메뉴 건너뛰기




Volumn 352, Issue 4, 2005, Pages 807-822

Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase

Author keywords

Adenylate kinase; Conformational change pathway; Elastic network; Minimum energy path

Indexed keywords

ADENYLATE KINASE;

EID: 24644483073     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.07.031     Document Type: Article
Times cited : (296)

References (117)
  • 1
    • 0032489015 scopus 로고    scopus 로고
    • The cell as a collection of protein machines: Preparing the next generation of molecular biologists
    • B. Alberts The cell as a collection of protein machines: preparing the next generation of molecular biologists Cell 92 1998 291 294
    • (1998) Cell , vol.92 , pp. 291-294
    • Alberts, B.1
  • 2
    • 0028335096 scopus 로고
    • Structural mechanisms for domain movements in proteins
    • M. Gerstein, A.M. Lesk, and C. Chothia Structural mechanisms for domain movements in proteins Biochemistry 33 1994 6739 6749
    • (1994) Biochemistry , vol.33 , pp. 6739-6749
    • Gerstein, M.1    Lesk, A.M.2    Chothia, C.3
  • 6
    • 1842861561 scopus 로고    scopus 로고
    • Biomolecular motors: The F1-ATPase paradigm
    • M. Karplus, and Y.Q. Gao Biomolecular motors: the F1-ATPase paradigm Curr. Opin. Struct. Biol. 14 2004 250 259
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 250-259
    • Karplus, M.1    Gao, Y.Q.2
  • 7
    • 0034637111 scopus 로고    scopus 로고
    • The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution
    • N. Ban, P. Nissen, J.H.P. Moore, and T. Steitz The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution Science 289 2000 905 920
    • (2000) Science , vol.289 , pp. 905-920
    • Ban, N.1    Nissen, P.2    Moore, J.H.P.3    Steitz, T.4
  • 8
    • 0041673353 scopus 로고    scopus 로고
    • The rotary motor of bacterial flagella
    • H.C. Berg The rotary motor of bacterial flagella Annu. Rev. Biochem. 72 2003 19 54
    • (2003) Annu. Rev. Biochem. , vol.72 , pp. 19-54
    • Berg, H.C.1
  • 9
    • 0030870719 scopus 로고    scopus 로고
    • The crystal structure of the asymmetric GroEL-GroES-(ADP)7 chaperonin complex
    • Z. Xu, A. Horwich, and P. Sigler The crystal structure of the asymmetric GroEL-GroES-(ADP)7 chaperonin complex Nature 388 1997 741 750
    • (1997) Nature , vol.388 , pp. 741-750
    • Xu, Z.1    Horwich, A.2    Sigler, P.3
  • 10
    • 0028114231 scopus 로고
    • Structure at 2.8 Å resolution of F1-ATPase from bovine heart mitochondria
    • J. Abrahams, A. Leslie, R. Lutter, and J. Walker Structure at 2.8 Å resolution of F1-ATPase from bovine heart mitochondria Nature 370 1994 621 628
    • (1994) Nature , vol.370 , pp. 621-628
    • Abrahams, J.1    Leslie, A.2    Lutter, R.3    Walker, J.4
  • 11
    • 0014958182 scopus 로고
    • Stereochemistry of cooperative effects in haemoglobin
    • M. Perutz Stereochemistry of cooperative effects in haemoglobin Nature 228 1970 726
    • (1970) Nature , vol.228 , pp. 726
    • Perutz, M.1
  • 13
    • 0033813317 scopus 로고    scopus 로고
    • Conformational changes studied by cryo-electron microscopy
    • H. Saibil Conformational changes studied by cryo-electron microscopy Nature Struct. Biol. 7 2000 711 714
    • (2000) Nature Struct. Biol. , vol.7 , pp. 711-714
    • Saibil, H.1
  • 15
    • 0347504884 scopus 로고    scopus 로고
    • Structure of the mitochondrial ATP synthase by electron cryomicroscopy
    • J.L. Rubinstein, J.E. Walker, and R. Henderson Structure of the mitochondrial ATP synthase by electron cryomicroscopy EMBO J. 22 2003 6182 6192
    • (2003) EMBO J. , vol.22 , pp. 6182-6192
    • Rubinstein, J.L.1    Walker, J.E.2    Henderson, R.3
  • 17
    • 2942516287 scopus 로고    scopus 로고
    • Atomic force microscopy imaging and pulling of nucleic acids
    • H.G. Hansma, K. Kasuya, and E. Oroudjev Atomic force microscopy imaging and pulling of nucleic acids Curr. Opin. Struct. Biol. 14 2004 380 385
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 380-385
    • Hansma, H.G.1    Kasuya, K.2    Oroudjev, E.3
  • 18
    • 0026544877 scopus 로고
    • Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 Å resolution. a model for a catalytic transition state
    • C. Müller, and G. Schulz Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 Å resolution. A model for a catalytic transition state J. Mol. Biol. 224 1992 159 177
    • (1992) J. Mol. Biol. , vol.224 , pp. 159-177
    • Müller, C.1    Schulz, G.2
  • 19
    • 0029644168 scopus 로고    scopus 로고
    • Adenylate kinase motions during catalysis: An energetic counterweight balancing substrate binding
