Molecular dynamics simulations of the thermal stability of tteRBP and ecRBP

References

• Adams , M.W.W. and Kelly , R.M. 1995 . Enzymes from microorganisms in extreme environments . Chemical & Engineering News , 73 : 32 – 42 .
   Web of Science ®Google Scholar
• Alexander, R., Maduskuie, T., McNamara, K., Smallwood, A., Wei, A., & Stouten, P. Unexpected binding mode of a bis-phenylamidine factor Xa inhibitor complexed to bovine trypsin (GROMACS Tutorial for Drug-Enzyme Complex).
   Google Scholar
• Amadei , A. , de groot , B.L. , Ceruso , M.A. , Paci , M. , Di Nola , A. and Berendsen , H.J. 1999 . A kinetic model for the internal motions of proteins: Diffusion between multiple harmonic wells . Proteins , 35 : 283 – 292 .
   PubMed Web of Science ®Google Scholar
• Amadei , A. , Linssen , A.B.M. and Berendsen , H.J.C. 1993 . Essential dynamics of proteins . Proteins , 17 : 412 – 425 .
   PubMed Web of Science ®Google Scholar
• Berendsen , H.J.C. , Postma , J.P.M. , van Gunsteren , W.F. , Dinola , A. and Haak , J.R. 1984 . Molecular dynamics with coupling to an external bath . The Journal of Chemical Physics , 81 : 3684 – 3690 .
   Web of Science ®Google Scholar
• Berendsen , H.J.C. , Van der Spoel , D. and van Drunen , R. 1995 . GROMACS-a message-passing parallel molecular dynamics implementation . Computer Physics Communications , 91 : 43 – 56 .
   Web of Science ®Google Scholar
• Bjorkman , A.J. , Binnie , R.A. , Zhang , H. , Cole , L.B. , Hermodson , M.A. and Mowbray , S.L. 1994 . Probing protein-protein interactions. The ribose-binding protein in bacterial transport and chemotaxis . Journal of Biological Chemistry , 269 : 30206 – 30211 .
   PubMed Web of Science ®Google Scholar
• Bjorkman , A.J. and Mowbray , S.L. 1998 . Multiple open forms of ribose-binding protein trace the path of its conformational change . Journal of Molecular Biology , 279 ( 3 ) : 651 – 664 .
   PubMed Web of Science ®Google Scholar
• Bohm , G. and Jaenicke , R. 1994 . Relevance of sequence statistics for the properties of extremophilic proteins . International Journal of Peptide and Protein Research , 43 ( 1 ) : 97 – 106 .
   PubMedGoogle Scholar
• Boos , W. and Shuman , H. 1998 . Maltose/Maltodextrin system of E. coli: Transport, metabolism, and regulation . Microbiology and Molecular Biology Reviews , 62 ( 1 ) : 204 – 229 .
   PubMed Web of Science ®Google Scholar
• Cornell , W.D. , Cieplak , P. , Bayly , C.I. , Gould , I.R. , Merz , K.M. , Ferguson , D.M. , … and Kollman , P.A. 1995 . A second generation force field for the simulation of proteins, nucleic acids, and organic molecules . Journal of the American Chemical Society , 117 : 5179 – 5197 .
   Web of Science ®Google Scholar
• Cuneo , M.J. , Tian , Y. , Allert , M. and Hellinga , H.W. 2008 . The backbone structure of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein is essentially identical to its mesophilic E. coli homolog . BMC Structural Biology , 8 : 1 – 11 .
   PubMed Web of Science ®Google Scholar
• Darden , T. , York , D. and Pedersen , L. 1998 . Particle mesh Ewald: An N-log(N) method for Ewald sums in large systems . The Journal of Chemical Physics , 98 : 10089 – 10092 .
   Google Scholar
• Davidson , A.L. , Shuman , H.A. and Nikaido , H. 1992 . Mechanism of maltose transport in E. coli: Transmembrane signaling by periplasmic binding proteins . Proceedings of the National Academy of Sciences, USA , 89 ( 6 ) : 2360 – 2364 .
