title: Mechanistic Insights into the Rate-Limiting Step in Purine-Specific Nucleoside Hydrolase.
abstract: A full enzymatic catalysis cycle in the inosine-adenosine-guanosine specific nucleoside hydrolase (IAG-NH) was assumed to be comprised of four steps: substrate binding, chemical reaction, base release, and ribose release. Nevertheless, the mechanistic details for the rate-limiting step of the entire enzymatic reaction are still unknown, even though the ribose release was likely to be the most difficult stage. Based on state-of-the-art quantum mechanics and molecular mechanics (QM/MM) molecular dynamics (MD) simulations, the ribose release process can be divided into two steps: "ribose dissociation" and "ribose release". The "ribose dissociation" includes "cleavage" and "exchange" stages, in which a metastable 6-fold intermediate will recover to an 8-fold coordination shell of Ca(2+) as observed in apo- IAG-NH. Extensive random acceleration molecular dynamics and MD simulations have been employed to verify plausible release channels, and the estimated barrier for the rate-determining step of the entire reaction is 13.0 kcal/mol, which is comparable to the experimental value of 16.7 kcal/mol. Moreover, the gating mechanism arising from loop1 and loop2, as well as key residues around the active pocket, has been found to play an important role in manipulating the ribose release.
authors.affiliation: School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou, 510006, People's Republic of China.
authors.forename: Nanhao
authors.initials: N
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen, 360015, People's Republic of China.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen, 360015, People's Republic of China.
authors.forename: Jianing
authors.initials: J
authors.lastname: Lu
authors.affiliation: School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou, 510006, People's Republic of China.
authors.forename: Ruibo
authors.initials: R
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen, 360015, People's Republic of China.
authors.forename: Zexing
authors.initials: Z
authors.lastname: Cao
mesh_terms: D002118:Calcium / Q000737:chemistry / Q000378:metabolism; D007700:Kinetics; D008958:Models, Molecular; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D009699:N-Glycosyl Hydrolases / Q000737:chemistry* / Q000378:metabolism; D011789:Quantum Theory
chemical_list: D009699:N-Glycosyl Hydrolases; C110539:inosine-adenosine-guanosine-preferring nucleoside hydrolase; D002118:Calcium