메뉴 건너뛰기




Volumn 4, Issue 3, 2013, Pages 491-495

Sirtuin deacetylation mechanism and catalytic role of the dynamic cofactor binding loop

Author keywords

ab initio QM MM molecular dynamics simulation; enzyme catalysis; free energy and umbrella sampling; protein deacetylation; reaction mechanisms

Indexed keywords

DEACETYLATION; ENZYME CATALYSIS; MOLECULAR DYNAMICS SIMULATIONS; REACTION MECHANISM; UMBRELLA SAMPLING;

EID: 84873434826     PISSN: None     EISSN: 19487185     Source Type: Journal    
DOI: 10.1021/jz302015s     Document Type: Article
Times cited : (26)

References (52)
  • 1
    • 67949102053 scopus 로고    scopus 로고
    • Recent Progress in the Biology and Physiology of Sirtuins
    • Finkel, T.; Deng, C. X.; Mostoslavsky, R. Recent Progress in the Biology and Physiology of Sirtuins Nature 2009, 460, 587-591
    • (2009) Nature , vol.460 , pp. 587-591
    • Finkel, T.1    Deng, C.X.2    Mostoslavsky, R.3
  • 2
    • 77949887506 scopus 로고    scopus 로고
    • Mammalian Sirtuins: Biological Insights and Disease Relevance
    • Haigis, M. C.; Sinclair, D. A. Mammalian Sirtuins: Biological Insights and Disease Relevance Annu. Rev. Pathol. Mech. Dis. 2010, 5, 253-295
    • (2010) Annu. Rev. Pathol. Mech. Dis. , vol.5 , pp. 253-295
    • Haigis, M.C.1    Sinclair, D.A.2
  • 5
    • 79957944140 scopus 로고    scopus 로고
    • Advances in Characterization of Human Sirtuin Isoforms: Chemistries, Targets and Therapeutic Applications
    • Cen, Y.; Youn, D. Y.; Sauve, A. A. Advances in Characterization of Human Sirtuin Isoforms: Chemistries, Targets and Therapeutic Applications Curr. Med. Chem. 2011, 18, 1919-1935
    • (2011) Curr. Med. Chem. , vol.18 , pp. 1919-1935
    • Cen, Y.1    Youn, D.Y.2    Sauve, A.A.3
  • 6
    • 77958523925 scopus 로고    scopus 로고
    • NAD(+)-Dependent Histone Deacetylases (Sirtuins) as Novel Therapeutic Targets
    • Uciechowska, U.; Sippl, W.; Jung, M. NAD(+)-Dependent Histone Deacetylases (Sirtuins) as Novel Therapeutic Targets Med. Res. Rev. 2010, 30, 861-889
    • (2010) Med. Res. Rev. , vol.30 , pp. 861-889
    • Uciechowska, U.1    Sippl, W.2    Jung, M.3
  • 9
    • 78650132019 scopus 로고    scopus 로고
    • Sirtuin Mechanism and Inhibition: Explored with N (ε)-acetyl-lysine Analogs
    • Hirsch, B. M.; Zheng, W. Sirtuin Mechanism and Inhibition: Explored with N (ε)-acetyl-lysine Analogs Mol. BioSyst. 2011, 7, 16-28
    • (2011) Mol. BioSyst. , vol.7 , pp. 16-28
    • Hirsch, B.M.1    Zheng, W.2
  • 10
    • 78751506349 scopus 로고    scopus 로고
    • Catalysis and Mechanistic Insights into Sirtuin Activation
    • Dittenhafer-Reed, K. E.; Feldman, J. L.; Denu, J. M. Catalysis and Mechanistic Insights into Sirtuin Activation ChemBioChem 2011, 12, 281-289
    • (2011) ChemBioChem , vol.12 , pp. 281-289
    • Dittenhafer-Reed, K.E.1    Feldman, J.L.2    Denu, J.M.3
  • 11
    • 79958244669 scopus 로고    scopus 로고
    • Computer- and Structure-Based Lead Design for Epigenetic Targets
    • Heinke, R.; Carlino, L.; Kannan, S.; Jung, M.; Sippl, W. Computer- and Structure-Based Lead Design for Epigenetic Targets Bioorg. Med. Chem. 2011, 19, 3605-3615
    • (2011) Bioorg. Med. Chem. , vol.19 , pp. 3605-3615
    • Heinke, R.1    Carlino, L.2    Kannan, S.3    Jung, M.4    Sippl, W.5
  • 12
    • 70149123204 scopus 로고    scopus 로고
    • Inhibition of Human Sirtuins by in Situ Generation of an Acetylated Lysine-ADP-Ribose Conjugate
    • Asaba, T.; Suzuki, T.; Ueda, R.; Tsumoto, H.; Nakagawa, H.; Miyata, N. Inhibition of Human Sirtuins by in Situ Generation of an Acetylated Lysine-ADP-Ribose Conjugate J. Am. Chem. Soc. 2009, 131, 6989-6996
