메뉴 건너뛰기




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

The allosteric mechanism of yeast chorismate mutase: A dynamic analysis

Author keywords

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

Indexed keywords

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

EID: 30444444229     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.10.064     Document Type: Article
Times cited : (30)

References (44)
  • 1
    • 0026012220 scopus 로고
    • Aromatic amino acid biosynthesis in the yeast Saccharomyces cerevisiae: A model system for the regulation of a eukaryotic biosynthetic pathway
    • 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
    • (1991) Microbiol. Rev. , vol.55 , pp. 349-370
    • Braus, G.H.1
  • 3
    • 0025325966 scopus 로고
    • Yeast allosteric chorismate mutase is locked in the activated state by a single amino acid substitution
    • 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
    • (1990) Biochemistry , vol.29 , pp. 3660-3668
    • Schmidheini, T.1    Mosch, H.U.2    Evans, J.N.3    Braus, G.4
  • 4
    • 0029867028 scopus 로고    scopus 로고
    • Crystal structure of the T state of allosteric yeast chorismate mutase and comparison with the R state
    • 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
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 3330-3334
    • Strater, N.1    Hakansson, K.2    Schnappauf, G.3    Braus, G.4    Lipscomb, W.N.5
  • 5
    • 0031573452 scopus 로고    scopus 로고
    • Mechanisms of catalysis and allosteric regulation of yeast chorismate mutase from crystal structures
    • 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
    • (1997) Structure , vol.5 , pp. 1437-1452
    • Strater, N.1    Schnappauf, G.2    Braus, G.3    Lipscomb, W.N.4
  • 6
    • 33845377155 scopus 로고
    • An inhibitor of chorismate mutase resembling the transition-state conformation
    • 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
    • (1985) J. Am. Chem. Soc. , vol.107 , pp. 7792-7793
    • Bartlett, P.A.1    Johnson, C.R.2
  • 7
    • 0001031179 scopus 로고
    • Proteins: A theoretical perspective of dynamics, structure, and thermodynamics
    • 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
    • (1988) Advan. Chem. Phys. , vol.1 , pp. 1-249
    • Brooks III, C.L.1    Karplus, M.2    Pettitt, B.M.3
  • 9
    • 0022419152 scopus 로고
    • Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme
    • 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
    • (1985) J. Mol. Biol. , vol.181 , pp. 423-447
    • Levitt, M.1    Sander, C.2    Stern, P.S.3
  • 10
    • 0000885331 scopus 로고
    • Harmonic analysis of large systems. I. Methodology
    • B.R. Brooks, D. Janezic, and M. Karplus Harmonic analysis of large systems. I. Methodology J. Comput. Chem. 16 1995 1522 1542
    • (1995) J. Comput. Chem. , vol.16 , pp. 1522-1542
    • Brooks, B.R.1    Janezic, D.2    Karplus, M.3
  • 11
    • 0020771265 scopus 로고
    • Dynamics of a small globular protein in terms of low-frequency vibrational modes
    • 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
    • (1983) Proc. Natl Acad. Sci. USA , vol.80 , pp. 3696-3700
    • Go, N.1    Noguti, T.2    Nishikawa, T.3
  • 12
    • 0022111715 scopus 로고
    • Normal modes for specific motions of macromolecules: Application to the hinge-bending mode of lysozyme
    • 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
    • (1985) Proc. Natl Acad. Sci. USA , vol.82 , pp. 4995-4999
    • Brooks, B.1    Karplus, M.2
  • 13
    • 0032555216 scopus 로고    scopus 로고
    • The allosteric mechanism of the chaperonin GroEL: A dynamic analysis
    • J. Ma, and M. Karplus The allosteric mechanism of the chaperonin GroEL: a dynamic analysis Proc. Natl Acad. Sci. USA 95 1998 8502 8507
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 8502-8507
    • Ma, J.1    Karplus, M.2
  • 14
    • 0032932341 scopus 로고    scopus 로고
    • Tertiary and quaternary conformational changes in aspartate transcarbamylase: A normal mode study
    • 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
    • (1999) Proteins: Struct. Funct. Genet. , vol.34 , pp. 96-112
    • Thomas, A.1    Hinsen, K.2    Field, M.J.3    Perahia, D.4
  • 15
    • 0141792364 scopus 로고    scopus 로고
    • Allosteric changes in protein structure computed by a simple mechanical model: Hemoglobin T↔R2 transition
    • 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
    • (2003) J. Mol. Biol. , vol.333 , pp. 153-168
    • Xu, C.1    Tobi, D.2    Bahar, I.3
  • 17
    • 0036721233 scopus 로고    scopus 로고
    • Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic
    • 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
    • (2002) Proteins: Struct. Funct. Genet. , vol.48 , pp. 682-695
    • Krebs, W.G.1    Alexandrov, V.2    Wilson, C.A.3    Echols, N.4    Yu, H.5    Gerstein, M.6
  • 18
    • 2342518038 scopus 로고    scopus 로고
    • On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models
    • 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
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 6957-6962
    • Delarue, M.1    Dumas, P.2
  • 19
    • 0027794972 scopus 로고
    • Targeted molecular dynamics simulation of conformational change-application to the T-R transition in insulin
    • 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
    • (1993) Mol. Sim. , vol.10 , pp. 291-308
    • Schlitter, J.1    Engels, M.2    Kruger, P.3    Jacoby, E.4    Wollmer, A.5
  • 20
    • 0030711616 scopus 로고    scopus 로고
    • Molecular switch in signal transduction: Reaction paths of the conformational changes in ras p21
    • 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
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 11905-11910