    • C. Müller, G. Schlauderer, J. Reinstein, and G. Schulz Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding Structure 4 1996 147 156
    • (1996) Structure , vol.4 , pp. 147-156
    • Müller, C.1    Schlauderer, G.2    Reinstein, J.3    Schulz, G.4
  • 21
    • 0036967107 scopus 로고    scopus 로고
    • The frontiers of time-resolved macromolecular crystallography: Movies and chirped X-ray pulses
    • K. Moffat The frontiers of time-resolved macromolecular crystallography: movies and chirped X-ray pulses Faraday Discuss. 122 2003 65 77 discussion 79-88
    • (2003) Faraday Discuss. , vol.122 , pp. 65-77
    • Moffat, K.1
  • 22
    • 0038047431 scopus 로고    scopus 로고
    • Watching a protein as it functions with 150-ps time-resolved X-ray crystallography
    • F. Schotte, M. Lim, T.A. Jackson, A.V. Smirnov, J. Soman, and J.S. Olson Watching a protein as it functions with 150-ps time-resolved X-ray crystallography Science 300 2003 1944 1947
    • (2003) Science , vol.300 , pp. 1944-1947
    • Schotte, F.1    Lim, M.2    Jackson, T.A.3    Smirnov, A.V.4    Soman, J.5    Olson, J.S.6
  • 26
    • 0001031179 scopus 로고
    • Proteins: A theoretical perspective of dynamics, structure, and thermodynamics
    • I. Prigogine S.A. Rice Wiley New York
    • C.L. Brooks, M. Karplus, and B.M. Pettitt Proteins: a theoretical perspective of dynamics, structure, and thermodynamics I. Prigogine S.A. Rice Advances in Chemical Physics vol. 71 1988 Wiley New York
    • (1988) Advances in Chemical Physics , vol.71
    • Brooks, C.L.1    Karplus, M.2    Pettitt, B.M.3
  • 27
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single parameter, atomic analysis
    • M.M. Tirion Large amplitude elastic motions in proteins from a single parameter, atomic analysis Phys. Rev. Letters 77 1996 1905 1908
    • (1996) Phys. Rev. Letters , vol.77 , pp. 1905-1908
    • Tirion, M.M.1
  • 28
    • 0035044995 scopus 로고    scopus 로고
    • Conformational change of proteins arising from normal mode calculations
    • F. Tama, and Y. 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.2
  • 29
    • 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
  • 30
    • 0036077875 scopus 로고    scopus 로고
    • Simplified normal mode analysis of conformational transitions in dna-dependent polymerases: The elastic network model
    • M. Delarue, and Y.H. Sanejouand Simplified normal mode analysis of conformational transitions in dna-dependent polymerases: the elastic network model J. Mol. Biol. 320 2002 1011 1024
    • (2002) J. Mol. Biol. , vol.320 , pp. 1011-1024
    • Delarue, M.1    Sanejouand, Y.H.2
  • 31
    • 0042424707 scopus 로고    scopus 로고
    • Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy
    • F. Tama, M. Valle, J. Frank, and C.L. Brooks Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy Proc. Natl Acad. Sci. USA 100 2003 9319 9323
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 9319-9323
    • Tama, F.1    Valle, M.2    Frank, J.3    Brooks, C.L.4
  • 32
    • 0141865614 scopus 로고    scopus 로고
    • Transconformations of the SERCA1 Ca-ATPase: A normal mode study
    • N. Reuter, K. Hinsen, and J.J. Lacapère Transconformations of the SERCA1 Ca-ATPase: a normal mode study Biophys. J. 85 2003 2186 2197
    • (2003) Biophys. J. , vol.85 , pp. 2186-2197
    • Reuter, N.1    Hinsen, K.2    Lacapère, J.J.3
  • 33
    • 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
  • 34
    • 0242268469 scopus 로고    scopus 로고
    • Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins
    • O. Miyashita, J. Onuchic, and P. Wolynes Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins Proc. Natl Acad. Sci. USA 100 2003 12570 12575
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 12570-12575
    • Miyashita, O.1    Onuchic, J.2    Wolynes, P.3
  • 36
    • 1642452881 scopus 로고    scopus 로고
    • The role of hydrogen bonding in the enzymatic reaction catalyzed by HIV-1 protease
    • J. Trylska, P. Grochowski, and J.A. McCammon The role of hydrogen bonding in the enzymatic reaction catalyzed by HIV-1 protease Protein Sci. 13 2004 513 528
    • (2004) Protein Sci. , vol.13 , pp. 513-528
    • Trylska, J.1    Grochowski, P.2    McCammon, J.A.3
  • 37
    • 9644266693 scopus 로고    scopus 로고
    • Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis
    • F. Tama, and C.L. Brooks Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis J. Mol. Biol. 345 2005 299 314
    • (2005) J. Mol. Biol. , vol.345 , pp. 299-314
    • Tama, F.1    Brooks, C.L.2
  • 38
    • 10044234207 scopus 로고    scopus 로고
    • The requirement for mechanical coupling between head and s2 domains in smooth muscle Myosin ATPase regulation and its implications for dimeric motor function
