title: Structural and molecular basis of cellulase Cel48F by computational modeling: Insight into catalytic and product release mechanism.
abstract: As a processive cellulase, Cel48F from Clostridium cellulolyticum plays a crucial role in cellulose fiber degradation. It has been confirmed in experiment that residue Glu44 will greatly affect the catalytic activity but the mechanism is still unknown. In this study, conventional molecular dynamics, steered molecular dynamics and free energy calculation were integrated to simulate the hydrolysis and product release process to gain insights into the factors that influence catalytic activity. Analysis of simulation results indicated that Glu44 could maintain the proper conformation of its substrate to ensure successful cleavage reaction or serve as a base required in the inverting mechanism in hydrolysis. After hydrolysis is completed, residues Glu44, Asp494, Trp611 and Glu55 participate in hydrogen bond rearrangement during product releasing process. This rearrangement can reduce the sliding barrier and stimulate the product to move toward the exit in the initial release stage. Dependent on the rearrangement, the product moves toward the exit and is exposed to an increasing amount of solvent molecules, which makes solvent effect more and more notable. With the assistance of solvent interaction, product can get rid of the enzyme more easily. However, the subsequent release process remains uncertain because of the disordered motion of solvent molecules. This work provides theoretical data as a basis of cellulase modification or mutation.
authors.affiliation: Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People's Republic of China.
authors.forename: Mengdan
authors.initials: M
authors.lastname: Qian
authors.affiliation: National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun 130012, People's Republic of China.
authors.forename: Shanshan
authors.initials: S
authors.lastname: Guan
authors.affiliation: National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun 130012, People's Republic of China.
authors.forename: Yaming
authors.initials: Y
authors.lastname: Shan
authors.affiliation: Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People's Republic of China. Electronic address: stringbell@jlu.edu.cn.
authors.forename: Hao
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People's Republic of China. Electronic address: ws@jlu.edu.cn.
authors.forename: Song
authors.initials: S
authors.lastname: Wang
mesh_terms: D000596:Amino Acids; D001665:Binding Sites; D055162:Biocatalysis; D002480:Cellulase / Q000737:chemistry*; D046973:Ruminiclostridium cellulolyticum / Q000201:enzymology*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D016297:Mutagenesis, Site-Directed; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D000596:Amino Acids; D012997:Solvents; D002480:Cellulase
keywords: Hydrolysis activity; MM/PBSA calculation; Molecular dynamics simulation; Mutant; Pathway; Substrate conformation