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 6989-6996
    • Asaba, T.1    Suzuki, T.2    Ueda, R.3    Tsumoto, H.4    Nakagawa, H.5    Miyata, N.6
  • 13
    • 77953292895 scopus 로고    scopus 로고
    • Sirtuins Inhibitors: The Approach to Affinity and Selectivity
    • Cen, Y. Sirtuins Inhibitors: The Approach to Affinity and Selectivity Biochim. Biophys. Acta 2010, 1804, 1635-1644
    • (2010) Biochim. Biophys. Acta , vol.1804 , pp. 1635-1644
    • Cen, Y.1
  • 14
    • 82955233648 scopus 로고    scopus 로고
    • Old Enzymes, New Tricks: Sirtuins Are NAD(+)-Dependent Deacylases
    • Hirschey, M. D. Old Enzymes, New Tricks: Sirtuins Are NAD(+)-Dependent Deacylases Cell Metab. 2011, 14, 718-719
    • (2011) Cell Metab. , vol.14 , pp. 718-719
    • Hirschey, M.D.1
  • 15
    • 77953291365 scopus 로고    scopus 로고
    • Sirtuin Chemical Mechanisms
    • Sauve, A. A. Sirtuin Chemical Mechanisms Biochim. Biophys. Acta 2010, 1804, 1591-1603
    • (2010) Biochim. Biophys. Acta , vol.1804 , pp. 1591-1603
    • Sauve, A.A.1
  • 16
    • 53649086367 scopus 로고    scopus 로고
    • Mechanisms and Molecular Probes of Sirtuins
    • Smith, B. C.; Hallows, W. C.; Denu, J. M. Mechanisms and Molecular Probes of Sirtuins Chem. Biol. 2008, 15, 1002-1013
    • (2008) Chem. Biol. , vol.15 , pp. 1002-1013
    • Smith, B.C.1    Hallows, W.C.2    Denu, J.M.3
  • 17
    • 34248595983 scopus 로고    scopus 로고
    • + cleavage
    • DOI 10.1021/ja070162w
    • Smith, B. C.; Denu, J. M. Sir2 Deacetylases Exhibit Nucleophilic Participation of Acetyl Lysine in NAD+ Cleavage J. Am. Chem. Soc. 2007, 129, 5802-5803 (Pubitemid 46748469)
    • (2007) Journal of the American Chemical Society , vol.129 , Issue.18 , pp. 5802-5803
    • Smith, B.C.1    Denu, J.M.2
  • 18
    • 33745534953 scopus 로고    scopus 로고
    • + and Acetylated Peptide
    • DOI 10.1016/j.str.2006.06.006, PII S0969212606002899
    • Hoff, K. G.; Avalos, J. L.; Sens, K.; Wolberger, C. Insights into the Sirtuin Mechanism From Ternary Complexes Containing NAD(+) and Acetylated Peptide Structure 2006, 14, 1231-1240 (Pubitemid 44176368)
    • (2006) Structure , vol.14 , Issue.8 , pp. 1231-1240
    • Hoff, K.G.1    Avalos, J.L.2    Sens, K.3    Wolberger, C.4
  • 22
    • 57549110245 scopus 로고    scopus 로고
    • Highly Dissociative and Concerted Mechanism for the Nicotinamide Cleavage Reaction in Sir2Tm Enzyme Suggested by Ab Initio QM/MM Molecular Dynamics Simulations
    • Hu, P.; Wang, S.; Zhang, Y. Highly Dissociative and Concerted Mechanism for the Nicotinamide Cleavage Reaction in Sir2Tm Enzyme Suggested By Ab Initio QM/MM Molecular Dynamics Simulations J. Am. Chem. Soc. 2008, 130, 16721-16728
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 16721-16728
    • Hu, P.1    Wang, S.2    Zhang, Y.3
  • 23
    • 77956246695 scopus 로고    scopus 로고
    • A Transition State of ADP-Ribosylation of Acetyllysine Catalyzed by Archaeoglobus Fulgidus Sir2 Determined by Kinetic Isotope Effects and Computational Approaches
    • Cen, Y.; Sauve, A. A Transition State of ADP-Ribosylation of Acetyllysine Catalyzed by Archaeoglobus Fulgidus Sir2 Determined by Kinetic Isotope Effects and Computational Approaches J. Am. Chem. Soc. 2010, 132, 12286-12298
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 12286-12298
    • Cen, Y.1    Sauve, A.2
  • 24
    • 77956509704 scopus 로고    scopus 로고
    • Investigation of the Catalytic Mechanism of Sir2 Enzyme with QM/MM Approach: SN1 vs SN2?
    • Liang, Z.; Shi, T.; Ouyang, S.; Li, H.; Yu, K.; Zhu, W.; Luo, C.; Jiang, H. Investigation of the Catalytic Mechanism of Sir2 Enzyme with QM/MM Approach: SN1 vs SN2? J. Phys. Chem. B 2010, 114, 11927-11933