   PubMed Web of Science ®Google Scholar
• Duan , Y. , Wu , C. , Chowdhury , S. , Lee , M.C. , Xiong , G. , Zhang , W. , … and Kollman , P. 2003 . A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations . A Journal of Computational Chemistry , 24 : 1999 – 2012 .
   PubMed Web of Science ®Google Scholar
• Essmann , U. , Perera , L. , Berkowitz , M. , Darden , T. , Lee , H. and Pedersen , L. 1995 . A smooth particle mesh Ewald method . The Journal of Chemical Physics , 103 : 8577 – 8593 .
   Web of Science ®Google Scholar
• Frisch , M.J. , Trucks , G.W. , Schlegel , H.B. , Scuseria , G.E. , Robb , M.A. , Cheeseman , J.R. , … and Pople , J.A. 2004 . Gaussian 03 , Wallingford , CT : Revision C 02 Gaussian Inc .
   Google Scholar
• Fukuchi , S. and Nishikawa , K. 2001 . Protein surface amino acid compositions distinctively differ between thermophilic and mesophilic bacteria . Journal of Molecular Biology , 309 ( 4 ) : 835 – 843 .
   PubMed Web of Science ®Google Scholar
• Hess , Berk . 2002 . Convergence of sampling in protein simulations . Physical Review E , 65 : 0319101 – 319110 .
   Web of Science ®Google Scholar
• Hess , B. , Bekker , H. , Berendsen , H.J.C. and Fraaije , J.G.E.M. 1997 . LINCS: A linear constraint solver for molecular simulations . Journal of Computational Chemistry , 18 : 1463 – 1472 .
   Web of Science ®Google Scholar
• Huber , R. , Huber , H. and Stretter , K.O. 2000 . Towards the ecology of hyperthermophiles: Biotops, new isolation strategies and novel metabolic properties . FEMS Microbiology Reviews , 24 : 615 – 623 .
   PubMed Web of Science ®Google Scholar
• Jorgensen , W. , Chandrasekhar , J. , Madura , J. , Impey , R. and Klein , M. 1983 . Comparison of simple potential functions for simulating liquid water . The Journal of Chemical Physics , 79 : 926 – 935 .
   Web of Science ®Google Scholar
• Lehmann , M. , Pasamontes , L. , Lassen , S.F. and Wyss , M. 2000 . The consensus concept for thermostability engineering of proteins . Biochemistry Biophysics Acta , 1543 : 408 – 415 .
   PubMed Web of Science ®Google Scholar
• Liang , H.K. , Huang , C.M. , Ko , M.T. and Hwang , J.K. 2005 . Amino acid coupling patterns in thermophilic proteins . Proteins , 59 ( 1 ) : 58 – 63 .
   PubMed Web of Science ®Google Scholar
• Lindahl , E. , Hess , B. and van der Spoel , D. 2001 . GROMACS 3.0: A package for molecular simulation and trajectory analysis . Journal of Molecular Modeling , 7 : 306 – 317 .
   Web of Science ®Google Scholar
• Magnusson , U. , Chaudhuri , B.N. , Ko , J. , Park , C. , Jones , T.A. and Mowbray , S.L. 2002 . Hinge-bending motion of D-Allose-binding protein from E. coli . Journal of Biological Chemistry , 277 ( 16 ) : 14077 – 14084 .
   PubMed Web of Science ®Google Scholar
• Miyamoto , S. and Kollman , P.A. 1992 . Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models . Journal of Computational Chemistry , 13 : 952 – 962 .
   Web of Science ®Google Scholar
• Neiditch , M.B. , Federle , M.J. , Pompeani , A.J. , Kelly , R.C. , Swem , D.L. , Jeffrey , P.D. , … and Hughson , F.M. 2006 . Ligand-induced asymmetry in histidine sensor kinase complex regulates quorum sensing . Cell , 126 ( 6 ) : 1095 – 1108 .
