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Volumn 52, Issue 2, 2012, Pages 449-456

Understanding product specificity of protein lysine methyltransferases from QM/MM molecular dynamics and free energy simulations: The effects of mutation on SET7/9 beyond the Tyr/Phe switch

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; COMPUTATIONAL CHEMISTRY; MOLECULAR DYNAMICS; MOLECULAR MODELING; QUANTUM THEORY; REACTION KINETICS;

EID: 84857562890     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci200364m     Document Type: Conference Paper
Times cited : (24)

References (44)
  • 1
    • 33745632390 scopus 로고    scopus 로고
    • The epigenetic magic of histone lysine methylation
    • Jenuwein, T. The epigenetic magic of histone lysine methylation FEBS J. 2006, 273, 3121-3135
    • (2006) FEBS J. , vol.273 , pp. 3121-3135
    • Jenuwein, T.1
  • 2
    • 27644589675 scopus 로고    scopus 로고
    • The diverse functions of histone lysine methylation
    • DOI 10.1038/nrm1761, PII N1761
    • Martin, C.; Zhang, Y. The diverse functions of histone lysine methylation Nat. Rev. Mol. Cell Biol. 2005, 6, 838-849 (Pubitemid 41568733)
    • (2005) Nature Reviews Molecular Cell Biology , vol.6 , Issue.11 , pp. 838-849
    • Martin, C.1    Zhang, Y.2
  • 3
    • 0034610814 scopus 로고    scopus 로고
    • The language of covalent histone modifications
    • DOI 10.1038/47412
    • Strahl, B. D.; Allis, C. D. The language of covalent histone modifications Nature 2000, 403, 41-45 (Pubitemid 30038513)
    • (2000) Nature , vol.403 , Issue.6765 , pp. 41-45
    • Strahl, B.D.1    Allis, C.D.2
  • 4
    • 20544461679 scopus 로고    scopus 로고
    • Structural and sequence motifs of protein (histone) methylation enzymes
    • DOI 10.1146/annurev.biophys.34.040204.144452
    • Cheng, X.; Collins, R. E.; Zhang, X. Structural and sequence motifs of protein (histone) methylation enzymes Annu. Rev. Biophys. Biomol. Struct. 2005, 34, 267-294 (Pubitemid 40847726)
    • (2005) Annual Review of Biophysics and Biomolecular Structure , vol.34 , pp. 267-294
    • Cheng, X.1    Collins, R.E.2    Zhang, X.3
  • 6
    • 35848961668 scopus 로고    scopus 로고
    • How chromatin-binding modules interpret histone modifications: Lessons from professional pocket pickers
    • DOI 10.1038/nsmb1338, PII NSMB1338
    • Taverna, S. D.; Li, H.; Ruthenburg, A. J.; Allis, C. D.; Patel, D. J. How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers Nat. Struct. Mol. Biol. 2007, 14, 1025-1040 (Pubitemid 350060344)
    • (2007) Nature Structural and Molecular Biology , vol.14 , Issue.11 , pp. 1025-1040
    • Taverna, S.D.1    Li, H.2    Ruthenburg, A.J.3    Allis, C.D.4    Patel, D.J.5
  • 7
    • 35848946372 scopus 로고    scopus 로고
    • Primers on chromatin
    • DOI 10.1038/nsmb1107-1110, PII NSMB11071110
    • Lall, S. Primers on chromatin Nat. Struct. Mol. Biol. 2007, 14, 1110-1115 (Pubitemid 350060326)
    • (2007) Nature Structural and Molecular Biology , vol.14 , Issue.11 , pp. 1110-1115
    • Lall, S.1
  • 8
    • 15044358494 scopus 로고    scopus 로고
    • Reading signals on the nucleosome with a new nomenclature for modified histones
    • Turner, B. M. Reading signals on the nucleosome with a new nomenclature for modified histones Nat. Struct. Mol. Biol. 2005, 12, 110-112
    • (2005) Nat. Struct. Mol. Biol. , vol.12 , pp. 110-112
    • Turner, B.M.1
  • 9
    • 0037020217 scopus 로고    scopus 로고
