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Volumn 71, Issue 1, 2008, Pages 131-143

Molecular dynamics simulations of domain motions of substrate-free S-adenosyl-L-homocysteine hydrolase in solution

Author keywords

Diffusion; Domain motions; Hinge bending; Molecular dynamics simulations; Protein dynamics; Rotational; S adenosyl L homocysteine hydrolase

Indexed keywords

ADENOSYLHOMOCYSTEINASE; NICOTINAMIDE ADENINE DINUCLEOTIDE; SOLVENT; TETRAMER;

EID: 40549140147     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21664     Document Type: Article
Times cited : (11)

References (46)
  • 3
    • 0000662412 scopus 로고
    • Methionine, homocysteine, and cysteine-metabolic interrelationships
    • Friedman M, editor. Boca Raton, FL: CRC Press;
    • Smolin LA, Benevenga NJ. Methionine, homocysteine, and cysteine-metabolic interrelationships. In: Absorption and utilization of amino acids, Vol. 1. Friedman M, editor. Boca Raton, FL: CRC Press; 1989. pp 157-187.
    • (1989) Absorption and utilization of amino acids , vol.1 , pp. 157-187
    • Smolin, L.A.1    Benevenga, N.J.2
  • 11
    • 0036510742 scopus 로고    scopus 로고
    • Inhibition of S-adenosylhomocysteine hydrolase by acyclic sugar adenosine analogue D-eritadenine. Crystal structure of S-adenosylhomocysteine hydrolase complexed with D-eritadenine
    • Huang Y, Komoto J, Takata Y, Powell DR, Gomi T, Ogawa H, Fujioka M, Takusagawa F. Inhibition of S-adenosylhomocysteine hydrolase by acyclic sugar adenosine analogue D-eritadenine. Crystal structure of S-adenosylhomocysteine hydrolase complexed with D-eritadenine. J Biol Chem 2002;277:7477-7482.
    • (2002) J Biol Chem , vol.277 , pp. 7477-7482
    • Huang, Y.1    Komoto, J.2    Takata, Y.3    Powell, D.R.4    Gomi, T.5    Ogawa, H.6    Fujioka, M.7    Takusagawa, F.8
  • 12
    • 0034644738 scopus 로고    scopus 로고
    • Effects of site-directed mutagenesis on structure and function of recombinant rat liver S-adenosylhomocysteine hydrolase. Crystal structure of D244E mutant enzyme
    • Komoto J, Huang Y, Gomi T, Ogawa H, Takata Y, Fujioka M and Takusagawa F. Effects of site-directed mutagenesis on structure and function of recombinant rat liver S-adenosylhomocysteine hydrolase. Crystal structure of D244E mutant enzyme. J Biol Chem 2000;275:32147-32156.
    • (2000) J Biol Chem , vol.275 , pp. 32147-32156
    • Komoto, J.1    Huang, Y.2    Gomi, T.3    Ogawa, H.4    Takata, Y.5    Fujioka, M.6    Takusagawa, F.7
  • 13
    • 33746888705 scopus 로고    scopus 로고
    • Effects of ligand binding and oxidation on hinge-bending motions in S-adenosyl-L-homocysteine hydrolase
    • Wang M, Unruh JR, Johnson CK, Kuczera K, Schowen RL, Borchardt RT. Effects of ligand binding and oxidation on hinge-bending motions in S-adenosyl-L-homocysteine hydrolase. Biochemistry 2006;45:7778-7786.
    • (2006) Biochemistry , vol.45 , pp. 7778-7786
    • Wang, M.1    Unruh, J.R.2    Johnson, C.K.3    Kuczera, K.4    Schowen, R.L.5    Borchardt, R.T.6
  • 15
    • 18544386701 scopus 로고    scopus 로고
    • Domain motions and the open-to-closed conformational transition of an enzyme: A normal mode analysis of S-adenosyl-L-homocysteine hydrolase
    • Wang M, Borchardt RT, Schowen RL, Kuczera K. Domain motions and the open-to-closed conformational transition of an enzyme: a normal mode analysis of S-adenosyl-L-homocysteine hydrolase. Biochemistry 2005;44:7228-7239.
    • (2005) Biochemistry , vol.44 , pp. 7228-7239
    • Wang, M.1    Borchardt, R.T.2    Schowen, R.L.3    Kuczera, K.4
  • 17
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • Karplus M, McCammon JA. Molecular dynamics simulations of biomolecules. Nat Struct Biol 2002;9:646-652.
    • (2002) Nat Struct Biol , vol.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 18
    • 0034665864 scopus 로고    scopus 로고
    • A dynamic model for the allosteric mechanism of GroEL
    • Ma JP, Sigler PB, Xu ZH, Karplus MA. A dynamic model for the allosteric mechanism of GroEL. J Mol Biol 2000;302:303-313.
