메뉴 건너뛰기




Volumn 67, Issue 2, 2007, Pages 325-337

Essential dynamics sampling study of adenylate kinase: Comparison to citrate synthase and implication for the hinge and shear mechanisms of domain motions

Author keywords

DynDom; Hinge bending; Molecular dynamics simulation; Principal component analysis

Indexed keywords

ADENYLATE KINASE; BACTERIAL ENZYME; CITRATE SYNTHASE; ESCHERICHIA COLI PROTEIN;

EID: 33947431555     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21280     Document Type: Article
Times cited : (44)

References (42)
  • 2
    • 0035958660 scopus 로고    scopus 로고
    • Investigation of the mechanism of domain closure in citrate synthase by molecular dynamics simulation
    • Roccatano D, Mark AE, Hayward S. Investigation of the mechanism of domain closure in citrate synthase by molecular dynamics simulation. J Mol Biol 2001;310:1039-1053.
    • (2001) J Mol Biol , vol.310 , pp. 1039-1053
    • Roccatano, D.1    Mark, A.E.2    Hayward, S.3
  • 3
    • 2442612037 scopus 로고    scopus 로고
    • Investigating the accessibility of the closed domain conformation of citrate synthase using essential dynamics sampling
    • Daidone I, Roccatano D, Hayward S. Investigating the accessibility of the closed domain conformation of citrate synthase using essential dynamics sampling. J Mol Biol 2004;339:515-325.
    • (2004) J Mol Biol , vol.339 , pp. 515-325
    • Daidone, I.1    Roccatano, D.2    Hayward, S.3
  • 4
    • 0242331659 scopus 로고    scopus 로고
    • The energetic cost of domain reorientation in maltose-binding protein as studied by NMR and fluorescence spectroscopy
    • Millet O, Hudson RP, Kay LE. The energetic cost of domain reorientation in maltose-binding protein as studied by NMR and fluorescence spectroscopy. Proc Natl Acad Sci USA 2003;100: 12700-12705.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 12700-12705
    • Millet, O.1    Hudson, R.P.2    Kay, L.E.3
  • 5
    • 27744606438 scopus 로고    scopus 로고
    • A salt-bridge motif involved in ligand binding and large-scale domain motions of the maltose-binding protein
    • Stockner T, Vogel HJ, Tieleman DP. A salt-bridge motif involved in ligand binding and large-scale domain motions of the maltose-binding protein. Biophys J 2005;89:3362-3371.
    • (2005) Biophys J , vol.89 , pp. 3362-3371
    • Stockner, T.1    Vogel, H.J.2    Tieleman, D.P.3
  • 6
    • 33748467645 scopus 로고    scopus 로고
    • Molecular dynamics simulations of NAD+-induced domain closure in horse liver alcohol dehydrogenase
    • Hayward S, Kitao A. Molecular dynamics simulations of NAD+-induced domain closure in horse liver alcohol dehydrogenase. Biophys J 2006;91:1823-1831.
    • (2006) Biophys J , vol.91 , pp. 1823-1831
    • Hayward, S.1    Kitao, A.2
  • 7
    • 0032006209 scopus 로고    scopus 로고
    • Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme
    • Hayward S, Berendsen HJC. Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme. Proteins 1998;30:144-154.
    • (1998) Proteins , vol.30 , pp. 144-154
    • Hayward, S.1    Berendsen, H.J.C.2
  • 8
    • 0036888353 scopus 로고    scopus 로고
    • Hayward S, Lee RA. Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50. J Mol Graph Model 2002;21:181-183
    • Hayward S, Lee RA. Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50. J Mol Graph Model 2002;21:181-183.
  • 9
    • 2442567233 scopus 로고    scopus 로고
    • Identification of specific interactions that drive ligand-induced closure in five enzymes with classic domain movements
