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Volumn 7, Issue 5, 2012, Pages

Qm/mm md and free energy simulations of g9a-like protein (glp) and its mutants: Understanding the factors that determine the product specificity

Author keywords

[No Author keywords available]

Indexed keywords

G9A LIKE PROTEIN; HISTONE LYSINE METHYLTRANSFERASE; LYSINE 6 AMINOTRANSFERASE; MUTANT PROTEIN; PHENYLALANINE; TYROSINE; UNCLASSIFIED DRUG;

EID: 84862060896     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0037674     Document Type: Article
Times cited : (17)

References (38)
  • 1
    • 0034610814 scopus 로고    scopus 로고
    • The language of covalent histone modifications
    • Strahl BD, Allis CD, (2000) The language of covalent histone modifications. Nature 403: 41-45.
    • (2000) Nature , vol.403 , pp. 41-45
    • Strahl, B.D.1    Allis, C.D.2
  • 2
    • 0037309997 scopus 로고    scopus 로고
    • Structure of SET domain proteins: a new twist on histone methylation
    • Marmorstein R, (2003) Structure of SET domain proteins: a new twist on histone methylation. Trends Biochem Sci 28: 59-62.
    • (2003) Trends Biochem Sci , vol.28 , pp. 59-62
    • Marmorstein, R.1
  • 3
    • 33745632390 scopus 로고    scopus 로고
    • The epigenetic magic of histone lysine methylation
    • Jenuwein T, (2006) The epigenetic magic of histone lysine methylation. FEBS J 273: 3121-3135.
    • (2006) FEBS J , vol.273 , pp. 3121-3135
    • Jenuwein, T.1
  • 4
    • 27644589675 scopus 로고    scopus 로고
    • The diverse functions of histone lysine methylation
    • Martin C, Zhang Y, (2005) The diverse functions of histone lysine methylation. Nat Rev Mol Cell Biol 6: 838-849.
    • (2005) Nat Rev Mol Cell Biol , vol.6 , pp. 838-849
    • Martin, C.1    Zhang, Y.2
  • 5
    • 35848961668 scopus 로고    scopus 로고
    • How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers
    • Taverna SD, Li H, Ruthenburg AJ, Allis CD, Patel DJ, (2007) How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat Struc Mol Biol 14: 1025-1040.
    • (2007) Nat Struc Mol Biol , vol.14 , pp. 1025-1040
    • Taverna, S.D.1    Li, H.2    Ruthenburg, A.J.3    Allis, C.D.4    Patel, D.J.5
  • 6
    • 35848946372 scopus 로고    scopus 로고
    • Primers on chromatin
    • Lall S, (2007) Primers on chromatin. Nat Struc Mol Biol 14: 1110-1115.
    • (2007) Nat Struc Mol Biol , vol.14 , pp. 1110-1115
    • Lall, S.1
  • 7
    • 15044358494 scopus 로고    scopus 로고
    • Reading signals on the nucleosome with a new nomenclature for modified histones
    • Turner BM, (2005) Reading signals on the nucleosome with a new nomenclature for modified histones. Nat Struc Mol Biol 12: 110-112.
    • (2005) Nat Struc Mol Biol , vol.12 , pp. 110-112
    • Turner, B.M.1
  • 8
    • 0037020217 scopus 로고    scopus 로고
    • Structure of the Neurospora SET domain protein DIM-5, a histone H3 lysine methyltransferase
    • Zhang X, Tamaru H, Khan SI, Horton JR, Keefe LJ, et al. (2002) Structure of the Neurospora SET domain protein DIM-5, a histone H3 lysine methyltransferase. Cell 111: 117-127.
    • (2002) Cell , vol.111 , pp. 117-127
    • Zhang, X.1    Tamaru, H.2    Khan, S.I.3    Horton, J.R.4    Keefe, L.J.5
  • 9
    • 0042164227 scopus 로고    scopus 로고
    • Structural basis for the product specificity of histone lysine methyltransferases
    • Zhang X, Yang Z, Khan SI, Horton JR, Tamaru H, et al. (2003) Structural basis for the product specificity of histone lysine methyltransferases. Mol Cell 12: 177-185.
    • (2003) Mol Cell , vol.12 , pp. 177-185
    • Zhang, X.1    Yang, Z.2    Khan, S.I.3    Horton, J.R.4    Tamaru, H.5
  • 10
    • 22344454519 scopus 로고    scopus 로고
    • Structural and functional analysis of SET8, a histone H4 Lys-20 methyltransferase
