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Volumn 127, Issue 6, 2005, Pages 1946-1957

Dynamic and electrostatic effects in enzymatic processes. An analysis of the nucleophilic substitution reaction in haloalkane dehalogenase

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL REACTIONS; ELECTROSTATICS; HYDROGEN BONDS; NEGATIVE IONS; SOLUTIONS; SUBSTRATES;

EID: 13644269269     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja046553h     Document Type: Article
Times cited : (40)

References (77)
  • 39
    • 0013308245 scopus 로고
    • These two values are based on extrapolations from other temperatures (Okamoto, K.; Kita, T.; Araki, K.; Shingu, H. Bull. Chem. Soc. Jpn. 1967, 40, 1912-1916) or on the use of nucleophilics parameters (see refs 22 and 24).
    • (1967) Bull. Chem. Soc. Jpn. , vol.40 , pp. 1912-1916
    • Okamoto, K.1    Kita, T.2    Araki, K.3    Shingu, H.4
  • 40
    • 13644260863 scopus 로고    scopus 로고
    • note
    • cat.
  • 60
    • 13644253325 scopus 로고    scopus 로고
    • note
    • We employed a parabolic energy penalty centered on the maximum of the PMF with different values of the force constant allowing a maximum fluctuation of the reaction coordinate of about kT, in terms of the PMF. Sets of initial configurations obtained with different values of the force constant led to the same transmission coefficient. In addition we also used constrained reaction coordinate dynamics and tested that averaged properties were the same that those obtained previously. For example, the averaged absolute gradient with respect to the reaction coordinate differed by less than 2% in the different simulations.
  • 64
    • 13644253327 scopus 로고    scopus 로고
    • note
    • The averaged charge on the link atom was independent of the reaction coordinate and has a mean value of 0.28 ± 0.02 au. In addition we verified that the charges on the carboxylate group remained unchanged when the link atom was displaced to a more distant position increasing the size of the QM region, both in the reactant and in the transition state.
  • 65
    • 13644268860 scopus 로고    scopus 로고
    • note
    • -1.
  • 67
    • 13644262748 scopus 로고    scopus 로고
    • note
    • The criterion was the distance of the first minimum of the radial distribution function for acetate and chloride anions in water as given in refs 54 and 55, respectively. These distances can lead to a slight underestimation of the coordination number for the neutral atoms.
  • 72
    • 13644268081 scopus 로고    scopus 로고
    • note
    • The averaged interaction energies were obtained from 10000 structures taken from MD simulations of the transition and reactant states in aqueous solution and in the enzyme. In these calculations we included all the QM region and those water molecules or residues presenting a hydrogen bond with the O2 atom. In the case of the enzyme the side chains of residues Glu56 and Trp125 were not considered in order to avoid the interaction with the chlorine atom.
  • 76
    • 13644259416 scopus 로고    scopus 로고
    • note
    • MM) favours the reaction in solution for this process where one moves from a charge-localized reactant state to a charge-delocalized transition state in which the solvent structure is less distorted. Note that both concepts are different as the reorganization energy also accounts for changes in the interactions.
  • 77
    • 13644255556 scopus 로고    scopus 로고
    • note
    • Estimated as 1/4 of the reorganization energy.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.