    • (2000) J Mol Biol , vol.302 , pp. 303-313
    • Ma, J.P.1    Sigler, P.B.2    Xu, Z.H.3    Karplus, M.A.4
  • 20
    • 0035815288 scopus 로고    scopus 로고
    • Dynamic coupling between the SH2 and SH3 domains of c-Src and hck underlies their inactivation by C-terminal tyrosine phosphorylation
    • Young MA, Gonfloni S, Superti-Furga G, Roux B, Kuriyan J. Dynamic coupling between the SH2 and SH3 domains of c-Src and hck underlies their inactivation by C-terminal tyrosine phosphorylation. Cell 2001;105:115-126.
    • (2001) Cell , vol.105 , pp. 115-126
    • Young, M.A.1    Gonfloni, S.2    Superti-Furga, G.3    Roux, B.4    Kuriyan, J.5
  • 21
    • 1542358827 scopus 로고    scopus 로고
    • Structure, dynamics and interaction with kinase targets: Computer simulations of calmodulin
    • Yang C, Jas GS, Kuczera K. Structure, dynamics and interaction with kinase targets: computer simulations of calmodulin. Biochim Biophys Acta 2004;1697:289-300.
    • (2004) Biochim Biophys Acta , vol.1697 , pp. 289-300
    • Yang, C.1    Jas, G.S.2    Kuczera, K.3
  • 22
    • 0037151004 scopus 로고    scopus 로고
    • Catalytic mechanism of S-adenosylhomocysteine hydrolase. Site-directed mutagenesis of Asp-130, Lys-185, Asp-189, and Asn-190
    • Takata Y, Yamada T, Huang Y, Komoto J, Gomi T, Ogawa H, Fujioka M, Takusagawa F. Catalytic mechanism of S-adenosylhomocysteine hydrolase. Site-directed mutagenesis of Asp-130, Lys-185, Asp-189, and Asn-190. J Biol Chem 2002;277:22670-22676.
    • (2002) J Biol Chem , vol.277 , pp. 22670-22676
    • Takata, Y.1    Yamada, T.2    Huang, Y.3    Komoto, J.4    Gomi, T.5    Ogawa, H.6    Fujioka, M.7    Takusagawa, F.8
  • 23
    • 0029633186 scopus 로고    scopus 로고
    • Pearlman DA, Case DA, Caldwell JW, Ross WR, Cheatham TE, III, DeBolt S, Ferguson D, Seibel G, Kollman P. AMBER, a computer program for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to elucidate the structures and energies of molecules. Comp Phys Commun 1995;91:1-41.
    • Pearlman DA, Case DA, Caldwell JW, Ross WR, Cheatham TE, III, DeBolt S, Ferguson D, Seibel G, Kollman P. AMBER, a computer program for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to elucidate the structures and energies of molecules. Comp Phys Commun 1995;91:1-41.
  • 25
    • 0001398008 scopus 로고    scopus 로고
    • How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
    • Wang J, Cieplak P, Kollman PA. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 2000;21:1049-1074.
    • (2000) J Comput Chem , vol.21 , pp. 1049-1074
    • Wang, J.1    Cieplak, P.2    Kollman, P.A.3
  • 27
    • 0037038533 scopus 로고    scopus 로고
    • Large and fast relaxations inside a protein: Calculation and measurement of reorganization energies in alcohol dehydrogenase
    • (b) Walker RC, de Souza MM, Mercer IP, Gould IR, Klug DR. Large and fast relaxations inside a protein: calculation and measurement of reorganization energies in alcohol dehydrogenase. J Phys Chem B 2002;106:11658-11665;
    • (2002) J Phys Chem B , vol.106 , pp. 11658-11665
    • Walker, R.C.1    de Souza, M.M.2    Mercer, I.P.3    Gould, I.R.4    Klug, D.R.5
  • 28
    • 0001015978 scopus 로고    scopus 로고
    • A molecular mechanics force field for NAD(+), NADH, and the pyrophosphate groups of nucleotides
    • (c) Pavelites JJ, Gao JL, Bash PA, Mackerell AD. A molecular mechanics force field for NAD(+), NADH, and the pyrophosphate groups of nucleotides. J Comput Chem 1997;18:221-239.
    • (1997) J Comput Chem , vol.18 , pp. 221-239
    • Pavelites, J.J.1    Gao, J.L.2    Bash, P.A.3    Mackerell, A.D.4
  • 31
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 1977;23:327.
    • (1977) J Comput Phys , vol.23 , pp. 327
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 32
    • 0033024177 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules: Long-range electrostatic effects