    • Couture JF, Collazo E, Brunzelle JS, Trievel RC, (2005) Structural and functional analysis of SET8, a histone H4 Lys-20 methyltransferase. Genes Dev 19: 1455-1465.
    • (2005) Genes Dev , vol.19 , pp. 1455-1465
    • Couture, J.F.1    Collazo, E.2    Brunzelle, J.S.3    Trievel, R.C.4
  • 11
    • 22344455665 scopus 로고    scopus 로고
    • Specificity and mechanism of the histone methyltransferase Pr-Set7
    • Xiao B, Jing C, Kelly G, Walker PA, Muskett FW, et al. (2005) Specificity and mechanism of the histone methyltransferase Pr-Set7. Genes Dev 19: 1444-1454.
    • (2005) Genes Dev , vol.19 , pp. 1444-1454
    • Xiao, B.1    Jing, C.2    Kelly, G.3    Walker, P.A.4    Muskett, F.W.5
  • 12
    • 0037421847 scopus 로고    scopus 로고
    • Structure and catalytic mechanism of the human histone methyltransferase SET7/9
    • Xiao B, Jing C, Wilson JR, Walker PA, Vasisht N, et al. (2003) Structure and catalytic mechanism of the human histone methyltransferase SET7/9. Nature 421: 652-656.
    • (2003) Nature , vol.421 , pp. 652-656
    • Xiao, B.1    Jing, C.2    Wilson, J.R.3    Walker, P.A.4    Vasisht, N.5
  • 14
    • 14044256546 scopus 로고    scopus 로고
    • In vitro and in vivo analyses of a Phe/Tyr switch controlling product specificity of histone lysine methyltransferases
    • Collins RE, Tachibana M, Tamaru H, Smith KM, Jia D, et al. (2005) In vitro and in vivo analyses of a Phe/Tyr switch controlling product specificity of histone lysine methyltransferases. J Biol Chem 280: 5563-5570.
    • (2005) J Biol Chem , vol.280 , pp. 5563-5570
    • Collins, R.E.1    Tachibana, M.2    Tamaru, H.3    Smith, K.M.4    Jia, D.5
  • 16
    • 79961241001 scopus 로고    scopus 로고
    • Structural and biochemical studies of human lysine methyltransferase Smyd3 reveal the important functional roles of its post-SET and TPR domains and the regulation of its activity by DNA binding
    • Xu ST, Wu J, Sun BF, Zhong C, Ding JP, (2011) Structural and biochemical studies of human lysine methyltransferase Smyd3 reveal the important functional roles of its post-SET and TPR domains and the regulation of its activity by DNA binding. Nucleic Acids Res 39: 4438-4449.
    • (2011) Nucleic Acids Res , vol.39 , pp. 4438-4449
    • Xu, S.T.1    Wu, J.2    Sun, B.F.3    Zhong, C.4    Ding, J.P.5
  • 17
    • 77957770113 scopus 로고    scopus 로고
    • SET7/9 Catalytic Mutants Reveal the Role of Active Site Water Molecules in Lysine Multiple Methylation
    • Del Rizzo PA, Couture JF, Dirk LMA, Strunk BS, Roiko MS, et al. (2010) SET7/9 Catalytic Mutants Reveal the Role of Active Site Water Molecules in Lysine Multiple Methylation. J Bio Chem 285: 31849-31858.
    • (2010) J Bio Chem , vol.285 , pp. 31849-31858
    • Del Rizzo, P.A.1    Couture, J.F.2    Dirk, L.M.A.3    Strunk, B.S.4    Roiko, M.S.5
  • 18
    • 71549139127 scopus 로고    scopus 로고
    • Energy Triplets for Writing Epigenetic Marks: Insights from QM/MM Free-Energy Simulations of Protein Lysine Methyltransferases
    • Xu Q, Chu YZ, Guo HB, Smith JC, Guo H, (2009) Energy Triplets for Writing Epigenetic Marks: Insights from QM/MM Free-Energy Simulations of Protein Lysine Methyltransferases. Chem Eur J 15: 12596-12599.
    • (2009) Chem Eur J , vol.15 , pp. 12596-12599
    • Xu, Q.1    Chu, Y.Z.2    Guo, H.B.3    Smith, J.C.4    Guo, H.5
  • 19
    • 77951116407 scopus 로고    scopus 로고
    • Understanding Energetic Origins of Product Specificity of SET8 from QM/MM Free Energy Simulations: What Causes the Stop of Methyl Addition during Histone Lysine Methylation?
    • Chu YZ, Xu Q, Guo H, (2008) Understanding Energetic Origins of Product Specificity of SET8 from QM/MM Free Energy Simulations: What Causes the Stop of Methyl Addition during Histone Lysine Methylation? J Chem Theory Comput 6: 1380-1389.