    • Ma, J.1    Karplus, M.2
  • 21
    • 0034665864 scopus 로고    scopus 로고
    • A dynamic model for the allosteric mechanism of GroEL
    • 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
    • (2000) J. Mol. Biol. , vol.302 , pp. 303-313
    • Ma, J.1    Sigler, P.B.2    Xu, Z.3    Karplus, M.4
  • 23
    • 0032539802 scopus 로고    scopus 로고
    • Separation of inhibition and activation of the allosteric yeast chorismate mutase
    • 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
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 2868-2873
    • Schnappauf, G.1    Lipscomb, W.N.2    Braus, G.H.3
  • 24
    • 0034821747 scopus 로고    scopus 로고
    • Allosteric regulation of catalytic activity: Escherichia coli aspartate transcarbamoylase versus yeast chorismate mutase
    • 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
    • (2001) Microbiol. Mol. Biol. Rev. , vol.65 , pp. 404-421
    • Helmstaedt, K.1    Krappmann, S.2    Braus, G.H.3
  • 25
    • 0035979270 scopus 로고    scopus 로고
    • Substrate conformational transitions in the active site of chorismate mutase: Their role in the catalytic mechanism
    • 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
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 9032-9037
    • Guo, H.1    Cui, Q.2    Lipscomb, W.N.3    Karplus, M.4
  • 26
    • 1642365068 scopus 로고    scopus 로고
    • New advances in normal mode analysis of supermolecular complexes and applications to structural refinement
    • J. Ma New advances in normal mode analysis of supermolecular complexes and applications to structural refinement Curr. Protein Pept. Sci. 5 2004 119 123
    • (2004) Curr. Protein Pept. Sci. , vol.5 , pp. 119-123
    • Ma, J.1
  • 27
    • 14844286108 scopus 로고    scopus 로고
    • Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes
    • J. Ma Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes Structure (Camb) 13 2005 373 380
    • (2005) Structure (Camb) , vol.13 , pp. 373-380
    • Ma, J.1
  • 28
    • 0037173062 scopus 로고    scopus 로고
    • How to describe protein motion without amino acid sequence and atomic coordinates
    • 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
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 8620-8625
    • Ming, D.1    Kong, Y.2    Lambert, M.A.3    Huang, Z.4    Ma, J.5
  • 29
    • 0037062479 scopus 로고    scopus 로고
    • Domain movements in human fatty acid synthase by quantized elastic deformational model
    • 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
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 7895-7899
    • Ming, D.1    Kong, Y.2    Wakil, S.J.3    Brink, J.4    Ma, J.5
  • 30
    • 0037666985 scopus 로고    scopus 로고
    • Conformational flexibility of pyruvate dehydrogenase complexes: A computational analysis by quantized elastic deformational model
    • 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
    • (2003) J. Mol. Biol. , vol.330 , pp. 129-135
    • Kong, Y.1    Ming, D.2    Wu, Y.3    Stoops, J.K.4    Zhou, Z.H.5    Ma, J.6
  • 31
    • 0034029144 scopus 로고    scopus 로고
    • Proteins with similar architecture exhibit similar large scale dynamic behavior
    • O. Keskin, R.L. Jernigan, and I. Bahar Proteins with similar architecture exhibit similar large scale dynamic behavior Biophys.J. 78 2000 2093 2106
    • (2000) Biophys.J. , vol.78 , pp. 2093-2106
    • Keskin, O.1    Jernigan, R.L.2    Bahar, I.3
  • 32
    • 78651189765 scopus 로고
    • On the nature of allosteric transitions: A plausible model
    • J. Monod, J. Wyman, and J.P. Changeux On the nature of allosteric transitions: a plausible model J. Mol. Biol. 12 1965 88 118
    • (1965) J. Mol. Biol. , vol.12 , pp. 88-118
    • Monod, J.1    Wyman, J.2    Changeux, J.P.3
  • 34
  • 35
    • 0011134241 scopus 로고    scopus 로고
    • Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions
    • 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
    • (1996) J. Comput. Chem. , vol.17 , pp. 520-552
    • Halgren, T.A.1
  • 36
    • 0035044995 scopus 로고    scopus 로고
    • Conformational change of proteins arising from normal mode calculations
    • F. Tama, and Y.H. Sanejouand Conformational change of proteins arising from normal mode calculations Protein Eng. 14 2001 1 6
    • (2001) Protein Eng. , vol.14 , pp. 1-6
    • Tama, F.1    Sanejouand, Y.H.2
  • 37
    • 0025732376 scopus 로고
    • Simulation analysis of the stability mutant R96H in T4 lysozyme
    • B. Tidor, and M. Karplus Simulation analysis of the stability mutant R96H in T4 lysozyme Biochemistry 30 1991 3217 3228
    • (1991) Biochemistry , vol.30 , pp. 3217-3228
    • Tidor, B.1    Karplus, M.2
  • 39
    • 0027992458 scopus 로고
    • The monofunctional chorismate mutase from Bacillus subtilis
    • 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
    • (1994) J. Mol. Biol. , vol.240 , pp. 476-500
    • Chook, Y.M.1    Gray, J.V.2    Ke, H.3    Lipscomb, W.N.4
  • 40
    • 33645858780 scopus 로고
    • Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water
    • W. Jorgensen Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water J. Am. Chem. Soc. 103 1981 335 340
    • (1981) J. Am. Chem. Soc. , vol.103 , pp. 335-340
    • Jorgensen, W.1
  • 42
    • 0036073866 scopus 로고    scopus 로고
    • A dynamic analysis of the rotation mechanism for conformational change in F(1)-ATPase
    • 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
    • (2002) Structure (Camb) , vol.10 , pp. 921-931
    • Ma, J.1    Flynn, T.C.2    Cui, Q.3    Leslie, A.G.4    Walker, J.E.5    Karplus, M.6
  • 44
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • 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
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.