    • Sagui C, Darden TA. Molecular dynamics simulations of biomolecules: long-range electrostatic effects. Annu Rev Biophys Biomol Struct 1999;28:155-179.
    • (1999) Annu Rev Biophys Biomol Struct , vol.28 , pp. 155-179
    • Sagui, C.1    Darden, T.A.2
  • 33
    • 84986512474 scopus 로고    scopus 로고
    • Brooks BR, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macro molecular energy, minimization and dynamics calculations. J Comput Chem 1983;4:187-217.
    • Brooks BR, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macro molecular energy, minimization and dynamics calculations. J Comput Chem 1983;4:187-217.
  • 34
    • 0000577041 scopus 로고
    • Nonlinear dynamics of proteins
    • Garcia AE. Nonlinear dynamics of proteins. Phys Rev Lett 1992;68:2696-2699.
    • (1992) Phys Rev Lett , vol.68 , pp. 2696-2699
    • Garcia, A.E.1
  • 36
    • 0000261794 scopus 로고
    • Polarized fluorescence and rotational Brownian motion
    • Ehrenberg M, Rigler R. Polarized fluorescence and rotational Brownian motion. Chem Phys Lett 1972;14:539-544.
    • (1972) Chem Phys Lett , vol.14 , pp. 539-544
    • Ehrenberg, M.1    Rigler, R.2
  • 37
    • 0343732186 scopus 로고
    • Theory of fluorescence depolarization anisotropic rotational diffusion
    • Chuang TJ, Eisenthal KB. Theory of fluorescence depolarization anisotropic rotational diffusion. J Chem Phys 1972;57:5094-5097.
    • (1972) J Chem Phys , vol.57 , pp. 5094-5097
    • Chuang, T.J.1    Eisenthal, K.B.2
  • 39
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Lee B, Richards FM. The interpretation of protein structures: estimation of static accessibility. J Mol Biol 1971;55:379-400.
    • (1971) J Mol Biol , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 40
    • 0034321041 scopus 로고    scopus 로고
    • Microscopic details of rotational diffusion of perylene in organic solvents: Molecular dynamics simulations and experiment vs. Debye-Stokes-Einstein theory
    • Jas GS, Larson EJ, Johnson CK, Kuczera K. Microscopic details of rotational diffusion of perylene in organic solvents: molecular dynamics simulations and experiment vs. Debye-Stokes-Einstein theory. J Phys Chem A 2000;104:9841-9852.
    • (2000) J Phys Chem A , vol.104 , pp. 9841-9852
    • Jas, G.S.1    Larson, E.J.2    Johnson, C.K.3    Kuczera, K.4
  • 41
    • 40549115744 scopus 로고    scopus 로고
    • Hu C, Kuczera K.Images and animations of S-adenosyl-L- homocysteine hydrolase dynamics in solution. http://129.237.102.17/~kuczera/ 1ky4.html, 2005.
    • Hu C, Kuczera K.Images and animations of S-adenosyl-L- homocysteine hydrolase dynamics in solution. http://129.237.102.17/~kuczera/ 1ky4.html, 2005.
  • 42
    • 33845553743 scopus 로고
    • Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. II. Analysis of experimental results
    • Lipari G, Szabo A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. II. Analysis of experimental results. J Am Chem Soc 1982;104:4559-4570.
    • (1982) J Am Chem Soc , vol.104 , pp. 4559-4570
    • Lipari, G.1    Szabo, A.2
  • 43
    • 33646719091 scopus 로고
    • Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. I. Theory and range of validity
    • Lipari G, Szabo A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. I. Theory and range of validity. J Am Chem Soc 1982;104:4546-4559.
    • (1982) J Am Chem Soc , vol.104 , pp. 4546-4559
    • Lipari, G.1    Szabo, A.2
  • 45
    • 0000658538 scopus 로고
    • Langevin modes of macromolecules
    • Lamm G, Sabo A. Langevin modes of macromolecules. J Chem Phys 1986;85:7334-7348.
    • (1986) J Chem Phys , vol.85 , pp. 7334-7348
    • Lamm, G.1    Sabo, A.2
  • 46
    • 0027732618 scopus 로고
    • Effect of solvent on collective motions in globular proteins
    • Hayward S, Kitao A, Hirata F, Go N. Effect of solvent on collective motions in globular proteins. J Mol Biol 1993;234:1207-1217.
    • (1993) J Mol Biol , vol.234 , pp. 1207-1217
    • Hayward, S.1    Kitao, A.2    Hirata, F.3    Go, N.4


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