    • (2008) J Chem Theory Comput , vol.6 , pp. 1380-1389
    • Chu, Y.Z.1    Xu, Q.2    Guo, H.3
  • 20
    • 34547433238 scopus 로고    scopus 로고
    • Mechanism of histone methylation catalyzed by protein lysine methyltransferase SET7/9 and origin of product specificity
    • Guo HB, Guo H, (2007) Mechanism of histone methylation catalyzed by protein lysine methyltransferase SET7/9 and origin of product specificity. Proc Natl Acad Sci USA 104: 8797-8802.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 8797-8802
    • Guo, H.B.1    Guo, H.2
  • 21
    • 45749140396 scopus 로고    scopus 로고
    • Product specificity and mechanism of protein lysine methyltransferases: Insights from the histone lysine methyltransferase SET8
    • Zhang XD, Bruice TC, (2008) Product specificity and mechanism of protein lysine methyltransferases: Insights from the histone lysine methyltransferase SET8. Biochemistry 47: 6671-6677.
    • (2008) Biochemistry , vol.47 , pp. 6671-6677
    • Zhang, X.D.1    Bruice, T.C.2
  • 22
    • 79956279966 scopus 로고    scopus 로고
    • Modeling a New Water Channel That Allows SET9 to Dimethylate p53
    • Bai QF, Shen YL, Yao XJ, Wang F, Du YP, et al. (2011) Modeling a New Water Channel That Allows SET9 to Dimethylate p53. Plos One 6: e19856.
    • (2011) Plos One , vol.6
    • Bai, Q.F.1    Shen, Y.L.2    Yao, X.J.3    Wang, F.4    Du, Y.P.5
  • 23
    • 41149125431 scopus 로고    scopus 로고
    • How do SET-domain protein lysine methyltransferases achieve the methylation state specificity? Revisited by ab initio QM/MM molecular dynamics simulations
    • Hu P, Wang S, Zhang Y, (2008) How do SET-domain protein lysine methyltransferases achieve the methylation state specificity? Revisited by ab initio QM/MM molecular dynamics simulations. J Am Chem Soc 130: 3806-3813.
    • (2008) J Am Chem Soc , vol.130 , pp. 3806-3813
    • Hu, P.1    Wang, S.2    Zhang, Y.3
  • 24
    • 34248219463 scopus 로고    scopus 로고
    • Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: The case of histone lysine methyltransferase SET7/9
    • Wang SL, Hu P, Zhang YK, (2007) Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: The case of histone lysine methyltransferase SET7/9. J Phys Chem B 111: 3758-3764.
    • (2007) J Phys Chem B , vol.111 , pp. 3758-3764
    • Wang, S.L.1    Hu, P.2    Zhang, Y.K.3
  • 25
    • 31944437048 scopus 로고    scopus 로고
    • Catalytic mechanism and product specificity of the histone lysine methyltransferase SET7/9: An ab initio QM/MM-FE study with multiple initial structures
    • Hu P, Zhang YK, (2006) Catalytic mechanism and product specificity of the histone lysine methyltransferase SET7/9: An ab initio QM/MM-FE study with multiple initial structures. J Am Chem Soc 128: 1272-1278.
    • (2006) J Am Chem Soc , vol.128 , pp. 1272-1278
    • Hu, P.1    Zhang, Y.K.2
  • 26
    • 44449162039 scopus 로고    scopus 로고
    • Enzymatic mechanism and product specificity of SET-domain protein lysine methyltransferases
    • Zhang X, Bruice TC, (2008) Enzymatic mechanism and product specificity of SET-domain protein lysine methyltransferases. Proc Natl Acad Sci USA 105: 5728-5732.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 5728-5732
    • Zhang, X.1    Bruice, T.C.2
  • 27
    • 84986513644 scopus 로고
    • A combined quantum-mechanical and molecular mechanical potential for molecular-dynamics simulations
    • Field MJ, Bash PA, Karplus M, (1990) A combined quantum-mechanical and molecular mechanical potential for molecular-dynamics simulations. J Comput Chem 11: 700-733.
    • (1990) J Comput Chem , vol.11 , pp. 700-733
    • Field, M.J.1    Bash, P.A.2    Karplus, M.3
  • 30