    • Hayward S. Identification of specific interactions that drive ligand-induced closure in five enzymes with classic domain movements. J Mol Biol 2004;339:1001-1021.
    • (2004) J Mol Biol , vol.339 , pp. 1001-1021
    • Hayward, S.1
  • 10
    • 0032769661 scopus 로고    scopus 로고
    • Structural principles governing domain motions in proteins
    • Hayward S. Structural principles governing domain motions in proteins. Proteins 1999;36:425-435.
    • (1999) Proteins , vol.36 , pp. 425-435
    • Hayward, S.1
  • 11
    • 0028335096 scopus 로고
    • Structural mechanisms for domain movements in proteins
    • Gerstein M, Lesk AM, Chothia C. Structural mechanisms for domain movements in proteins. Biochemistry 1994;33:6739-6749.
    • (1994) Biochemistry , vol.33 , pp. 6739-6749
    • Gerstein, M.1    Lesk, A.M.2    Chothia, C.3
  • 12
    • 0029644168 scopus 로고    scopus 로고
    • Adenylate kinase motions during catalysis: An energetic counterweight balancing substrate binding
    • Muller CW, Schlauderer GJ, Reinstein J, Schulz GE. Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding. Structure 1996;4:147-156.
    • (1996) Structure , vol.4 , pp. 147-156
    • Muller, C.W.1    Schlauderer, G.J.2    Reinstein, J.3    Schulz, G.E.4
  • 14
    • 0028958522 scopus 로고
    • Mechanism of adenylate kinase-the essential lysine helps to orient the phosphates and the active-site residues to proper conformations
    • Byeon IJL, Shi ZT, Tsai MD. Mechanism of adenylate kinase-the essential lysine helps to orient the phosphates and the active-site residues to proper conformations. Biochemistry 1995;34: 3172-3182.
    • (1995) Biochemistry , vol.34 , pp. 3172-3182
    • Byeon, I.J.L.1    Shi, Z.T.2    Tsai, M.D.3
  • 15
    • 33144487234 scopus 로고    scopus 로고
    • Roles of static and dynamic domains in stability and catalysis of adenylate kinase
    • Bae E, Phillips GN. Roles of static and dynamic domains in stability and catalysis of adenylate kinase. Proc Natl Acad Sci USA 2006;103:2132-2137.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 2132-2137
    • Bae, E.1    Phillips, G.N.2
  • 16
    • 0029644728 scopus 로고
    • Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases
    • Vonrhein C, Schlauderer GJ, Schulz GE. Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases. Structure 1995;3:483-490.
    • (1995) Structure , vol.3 , pp. 483-490
    • Vonrhein, C.1    Schlauderer, G.J.2    Schulz, G.E.3
  • 17
    • 0028491137 scopus 로고
    • Nucleotide-binding properties of adenylate kinase from Escherichia coli-a molecular-dynamics study in aqueous and vacuum environments
    • Kern P, Brunne RM, Folkers G. Nucleotide-binding properties of adenylate kinase from Escherichia coli-a molecular-dynamics study in aqueous and vacuum environments. J Comput-Aided Mol Des 1994;8:367-388.
    • (1994) J Comput-Aided Mol Des , vol.8 , pp. 367-388
    • Kern, P.1    Brunne, R.M.2    Folkers, G.3
  • 18
    • 0029886930 scopus 로고    scopus 로고
    • Study of global motions in proteins by weighted masses molecular dynamics: Adenylate kinase as a test case
    • Elamrani S, Berry MB, Phillips GN, McCammon JA. Study of global motions in proteins by weighted masses molecular dynamics: adenylate kinase as a test case. Proteins 1996;25: 79-88.
    • (1996) Proteins , vol.25 , pp. 79-88
    • Elamrani, S.1    Berry, M.B.2    Phillips, G.N.3    McCammon, J.A.4
  • 19
    • 10844273276 scopus 로고    scopus 로고
