Dynamical flexibility and proton transfer in the arginase active site probed by ab initio molecular dynamics.
We have used ab initio molecular dynamics (AIMD) to investigate the dynamical flexibility of the bridged binuclear structural motif in the active site of arginase. Dynamical transformations play a crucial role in catalysis. We have provided direct insight into the motions of the first-shell ligands with emphasis on the chelating and bridging carboxylates. In the case of the terminal Asp234 residue we observe changes in the binding mode (carboxylate shifts). AIMD dynamics of sufficient duration has allowed us to observe proton transfer from the bridging nucleophile to the catalytically essential Asp 128 residue and to map the underlying free energy surface in terms of simple reaction coordinates, such as the oxygen-oxygen distance Ro-o and the asymmetric stretch delta. This has provided valuable insight into the nature of the last step of the catalytic cycle. In addition, constrained molecular dynamics permitted us to compare the deprotonation free energy of the bridging nucleophile in the case of native versus metal-depleted arginase.
Ivanov
Ivaylo
I
Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, USA. iivanov@cmm.chem.upenn.edu
Klein
Michael L
ML
D001119:Arginase / Q000737:chemistry* / Q000378:metabolism*; D001665:Binding Sites; D008956:Models, Chemical; D008958:Models, Molecular; D017510:Protein Folding; D011522:Protons; D013816:Thermodynamics
D011522:Protons; D001119:Arginase