Publication： Journal of American Chemical Society

Date of Publication: February 18, 2010

Authors： Sangbae Lee, Mengen Chen, Wei Yang, and Nigel G. J. Richards

DOI 10.1021/ja101446u

The importance of understanding the conformational energetics and dynamical properties of active site loops has driven the development of a number of sophisticated experimental biophysical methods to monitor the conformational transitions of these regions and their role in catalysis and/or binding. Computational methods offer an alternate approach to evaluating these motions, but the determination of free energies using molecular dynamics is greatly complicated by the “lagging Hamiltonian” problem, which arises from the relatively long times that are needed for the protein environment to relax about a given loop conformation. As a result, substantial effort is required to ensure adequate sampling for calculations employing perturbation4 or thermodynamic integration methods, limiting their application in studies of large molecular systems. In an effort to overcome this problem, Yang and co-workers have introduced an “Orthogonal Space Random Walk” (OSRW) sampling algorithm, which allows synchronous acceleration of the sampling of order parameter moves and their coupled protein reorganizations. We now report the application of this method to compute the conformational energetics of the functionally important tetraglycine loop in the active site of Oxalobacter formigenes formyl-CoA:oxalate transferase (FRC). Thus, OSRW-derived free energy profiles were computed for the interconversion of “open” and “closed” loop structures in FRC and correlated with the steady-state kinetic properties of the enzyme. In addition, the energetic and structural effects of introducing an alanine residue at each position of the tetraglycine loop were calculated. Taken overall, this comparison study demonstrates the capability of the OSRW strategy in predicting the free energy surfaces associated with active site loop motions.