    • Structure of the Neurospora SET domain protein DIM-5, a histone H3 lysine methyltransferase
    • Zhang, X.; Tamaru, H.; Khan, S. I.; Horton, J. R.; Keefe, L. J.; Selker, E. U.; Cheng, X. Structure of the Neurospora SET domain protein DIM-5, a histone H3 lysine methyltransferase Cell 2002, 111, 117-27
    • (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    Selker, E.U.6    Cheng, X.7
  • 10
    • 0042164227 scopus 로고    scopus 로고
    • Structural basis for the product specificity of histone lysine methyltransferases
    • DOI 10.1016/S1097-2765(03)00224-7
    • Zhang, X.; Yang, Z.; Khan, S. I.; Horton, J. R.; Tamaru, H.; Selker, E. U.; Cheng, X. Structural basis for the product specificity of histone lysine methyltransferases Mol. Cell 2003, 12, 177-85 (Pubitemid 36957834)
    • (2003) Molecular Cell , vol.12 , Issue.1 , pp. 177-185
    • Zhang, X.1    Yang, Z.2    Khan, S.I.3    Horton, J.R.4    Tamaru, H.5    Selker, E.U.6    Cheng, X.7
  • 11
    • 22344454519 scopus 로고    scopus 로고
    • Structural and functional analysis of SET8, a histone H4 Lys-20 methyltransferase
    • DOI 10.1101/gad.1318405
    • Couture, J. F.; Collazo, E.; Brunzelle, J. S.; Trievel, R. C. Structural and functional analysis of SET8, a histone H4 Lys-20 methyltransferase Genes Dev. 2005, 19, 1455-1465 (Pubitemid 41003012)
    • (2005) Genes and Development , vol.19 , Issue.12 , pp. 1455-1465
    • Couture, J.-F.1    Collazo, E.2    Brunzelle, J.S.3    Trievel, R.C.4
  • 15
  • 16
    • 0035816682 scopus 로고    scopus 로고
    • SET domain-containing protein, G9a, is a novel lysine-preferring mammalian histone methyltransferase with hyperactivity and specific selectivity to lysines 9 and 27 of histone H3
    • Tachibana, M.; Sugimoto, K.; Fukushima, T.; Shinkai, Y. SET domain-containing protein, G9a, is a novel lysine-preferring mammalian histone methyltransferase with hyperactivity and specific selectivity to lysines 9 and 27 of histone H3 J. Biol. Chem. 2001, 276, 25309-25317
    • (2001) J. Biol. Chem. , vol.276 , pp. 25309-25317
    • Tachibana, M.1    Sugimoto, K.2    Fukushima, T.3    Shinkai, Y.4
  • 18
    • 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, S. T.; Wu, J.; Sun, B. F.; Zhong, C.; Ding, J. P. 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. 2011, 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
  • 21
    • 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, Y-Z; Guo, H-B; Smith, J. C.; Guo, H. Energy Triplets for Writing Epigenetic Marks: Insights from QM/MM Free-Energy Simulations of Protein Lysine Methyltransferases Chemistry 2009, 15, 12596-12599
    • (2009) Chemistry , vol.15 , pp. 12596-12599
    • Xu, Q.1    Chu, Y.-Z.2    Guo, H.-B.3    Smith, J.C.4    Guo, H.5
  • 22
    • 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, Y. Z.; Xu, Q.; Guo, H. 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. 2010, 6, 1380-1389
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 1380-1389
    • Chu, Y.Z.1    Xu, Q.2    Guo, H.3
  • 23
    • 34547433238 scopus 로고    scopus 로고
    • Mechanism of histone methylation catalyzed by protein lysine methyltransferase SET7/9 and origin of product specificity
    • DOI 10.1073/pnas.0702981104
    • Guo, H. B.; Guo, H. Mechanism of histone methylation catalyzed by protein lysine methyltransferase SET7/9 and origin of product specificity Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 8797-8802 (Pubitemid 47175391)
