Conformational equilibria and free energy profiles for the allosteric transition of the ribose-binding protein

Journal of Molecular Biology

Volumn 353, Issue 1, 2005, Pages 196-210

  Ravindranathan, Krishna Pratap ^a   Gallicchio, Emilio ^a   Levy, Ronald M ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

Free energy profiles; Ligand induced conformational change; Protein allostery; Ribose binding protein; Umbrella sampling molecular dynamics

Indexed keywords

BINDING PROTEIN; HYDROGEN; PERMEASE; RIBOSE; RIBOSE BINDING PROTEIN; UNCLASSIFIED DRUG;

ALLOSTERISM; ARTICLE; COMPUTER SIMULATION; CONFORMATIONAL TRANSITION; ENERGY; ENTROPY; HISTOGRAM; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR MODEL; PREDICTION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN TRANSPORT; STATISTICAL SIGNIFICANCE; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

BACTERIA (MICROORGANISMS);

EID: 25144472137     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.08.009     Document Type: Article

References (47)

1. B. Alberts, D. Bray, J. Lewis, M. Raff, K. Roberts, and J.D. Watson Molecular Biology of the Cell 2002 Garland Science New York
2. M. Gerstein, A. Lesk, and C. Chothia Structural mechanisms for domain movements in proteins Biochemistry 33 1994 6739 6749
3. M. Gerstein, and W.A. Krebs Database of molecular motions Nucl. Acids Res. 26 1998 4280 4290
4. B. Mao, and J.A. McCammon Theoretical study of hinge-binding protein: internal energy and free energy changes J. Biol. Chem. 258 1983 12543 12547
5. J. Ma, P.B. Sigler, Z. Xu, and M. Karplus A dynamic model for the allosteric mechanism of GroEl J. Mol. Biol. 302 2000 303 313
6. M.A. Young, S. Gonfloni, G. Superti-Furga, B. Roux, and J. Kuriyan Dynamic coupling between the SH2 and SH3 Domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation Cell 105 2001 115 126
7. E. Villa, A. Balaeff, and K. Schulten Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation Proc. Natl Acad. Sci. USA 102 2005 6683 6788
8. M.M. Tirion Large amplitude elastic motions in proteins from a single-parameter, atomic analysis Phys. Rev. Letters 77 1996 1905 1908
9. Y. Wang, A.J. Rader, I. Bahar, and R. Jernigan Global ribosome motions revealed by elastic network model J. Struct. Biol. 147 2004 302 314
10. V. Mekler, E. Kortkhonjia, J. Mukhopadhyay, J. Knight, A. Revyakin, and A.N. Kapanidis Structural organisation of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex Cell 108 2002 599 614
11. S.A. Darst, N. Opalka, P. Chacon, P. Polyakov, C. Richter, G. Zhang, and W. Wriggers Conformational flexibility of bacterial RNA polymerase Proc. Natl Acad. Sci. USA 99 2002 4296 4301
12. F. Tama, W. Wriggers, and C.L. Brooks III Exploring global distortions of biological macromolecules and assembles from low-resolution structural information and elastic network theory J. Mol. Biol. 321 2002 297 305
13. J.F. Falke, R.B. Bass, S.L. Butler, S.A. Chervitz, and M.A. Danielson The two component signalling pathway of bacterial chemotaxis: a molecular view of signal transduction by receptors, kinases, and adaptation enzymes Annu. Rev. Cell. Dev. Biol. 13 1997 457 512
14. A.M. Stock, and S.L. Mowbray Bacterial chemotaxis: a field in motion Curr. Opin. Struct. Biol. 5 1995 744 751
15. S. Mowbray, and L. Cole The 1.7 Å X-ray structure of the periplasmic ribose receptor of Escherichia coli J. Mol. Biol. 225 1992 155 175
16. A. Björkman, and S. Mowbray Multiple open forms of ribose binding protein trace the path of its conformational change J. Mol. Biol. 279 1998 651 664
17. B.H. Shilton, M.M. Flocco, M. Nilsson, and S.L. Mowbray Conformational changes of three periplasmic receptors for bacterial chemotaxis and transport: the maltose-,glucose/galactose- and ribose-binding proteins J. Mol. Biol. 264 1996 350 363
18. L.A. Luck, and J.J. Falke Open conformation of substrate binding cleft: 19F NMR studies of cleft angle in the d-galactose chemosensory receptor Biochemistry 30 1991 6484 6490
19. C.L. Careaga, J. Sutherland, J. Sabeti, and J.J. Falke Large amplitude twisting motions of an interdomain hinge: a disulfide trapping study of the glucose-galactose binding protein Biochemistry 34 1995 3048 3055
20. N.K. Vyas, M.N. Vyas, and F.A. Quiocho Sugar and signal-transducer binding sites of the Escherichia coli galactose chemoreceptor protein Science 242 1988 1290 1295