    • F. Tama, M. Feig, J. Liu, C.L. Brooks, and K.A. Taylor The requirement for mechanical coupling between head and s2 domains in smooth muscle Myosin ATPase regulation and its implications for dimeric motor function J. Mol. Biol. 345 2005 837 854
    • (2005) J. Mol. Biol. , vol.345 , pp. 837-854
    • Tama, F.1    Feig, M.2    Liu, J.3    Brooks, C.L.4    Taylor, K.A.5
  • 39
    • 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 13 2005 373 380
    • (2005) Structure , vol.13 , pp. 373-380
    • Ma, J.1
  • 40
    • 17044393884 scopus 로고    scopus 로고
    • Coarse-grained models for proteins
    • V. Tozzini Coarse-grained models for proteins Curr. Opin. Struct. Biol. 15 2005 144 150
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 144-150
    • Tozzini, V.1
  • 41
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    • I. Bahar, A. Atilgan, and B. Erman Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential Fold. Des. 2 1997 173 181
    • (1997) Fold. Des. , vol.2 , pp. 173-181
    • Bahar, I.1    Atilgan, A.2    Erman, B.3
  • 42
    • 0035865950 scopus 로고    scopus 로고
    • Learning effective amino acid interactions through iterative stochastic techniques
    • C. Micheletti, F. Seno, J. Banavar, and A. Maritan Learning effective amino acid interactions through iterative stochastic techniques Proteins: Struct. Funct. Genet. 42 2001 422 431
    • (2001) Proteins: Struct. Funct. Genet. , vol.42 , pp. 422-431
    • Micheletti, C.1    Seno, F.2    Banavar, J.3    Maritan, A.4
  • 43
    • 0037022347 scopus 로고    scopus 로고
    • Flexibility and packing in proteins
    • B. Halle Flexibility and packing in proteins Proc. Natl Acad. Sci. USA 99 2002 1274 1279
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 1274-1279
    • Halle, B.1
  • 44
    • 51149216498 scopus 로고
    • Analysis of contribution of internal vibrations to statistical weights of equilibrium conformations of macromolecules
    • N. Go, and H. Scheraga Analysis of contribution of internal vibrations to statistical weights of equilibrium conformations of macromolecules J. Chem. Phys. 51 1969 4751 4767
    • (1969) J. Chem. Phys. , vol.51 , pp. 4751-4767
    • Go, N.1    Scheraga, H.2
  • 45
    • 18344362394 scopus 로고
    • Use of classical statistical-mechanics in treatment of polymer-chain conformation
    • N. Go, and H. Scheraga Use of classical statistical-mechanics in treatment of polymer-chain conformation Macromolecules 9 1976 535 542
    • (1976) Macromolecules , vol.9 , pp. 535-542
    • Go, N.1    Scheraga, H.2
  • 46
    • 0017024625 scopus 로고
    • Statistical thermodynamics of random networks
    • P.J. Flory Statistical thermodynamics of random networks Proc. Roy. Soc. ser. A 351 1976 351 380
    • (1976) Proc. Roy. Soc. Ser. a , vol.351 , pp. 351-380
    • Flory, P.J.1
  • 48
    • 0035996990 scopus 로고    scopus 로고
    • Dynamics of proteins in crystals: Comparison of experiment with simple models
    • S. Kundu, J.S. Melton, D.C. Sorensen, and G.N. Phillips Dynamics of proteins in crystals: comparison of experiment with simple models Biophys. J. 83 2002 723 732
    • (2002) Biophys. J. , vol.83 , pp. 723-732
    • Kundu, S.1    Melton, J.S.2    Sorensen, D.C.3    Phillips, G.N.4
  • 49
    • 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
  • 50
    • 0345687171 scopus 로고    scopus 로고
    • A comparative study of motor-protein motions by using a simple elastic-network model
    • W. Zheng, and S. Doniach A comparative study of motor-protein motions by using a simple elastic-network model Proc. Natl Acad. Sci. USA 100 2003 13253 13258
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 13253-13258
    • Zheng, W.1    Doniach, S.2
  • 51
    • 18144418170 scopus 로고    scopus 로고
    • Protein structural change upon ligand binding: Linear response theory
    • M. Ikeguchi, J. Ueno, M. Sato, and A. Kidera Protein structural change upon ligand binding: linear response theory Phys. Rev. Letters 94 2005 078102
    • (2005) Phys. Rev. Letters , vol.94 , pp. 078102
    • Ikeguchi, M.1    Ueno, J.2    Sato, M.3    Kidera, A.4
  • 52
    • 0036775029 scopus 로고    scopus 로고
    • Elastic models of conformational transitions in macromolecules
    • M.K. Kim, G.S. Chirikjian, and R.L. Jernigan Elastic models of conformational transitions in macromolecules J. Mol. Graph. Model 21 2002 151 160
    • (2002) J. Mol. Graph. Model , vol.21 , pp. 151-160
    • Kim, M.K.1    Chirikjian, G.S.2    Jernigan, R.L.3
  • 53
    • 13444305369 scopus 로고    scopus 로고
    • Simple energy landscape model for the kinetics of functional transitions in proteins
