evolutionary constraint that extends from their catalytic site and affects even distant sites, where site-specific evolutionary rate increases monotonically with distance. While protein-protein sites in enzymes was previously shown to induce only a weak conservation gradient, a comprehensive relationship between different types of functional sites in proteins and the magnitude of evolutionary rate gradients they induce has yet to be established. Here, we systematically calculate the evolutionary rate (dN/dS) of sites as a function of distance from different types of binding sites on enz...
Subjects
free text keywords: Molecular Biology, Binding site, Enzyme, chemistry.chemical_classification, chemistry, Catalysis, Biochemistry, Biophysics, Ligand (biochemistry), Allosteric regulation, Biology, Genetics, Function (biology)
26 references, page 1 of 2

Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D. J. (1997).

Echave, J., Spielman, S. J., & Wilke, C. O. (2016). Causes of evolutionary rate variation among protein sites. Nature Reviews Genetics, 17(2), 109-121. https://doi.org/10.1038/nrg.2015.18

Franzosa, E. A., & Xia, Y. (2009). Structural determinants of protein evolution are context-sensitive at the residue level. Molecular Biology and Evolution, 26(10), 2387-2395. https://doi.org/10.1093/molbev/msp146

Franzosa, E. A., Xue, R., & Xia, Y. (2013). Quantitative residue-level structure-evolution relationships in the yeast membrane proteome. Genome Biology and Evolution, 5(4), 734-744. https://doi.org/10.1093/gbe/evt039 [OpenAIRE]

Furnham, N., Holliday, G. L., De Beer, T. A. P., Jacobsen, J. O. B., Pearson, W. R., & Thornton, J. M. (2014). The Catalytic Site Atlas 2.0: Cataloging catalytic sites and residues identified in enzymes. Nucleic Acids Research, 42(D1), D485-D489. https://doi.org/10.1093/nar/gkt1243

Gerlt, J. A., & Babbitt, P. C. (2001). Divergent Evolution of Enzymatic Function: Mechanistically Diverse Superfamilies and Functionally Distinct Suprafamilies. Annual Review of Biochemistry, 70(1), 209-246. https://doi.org/10.1146/annurev.biochem.70.1.209

Hegyi, H., & Gerstein, M. (1999). The relationship between protein structure and function: a comprehensive survey with application to the yeast genome. Journal of Molecular Biology, 288(1), 147-164. https://doi.org/10.1006/JMBI.1999.2661 [OpenAIRE]

Jack, B. R., Meyer, A. G., Echave, J., & Wilke, C. O. (2016). Functional sites induce long-range evolutionary constraints in enzymes. PLOS Biology, 14(5), e1002452.

Luo, J., van Loo, B., & Kamerlin, S. C. L. (2012). Catalytic promiscuity in Pseudomonas aeruginosa arylsulfatase as an example of chemistry-driven protein evolution. FEBS Letters, 586(11), 1622- 1630. https://doi.org/10.1016/j.febslet.2012.04.012

Marcos, M. L., & Echave, J. (2015). Too packed to change: side-chain packing and site-specific substitution rates in protein evolution. PeerJ, 3, e911. https://doi.org/10.7717/peerj.911

Martin, A. C., Orengo, C. A., Hutchinson, E. G., Jones, S., Karmirantzou, M., Laskowski, R. A., Mitchell, J. B., Taroni, C., & Thornton, J. M. (1998). Protein folds and functions. Structure (London, England : 1993), 6(7), 875-884. https://doi.org/10.1016/S0969-2126(98)00089-6 [OpenAIRE]

Nelson, E. D., & Grishin, N. V. (2016a). Evolution of off-lattice model proteins under ligand binding constraints. Physical Review E, 94(2), 022410. https://doi.org/10.1103/PhysRevE.94.022410

Nelson, E. D., & Grishin, N. V. (2016b). Long-Range Epistasis Mediated by Structural Change in a Model of Ligand Binding Proteins. PLOS ONE, 11(11), e0166739. https://doi.org/10.1371/journal.pone.0166739

Oberai, A., Joh, N. H., Pettit, F. K., & Bowie, J. U. (2009). Structural imperatives impose diverse evolutionary constraints on helical membrane proteins. Proceedings of the National Academy of Sciences of the United States of America, 106(42), 17747-17750. [OpenAIRE]

Overington, J., Donnelly, D., Johnson, M. S., Sali, A., & Blundell, T. L. (1992). Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds. Protein Science : A Publication of the Protein Society, 1(2), 216-226. https://doi.org/10.1002/pro.5560010203