    • (2010) J. Phys. Chem. B , vol.114 , pp. 11927-11933
    • Liang, Z.1    Shi, T.2    Ouyang, S.3    Li, H.4    Yu, K.5    Zhu, W.6    Luo, C.7    Jiang, H.8
  • 25
    • 1642297558 scopus 로고    scopus 로고
    • Structural basis for the mechanism and regulation of Sir2 enzymes
    • DOI 10.1016/S1097-2765(04)00082-6, PII S1097276504000826
    • Avalos, J. L.; Boeke, J. D.; Wolberger, C. Structural Basis for the Mechanism and Regulation of Sir2 Enzymes Mol. Cell 2004, 13, 639-648 (Pubitemid 38368122)
    • (2004) Molecular Cell , vol.13 , Issue.5 , pp. 639-648
    • Avalos, J.L.1    Boeke, J.D.2    Wolberger, C.3
  • 26
    • 33744956371 scopus 로고    scopus 로고
    • Use of substrate analogs and mutagenesis to study substrate binding and catalysis in the Sir2 family of NAD-dependent protein deacetylases
    • DOI 10.1074/jbc.M511482200
    • Khan, A. N.; Lewis, P. N. Use of Substrate Analogs and Mutagenesis to Study Substrate Binding and Catalysis in the Sir2 Family of NAD-dependent Protein Deacetylases J. Biol. Chem. 2006, 281, 11702-11711 (Pubitemid 43855428)
    • (2006) Journal of Biological Chemistry , vol.281 , Issue.17 , pp. 11702-11711
    • Khan, A.N.1    Lewis, P.N.2
  • 27
    • 0035951072 scopus 로고    scopus 로고
    • +-dependent deacetylation reactions
    • DOI 10.1021/bi011858j
    • Sauve, A. A.; Celic, I.; Avalos, J.; Deng, H. T.; Boeke, J. D.; Schramm, V. L. Chemistry of Gene Silencing: The Mechanism of NAD(+)-Dependent Deacetylation Reactions Biochemistry 2001, 40, 15456-15463 (Pubitemid 34015172)
    • (2001) Biochemistry , vol.40 , Issue.51 , pp. 15456-15463
    • Sauve, A.A.1    Celic, I.2    Avalos, J.3    Deng, H.4    Boeke, J.D.5    Schramm, V.L.6
  • 28
    • 0041571570 scopus 로고    scopus 로고
    • Sir2 regulation by nicotinamide results from switching between base exchange and deacetylation chemistry
    • DOI 10.1021/bi034959l
    • Sauve, A. A.; Schramm, V. L. Sir2 Regulation by Nicotinamide Results from Switching Between Base Exchange and Deacetylation Chemistry Biochemistry 2003, 42, 9249-9256 (Pubitemid 36959231)
    • (2003) Biochemistry , vol.42 , Issue.31 , pp. 9249-9256
    • Sauve, A.A.1    Schramm, V.L.2
  • 29
    • 30144431571 scopus 로고    scopus 로고
    • Sir2 protein deacetylases: Evidence for chemical intermediates and functions of a conserved histidine
    • DOI 10.1021/bi052014t
    • Smith, B. C.; Denu, J. M. Sir2 Protein Deacetylases: Evidence for Chemical Intermediates and Functions of a Conserved Histidine Biochemistry 2006, 45, 272-282 (Pubitemid 43054104)
    • (2006) Biochemistry , vol.45 , Issue.1 , pp. 272-282
    • Smith, B.C.1    Denu, J.M.2
  • 30
    • 84865225339 scopus 로고    scopus 로고
    • The Bicyclic Intermediate Structure Provides Insights into the Desuccinylation Mechanism of Human Sirtuin 5 (SIRT5)
    • Zhou, Y.; Zhang, H.; He, B.; Du, J.; Lin, H.; Cerione, R. A.; Hao, Q. The Bicyclic Intermediate Structure Provides Insights into the Desuccinylation Mechanism of Human Sirtuin 5 (SIRT5) J. Biol. Chem. 2012, 287, 28307-28314
    • (2012) J. Biol. Chem. , vol.287 , pp. 28307-28314
    • Zhou, Y.1    Zhang, H.2    He, B.3    Du, J.4    Lin, H.5    Cerione, R.A.6    Hao, Q.7
  • 31
    • 84871171710 scopus 로고    scopus 로고
    • Structural Basis for Sirtuin Activity and Inhibition
    • Yuan, H.; Marmorstein, R. Structural Basis for Sirtuin Activity and Inhibition J. Biol. Chem. 2012, 287, 42428-42435
    • (2012) J. Biol. Chem. , vol.287 , pp. 42428-42435
    • Yuan, H.1    Marmorstein, R.2
  • 32
    • 0001582558 scopus 로고    scopus 로고
    • A pseudobond approach to combining quantum mechanical and molecular mechanical methods
