The allosteric mechanism of yeast chorismate mutase: A dynamic analysis

Journal of Molecular Biology

Volumn 356, Issue 1, 2006, Pages 237-247

  Kong, Yifei ^a   Ma, Jianpeng ^b,c   Karplus, Martin ^a   Lipscomb, William N ^a  

^a HARVARD UNIVERSITY   (United States)

^b BAYLOR COLLEGE OF MEDICINE   (United States)

^c The NanoCarbon Center and Welch Institute for Advanced Materials   (United States)

Author keywords

Allosteric mechanism; Normal mode analysis; Targeted molecular dynamics; Yeast chorismate mutase

Indexed keywords

CHORISMATE MUTASE; LIGAND; UNCLASSIFIED DRUG; YEAST CHORISMATE MUTASE;

ALLOSTERISM; ARTICLE; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME STRUCTURE; ENZYME SUBSTRATE; LIGAND BINDING; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; YEAST;

EID: 30444444229     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.10.064     Document Type: Article

References (44)

1. G.H. Braus Aromatic amino acid biosynthesis in the yeast Saccharomyces cerevisiae: a model system for the regulation of a eukaryotic biosynthetic pathway Microbiol. Rev. 55 1991 349 370
2. U. Weiss, and J.M. Edwards The Biosynthesis of Aromatic Amino Compounds 1980 Wiley New York
3. T. Schmidheini, H.U. Mosch, J.N. Evans, and G. Braus Yeast allosteric chorismate mutase is locked in the activated state by a single amino acid substitution Biochemistry 29 1990 3660 3668
4. N. Strater, K. Hakansson, G. Schnappauf, G. Braus, and W.N. Lipscomb Crystal structure of the T state of allosteric yeast chorismate mutase and comparison with the R state Proc. Natl Acad. Sci. USA 93 1996 3330 3334
5. N. Strater, G. Schnappauf, G. Braus, and W.N. Lipscomb Mechanisms of catalysis and allosteric regulation of yeast chorismate mutase from crystal structures Structure 5 1997 1437 1452
6. P.A. Bartlett, and C.R. Johnson An inhibitor of chorismate mutase resembling the transition-state conformation J. Am. Chem. Soc. 107 1985 7792 7793
7. C.L. Brooks III, M. Karplus, and B.M. Pettitt Proteins: a theoretical perspective of dynamics, structure, and thermodynamics Advan. Chem. Phys. 1 1988 1 249
8. B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan, and M. Karplus CHARMM: a program for macromolecular energy, minimization, and dynamics calculations J. Comput. Chem. 4 1983 187 217
9. M. Levitt, C. Sander, and P.S. Stern Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme J. Mol. Biol. 181 1985 423 447
10. B.R. Brooks, D. Janezic, and M. Karplus Harmonic analysis of large systems. I. Methodology J. Comput. Chem. 16 1995 1522 1542
11. N. Go, T. Noguti, and T. Nishikawa Dynamics of a small globular protein in terms of low-frequency vibrational modes Proc. Natl Acad. Sci. USA 80 1983 3696 3700
12. B. Brooks, and M. Karplus Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme Proc. Natl Acad. Sci. USA 82 1985 4995 4999
13. J. Ma, and M. Karplus The allosteric mechanism of the chaperonin GroEL: a dynamic analysis Proc. Natl Acad. Sci. USA 95 1998 8502 8507
14. A. Thomas, K. Hinsen, M.J. Field, and D. Perahia Tertiary and quaternary conformational changes in aspartate transcarbamylase: a normal mode study Proteins: Struct. Funct. Genet. 34 1999 96 112
15. C. Xu, D. Tobi, and I. Bahar Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T↔R2 transition J. Mol. Biol. 333 2003 153 168
16. 2+-ATPase Biophys. J. 86 2004 743 763
17. W.G. Krebs, V. Alexandrov, C.A. Wilson, N. Echols, H. Yu, and M. Gerstein Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic Proteins: Struct. Funct. Genet. 48 2002 682 695
18. M. Delarue, and P. Dumas On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models Proc. Natl Acad. Sci. USA 101 2004 6957 6962
19. J. Schlitter, M. Engels, P. Kruger, E. Jacoby, and A. Wollmer Targeted molecular dynamics simulation of conformational change-application to the T-R transition in insulin Mol. Sim. 10 1993 291 308