    • O. Miyashita, P. Wolynes, and J. Onuchic Simple energy landscape model for the kinetics of functional transitions in proteins J. Phys. Chem. B 109 2005 1959 1969
    • (2005) J. Phys. Chem. B , vol.109 , pp. 1959-1969
    • Miyashita, O.1    Wolynes, P.2    Onuchic, J.3
  • 54
    • 0000231955 scopus 로고
    • Conjugate peak refinement - An algorithm for finding reaction paths and accurate transition-states in systems with many degrees of freedom
    • S. Fischer, and M. Karplus Conjugate peak refinement - an algorithm for finding reaction paths and accurate transition-states in systems with many degrees of freedom Chem. Phys. Letters 194 1992 252 261
    • (1992) Chem. Phys. Letters , vol.194 , pp. 252-261
    • Fischer, S.1    Karplus, M.2
  • 55
    • 0031680034 scopus 로고    scopus 로고
    • Adenylate kinase: Kinetic behavior in intact cells indicates it is integral to multiple cellular processes
    • P. Dzeja, R. Zeleznikar, and N. Goldberg Adenylate kinase: kinetic behavior in intact cells indicates it is integral to multiple cellular processes Mol. Cell. Biochem. 184 1998 169 182
    • (1998) Mol. Cell. Biochem. , vol.184 , pp. 169-182
    • Dzeja, P.1    Zeleznikar, R.2    Goldberg, N.3
  • 56
    • 0001607723 scopus 로고
    • Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold
    • J. Walker, M. Saraste, M. Runswick, and N. Gay Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold EMBO J. 1 1982 945 951
    • (1982) EMBO J. , vol.1 , pp. 945-951
    • Walker, J.1    Saraste, M.2    Runswick, M.3    Gay, N.4
  • 57
    • 0028958522 scopus 로고
    • Mechanism of adenylate kinase. the "essential lysine" helps to orient the phosphates and the active site residues to proper conformations
    • L. Byeon, Z. Shi, and M. Tsai Mechanism of adenylate kinase. The "essential lysine" helps to orient the phosphates and the active site residues to proper conformations Biochemistry 34 1995 3172 3182
    • (1995) Biochemistry , vol.34 , pp. 3172-3182
    • Byeon, L.1    Shi, Z.2    Tsai, M.3
  • 58
    • 0142011067 scopus 로고    scopus 로고
    • Evolution and classification of P-loop kinases and related proteins
    • D.D. Leipe, E.V. Koonin, and L. Aravind Evolution and classification of P-loop kinases and related proteins J. Mol. Biol. 333 2003 781 815
    • (2003) J. Mol. Biol. , vol.333 , pp. 781-815
    • Leipe, D.D.1    Koonin, E.V.2    Aravind, L.3
  • 59
    • 0036290378 scopus 로고    scopus 로고
    • A novel view of domain flexibility in E. coli adenylate kinase based on structural mode-coupling (15)N NMR relaxation
    • V. Tugarinov, Y.E. Shapiro, Z. Liang, J.H. Freed, and E. Meirovitch A novel view of domain flexibility in E. coli adenylate kinase based on structural mode-coupling (15)N NMR relaxation J. Mol. Biol. 315 2002 155 170
    • (2002) J. Mol. Biol. , vol.315 , pp. 155-170
    • Tugarinov, V.1    Shapiro, Y.E.2    Liang, Z.3    Freed, J.H.4    Meirovitch, E.5
  • 61
    • 6344231648 scopus 로고    scopus 로고
    • Escherichia coli adenylate kinase dynamics: Comparison of elastic network model modes with mode-coupling (15)N-NMR relaxation data
    • N.A. Temiz, E. Meirovitch, and I. Bahar Escherichia coli adenylate kinase dynamics: comparison of elastic network model modes with mode-coupling (15)N-NMR relaxation data Proteins: Struct. Funct. Genet. 57 2004 468 480
    • (2004) Proteins: Struct. Funct. Genet. , vol.57 , pp. 468-480
    • Temiz, N.A.1    Meirovitch, E.2    Bahar, I.3
  • 63
    • 0033550299 scopus 로고    scopus 로고
    • Salt bridge stability in monomeric proteins
    • S. Kumar, and R. Nussinov Salt bridge stability in monomeric proteins J. Mol. Biol. 293 1999 1241 1255
    • (1999) J. Mol. Biol. , vol.293 , pp. 1241-1255
    • Kumar, S.1    Nussinov, R.2
  • 64
    • 0035937443 scopus 로고    scopus 로고
    • Two-state allosteric behavior in a single-domain signaling protein
    • B. Volkman, D. Lipson, D. Wemmer, and D. Kern Two-state allosteric behavior in a single-domain signaling protein Science 291 2001 2429 2433
    • (2001) Science , vol.291 , pp. 2429-2433
    • Volkman, B.1    Lipson, D.2    Wemmer, D.3    Kern, D.4
  • 66
    • 0029644728 scopus 로고
    • Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases
    • C. Vonrhein, G. Schlauderer, and G. Schulz Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases Structure 3 1995 483 490
    • (1995) Structure , vol.3 , pp. 483-490
    • Vonrhein, C.1    Schlauderer, G.2    Schulz, G.3
  • 67
    • 0027528934 scopus 로고
    • Domain closure in adenylate kinase. Joints on either side of two helices close like neighboring fingers