    • DOI 10.1063/1.478083, PII S0021960699302014
    • Zhang, Y.; Lee, T. S.; Yang, W. A Pseudobond Approach to Combining Quantum Mechanical and Molecular Mechanical Methods J. Chem. Phys. 1999, 110, 46-54 (Pubitemid 129708024)
    • (1999) Journal of Chemical Physics , vol.110 , Issue.1 , pp. 46-54
    • Zhang, Y.1    Lee, T.-S.2    Yang, W.3
  • 33
    • 22944472113 scopus 로고    scopus 로고
    • Improved Pseudobonds for Combined Ab Initio Quantum Mechanical/Molecular Mechanical Methods
    • Zhang, Y. Improved Pseudobonds for Combined Ab Initio Quantum Mechanical/Molecular Mechanical Methods J. Chem. Phys. 2005, 122, 024114
    • (2005) J. Chem. Phys. , vol.122 , pp. 024114
    • Zhang, Y.1
  • 36
    • 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
  • 37
    • 73349112879 scopus 로고    scopus 로고
    • Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations of the Hydrolysis Reaction Catalyzed by Protein Arginine Deiminase 4
    • Ke, Z.; Wang, S.; Xie, D.; Zhang, Y. Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations of the Hydrolysis Reaction Catalyzed by Protein Arginine Deiminase 4 J. Phys.Chem. B 2009, 113, 16705-16710
    • (2009) J. Phys.Chem. B , vol.113 , pp. 16705-16710
    • Ke, Z.1    Wang, S.2    Xie, D.3    Zhang, Y.4
  • 38
    • 70349266325 scopus 로고    scopus 로고
    • Active Site Cysteine Is Protonated in the PAD4Michaelis Complex: Evidence from Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations
    • Ke, Z.; Zhou, Y.; Hu, P.; Wang, S.; Xie, D.; Zhang, Y. Active Site Cysteine Is Protonated in the PAD4Michaelis Complex: Evidence from Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations J. Phys. Chem. B 2009, 113, 12750-12758
    • (2009) J. Phys. Chem. B , vol.113 , pp. 12750-12758
    • Ke, Z.1    Zhou, Y.2    Hu, P.3    Wang, S.4    Xie, D.5    Zhang, Y.6
  • 39
    • 34248219463 scopus 로고    scopus 로고
    • Ab Initio Quantum Mechanical/Molecular Mechanical Moleculardynamics Simulation of Enzyme Catalysis: The Case of Histone Lysine Methyltransferase SET7/9
    • Wang, S.; Hu, P.; Zhang, Y. Ab Initio Quantum Mechanical/Molecular Mechanical Moleculardynamics Simulation of Enzyme Catalysis: The Case of Histone Lysine Methyltransferase SET7/9 J. Phys.Chem. B 2007, 111, 3758-37564
    • (2007) J. Phys.Chem. B , vol.111 , pp. 3758-37564
    • Wang, S.1    Hu, P.2    Zhang, Y.3
  • 40
    • 77955808765 scopus 로고    scopus 로고
    • A Proton-Shuttle Reaction Mechanism for Histone Deacetylase 8 and the Catalytic Role of Metal Ions
    • Wu, R.; Wang, S.; Zhou, N.; Cao, Z.; Zhang, Y. A Proton-Shuttle Reaction Mechanism for Histone Deacetylase 8 and the Catalytic Role of Metal Ions J. Am. Chem. Soc. 2010, 132, 9471-9479
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 9471-9479
    • Wu, R.1    Wang, S.2    Zhou, N.3    Cao, Z.4    Zhang, Y.5
  • 41
    • 77954339384 scopus 로고    scopus 로고
    • Catalytic Reaction Mechanism of Acetylcholinesterase Determined by Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations
    • Zhou, Y.; Wang, S.; Zhang, Y. Catalytic Reaction Mechanism of Acetylcholinesterase Determined by Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations J. Phys. Chem. B 2010, 114, 8817-8825
    • (2010) J. Phys. Chem. B , vol.114 , pp. 8817-8825
    • Zhou, Y.1    Wang, S.2    Zhang, Y.3
  • 42
    • 79960593151 scopus 로고    scopus 로고
    • Molecular Mechanism for Eliminylation, a Newly Discovered Post-Translational Modification
    • Ke, Z.; Smith, G. K.; Zhang, Y.; Guo, H. Molecular Mechanism for Eliminylation, a Newly Discovered Post-Translational Modification J. Am. