title: Comparative thermal unfolding study of psychrophilic and mesophilic subtilisin-like serine proteases by molecular dynamics simulations.
abstract: Molecular dynamics (MD) simulations of a subtilisin-like serine protease VPR from the psychrophilic marine bacterium Vibrio sp. PA-44 and its mesophilic homologue, proteinase K (PRK), have been performed for 20 ns at four different temperatures (300, 373, 473, and 573 K). The comparative analyses of MD trajectories reveal that at almost all temperatures, VPR exhibits greater structural fluctuations/deviations, more unstable regular secondary structural elements, and higher global flexibility than PRK. Although these two proteases follow similar unfolding pathways at high temperatures, VPR initiates unfolding at a lower temperature and unfolds faster at the same high temperatures than PRK. These observations collectively indicate that VPR is less stable and more heat-labile than PRK. Analyses of the structural/geometrical properties reveal that, when compared to PRK, VPR has larger radius of gyration (Rg), less intramolecular contacts and hydrogen bonds (HBs), more protein-solvent HBs, and smaller burial of nonpolar area and larger exposure of polar area. These suggest that the increased flexibility of VPR would be most likely caused by its reduced intramolecular interactions and more favourable protein-solvent interactions arising from the larger exposure of the polar area, whereas the enhanced stability of PRK could be ascribed to its increased intramolecular interactions arising from the better optimized hydrophobicity. The factors responsible for the significant differences in local flexibility between these two proteases were also analyzed and ascertained. This study provides insights into molecular basis of thermostability of homologous serine proteases adapted to different temperatures.
authors.affiliation: a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China.
authors.forename: Xing
authors.initials: X
authors.lastname: Du
authors.affiliation: b Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming 650032 , PR China.
authors.forename: Peng
authors.initials: P
authors.lastname: Sang
authors.affiliation: a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China.
authors.forename: Yuan-Ling
authors.initials: YL
authors.lastname: Xia
authors.affiliation: a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Li
authors.affiliation: a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China.
authors.forename: Jing
authors.initials: J
authors.lastname: Liang
authors.affiliation: c Department of Applied Mathematics , Yunnan Agricultural University , Kunming 650201 , PR China.
authors.forename: Shi-Meng
authors.initials: SM
authors.lastname: Ai
authors.affiliation: a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China.|d Key Laboratory for Tumor Molecular Biology of High Education in Yunnan Province, School of Life Sciences , Yunnan University , Kunming 650223 , PR China.
authors.forename: Xing-Lai
authors.initials: XL
authors.lastname: Ji
authors.affiliation: a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China.|e Human Genetics Center and Division of Biostatistics, School of Public Health , The University of Texas Health Science Center , Houston , TX , 77030 , USA.
authors.forename: Yun-Xin
authors.initials: YX
authors.lastname: Fu
authors.affiliation: a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China.|d Key Laboratory for Tumor Molecular Biology of High Education in Yunnan Province, School of Life Sciences , Yunnan University , Kunming 650223 , PR China.
authors.forename: Shu-Qun
authors.initials: SQ
authors.lastname: Liu
mesh_terms: D059001:Aquatic Organisms; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D018360:Crystallography, X-Ray; D019286:Endopeptidase K / Q000737:chemistry* / Q000378:metabolism; D004795:Enzyme Stability; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D000072756:Protein Conformation, alpha-Helical; D000072757:Protein Conformation, beta-Strand; D054730:Protein Interaction Domains and Motifs; D017433:Protein Structure, Secondary; D058767:Protein Unfolding; D012697:Serine Endopeptidases / Q000737:chemistry* / Q000378:metabolism; D055672:Static Electricity; D040681:Structural Homology, Protein; D013379:Substrate Specificity; D013696:Temperature; D013816:Thermodynamics; D014733:Vibrio / Q000737:chemistry / Q000201:enzymology*
chemical_list: D001426:Bacterial Proteins; D012697:Serine Endopeptidases; D019286:Endopeptidase K
keywords: hydrophobicity; protein unfolding; protein-solvent interactions; stability and flexibility; temperature adaption