    • M. Gerstein, G. Schulz, and C. Chothia Domain closure in adenylate kinase. Joints on either side of two helices close like neighboring fingers J. Mol. Biol. 229 1993 494 501
    • (1993) J. Mol. Biol. , vol.229 , pp. 494-501
    • Gerstein, M.1    Schulz, G.2    Chothia, C.3
  • 68
    • 0029897810 scopus 로고    scopus 로고
    • The structure of bovine mitochondrial adenylate kinase: Comparison with isoenzymes in other compartments
    • G. Schlauderer, and G. Schulz The structure of bovine mitochondrial adenylate kinase: comparison with isoenzymes in other compartments Protein Sci. 5 1996 434 441
    • (1996) Protein Sci. , vol.5 , pp. 434-441
    • Schlauderer, G.1    Schulz, G.2
  • 69
    • 0029866802 scopus 로고    scopus 로고
    • Structure of a mutant adenylate kinase ligated with an ATP-analogue showing domain closure over ATP
    • G. Schlauderer, K. Proba, and G. Schulz Structure of a mutant adenylate kinase ligated with an ATP-analogue showing domain closure over ATP J. Mol. Biol. 256 1996 223 227
    • (1996) J. Mol. Biol. , vol.256 , pp. 223-227
    • Schlauderer, G.1    Proba, K.2    Schulz, G.3
  • 70
    • 0027506631 scopus 로고
    • Crystal-structures of 2 mutants of adenylate kinase from Escherichia coli that modify the gly-loop
    • C.W. Muller, and G.E. Schulz Crystal-structures of 2 mutants of adenylate kinase from Escherichia coli that modify the gly-loop Proteins: Struct. Funct. Genet. 15 1993 42
    • (1993) Proteins: Struct. Funct. Genet. , vol.15 , pp. 42
    • Muller, C.W.1    Schulz, G.E.2
  • 71
    • 0028338283 scopus 로고
    • The closed conformation of a highly flexible protein: The structure of E. coli adenylate kinase with bound AMP and AMPPNP
    • M. Berry, B. Meador, T. Bilderback, P. Liang, M. Glaser, and G. Phillips The closed conformation of a highly flexible protein: the structure of E. coli adenylate kinase with bound AMP and AMPPNP Proteins: Struct. Funct. Genet. 19 1994 183 198
    • (1994) Proteins: Struct. Funct. Genet. , vol.19 , pp. 183-198
    • Berry, M.1    Meador, B.2    Bilderback, T.3    Liang, P.4    Glaser, M.5    Phillips, G.6
  • 72
    • 0028998836 scopus 로고
    • High-resolution structures of adenylate kinase from yeast ligated with inhibitor Ap5A, showing the pathway of phosphoryl transfer
    • U. Abele, and G. Schulz High-resolution structures of adenylate kinase from yeast ligated with inhibitor Ap5A, showing the pathway of phosphoryl transfer Protein Sci. 4 1995 1262 1271
    • (1995) Protein Sci. , vol.4 , pp. 1262-1271
    • Abele, U.1    Schulz, G.2
  • 73
    • 0029031161 scopus 로고
    • Stability, activity and structure of adenylate kinase mutants
    • P. Spuergin, U. Abele, and G. Schulz Stability, activity and structure of adenylate kinase mutants Eur. J. Biochem. 231 1995 405 413
    • (1995) Eur. J. Biochem. , vol.231 , pp. 405-413
    • Spuergin, P.1    Abele, U.2    Schulz, G.3
  • 74
    • 0032515929 scopus 로고    scopus 로고
    • The crystal structure of phosphoribulokinase from Rhodobacter sphaeroides reveals a fold similar to that of adenylate kinase
    • D. Harrison, J. Runquist, A. Holub, and H. Miziorko The crystal structure of phosphoribulokinase from Rhodobacter sphaeroides reveals a fold similar to that of adenylate kinase Biochemistry 37 1998 5074 5085
    • (1998) Biochemistry , vol.37 , pp. 5074-5085
    • Harrison, D.1    Runquist, J.2    Holub, A.3    Miziorko, H.4
  • 75
    • 0038690122 scopus 로고    scopus 로고
    • Structures of thermophilic and mesophilic adenylate kinases from the genus Methanococcus
    • A.R. Criswell, E. Bae, B. Stec, J. Konisky, and G.N. Phillips Structures of thermophilic and mesophilic adenylate kinases from the genus Methanococcus J. Mol. Biol. 330 2003 1087 1099
    • (2003) J. Mol. Biol. , vol.330 , pp. 1087-1099
    • Criswell, A.R.1    Bae, E.2    Stec, B.3    Konisky, J.4    Phillips, G.N.5
  • 76
    • 0014429881 scopus 로고
    • Initial velocity and equilibrium kinetics of myokinase
    • D. Rhoads, and J. Lowenstein Initial velocity and equilibrium kinetics of myokinase J. Biol. Chem. 243 1968 3963 3972
    • (1968) J. Biol. Chem. , vol.243 , pp. 3963-3972
    • Rhoads, D.1    Lowenstein, J.2
  • 77
    • 0242331659 scopus 로고    scopus 로고
    • The energetic cost of domain reorientation in maltose-binding protein as studied by NMR and fluorescence spectroscopy
    • O. Millet, R.P. Hudson, and L.E. Kay The energetic cost of domain reorientation in maltose-binding protein as studied by NMR and fluorescence spectroscopy Proc. Natl Acad. Sci. USA 100 2003 12700 12705
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 12700-12705
    • Millet, O.1    Hudson, R.P.2    Kay, L.E.3
