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Volumn 106, Issue 37, 2009, Pages 15673-15678

Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase

Author keywords

Coarse grained; Potential function; Transition pathways

Indexed keywords

ADENYLATE KINASE;

EID: 70349462451     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0907684106     Document Type: Article
Times cited : (27)

References (37)
  • 1
    • 0346220393 scopus 로고    scopus 로고
    • The role of dynamics in allosteric regulation
    • Kern D, Zuiderweg ERP (2003) The role of dynamics in allosteric regulation. Curr Opin Struct Biol 13:748-757.
    • (2003) Curr Opin Struct Biol , vol.13 , pp. 748-757
    • Kern, D.1    Zuiderweg, E.R.P.2
  • 2
    • 0031922657 scopus 로고    scopus 로고
    • Conformational dynamics and enzyme activity
    • Yon JM, Perahia D, Ghelis C (1998) Conformational dynamics and enzyme activity. Biochimie 80:33-42.
    • (1998) Biochimie , vol.80 , pp. 33-42
    • Yon, J.M.1    Perahia, D.2    Ghelis, C.3
  • 3
    • 33646943202 scopus 로고    scopus 로고
    • Molecular dynamics: Survey of methods for simulating the activity of proteins
    • Adcock SA, McCammon JA (2006) Molecular dynamics: Survey of methods for simulating the activity of proteins. Chem Rev 106:1589-1615.
    • (2006) Chem Rev , vol.106 , pp. 1589-1615
    • Adcock, S.A.1    McCammon, J.A.2
  • 4
    • 25844431698 scopus 로고    scopus 로고
    • Coarse-grained normal mode analysis in structural biology
    • DOI 10.1016/j.sbi.2005.08.007, PII S0959440X05001557, Carbohydrates and Glycoconjugates/Biophysical Methods
    • Bahar I, Rader AJ (2005) Coarse-grained normal mode analysis in structural biology. Curr Opin Struct Biol 15:586-592. (Pubitemid 41393491)
    • (2005) Current Opinion in Structural Biology , vol.15 , Issue.5 , pp. 586-592
    • Bahar, I.1    Rader, A.J.2
  • 5
    • 0029644728 scopus 로고
    • Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases
    • Vonrhein C, Schlauderer GJ, Schulz GE (1995) Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases. Structure 3:483-490.
    • (1995) Structure , vol.3 , pp. 483-490
    • Vonrhein, C.1    Schlauderer, G.J.2    Schulz, G.E.3
  • 6
    • 0029644168 scopus 로고    scopus 로고
    • Adenylate kinase motions during catalysis: An energetic counterweight balancing substrate binding
    • Muller CW, Schlauderer GJ, Reinstein J, Schulz GE (1996) Adenylate kinase motions during catalysis: An energetic counterweight balancing substrate binding. Structure 4:147-156. (Pubitemid 126658978)
    • (1996) Structure , vol.4 , Issue.2 , pp. 147-156
    • Muller, C.W.1    Schlauderer, G.J.2    Reinstein, J.3    Schulz, G.E.4
  • 7
    • 0029866802 scopus 로고    scopus 로고
    • Structure of a mutant adenylate kinase ligated with an ATP-analogue showing domain closure over ATP
    • DOI 10.1006/jmbi.1996.0080
    • Schlauderer GJ, Proba K, Schulz GE (1996) Structure of a mutant adenylate kinase ligated with an ATP-analogue showing domain closure over ATP. J Mol Biol 256:223-227. (Pubitemid 26105586)
    • (1996) Journal of Molecular Biology , vol.256 , Issue.2 , pp. 223-227
    • Schlauderer, G.J.1    Proba, K.2    Schulz, G.E.3
  • 8
    • 0029897810 scopus 로고    scopus 로고
    • The structure of bovine mitochondrial adenylate kinase: Comparison with isoenzymes in other compartments
    • Schlauderer GJ, Schulz GE (1996) The structure of bovine mitochondrial adenylate kinase: Comparison with isoenzymes in other compartments. Protein Sci 5:434-441.
    • (1996) Protein Sci , vol.5 , pp. 434-441
    • Schlauderer, G.J.1    Schulz, G.E.2
  • 9
    • 36849048228 scopus 로고    scopus 로고
    • Intrinsic motions along an enzymatic reaction trajectory
    • Henzler-Wildman KA, et al. (2007) Intrinsic motions along an enzymatic reaction trajectory. Nature 450:838-844.
    • (2007) Nature , vol.450 , pp. 838-844
    • Henzler-Wildman, K.A.1
  • 10
    • 36749083505 scopus 로고    scopus 로고
    • Illuminating the mechanistic roles of enzyme conformational dynamics
    • Hanson JA, et al. (2007) Illuminating the mechanistic roles of enzyme conformational dynamics. Proc Natl Acad Sci USA 104:18055-18060.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 18055-18060