20. J. Ma, and M. Karplus Molecular switch in signal transduction: reaction paths of the conformational changes in ras p21 Proc. Natl Acad. Sci. USA 94 1997 11905 11910
21. 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
22. J. Ma, X. Zheng, G. Schnappauf, G. Braus, M. Karplus, and W.N. Lipscomb Yeast chorismate mutase in the R state: simulations of the active site Proc. Natl Acad. Sci. USA 95 1998 14640 14645
23. G. Schnappauf, W.N. Lipscomb, and G.H. Braus Separation of inhibition and activation of the allosteric yeast chorismate mutase Proc. Natl Acad. Sci. USA 95 1998 2868 2873
24. K. Helmstaedt, S. Krappmann, and G.H. Braus Allosteric regulation of catalytic activity: Escherichia coli aspartate transcarbamoylase versus yeast chorismate mutase Microbiol. Mol. Biol. Rev. 65 2001 404 421
25. H. Guo, Q. Cui, W.N. Lipscomb, and M. Karplus Substrate conformational transitions in the active site of chorismate mutase: their role in the catalytic mechanism Proc. Natl Acad. Sci. USA 98 2001 9032 9037
26. J. Ma New advances in normal mode analysis of supermolecular complexes and applications to structural refinement Curr. Protein Pept. Sci. 5 2004 119 123
27. J. Ma Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes Structure (Camb) 13 2005 373 380
28. D. Ming, Y. Kong, M.A. Lambert, Z. Huang, and J. Ma How to describe protein motion without amino acid sequence and atomic coordinates Proc. Natl Acad. Sci. USA 99 2002 8620 8625
29. D. Ming, Y. Kong, S.J. Wakil, J. Brink, and J. Ma Domain movements in human fatty acid synthase by quantized elastic deformational model Proc. Natl Acad. Sci. USA 99 2002 7895 7899
30. Y. Kong, D. Ming, Y. Wu, J.K. Stoops, Z.H. Zhou, and J. Ma Conformational flexibility of pyruvate dehydrogenase complexes: a computational analysis by quantized elastic deformational model J. Mol. Biol. 330 2003 129 135
31. O. Keskin, R.L. Jernigan, and I. Bahar Proteins with similar architecture exhibit similar large scale dynamic behavior Biophys.J. 78 2000 2093 2106
32. J. Monod, J. Wyman, and J.P. Changeux On the nature of allosteric transitions: a plausible model J. Mol. Biol. 12 1965 88 118
33. Y. Xue, W.N. Lipscomb, R. Graf, G. Schnappauf, and G. Braus The crystal structure of allosteric chorismate mutase at 2.2-Å resolution Proc. Natl Acad. Sci. USA 91 1994 10814 10818
34. T. Lazaridis, and M. Karplus Effective energy function for proteins in solution Proteins: Struct. Funct. Genet. 35 1999 133 152
35. T.A. Halgren Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions J. Comput. Chem. 17 1996 520 552
36. F. Tama, and Y.H. Sanejouand Conformational change of proteins arising from normal mode calculations Protein Eng. 14 2001 1 6
37. B. Tidor, and M. Karplus Simulation analysis of the stability mutant R96H in T4 lysozyme Biochemistry 30 1991 3217 3228
38. H.J.C. Berendsen, J.P.M. Postma, W.F.v. Gunsteren, A. DiNola, and J.R. Haak Molecular dynamics with coupling to an external bath J. Chem. Phys. 81 1984 3684 3690
39. Y.M. Chook, J.V. Gray, H. Ke, and W.N. Lipscomb The monofunctional chorismate mutase from Bacillus subtilis J. Mol. Biol. 240 1994 476 500
40. W. Jorgensen Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water J. Am. Chem. Soc. 103 1981 335 340
41. S.H. Northrup, M.R. Pear, J.A. McCammon, and M. Karplus Molecular dynamics of ferrocytochrome c Nature 286 1980 304 305
42. J. Ma, T.C. Flynn, Q. Cui, A.G. Leslie, J.E. Walker, and M. Karplus A dynamic analysis of the rotation mechanism for conformational change in F(1)-ATPase Structure (Camb) 10 2002 921 931
43. M.P. Allen, and D.J. Tildesley Computer Simulation of Liquids 1980 Clarendon Press Oxford
44. J.P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comput. Phys. 23 1977 327 341