Combined ab initio and free energy calculations to study reactions in enzymes and solution: Amide hydrolysis in trypsin and aqueous solution

Journal of the American Chemical Society

Volumn 120, Issue 14, 1998, Pages 3448-3457

  Stanton, Robert V ^a   Peräkylä, Mikael ^a   Bakowies, Dirk ^a   Kollman, Peter A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CATALYSIS; ELECTRIC POTENTIAL; ENZYME MECHANISM; HYDROLYSIS; QUANTUM MECHANICS;

EID: 2642622572     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja972723x     Document Type: Article

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56. γ(Ser) The geometry optimizations were performed in mixed internal and Cartesian coordinates. Defining the MM anchor atoms (dummy atoms in QM optimizations) in Cartesian coordinates and relating the QM atoms by Z-matrix coordinates to the MM coordinate frame avoids the necessity of subsequent rigid body rotations to reinsert the QM monomers into the protein coordinate frame. Performing MP2//6-31+G* calculations for the QM models of MICO and TET, we obtained results similar to those reported in Table 3. For MICO, variant A leads to a slightly higher energy (+1.2 kcal/ mol) and variant B leads to a slightly lower energy (-0.3 kcal/mol). For TET, we now calculate energies that are 0.6 and 3.0 kcal/mol lower with variants A and B, respectively. All of these discrepancies are well within the expected accuracy of our combined QM-FE approach. Hence we conclude that the relative quantum mechanical energy (ΔE) is not highly sensitive to the exact choice of constraints in the QM geometry optimizations.
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