26 references, page 1 of 2
Abstract
<jats:title>Abstract</jats:title><jats:p>Enzymes exhibit a strong long-range evolutionary constraint that extends from their catalytic site and affects even distant sites, where site-specific evolutionary rate increases monotonically with distance. While protein-protein sites in enzymes was previously shown to induce only a weak conservation gradient, a comprehensive relationship between different types of functional sites in proteins and the magnitude of evolutionary rate gradients they induce has yet to be established. Here, we systematically calculate the evolutionary rate (dN/dS) of sites as a function of distance from different types of binding sites on enz...
Subjects
free text keywords: Molecular Biology, Binding site, Enzyme, chemistry.chemical_classification, chemistry, Catalysis, Biochemistry, Biophysics, Ligand (biochemistry), Allosteric regulation, Biology, Genetics, Function (biology)
26 references, page 1 of 2

Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D. J. (1997).

Echave, J., Spielman, S. J., & Wilke, C. O. (2016). Causes of evolutionary rate variation among protein sites. Nature Reviews Genetics, 17(2), 109-121. https://doi.org/10.1038/nrg.2015.18

Franzosa, E. A., & Xia, Y. (2009). Structural determinants of protein evolution are context-sensitive at the residue level. Molecular Biology and Evolution, 26(10), 2387-2395. https://doi.org/10.1093/molbev/msp146

Franzosa, E. A., Xue, R., & Xia, Y. (2013). Quantitative residue-level structure-evolution relationships in the yeast membrane proteome. Genome Biology and Evolution, 5(4), 734-744. https://doi.org/10.1093/gbe/evt039 [OpenAIRE]

Furnham, N., Holliday, G. L., De Beer, T. A. P., Jacobsen, J. O. B., Pearson, W. R., & Thornton, J. M. (2014). The Catalytic Site Atlas 2.0: Cataloging catalytic sites and residues identified in enzymes. Nucleic Acids Research, 42(D1), D485-D489. https://doi.org/10.1093/nar/gkt1243

Gerlt, J. A., & Babbitt, P. C. (2001). Divergent Evolution of Enzymatic Function: Mechanistically Diverse Superfamilies and Functionally Distinct Suprafamilies. Annual Review of Biochemistry, 70(1), 209-246. https://doi.org/10.1146/annurev.biochem.70.1.209

Hegyi, H., & Gerstein, M. (1999). The relationship between protein structure and function: a comprehensive survey with application to the yeast genome. Journal of Molecular Biology, 288(1), 147-164. https://doi.org/10.1006/JMBI.1999.2661 [OpenAIRE]

Jack, B. R., Meyer, A. G., Echave, J., & Wilke, C. O. (2016). Functional sites induce long-range evolutionary constraints in enzymes. PLOS Biology, 14(5), e1002452.

Luo, J., van Loo, B., & Kamerlin, S. C. L. (2012). Catalytic promiscuity in Pseudomonas aeruginosa arylsulfatase as an example of chemistry-driven protein evolution. FEBS Letters, 586(11), 1622- 1630. https://doi.org/10.1016/j.febslet.2012.04.012

Marcos, M. L., & Echave, J. (2015). Too packed to change: side-chain packing and site-specific substitution rates in protein evolution. PeerJ, 3, e911. https://doi.org/10.7717/peerj.911

Martin, A. C., Orengo, C. A., Hutchinson, E. G., Jones, S., Karmirantzou, M., Laskowski, R. A., Mitchell, J. B., Taroni, C., & Thornton, J. M. (1998). Protein folds and functions. Structure (London, England : 1993), 6(7), 875-884. https://doi.org/10.1016/S0969-2126(98)00089-6 [OpenAIRE]

Nelson, E. D., & Grishin, N. V. (2016a). Evolution of off-lattice model proteins under ligand binding constraints. Physical Review E, 94(2), 022410. https://doi.org/10.1103/PhysRevE.94.022410

Nelson, E. D., & Grishin, N. V. (2016b). Long-Range Epistasis Mediated by Structural Change in a Model of Ligand Binding Proteins. PLOS ONE, 11(11), e0166739. https://doi.org/10.1371/journal.pone.0166739

Oberai, A., Joh, N. H., Pettit, F. K., & Bowie, J. U. (2009). Structural imperatives impose diverse evolutionary constraints on helical membrane proteins. Proceedings of the National Academy of Sciences of the United States of America, 106(42), 17747-17750. [OpenAIRE]

Overington, J., Donnelly, D., Johnson, M. S., Sali, A., & Blundell, T. L. (1992). Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds. Protein Science : A Publication of the Protein Society, 1(2), 216-226. https://doi.org/10.1002/pro.5560010203

26 references, page 1 of 2
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