    • Associative mechanism for phosphoryl transfer: A molecular dynamics simulation of Escherichia coli adenylate kinase complexed with its substrates
    • Krishnamurthy H, Lou HF, Kimple A, Vieille C, Cukier RI. Associative mechanism for phosphoryl transfer: a molecular dynamics simulation of Escherichia coli adenylate kinase complexed with its substrates. Proteins 2005;58:88-100.
    • (2005) Proteins , vol.58 , pp. 88-100
    • Krishnamurthy, H.1    Lou, H.F.2    Kimple, A.3    Vieille, C.4    Cukier, R.I.5
  • 21
    • 0000398122 scopus 로고    scopus 로고
    • An iso-random BiBi mechanism for adenylate kinase
    • Sheng XR, Li X, Pan XM. An iso-random BiBi mechanism for adenylate kinase. J Biol Chem 1999;274:22238-22242.
    • (1999) J Biol Chem , vol.274 , pp. 22238-22242
    • Sheng, X.R.1    Li, X.2    Pan, X.M.3
  • 23
    • 0028338283 scopus 로고
    • The closed conformation of a highly flexible protein-the structure of Escherichia coli adenylate kinase with bound amp and amppnp
    • Berry MB, Meador B, Bilderback T, Liang P, Glaser M, Phillips GN. The closed conformation of a highly flexible protein-the structure of Escherichia coli adenylate kinase with bound amp and amppnp. Proteins 1994;19:183-198.
    • (1994) Proteins , vol.19 , pp. 183-198
    • Berry, M.B.1    Meador, B.2    Bilderback, T.3    Liang, P.4    Glaser, M.5    Phillips, G.N.6
  • 26
    • 0002775934 scopus 로고
    • Interaction models for water in relation to protein hydration
    • Pullman B, editor, Dordrecht, Holland: Reidel;
    • Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans HJ. Interaction models for water in relation to protein hydration. In: Pullman B, editor. Intermolecular forces. Dordrecht, Holland: Reidel; 1981. pp 331-342.
    • (1981) Intermolecular forces , pp. 331-342
    • Berendsen, H.J.C.1    Postma, J.P.M.2    van Gunsteren, W.F.3    Hermans, H.J.4
  • 28
    • 84986440341 scopus 로고
    • SETTLE: An analytical version of the SHAKE and RATTLE algorithms for rigid water models
    • Miyamoto S, Kollman PA. SETTLE: an analytical version of the SHAKE and RATTLE algorithms for rigid water models. J Comput Chem 1992;13:952-962.
    • (1992) J Comput Chem , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 29
    • 33846823909 scopus 로고
    • Particle mesh Ewald-an N. Log(N) method for Ewald sums in large systems
    • Darden T, York D, Pedersen L. Particle mesh Ewald-an N. Log(N) method for Ewald sums in large systems. J Chem Phys 1993;98:10089-10092.
    • (1993) J Chem Phys , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 30
    • 0030888546 scopus 로고    scopus 로고
    • Model free methods to analyze domain motions in proteins from simulation. A comparison of a normal mode analysis and a molecular dynamics simulation of lysozyme
    • Hayward S, Kitao A, Berendsen HJC. Model free methods to analyze domain motions in proteins from simulation. A comparison of a normal mode analysis and a molecular dynamics simulation of lysozyme. Proteins 1997;27:425-437.
    • (1997) Proteins , vol.27 , pp. 425-437
    • Hayward, S.1    Kitao, A.2    Berendsen, H.J.C.3
  • 33
    • 20844448232 scopus 로고    scopus 로고
    • A comprehensive and non-redundant database of protein domain movements
    • Qi G, Lee RA, Hayward S. A comprehensive and non-redundant database of protein domain movements. Bioinformatics 2005;21:2832-2838.
    • (2005) Bioinformatics , vol.21 , pp. 2832-2838
    • Qi, G.1    Lee, R.A.2    Hayward, S.3
  • 34
    • 0031450906 scopus 로고    scopus 로고
    • Structure, catalysis and supramolecular assembly of adenylate kinase from maize
