title: Molecular dynamics simulations of the thermal stability of tteRBP and ecRBP.
abstract: Molecular dynamics simulations were performed for investigating the thermal stability of the extremely thermophilic Thermoanaerobacter tengcongensis ribose binding protein (tteRBP) and the mesophilic homologous Escherichia coli ribose binding protein (ecRBP). The simulations for the two proteins were carried out under the room temperature (300 K) and the optimal activity temperature (tteRBP 375 K and ecRBP 329 K), respectively. The comparative analyses of the trajectories show that the two proteins have stable overall structures at the two temperatures; further analyses indicate that they both have strong side-chain interactions and different backbone flexibilities at the different temperatures. The tteRBP 375 K and ecRBP 329 K have stronger internal motion and higher flexibility than tteRBP 300 K and ecRBP 300 K, respectively, it is noted that the flexibility of tteRBP is much higher than that of ecRBP at the two temperatures. Therefore, tteRBP 375 K can adapt to high temperature due to its higher flexibility of backbone. Combining with the researches by Cuneo et al., it is concluded that the side-chain interactions and flexibility of backbone are both the key factors to maintain thermal stability of the two proteins. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:22.
authors.affiliation: a State Key Laboratory of Theoretical and Computational Chemistry , Institute of Theoretical Chemistry, Jilin University , Changchun , 130023 , P.R. China.
authors.forename: Xian-Li
authors.initials: XL
authors.lastname: Feng
authors.forename: Xi
authors.initials: X
authors.lastname: Zhao
authors.forename: Hui
authors.initials: H
authors.lastname: Yu
authors.forename: Tie-Dong
authors.initials: TD
authors.lastname: Sun
authors.forename: Xu-Ri
authors.initials: XR
authors.lastname: Huang
mesh_terms: D000465:Algorithms; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D033902:Periplasmic Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D012266:Ribose / Q000737:chemistry / Q000378:metabolism; D046968:Thermoanaerobacter / Q000201:enzymology
chemical_list: D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; D033902:Periplasmic Binding Proteins; C028003:RbsB protein, E coli; D012266:Ribose