    • (2007) Proceedings of the National Academy of Sciences of the United States of America , vol.104 , Issue.21 , pp. 8797-8802
    • Guo, H.-B.1    Guo, H.2
  • 24
    • 45749140396 scopus 로고    scopus 로고
    • Product specificity and mechanism of protein lysine methyltransferases: Insights from the histone lysine methyltransferase SET8
    • DOI 10.1021/bi800244s
    • Zhang, X. D.; Bruice, T. C. Product specificity and mechanism of protein lysine methyltransferases: Insights from the histone lysine methyltransferase SET8 Biochemistry 2008, 47, 6671-6677 (Pubitemid 351874293)
    • (2008) Biochemistry , vol.47 , Issue.25 , pp. 6671-6677
    • Zhang, X.1    Bruice, T.C.2
  • 26
    • 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
    • DOI 10.1021/ja075896n
    • Hu, P.; Wang, S.; Zhang, Y. 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. 2008, 130, 3806-3813 (Pubitemid 351429846)
    • (2008) Journal of the American Chemical Society , vol.130 , Issue.12 , pp. 3806-3813
    • Hu, P.1    Wang, S.2    Zhang, Y.3
  • 27
    • 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
    • DOI 10.1021/jp067147i
    • Wang, S. L.; Hu, P.; Zhang, Y. K. Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: The case of histone lysine methyltransferase SET7/9 J. Phys. Chem. B 2007, 111, 3758-3764 (Pubitemid 46724005)
    • (2007) Journal of Physical Chemistry B , vol.111 , Issue.14 , pp. 3758-3764
    • Wang, S.1    Hu, P.2    Zhang, Y.3
  • 28
    • 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
    • DOI 10.1021/ja056153+
    • Hu, P.; Zhang, Y. K. 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. 2006, 128, 1272-1278 (Pubitemid 43190640)
    • (2006) Journal of the American Chemical Society , vol.128 , Issue.4 , pp. 1272-1278
    • Hu, P.1    Zhang, Y.2
  • 30
    • 77952400211 scopus 로고    scopus 로고
    • Quantum Chemical Modeling of Enzymatic Reactions: The Case of Histone Lysine Methyltransferase
    • Georgieva, P.; Himo, F. Quantum Chemical Modeling of Enzymatic Reactions: The Case of Histone Lysine Methyltransferase J. Comput. Chem. 2010, 31, 1707-1714
    • (2010) J. Comput. Chem. , vol.31 , pp. 1707-1714
    • Georgieva, P.1    Himo, F.2
  • 31
    • 84986513644 scopus 로고
    • A combined quantum-mechanical and molecular mechanical potential for molecular-dynamics simulations
    • Field, M. J.; Bash, P. A.; Karplus, M. A combined quantum-mechanical and molecular mechanical potential for molecular-dynamics simulations J. Comput. Chem. 1990, 11, 700-733
    • (1990) J. Comput. Chem. , vol.11 , pp. 700-733
    • Field, M.J.1    Bash, P.A.2    Karplus, M.3
  • 33
    • 0022068152 scopus 로고
    • Active-site dynamics in protein molecules - A stochastic boundary molecular-dynamics approach
    • Brooks, C. L.; Brunger, A.; Karplus, M. Active-site dynamics in protein molecules-a stochastic boundary molecular-dynamics approach Biopolymers 1985, 24, 843-865
    • (1985) Biopolymers , vol.24 , pp. 843-865
    • Brooks, C.L.1    Brunger, A.2    Karplus, M.3
  • 34
    • 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. A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method J. Phys. Chem. B 2001, 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
  • 37
    • 0000036869 scopus 로고    scopus 로고
    • Simulation of activation free energies in molecular systems
    • Neria, E.; Fischer, S.; Karplus, M. Simulation of activation free energies in molecular systems J. Chem. Phys. 1996, 105, 1902-1921 (Pubitemid 126612899)