  • 78
    • 0036385839 scopus 로고    scopus 로고
    • Elastic properties of proteins: Insight on the folding process and evolutionary selection of native structures
    • C. Micheletti, G. Lattanzi, and A. Maritan Elastic properties of proteins: insight on the folding process and evolutionary selection of native structures J. Mol. Biol. 321 2002 909 921
    • (2002) J. Mol. Biol. , vol.321 , pp. 909-921
    • Micheletti, C.1    Lattanzi, G.2    Maritan, A.3
  • 79
    • 0036904038 scopus 로고    scopus 로고
    • Changes in flexibility upon binding: Application of the self-consistent pair contact probability method to protein-protein interactions
    • L. Canino, T. Shen, and J. McCammon Changes in flexibility upon binding: application of the self-consistent pair contact probability method to protein-protein interactions J. Chem. Phys. 117 2002 9927 9933
    • (2002) J. Chem. Phys. , vol.117 , pp. 9927-9933
    • Canino, L.1    Shen, T.2    McCammon, J.3
  • 80
    • 0345064192 scopus 로고    scopus 로고
    • Hyperelasticity governs dynamic fracture at a critical length scale
    • M.J. Buehler, F.F. Abraham, and H. Gao Hyperelasticity governs dynamic fracture at a critical length scale Nature 426 2003 141 146
    • (2003) Nature , vol.426 , pp. 141-146
    • Buehler, M.J.1    Abraham, F.F.2    Gao, H.3
  • 81
    • 0002133110 scopus 로고    scopus 로고
    • MBO(N)D: A multibody method for long-time molecular dynamics simulations
    • H. Chun, C. Padilla, D. Chin, M. Watanabe, V. Karlov, and H. Alper MBO(N)D: a multibody method for long-time molecular dynamics simulations J. Comp. Chem. 21 2000 159 184
    • (2000) J. Comp. Chem. , vol.21 , pp. 159-184
    • Chun, H.1    Padilla, C.2    Chin, D.3    Watanabe, M.4    Karlov, V.5    Alper, H.6
  • 82
    • 18544382532 scopus 로고    scopus 로고
    • An overview of multiscale simulations of materials
    • M. Rieth W. Schommers chapt. 22 American Scientific New York
    • G. Lu, and E. Kaxiras An overview of multiscale simulations of materials M. Rieth W. Schommers Handbook of Theoretical and Computational Nanotechnology chapt. 22 2005 American Scientific New York
    • (2005) Handbook of Theoretical and Computational Nanotechnology
    • Lu, G.1    Kaxiras, E.2
  • 83
    • 0036424048 scopus 로고    scopus 로고
    • Transition path sampling: Throwing ropes over rough mountain passes, in the dark
    • P.G. Bolhuis, D. Chandler, C. Dellago, and P.L. Geissler Transition path sampling: throwing ropes over rough mountain passes, in the dark Annu. Rev. Phys. Chem. 53 2002 291 318
    • (2002) Annu. Rev. Phys. Chem. , vol.53 , pp. 291-318
    • Bolhuis, P.G.1    Chandler, D.2    Dellago, C.3    Geissler, P.L.4
  • 84
    • 17044437988 scopus 로고    scopus 로고
    • Metastability, conformation dynamics, and transition pathways in complex systems
    • S. Attinger P. Koumoutsakos Springer Berlin
    • E.W. Vanden-Eijnden Metastability, conformation dynamics, and transition pathways in complex systems S. Attinger P. Koumoutsakos Multiscale Modelling and Simulation vol. 35 2004 Springer Berlin
    • (2004) Multiscale Modelling and Simulation , vol.35
    • Vanden-Eijnden, E.W.1
  • 85
    • 3042660129 scopus 로고
    • A statistical method for identifying transition-states in high dimensional problems
    • L.R. Pratt A statistical method for identifying transition-states in high dimensional problems J. Chem. Phys. 85 1986 5045 5048
    • (1986) J. Chem. Phys. , vol.85 , pp. 5045-5048
    • Pratt, L.R.1
  • 86
    • 0000729781 scopus 로고    scopus 로고
    • Transition path sampling and the calculation of rate constants
    • C. Dellago, P.G. Bolhuis, F.S. Csajka, and D. Chandler Transition path sampling and the calculation of rate constants J. Chem. Phys. 108 1998 1964 1977
    • (1998) J. Chem. Phys. , vol.108 , pp. 1964-1977
    • Dellago, C.1    Bolhuis, P.G.2    Csajka, F.S.3    Chandler, D.4
  • 87
    • 0032533790 scopus 로고    scopus 로고
    • Analysis of domain motions by approximate normal mode calculations
    • K. Hinsen Analysis of domain motions by approximate normal mode calculations Proteins: Struct. Funct. Genet. 33 1998 417 429
    • (1998) Proteins: Struct. Funct. Genet. , vol.33 , pp. 417-429
    • Hinsen, K.1
  • 88
    • 0037079578 scopus 로고    scopus 로고
    • Dynamics of large proteins through hierarchical levels of coarse-grained structures
    • P. Doruker, R.L. Jernigan, and I. Bahar Dynamics of large proteins through hierarchical levels of coarse-grained structures J. Comput. Chem. 23 2002 119 127
    • (2002) J. Comput. Chem. , vol.23 , pp. 119-127
    • Doruker, P.1    Jernigan, R.L.2    Bahar, I.3
