The role of protein-ligand contacts in allosteric regulation of the Escherichia coli Catabolite Activator Protein

Townsend, P.D.; Rodgers, T.L.; Glover, L.C.; Korhonen, H.J.; Richards, S.A.; Colwell, L.J.; Pohl, E.; Wilson, M.R.; Hodgson, D.R.W.; McLeish, T.C.B.; Cann, M.J.

Abstract

Allostery is a fundamental process by which ligand binding to a protein alters its activity at a distant site. Both experimental and theoretical evidence demonstrate that allostery can be communicated through altered slow relaxation protein dynamics without conformational change. The Catabolite Activator Protein (CAP) of Escherichia coli is an exemplar for the analysis of such entropically driven allostery. Negative allostery in CAP occurs between identical cAMP binding sites. Changes to the cAMP-binding pocket can therefore impact the allosteric properties of CAP. Here we demonstrate, through a combination of coarse-grained modelling, isothermal calorimetry, and structural analysis, that decreasing the affinity of CAP for cAMP enhances negative cooperativity through an entropic penalty for ligand binding. The use of variant cAMP ligands indicates the data is not explained by structural heterogeneity between protein mutants. We observe computationally that altered interaction strength between CAP and cAMP variously modifies the change in allosteric cooperativity due to second-site CAP mutations. As the degree of correlated motion between the cAMP contacting site and a second site on CAP increases, there is a tendency for computed double mutations at these sites to drive CAP towards non-cooperativity. Naturally occurring pairs of covarying residues in CAP do not display this tendency, suggesting a selection pressure to fine tune allostery on changes to the CAP ligand-binding pocket without a drive to a non-cooperative state. In general, we hypothesize an evolutionary selection pressure to retain slow relaxation dynamics-induced allostery in proteins in which evolution of the ligand-binding site is occurring.

Citation

Townsend, P., Rodgers, T., Glover, L., Korhonen, H., Richards, S., Colwell, L., …Cann, M. (2015). The role of protein-ligand contacts in allosteric regulation of the Escherichia coli Catabolite Activator Protein. Journal of Biological Chemistry, 290(36), 22225-22235. https://doi.org/10.1074/jbc.m115.669267

• Journal Article Type: Article
• Acceptance Date: Jul 16, 2015
• Online Publication Date: Jul 16, 2015
• Publication Date: Sep 4, 2015
• Deposit Date: Jul 7, 2015
• Publicly Available Date: Sep 4, 2015
• Journal: Journal of Biological Chemistry
• Print ISSN: 0021-9258
• Electronic ISSN: 1083-351X
• Publisher: American Society for Biochemistry and Molecular Biology
• Peer Reviewed: Peer Reviewed
• Volume: 290
• Issue: 36
• Pages: 22225-22235
• DOI: https://doi.org/10.1074/jbc.m115.669267
• Keywords: Allosteric regulation, Biophysics, Calorimetry, Cyclic AMP (cAMP), Nucleoside/nucleotide analogue, Protein dynamic.
• Public URL: https://durham-repository.worktribe.com/output/1405441