title: Molecular Dynamics and Free Energy Simulations of Phenylacetate and CO2Release from AMDase and Its G74C/C188S Mutant: A Possible Rationale for the Reduced Activity of the Latter.
abstract: Arylmalonate decarboxylase (AMDase) catalyzes the decarboxylation of α-aryl-α-methyl malonates to produce optically pure α-arylpropionates of industrial and medicinal importance. Herein, atomistic molecular dynamics simulations have been carried out to delineate the mechanism of the release of product molecules phenylacetate (PAC) and carbon dioxide (CO2), from the wild-type (WT) and its G74C/C188S mutant enzymes. Both of the product molecules follow a crystallographically characterized solvent-accessible channel to come out of the protein interior. A higher free energy barrier for the release of PAC from G74C/C188S compared to that in the WT is consistent with the experimentally observed compromised efficiency of the mutant. The release of CO2precedes that of PAC; free energy barriers for CO2and PAC release in the WT enzyme are calculated to be ∼1-2 and ∼23 kcal/mol, respectively. Postdecarboxylation, CO2moves toward a hydrophobic pocket formed by Pro 14, Leu 38, Leu 40, Leu 77, and the side chain of Tyr 48 which serves as its temporary "reservoir". CO2releases following a channel mainly decorated by apolar residues, unlike in the case of oxalate decarboxylase where polar residues mediate its transport.
authors: Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore 560 064, India.
authors: Tarak
authors: T
authors: Karmakar
authors: Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore 560 064, India.
authors: Sundaram
authors: S
authors: Balasubramanian
mesh_terms: D002245:Carbon Dioxide / Q000737:chemistry / Q000378:metabolism*; D002262:Carboxy-Lyases / Q000235:genetics / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D009154:Mutation; D010648:Phenylacetates / Q000737:chemistry / Q000378:metabolism*; D013816:Thermodynamics
chemical_list: D010648:Phenylacetates; D002245:Carbon Dioxide; D002262:Carboxy-Lyases; C071852:malonate decarboxylase; C025136:phenylacetic acid