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Molecular dynamics simulation of the processive endocellulase Cel48F from Clostridium cellulolyticum : a novel “water‐control mechanism” in enzymatic hydrolysis of cellulose
Author(s) -
Zhang Hao,
Zhang Jilong,
Sun Lu,
Niu Xiaodi,
Wang Song,
Shan Yaming
Publication year - 2014
Publication title -
journal of molecular recognition
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.401
H-Index - 79
eISSN - 1099-1352
pISSN - 0952-3499
DOI - 10.1002/jmr.2364
Subject(s) - cellobiose , chemistry , hydrolysis , cellulose , glycoside hydrolase , molecular dynamics , substrate (aquarium) , active site , cellulase , stereochemistry , anomer , hydrolase , enzyme , biochemistry , computational chemistry , biology , ecology
Glycoside hydrolase of Cel48F from Clostridium cellulolyticum is an important processive cellulose, which can hydrolyze cellulose into cellobiose. Molecular dynamics simulations were used to investigate the hydrolysis mechanism of cellulose. The two conformations of the Cel48F‐cellotetrose complex in which the cellotetroses are bound at different sites (known as the sliding conformation and the hydrolyzing conformation) were simulated. By comparing these two conformations, a water‐control mechanism is proposed, in which the hydrolysis proceeds by providing a water molecule for every other glucosidic linkage. The roles of certain key residues are determined: Glu55 and Asp230 are the most probable candidates for acid and base, respectively, in the mechanism of inverting anomeric carbon. Met414 and Trp417 constitute the water‐control system. Glu44 might keep the substrate at a certain location within the active site or help the substrate chain to move from the sliding conformation to the hydrolyzing conformation. The other hydrophobic residues around the substrate can decrease the sliding energy barrier or provide a hydrophobic environment to resist entry of the surrounding water molecules into the active site, except for those coming from a specific water channel. Copyright © 2014 John Wiley & Sons, Ltd.