    • Hanson, J.A.1
  • 12
    • 33947431555 scopus 로고    scopus 로고
    • Essential dynamics sampling study of adenylate kinase: Comparison to citrate synthase and implication for the hinge and shear mechanisms of domain motions
    • DOI 10.1002/prot.21280
    • Snow C, Qi GY, Hayward S (2007) Essential dynamics sampling study of adenylate kinase: Comparison to citrate synthase and implication for the hinge and shear mechanisms of domain motions. Proteins 67:325-337. (Pubitemid 46449410)
    • (2007) Proteins: Structure, Function and Genetics , vol.67 , Issue.2 , pp. 325-337
    • Snow, C.1    Qi, G.2    Hayward, S.3
  • 13
    • 48149084621 scopus 로고    scopus 로고
    • The atomistic mechanism of conformational transition in adenylate kinase: A TEE-REX molecular dynamics study
    • Kubitzki MB, de Groot BL (2008) The atomistic mechanism of conformational transition in adenylate kinase: A TEE-REX molecular dynamics study. Structure 16:1175-1182.
    • (2008) Structure , vol.16 , pp. 1175-1182
    • Kubitzki, M.B.1    De Groot, B.L.2
  • 14
    • 36849039429 scopus 로고    scopus 로고
    • A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
    • Henzler-Wildman KA, et al. (2007) A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 450:913-916.
    • (2007) Nature , vol.450 , pp. 913-916
    • Henzler-Wildman, K.A.1
  • 15
    • 33846847773 scopus 로고    scopus 로고
    • Conformational Transitions of Adenylate Kinase: Switching by Cracking
    • DOI 10.1016/j.jmb.2006.11.085, PII S0022283606016445
    • Whitford PC, Miyashita O, Levy Y, Onuchic JN (2007) Conformational transitions of adenylate kinase: Switching by cracking. J Mol Biol 366:1661-1671. (Pubitemid 46215597)
    • (2007) Journal of Molecular Biology , vol.366 , Issue.5 , pp. 1661-1671
    • Whitford, P.C.1    Miyashita, O.2    Levy, Y.3    Onuchic, J.N.4
  • 16
    • 34548304871 scopus 로고    scopus 로고
    • Protein conformational transitions explored by mixed elastic network models
    • Zheng WJ, Brooks BR, Hummer G (2007) Protein conformational transitions explored by mixed elastic network models. Proteins 69:43-57.
    • (2007) Proteins , vol.69 , pp. 43-57
    • Zheng, W.J.1    Brooks, B.R.2    Hummer, G.3
  • 17
    • 37349101940 scopus 로고    scopus 로고
    • An NMA-guided path planning approach for computing large-amplitude conformational changes in proteins
    • DOI 10.1002/prot.21570
    • Kirillova S, Cortes J, Stefaniu A, Simeon T (2008) An NMA-guided path planning approach for computing large-amplitude conformational changes in proteins. Proteins 70:131-143. (Pubitemid 350293455)
    • (2008) Proteins: Structure, Function and Genetics , vol.70 , Issue.1 , pp. 131-143
    • Kirillova, S.1    Cortes, J.2    Stefaniu, A.3    Simeon, T.4
  • 18
    • 24644483073 scopus 로고    scopus 로고
    • Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase
    • DOI 10.1016/j.jmb.2005.07.031, PII S0022283605008193
    • Maragakis P, Karplus M (2005) Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase. J Mol Biol 352:807-822. (Pubitemid 41267070)
    • (2005) Journal of Molecular Biology , vol.352 , Issue.4 , pp. 807-822
    • Maragakis, P.1    Karplus, M.2
  • 19
    • 70349458094 scopus 로고    scopus 로고
    • A force field for virtual atom molecular mechanics of proteins
    • Korkut A, Hendrickson WA (2009) A force field for virtual atom molecular mechanics of proteins. Proc Natl Acad Sci USA 106:15667-15672.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 15667-15672
    • Korkut, A.1    Hendrickson, W.A.2
  • 21
    • 0037441653 scopus 로고    scopus 로고
    • Structure validation by C alpha geometry: Phi, psi and C-beta deviation
    • Lovell SC, et al. (2003) Structure validation by C alpha geometry: Phi, psi and C-beta deviation. Proteins 50:437-450.
    • (2003) Proteins , vol.50 , pp. 437-450
    • Lovell, S.C.1
  • 22
    • 0030832809 scopus 로고    scopus 로고
    • Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches
    • DOI 10.1002/(SICI)1097-0134(199711)29:3<292::AID-PROT4>3.0.CO;2-D
    • Bahar I, Kaplan M, Jernigan RL (1997) Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches. Proteins 29:292-308. (Pubitemid 27484221)