21. S. Kumar, B. Ma, C.J. Tsai, N. Sinha, and R. Nussinov Folding and binding cascades: dynamic landscapes and population shifts Protein Sci. 2000 2000 10 19
22. K. Gunasekaran, B. Ma, and R. Nussinov Is allostery an intrinsic property of all dynamic proteins? Proteins: Struct. Funct. Bioinf. 57 2004 433 443
23. + channel Nature 414 2001 73 77
24. B. Roux The calculation of the potential of mean force using computer simulations Comput. Phys. Commun. 91 1995 275 282
25. S. Kumar, D. Bouzida, R.H. Swendsen, P.A. Kollman, and J.M. Rosenberg The weighted histogram analysis method for free energy calculations of biomolecules. I. The method J. Comput. Chem. 13 1992 1011 1021
26. R.A. Binnie, H. Zhang, S. Mowbray, and M.A. Hermodson Functional mapping of the surface of Escherichia coli ribose-binding protein: mutations that affect chemotaxis and transport Protein Sci. 1 1992 1642 1651
27. M.M. Flocco, and S.L. Mowbray The 1.9 Å X-ray structure of a closed unliganded form of the periplasmic glucose/galactose receptor from Salmonella typhimurium J. Biol. Chem. 269 1994 8931 8936
28. W.G. Krebs, and M. Gerstein The Morph server: a standardised system for analyzing and visualizing macromolecular motions in a database framework Nucl. Acids Res. 28 2000 1665 1675
29. J.A. McCammon, and S.C. Harvey Dynamics of Proteins and Nucleic Acids 1987 Cambridge University Press Cambridge
30. D.B. Kitchen, D.A. Hirata, J.D. Kofke, M. Westbrook, M. Yarmush, and R.M. Levy Conserving energy during molecular dynamics simulations of water, proteins and proteins in water J. Comput. Chem. 11 1990 1169 1180
31. J.L. Banks, S.B. Beard, Y. Cao, A.E. Cho, W. Damm, and R. Farid Integrated modelling program, applied chemical theory (IMPACT) J. Comput. Chem 2005 In the press
32. E. Gallicchio, M. Andrec, A.K. Felts, and R.M. Levy T-WHAM, replica exchange, and transition paths J. Phys. Chem. B 109 2005 6722 6731
33. W.L. Jorgensen, D.S. Maxwell, and J. Tirado-Rives Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids J. Am. Chem. Soc. 118 1996 11225 11236
34. J. Trylska, J.A. McCammon, and C.L. Brooks III Exploring assembly energetics of the 30S ribosomal subunit using an implicit solvent approach J. Am. Chem. Soc. 127 2005 11125 11133
35. M. Vendruscolo, E. Paci, M. Karplus, and C.M. Dobson Structures and relative free energies of partially folded states of proteins Proc. Natl Acad. Sci. USA 100 2003 14817 14821
36. E. Gallicchio, and R.M. Levy AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling J. Comput. Chem. 25 2004 479 499
37. D. Qui, P.S. Shenkin, F.P. Hollinger, and C.W. Still The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii J. Phys. Chem. A 101 1997 3005 3014
38. D. Bashford, and D.A. Case Generalized Born models of macromolecular solvation effects Annu. Rev. Phys. Chem. 51 2000 129 152
39. E. Gallicchio, L.Y. Zhang, and R.M. Levy The SGB/NP hydration free energy model based on the surface generalized Born solvent reaction field and novel non-polar hydration free energy estimators J. Comput. Chem. 23 2002 517 529
40. R.M. Levy, L.Y. Zhang, E. Gallicchio, and A.K. Felts On the non-polar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy J. Am. Chem. Soc. 125 2003 9523 9530
41. Y. Su, and E. Gallicchio The non-polar solvent potential of mean force for the dimerization of alanine dipeptide: the role of solute-solvent van der Waals interactions Biophys. Chem. 109 2004 251 260
42. A.K. Felts, Y. Harano, E. Gallicchio, and R.M. Levy Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model Proteins: Struct. Funct. Bioinf. 56 2004 310 321
43. M. Andrec, A.K. Felts, E. Gallicchio, and R.M. Levy Protein folding pathways from replica exchange simulations and a kinetic network model Proc. Natl Acad. Sci. USA 102 2005 6801 6806
44. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, and H. Weissig The Protein Data Bank Nucl. Acids Res. 28 2000 235 242
45. H.C. Berendsen, J.P.M. Postma, W.F. van Gunsternen, A. DiNola, and J.R. Haak Molecular dynamics with coupling to an external bath J. Chem. Phys. 81 1984 3684 3690
46. C. Bartels, and M. Karplus Multidimensional adaptive umbrella sampling: applications to main chain and side chain peptide conformations J. Comput. Chem. 18 1997 1450 1462
47. P.J. Kraulis MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures J. Appl. Crystallog. 24 1991 946 950