    • Wild K, Grafmuller R, Wagner E, Schulz GE. Structure, catalysis and supramolecular assembly of adenylate kinase from maize. Eur J Biochem 1997;250:326-331.
    • (1997) Eur J Biochem , vol.250 , pp. 326-331
    • Wild, K.1    Grafmuller, R.2    Wagner, E.3    Schulz, G.E.4
  • 35
    • 0026079373 scopus 로고
    • The refined structure of the complex between adenylate kinase from beef-heart mitochondrial matrix and its substrate Amp at 1.85 A resolution
    • Diederichs K, Schulz GE. The refined structure of the complex between adenylate kinase from beef-heart mitochondrial matrix and its substrate Amp at 1.85 A resolution. J Mol Biol 1991;217: 541-549.
    • (1991) J Mol Biol , vol.217 , pp. 541-549
    • Diederichs, K.1    Schulz, G.E.2
  • 36
    • 0028998836 scopus 로고
    • High-resolution structures of adenylate kinase from yeast ligated with inhibitor Ap(5)a, showing the pathway of phosphoryl transfer
    • Abele U, Schulz GE. High-resolution structures of adenylate kinase from yeast ligated with inhibitor Ap(5)a, showing the pathway of phosphoryl transfer. Protein Sci 1995;4:1262-1271.
    • (1995) Protein Sci , vol.4 , pp. 1262-1271
    • Abele, U.1    Schulz, G.E.2
  • 37
    • 0038156098 scopus 로고    scopus 로고
    • The DynDom database of protein domain motions
    • Lee RA, Razaz M, Hayward S. The DynDom database of protein domain motions. Bioinformatics 2003;19:1290-1291.
    • (2003) Bioinformatics , vol.19 , pp. 1290-1291
    • Lee, R.A.1    Razaz, M.2    Hayward, S.3
  • 38
    • 24644483073 scopus 로고    scopus 로고
    • Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase
    • Maragakis P, Karplus M. Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase. J Mol Biol 2005;352:807-822.
    • (2005) J Mol Biol , vol.352 , pp. 807-822
    • Maragakis, P.1    Karplus, M.2
  • 39
    • 0025047629 scopus 로고
    • A mutant T4 lysozyme displays five different crystal conformations
    • Faber HR, Matthews BW. A mutant T4 lysozyme displays five different crystal conformations. Nature 1990;348:263-266.
    • (1990) Nature , vol.348 , pp. 263-266
    • Faber, H.R.1    Matthews, B.W.2
  • 40
    • 1842326248 scopus 로고    scopus 로고
    • Conformation of T4 lysozyme in solution. Hinge-bending motion and the substrate-induced conformational transition studied by site-directed spin labeling
    • McHaourab HS, Oh KJ, Fang CJ, Hubbell WL. Conformation of T4 lysozyme in solution. Hinge-bending motion and the substrate-induced conformational transition studied by site-directed spin labeling. Biochemistry 1997;36:307-316.
    • (1997) Biochemistry , vol.36 , pp. 307-316
    • McHaourab, H.S.1    Oh, K.J.2    Fang, C.J.3    Hubbell, W.L.4
  • 41
    • 25144472137 scopus 로고    scopus 로고
    • Conformational equilibria and free energy profiles for the allosteric transition of the ribose-binding protein
    • Ravindranathan KP, Gallicchio E, Levy RM. Conformational equilibria and free energy profiles for the allosteric transition of the ribose-binding protein. J Mol Biol 2005;353:196-210.
    • (2005) J Mol Biol , vol.353 , pp. 196-210
    • Ravindranathan, K.P.1    Gallicchio, E.2    Levy, R.M.3
  • 42
    • 0032530836 scopus 로고    scopus 로고
    • A database of macromolecular movements
    • Gerstein M, Krebs W. A database of macromolecular movements. Nucleic Acids Res 1998;26:4280-4290.
    • (1998) Nucleic Acids Res , vol.26 , pp. 4280-4290
    • Gerstein, M.1    Krebs, W.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.