    • 0000036869 scopus 로고    scopus 로고
    • Simulation of activation free energies in molecular systems
    • Neria E, Fischer S, Karplus M, (1996) Simulation of activation free energies in molecular systems. J Chem Phys 105: 1902-1921.
    • (1996) J Chem Phys , vol.105 , pp. 1902-1921
    • Neria, E.1    Fischer, S.2    Karplus, M.3
  • 31
    • 0022068152 scopus 로고
    • Active-site dynamics in protein molecules - a stochastic boundary molecular-dynamics approach
    • Brooks CL, Brunger A, Karplus M, (1985) Active-site dynamics in protein molecules - a stochastic boundary molecular-dynamics approach. Biopolymers 24: 843-865.
    • (1985) Biopolymers , vol.24 , pp. 843-865
    • Brooks, C.L.1    Brunger, A.2    Karplus, M.3
  • 32
    • 0035138648 scopus 로고    scopus 로고
    • A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method
    • Cui Q, Elstner M, Kaxiras E, Frauenheim T, Karplus M, (2001) A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method. J Phys Chem B 105: 569-585.
    • (2001) J Phys Chem B , vol.105 , pp. 569-585
    • Cui, Q.1    Elstner, M.2    Kaxiras, E.3    Frauenheim, T.4    Karplus, M.5
  • 33
    • 0041784950 scopus 로고    scopus 로고
    • All-atom empirical potential for molecular modeling and dynamics studies of proteins
    • MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102: 3586-3616.
    • (1998) J Phys Chem B , vol.102 , pp. 3586-3616
    • MacKerell, A.D.1    Bashford, D.2    Bellott, M.3    Dunbrack, R.L.4    Evanseck, J.D.5
  • 34
    • 16444385400 scopus 로고
    • Monte-carlo free-energy estimates using non-boltzmann sampling - application to subcritical lennard -jones fluid
    • Torrie GM, Valleau JP, (1974) Monte-carlo free-energy estimates using non-boltzmann sampling - application to subcritical lennard-jones fluid. Chem Phys Lett 28: 578-581.
    • (1974) Chem Phys Lett , vol.28 , pp. 578-581
    • Torrie, G.M.1    Valleau, J.P.2
  • 35
    • 84986519238 scopus 로고
    • The weighted histogram analysis method for free-energy calculations on biomolecules. 1. The method
    • Kumar S, Bouzida D, Swendsen RH, Kollman PA, Rosenberg JM, (1992) The weighted histogram analysis method for free-energy calculations on biomolecules. 1. The method. J Comput Chem 13: 1011-1021.
    • (1992) J Comput Chem , vol.13 , pp. 1011-1021
    • Kumar, S.1    Bouzida, D.2    Swendsen, R.H.3    Kollman, P.A.4    Rosenberg, J.M.5
  • 36
    • 73349135352 scopus 로고    scopus 로고
    • Boxed Molecular Dynamics: A Simple and General Technique for Accelerating Rare Event Kinetics and Mapping Free Energy in Large Molecular Systems
    • Glowacki DR, Paci E, Shalashilin DV, (2009) Boxed Molecular Dynamics: A Simple and General Technique for Accelerating Rare Event Kinetics and Mapping Free Energy in Large Molecular Systems. Journal of Physical Chemistry B 113: 16603-16611.
    • (2009) Journal of Physical Chemistry B , vol.113 , pp. 16603-16611
    • Glowacki, D.R.1    Paci, E.2    Shalashilin, D.V.3
  • 37
    • 80051906268 scopus 로고    scopus 로고
    • Communication: Conformation state diagram of polypeptides: A chain length induced alpha-beta transition
    • Ricchiuto P, Brukhno AV, Paci E, Auer S, (2011) Communication: Conformation state diagram of polypeptides: A chain length induced alpha-beta transition. Journal of Chemical Physics 135.
    • (2011) Journal of Chemical Physics , vol.135
    • Ricchiuto, P.1    Brukhno, A.V.2    Paci, E.3    Auer, S.4
  • 38
    • 0029878720 scopus 로고    scopus 로고
    • VMD: visual molecular dynamics
    • Humphrey W DA, Schulten K, (1996) VMD: visual molecular dynamics. J Mol Graph 14: 27-38.
    • (1996) J Mol Graph , vol.14 , pp. 27-38
    • Humphrey, W.D.A.1    Schulten, K.2


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