    • (1997) Proteins: Structure, Function and Genetics , vol.29 , Issue.3 , pp. 292-308
    • Bahar, I.1    Kaplan, M.2    Jernigan, R.L.3
  • 23
    • 0000933280 scopus 로고
    • Transformations to optimize the superposition of similar structures
    • Hendrickson WA (1979) Transformations to optimize the superposition of similar structures. Acta Crystallogr A 35:158-163.
    • (1979) Acta Crystallogr A , vol.35 , pp. 158-163
    • Hendrickson, W.A.1
  • 24
    • 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
    • Diederichs K, Schulz GE (1991) 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 217:541-549. (Pubitemid 121003300)
    • (1991) Journal of Molecular Biology , vol.217 , Issue.3 , pp. 541-549
    • Diederichs, K.1    Schulz, G.E.2
  • 26
    • 36549043024 scopus 로고    scopus 로고
    • Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation
    • DOI 10.1016/j.sbi.2007.09.011, PII S0959440X07001534, Catalysis and Regulation /Protein
    • Bahar I, Chennubhotla C, Tobi D (2007) Intrinsic dynamics of enzymes in the unbound state and, relation to allosteric regulation. Curr Opin Struct Biol 17:633-640. (Pubitemid 350180409)
    • (2007) Current Opinion in Structural Biology , vol.17 , Issue.6 , pp. 633-640
    • Bahar, I.1    Chennubhotla, C.2    Tobi, D.3
  • 27
    • 45849131354 scopus 로고    scopus 로고
    • Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution
    • Lange OF, et al. (2008) Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science 320:1471-1475.
    • (2008) Science , vol.320 , pp. 1471-1475
    • Lange, O.F.1
  • 28
    • 0028335096 scopus 로고
    • Structural mechanisms for domain movements in proteins
    • DOI 10.1021/bi00188a001
    • Gerstein M, Lesk AM, Chothia C (1994) Structural mechanisms for domain movements in proteins. Biochemistry 33:6739-6749. (Pubitemid 24190795)
    • (1994) Biochemistry , vol.33 , Issue.22 , pp. 6739-6749
    • Gerstein, M.1    Lesk, A.M.2    Chothia, C.3
  • 31
    • 0022419152 scopus 로고
    • Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme
    • Levitt M, Sander C, Stern PS (1985) Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme. J Mol Biol 181:423-447.
    • (1985) J Mol Biol , vol.181 , pp. 423-447
    • Levitt, M.1    Sander, C.2    Stern, P.S.3
  • 32
    • 0029560322 scopus 로고
    • Hinge-bending motion in citrate synthase arising from normal mode calculations
    • DOI 10.1002/prot.340230410
    • Marques O, Sanejouand YH (1995) Hinge-bending motion in citrate synthase arising from normal mode calculations. Proteins 23:557-560. (Pubitemid 26009518)
    • (1995) Proteins: Structure, Function and Genetics , vol.23 , Issue.4 , pp. 557-560
    • Marques, O.1    Sanejouand, Y.-H.2
  • 33
    • 0030700726 scopus 로고    scopus 로고
    • Ligand-induced conformational changes in ras p21: A normal mode and energy minimization analysis
    • DOI 10.1006/jmbi.1997.1313
    • Ma J, Karplus M (1997) Ligand-induced conformational changes in ras p21: A normal mode and energy minimization analysis. J Mol Biol 274:114-131. (Pubitemid 27519461)
    • (1997) Journal of Molecular Biology , vol.274 , Issue.1 , pp. 114-131
    • Ma, J.1    Karplus, M.2
  • 35
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure-pattern-recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C (1983) Dictionary of protein secondary structure-pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 36
    • 0026829432 scopus 로고
    • TNPACK - A truncated Newton minimization package for large-scale problems: II. Implementation examples
    • DOI 10.1145/128745.150975
    • Schlick T, Fogelson A (1992) Tnpack-a Truncated Newton Minimization Package for large-scale problems. 2. Implementation examples.ACMTrans Math Software 18:71-111. (Pubitemid 23599656)
    • (1992) ACM Transactions on Mathematical Software , vol.18 , Issue.1 , pp. 71-111
    • Schlick, T.1    Fogelson, A.2
  • 37
    • 34547592557 scopus 로고    scopus 로고
    • MolProbity: All-atom contacts and structure validation for proteins and nucleic acids
    • Davis IW, et al. (2007) MolProbity: All-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35:W375-W383.
    • (2007) Nucleic Acids Res , vol.35
    • Davis, I.W.1


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