Probing protein environment in an enzymatic process: All-electron quantum chemical analysis combined with ab initio quantum mechanical/molecular mechanical modeling of chorismate mutase.
In this study, we investigated the electronic character of protein environment in enzymatic processes by performing all-electron QM calculations based on the fragment molecular orbital (FMO) method. By introducing a new computational strategy combining all-electron QM analysis with ab initio QM/MM modeling, we investigated the details of molecular interaction energy between a reactive substrate and amino acid residues at a catalytic site. For a practical application, we selected the chorismate mutase catalyzed reaction as an example. Because the computational time required to perform all-electron QM reaction path searches was very large, we employed the ab initio QM/MM modeling technique to construct reliable reaction profiles and performed all-electron FMO calculations for the selected geometries. The main focus of the paper is to analyze the details of electrostatic stabilization, which is considered to be the major feature of enzymatic catalyses, and to clarify how the electronic structure of proteins is polarized in response to the change in electron distribution of the substrate. By performing interaction energy decomposition analysis from a quantum chemical viewpoint, we clarified the relationship between the location of amino acid residues on the protein domain and the degree of electronic polarization of each residue. In particular, in the enzymatic transition state, Arg7, Glu78, and Arg90 are highly polarized in response to the delocalized electronic character of the substrate, and as a result, a large amount of electrostatic stabilization energy is stored in the molecular interaction between the enzyme and the substrate and supplied for transition state stabilization.
Ishida
Toyokazu
T
Research Institute for Computational Science (RICS), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba, 305-3568, Japan. toyokazu.ishida@aist.go.jp
D001412:Bacillus subtilis / Q000201:enzymology*; D055162:Biocatalysis; D020134:Catalytic Domain; D002826:Chorismate Mutase / Q000737:chemistry* / Q000378:metabolism; D004583:Electrons; D008958:Models, Molecular; D011485:Protein Binding; D055550:Protein Stability; D011789:Quantum Theory; D015203:Reproducibility of Results; D055672:Static Electricity; D013816:Thermodynamics
D002826:Chorismate Mutase