  • 89
    • 21144473420 scopus 로고
    • Electron transfer reactions in chemistry. theory and experiment
    • R.A. Marcus Electron transfer reactions in chemistry. theory and experiment Rev. Mod. Phys. 65 1993 599 610 nobel lecture
    • (1993) Rev. Mod. Phys. , vol.65 , pp. 599-610
    • Marcus, R.A.1
  • 90
    • 33846327366 scopus 로고
    • Potential energy surface for H3
    • R.N. Porter, and M. Karplus Potential energy surface for H3 J. Chem. Phys. 40 1964 1105 1115
    • (1964) J. Chem. Phys. , vol.40 , pp. 1105-1115
    • Porter, R.N.1    Karplus, M.2
  • 91
    • 36849129194 scopus 로고
    • Exchange reactions with activation energy. I. Simple barrier potential for (H,H2)
    • M. Karplus, and R.D. Sharma Exchange reactions with activation energy. I. Simple barrier potential for (H,H2) J. Chem. Phys. 43 1965 3259 3287
    • (1965) J. Chem. Phys. , vol.43 , pp. 3259-3287
    • Karplus, M.1    Sharma, R.D.2
  • 92
    • 4243810035 scopus 로고
    • Simulation of enzyme-reactions using valence-bond force-fields and other hybrid quantum-classical approaches
    • J. Aqvist, and A. Warshel Simulation of enzyme-reactions using valence-bond force-fields and other hybrid quantum-classical approaches Chem. Rev. 93 1993 2523 2544 and references therein
    • (1993) Chem. Rev. , vol.93 , pp. 2523-2544
    • Aqvist, J.1    Warshel, A.2
  • 93
    • 0031567076 scopus 로고    scopus 로고
    • Molecular dynamics of an enzyme reaction: Proton transfer in TIM
    • E. Neria, and M. Karplus Molecular dynamics of an enzyme reaction: proton transfer in TIM Chem. Phys. Letters 267 1997 23 30
    • (1997) Chem. Phys. Letters , vol.267 , pp. 23-30
    • Neria, E.1    Karplus, M.2
  • 94
    • 0018796418 scopus 로고
    • Picosecond dynamics of tyrosine side chains in proteins
    • J. McCammon, P. Wolynes, and M. Karplus Picosecond dynamics of tyrosine side chains in proteins Biochemistry 18 1979 927 942
    • (1979) Biochemistry , vol.18 , pp. 927-942
    • McCammon, J.1    Wolynes, P.2    Karplus, M.3
  • 95
    • 0000055722 scopus 로고
    • Diffusion-controlled reactions - A variational formula for the optimum reaction coordinate
    • M. Berkowitz, J.D. Morgan, J.A. McCammon, and S.H. Northrup Diffusion-controlled reactions - a variational formula for the optimum reaction coordinate J. Chem. Phys. 79 1983 5563
    • (1983) J. Chem. Phys. , vol.79 , pp. 5563
    • Berkowitz, M.1    Morgan, J.D.2    McCammon, J.A.3    Northrup, S.H.4
  • 96
    • 0031256658 scopus 로고    scopus 로고
    • The maxflux algorithm for calculating variationally optimized reaction paths for conformational transitions in many body systems at finite temperature
    • S.H. Huo, and J.E. Straub The maxflux algorithm for calculating variationally optimized reaction paths for conformational transitions in many body systems at finite temperature J. Chem. Phys. 107 1997 5000 5006
    • (1997) J. Chem. Phys. , vol.107 , pp. 5000-5006
    • Huo, S.H.1    Straub, J.E.2
  • 97
    • 0038340986 scopus 로고    scopus 로고
    • A temperature-dependent nudged-elastic-band algorithm
    • R. Crehuet, and M.J. Field A temperature-dependent nudged-elastic-band algorithm J. Chem. Phys. 118 2003 9563 9571
    • (2003) J. Chem. Phys. , vol.118 , pp. 9563-9571
    • Crehuet, R.1    Field, M.J.2
  • 99
    • 0344931796 scopus 로고    scopus 로고
    • Retinoic acid receptor: A simulation analysis of retinoic acid binding and the resulting conformational changes
    • A. Blondel, J.P. Renaud, S. Fischer, D. Moras, and M. Karplus Retinoic acid receptor: a simulation analysis of retinoic acid binding and the resulting conformational changes J. Mol. Biol. 291 1999 101 115
    • (1999) J. Mol. Biol. , vol.291 , pp. 101-115
    • Blondel, A.1    Renaud, J.P.2    Fischer, S.3    Moras, D.4    Karplus, M.5
  • 100
    • 0037795659 scopus 로고    scopus 로고
    • Time-resolved computational protein biochemistry: Solvent effects on interactions, conformational transitions and equilibrium fluctuations
    • A.L. Tournier, D. Huang, S.M. Schwarzl, S. Fischer, and J.C. Smith Time-resolved computational protein biochemistry: solvent effects on interactions, conformational transitions and equilibrium fluctuations Faraday Discuss. 122 2003 243 251 (discussion 269-82)
    • (2003) Faraday Discuss. , vol.122 , pp. 243-251
    • Tournier, A.L.1    Huang, D.2    Schwarzl, S.M.3    Fischer, S.4    Smith, J.C.5
  • 101
    • 0036888353 scopus 로고    scopus 로고
    • Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50
    • S. Hayward, and R.A. Lee Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50 J. Mol. Graph Model 21 2002 181 183
