title: Domain Motions and Functionally-Key Residues of L-Alanine Dehydrogenase Revealed by an Elastic Network Model.
abstract: Mycobacterium tuberculosis L-alanine dehydrogenase (L-MtAlaDH) plays an important role in catalyzing L-alanine to ammonia and pyruvate, which has been considered to be a potential target for tuberculosis treatment. In the present work, the functional domain motions encoded in the structure of L-MtAlaDH were investigated by using the Gaussian network model (GNM) and the anisotropy network model (ANM). The slowest modes for the open-apo and closed-holo structures of the enzyme show that the domain motions have a common hinge axis centered in residues Met133 and Met301. Accompanying the conformational transition, both the 1,4-dihydronicotinamide adenine dinucleotide (NAD)-binding domain (NBD) and the substrate-binding domain (SBD) move in a highly coupled way. The first three slowest modes of ANM exhibit the open-closed, rotation and twist motions of L-MtAlaDH, respectively. The calculation of the fast modes reveals the residues responsible for the stability of the protein, and some of them are involved in the interaction with the ligand. Then, the functionally-important residues relevant to the binding of the ligand were identified by using a thermodynamic method. Our computational results are consistent with the experimental data, which will help us to understand the physical mechanism for the function of L-MtAlaDH.
authors.affiliation: College of Science, Yanshan University, Qinhuangdao 066004, China. lxy@ysu.edu.cn.
authors.forename: Xing-Yuan
authors.initials: XY
authors.lastname: Li
authors.affiliation: College of Science, Yanshan University, Qinhuangdao 066004, China. ysu-zjc@163.com.
authors.forename: Jing-Chao
authors.initials: JC
authors.lastname: Zhang
authors.affiliation: College of Science, Yanshan University, Qinhuangdao 066004, China. yywlxzyy@163.com.
authors.forename: Yan-Ying
authors.initials: YY
authors.lastname: Zhu
authors.affiliation: College of Science, Yanshan University, Qinhuangdao 066004, China. jiguosu@ysu.edu.cn.
authors.forename: Ji-Guo
authors.initials: JG
authors.lastname: Su
mesh_terms: D050788:Alanine Dehydrogenase / Q000737:chemistry*; D016880:Anisotropy; D001426:Bacterial Proteins / Q000737:chemistry*; D020134:Catalytic Domain; D003198:Computer Simulation; D004548:Elasticity; D008958:Models, Molecular; D009169:Mycobacterium tuberculosis / Q000201:enzymology; D011485:Protein Binding; D017433:Protein Structure, Secondary; D013816:Thermodynamics
chemical_list: D001426:Bacterial Proteins; D050788:Alanine Dehydrogenase
keywords: Gaussian network model; Mycobacterium tuberculosis l-alanine dehydrogenase; anisotropy network model; domain motions; functionally-key residues; thermodynamic cycle method