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A Combination of Computational and Experimental Approaches to Investigate the Binding Behavior of B.sub Lipase A Mutants with Substrate p NPP
Author(s) -
Ni Zhong,
Jin Xin,
Zhou Peng,
Wu Qi,
Lin XianFu
Publication year - 2011
Publication title -
molecular informatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.481
H-Index - 68
eISSN - 1868-1751
pISSN - 1868-1743
DOI - 10.1002/minf.201000110
Subject(s) - oniom , lipase , chemistry , docking (animal) , qm/mm , active site , molecular dynamics , enzyme catalysis , stereochemistry , substrate (aquarium) , bacillus subtilis , mutagenesis , binding site , enzyme , computational chemistry , catalysis , mutant , biochemistry , biology , medicine , ecology , genetics , nursing , bacteria , gene
The formation of so‐called enzyme–substrate complex is the key step for a successful enzyme‐catalysis reaction. Enzymes use substrate‐binding energy both to promote ground‐state association and to stabilize the reaction transition state selectively. Some residues besides the catalytic triads play important roles toward the substrate binding process. In this study, we employed ONIOM methodology and docking to explore the influence of individual amino acids of Bacillus subtilis ( B.sub ) lipase A on the hydrolysis reaction, with the aim to guide mutagenesis experiments on the basis of computational framework. Subsequently, the B.sub lipase A is modified experimentally with different non‐polar residues at the position 12, which is spatially adjacent to the active site, by using site‐directed mutagenesis. We obtain a good correlation model between the computationally predicted binding energies and the experimental measured affinities, with a correlation coefficient r =0.78. It is largely unexplored that the combination of docking and quantum mechanical/molecular mechanical (QM/MM) analyses is used in conjunction with experimental procedure to investigate the enzyme catalysis process. We therefore expect that this work could provide a new pathway for exploring the molecular mechanism of enzyme–substrate recognition and interaction.