    • (2002) J. Mol. Graph Model , vol.21 , pp. 181-183
    • Hayward, S.1    Lee, R.A.2
  • 102
    • 0142227208 scopus 로고    scopus 로고
    • The structure of ClpB: A molecular chaperone that rescues proteins from an aggregated state
    • S. Lee, M.E. Sowa, Y. hei Watanabe, P.B. Sigler, W. Chiu, M. Yoshida, and F.T.F. Tsai The structure of ClpB: a molecular chaperone that rescues proteins from an aggregated state Cell 115 2003 229 240
    • (2003) Cell , vol.115 , pp. 229-240
    • Lee, S.1    Sowa, M.E.2    Hei Watanabe, Y.3    Sigler, P.B.4    Chiu, W.5    Yoshida, M.6    Tsai, F.T.F.7
  • 103
    • 0031715982 scopus 로고    scopus 로고
    • Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
    • I. Shindyalov, and P. Bourne Protein structure alignment by incremental combinatorial extension (CE) of the optimal path Protein Eng. 11 1998 739 747
    • (1998) Protein Eng. , vol.11 , pp. 739-747
    • Shindyalov, I.1    Bourne, P.2
  • 104
    • 0035165967 scopus 로고    scopus 로고
    • A database and tools for 3-D protein structure comparison and alignment using the combinatorial extension (CE) algorithm
    • I. Shindyalov, and P. Bourne A database and tools for 3-D protein structure comparison and alignment using the combinatorial extension (CE) algorithm Nucl. Acids Res. 29 2001 228 229
    • (2001) Nucl. Acids Res. , vol.29 , pp. 228-229
    • Shindyalov, I.1    Bourne, P.2
  • 105
    • 0031715982 scopus 로고    scopus 로고
    • Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
    • I. Shindyalov, and P. Bourne Protein structure alignment by incremental combinatorial extension (CE) of the optimal path Protein Eng. 9 1998 739 747
    • (1998) Protein Eng. , vol.9 , pp. 739-747
    • Shindyalov, I.1    Bourne, P.2
  • 106
    • 0037305856 scopus 로고    scopus 로고
    • Crystal structure of a trimeric form of dephosphocoenzyme a kinase from Escherichia coli
    • N. O'Toole, J.A.R.G. Barbosa, Y. Li, L.W. Hung, A. Matte, and M. Cygler Crystal structure of a trimeric form of dephosphocoenzyme A kinase from Escherichia coli Protein Sci. 12 2003 327 336
    • (2003) Protein Sci. , vol.12 , pp. 327-336
    • O'Toole, N.1    Barbosa, J.A.R.G.2    Li, Y.3    Hung, L.W.4    Matte, A.5    Cygler, M.6
  • 107
  • 108
    • 0029619259 scopus 로고
    • Knowledge-based protein secondary structure assignment
    • D. Frishman, and P. Argos Knowledge-based protein secondary structure assignment Proteins: Struct. Funct. Genet. 23 1995 566 579
    • (1995) Proteins: Struct. Funct. Genet. , vol.23 , pp. 566-579
    • Frishman, D.1    Argos, P.2
  • 110
    • 0000036869 scopus 로고    scopus 로고
    • Simulation of activation free energies in molecular systems
    • E. Neria, S. Fischer, and M. Karplus Simulation of activation free energies in molecular systems J. Chem. Phys. 105 1996 1902 1921
    • (1996) J. Chem. Phys. , vol.105 , pp. 1902-1921
    • Neria, E.1    Fischer, S.2    Karplus, M.3
  • 112
  • 113
    • 0023887425 scopus 로고
    • Refined structure of porcine cytosolic adenylate kinase at 2.1 Å resolution
    • D. Dreusicke, P. Karplus, and G. Schulz Refined structure of porcine cytosolic adenylate kinase at 2.1 Å resolution J. Mol. Biol. 199 1988 359 371
    • (1988) J. Mol. Biol. , vol.199 , pp. 359-371
    • Dreusicke, D.1    Karplus, P.2    Schulz, G.3
  • 114
    • 0031450906 scopus 로고    scopus 로고
    • Structure, catalysis and supramolecular assembly of adenylate kinase from maize
    • K. Wild, R. Grafmüller, E. Wagner, and G. Schulz Structure, catalysis and supramolecular assembly of adenylate kinase from maize Eur. J. Biochem. 250 1997 326 331
    • (1997) Eur. J. Biochem. , vol.250 , pp. 326-331
    • Wild, K.1    Grafmüller, R.2    Wagner, E.3    Schulz, G.4
  • 115
    • 0026079373 scopus 로고
    • The refined structure of the complex between adenylate kinase from beef heart mitochondrial matrix and its substrate AMP at 1.85 Å resolution
    • K. Diederichs, and G. Schulz The refined structure of the complex between adenylate kinase from beef heart mitochondrial matrix and its substrate AMP at 1.85 Å resolution J. Mol. Biol. 217 1991 541 549
    • (1991) J. Mol. Biol. , vol.217 , pp. 541-549
    • Diederichs, K.1    Schulz, G.2
  • 116
    • 0026520374 scopus 로고
    • Refined structure of the complex between guanylate kinase and its substrate GMP at 2.0 Å resolution
    • T. Stehle, and G. Schulz Refined structure of the complex between guanylate kinase and its substrate GMP at 2.0 Å resolution J. Mol. Biol. 224 1992 1127 1141
    • (1992) J. Mol. Biol. , vol.224 , pp. 1127-1141
    • Stehle, T.1    Schulz, G.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.