Determination of the Reaction Coordinate for a Key Conformational Fluctuation in Human Carbonic Anhydrase II

• Published in: The journal of physical chemistry. B 2015-08, Vol.119 (34), p.11403-11415
• Main Authors: Paul, Sanjib, Taraphder, Srabani
• Format: Article
• Language: English
• Subjects: Barriers; Carbonic anhydrase; Carbonic Anhydrase II - chemistry; Crystallography, X-Ray; Free energy; Human; Humans; Mathematical models; Models, Molecular; Order parameters; Protein Conformation; Proteins; Residues
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/acs.jpcb.5b03655

During the reversible hydration of carbon dioxide into bicarbonate by the enzyme human carbonic anhydrase II, the rate-determining step of proton transfer across the active site has been suggested to involve side chain rotation of the residue His-64 shuttling an excess proton in and out of the active site. In the present article, we have determined the reaction coordinate for this catalytically important conformational transition starting from a set of 32 order parameters (or candidate collective variables). Following the original work by Peters and Trout (J. Chem. Phys. 2006, 125, 054108), unbiased dynamical transition paths connecting the two major side chain conformations are harvested using an aimless shooting algorithm, and the reaction coordinate is determined using the method of forward-trajectory likelihood maximization. Several different models are tested involving a single order parameter or linear combinations of several of them chosen from the preselected set. An optimum reaction coordinate, identified using a Bayesian information criterion, is found to be a linear combination of 4 order parameters. This reaction coordinate is subsequently utilized to explore the associated free energy profile and diffusive barrier crossing dynamics. To the best of our knowledge, previous instances of this calculation include only alanine dipeptide and photoactive yellow protein (125 residues) in explicit water solvent. The present work is the first report of a quantitative determination of the reaction coordinate for conformational transition in a protein having as many as 259 residues in the presence of explicit water and sampled near the free energy barrier for about 1 μs.