   PubMed Web of Science ®Google Scholar
• Persidis , A. 1998 . Extremophiles: Unusual and useful molecules are found in life on the edge of environmental tolerance . Nature Biotechnology , 16 : 593 – 594 .
   PubMed Web of Science ®Google Scholar
• Sharff , A.J. , Rodseth , L.E. , Spurlino , J.C. and Quiocho , F.A. 1992 . Crystallographic evidence of a large ligand-induced hinge-twist motion between the two domains of the maltodextrin binding protein involved in active transport and chemotaxis . Biochemistry , 31 ( 44 ) : 10657 – 10663 .
   PubMed Web of Science ®Google Scholar
• Sobolev , V. , Wade , R.C. , Vriend , G. and Edelman , M. 1996 . Molecular docking using surface complementarity . Proteins , 25 : 120 – 129 .
   PubMed Web of Science ®Google Scholar
• Spassov , V.Z. , Karshikoff , A.D. and Ladenstein , R. 1994 . Optimization of the elect rostatic interactions in proteins of different functional and folding type . Protein Science , 3 : 1556 – 1569 .
   PubMed Web of Science ®Google Scholar
• Spoel , D.V.D. , Lindahl , E. , Hess , B. , Groenhof , G. , Mark , A.E. and Berendsen , H.J.C. 2005 . Predicting protein ligand binding motions with the conformation explorer . Journal of Computational Chemistry , 26 : 1701 – 1718 .
   PubMed Web of Science ®Google Scholar
• Van Aalten , D.M.F. , Amadei , A. , Bywater , R. , Findlay , J.B.C. , Berendsen , H.J.C. , Sander , C. and Stouten , P.F.W. 1996 . Dynamics of proteins in different solvent systems: Analysis of essential motion in lipases . Biophysical Journal , 70 : 684 – 692 .
   PubMed Web of Science ®Google Scholar
• Van Aalten , D.M.F. , Findlay , J.B.C. , Amadei , A. and Berendsen , H.J.C. 1995 . Essential dynamics of the cellular retinol-binding protein: Evidence for ligand induced conformational changes . Protein Engineering , 89 : 1129 – 1136 .
   Google Scholar
• Vihinen , M. and Mantsala , P. 1989 . Microbial amylolytic enzymes critical reviews . Biochemistry and Molecular Biology , 24 : 329 – 418 .
   Google Scholar
• Vogt , G. and Argos , P. 1997 . Protein thermal stability: Hydrogen bonds or internal packing? . Folding and Design , 2 : S40 – S46 .
   PubMedGoogle Scholar
• Vogt , G. , Woell , S. and Argos , P. 1997 . Protein thermal stability, hydrogen bonds, and ion pairs . Journal of Molecular Biology , 269 : 631 – 643 .
   PubMed Web of Science ®Google Scholar
• Xiao , L. and Honig , B. 1999 . Electrostatic contributions to the stability of hyperthermophilic proteins . Journal of Molecular Biology , 289 : 1435 – 1444 .
   PubMed Web of Science ®Google Scholar
• Yanfen , X. , Yi , X. , Liu , Y. , Ma , Y. and Zhou , P. 2001 . Thermoanaerobacter tengcongensis sp. Nov., a novel anaerobic, saccharolytic, thermophilic bacterium isolated from a hot spring in Tengcong, China . International Journal of Systematic and Evolutionary Microbiology , 51 : 1335 – 1341 .
   PubMed Web of Science ®Google Scholar
• Yip , K.S.P. , Stillman , T.J. , Britton , K.L. , Artymiuk , P.J. , Baker , P.J. , Sedelnikova , S.E. , … and Rice , D.W. 1995 . The Structure of pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion-pair networks in maintaining enzyme stability at extreme temperatures . Structure , 3 : 1147 – 1158 .
   PubMed Web of Science ®Google Scholar