    • (1996) Journal of Chemical Physics , vol.105 , Issue.5 , pp. 1902-1921
    • Neria, E.1    Fischer, S.2    Karplus, M.3
  • 38
    • 16444385400 scopus 로고
    • Monte-carlo free-energy estimates using non-boltzmann sampling - Application to subcritical lennard-jones fluid
    • Torrie, G. M.; Valleau, J. P. Monte-carlo free-energy estimates using non-boltzmann sampling-application to subcritical lennard-jones fluid Chem. Phys. Lett. 1974, 28, 578-581
    • (1974) Chem. Phys. Lett. , vol.28 , pp. 578-581
    • Torrie, G.M.1    Valleau, J.P.2
  • 39
    • 84986519238 scopus 로고
    • The weighted histogram analysis method for free-energy calculations on biomolecules 0.1. The method
    • Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. The weighted histogram analysis method for free-energy calculations on biomolecules 0.1. The method J. Comput. Chem. 1992, 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
  • 40
    • 84961978260 scopus 로고    scopus 로고
    • Direct Evidence for Methyl Group Coordination by Carbon-Oxygen Hydrogen Bonds in the Lysine Methyltransferase SET7/9
    • Horowitz, S.; Yesselman, J. D.; Al-Hashimi, H. M.; Trievel, R. C. Direct Evidence for Methyl Group Coordination by Carbon-Oxygen Hydrogen Bonds in the Lysine Methyltransferase SET7/9 J. Biol. Chem. 2011, 286, 18658-18663
    • (2011) J. Biol. Chem. , vol.286 , pp. 18658-18663
    • Horowitz, S.1    Yesselman, J.D.2    Al-Hashimi, H.M.3    Trievel, R.C.4
  • 41
    • 33745842198 scopus 로고    scopus 로고
    • Catalytic roles for carbon-oxygen hydrogen bonding in SET domain lysine methyltransferases
    • DOI 10.1074/jbc.M602257200
    • Couture, J. F.; Hauk, G.; Thompson, M. J.; Blackburn, G. M.; Trievel, R. C. Catalytic roles for carbon-oxygen hydrogen bonding in SET domain lysine methyltransferases J. Biol. Chem. 2006, 281, 19280-19287 (Pubitemid 44035432)
    • (2006) Journal of Biological Chemistry , vol.281 , Issue.28 , pp. 19280-19287
    • Couture, J.-F.1    Hauk, G.2    Thompson, M.J.3    Blackburn, G.M.4    Trievel, R.C.5
  • 42
    • 0000724150 scopus 로고
    • Solvent influence on the stability of the peptide hydrogen-bond - A supramolecular cooperative effect
    • Guo, H.; Karplus, M. Solvent influence on the stability of the peptide hydrogen-bond-a supramolecular cooperative effect J. Phys. Chem. 1994, 98, 7104-7105
    • (1994) J. Phys. Chem. , vol.98 , pp. 7104-7105
    • Guo, H.1    Karplus, M.2
  • 43
    • 9944222091 scopus 로고    scopus 로고
    • δ- H•••O=C hydrogen bonds involving proline residues in helices
    • δ-H•••O=C hydrogen bonds involving proline residues in helices J. Phys. Chem. B 2004, 108, 18065-18072
    • (2004) J. Phys. Chem. B , vol.108 , pp. 18065-18072
    • Guo, H.B.1    Beahm, R.F.2    Guo, H.3
  • 44
    • 84857544999 scopus 로고    scopus 로고
    • A peptide-linkage deletion procedure for estimate of energetic contributions of individual peptide groups in a complex environment: Application to parallel β-Sheets
    • Guo, H. B.; Gorin, A.; Guo, H. A peptide-linkage deletion procedure for estimate of energetic contributions of individual peptide groups in a complex environment: Application to parallel β-Sheets Interdiscip. Sci. 2009, 1, 12-20
    • (2009) Interdiscip. Sci. , vol.1 , pp. 12-20
    • Guo, H.B.1    Gorin, A.2    Guo, H.3


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