title: Dynamical study, hydrogen bond analysis, and constant pH simulations of the beta carbonic anhydrase of Methanobacterium thermoautotrophicum.
abstract: Within the five classes (α, β, γ, δ, and ζ) of carbonic anhydrases (CAs) the first two, containing mammal and plant representatives, are the most studied among all CAs. In this study, we have focused our investigation on the beta-class carbonic anhydrase of Methanobacterium thermoautotrophicum. We investigated both the importance of the Asp-Arg dyad near the catalytic zinc-bound water and the possible roles that water molecules within the active site and residues near the entrance of the catalytic cleft have on the first step of the enzyme's reaction mechanism. Hydrogen-bonding analysis of selected residues within the active site and constant pH replica exchange molecular dynamics constant pH replica exchange simulations were performed. The latter was done in order to evaluate the pKa values of possible proton acceptors. We found an intricate hydrogen-bonding network involving two acidic residues within the active site, Asp16 and Asp34, and the catalytic water molecule. We also observed a very strong interaction between the zinc-bound water and residues Asp34 and Arg36. This interaction was not significantly affected by the change in the protonation state of both the catalytic water and aspartate residue 34. The pKa analysis show that the effect of the R36A mutation affects not only the possible proton acceptors, but also the catalytic water itself.
authors: a Laboratório de Modelagem Molecular - LABMMOL, Instituto de Química, Programa de PG em Química , Universidade Federal do Rio de Janeiro , Av. Athos da Silveira Ramos Nº 149, CT, Bloco A, sala 609, Cidade Universitário, Ilha do Fundão, Rio de Janeiro, RJ 21941-909 , Brazil.
authors: Fabrício
authors: F
authors: Bracht
authors: a Laboratório de Modelagem Molecular - LABMMOL, Instituto de Química, Programa de PG em Química , Universidade Federal do Rio de Janeiro , Av. Athos da Silveira Ramos Nº 149, CT, Bloco A, sala 609, Cidade Universitário, Ilha do Fundão, Rio de Janeiro, RJ 21941-909 , Brazil.
authors: Ricardo Bicca
authors: RB
authors: de Alencastro
mesh_terms: D000595:Amino Acid Sequence; D002256:Carbonic Anhydrases / Q000737:chemistry*; D020134:Catalytic Domain; D006531:HEPES / Q000737:chemistry; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D017014:Methanobacterium / Q000201:enzymology*; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D055503:Protein Multimerization
chemical_list: D002256:Carbonic Anhydrases; D006531:HEPES
keywords: beta Carbonic anhydrase; hydrogen bonding; molecular dynamics; pKa; salt bridge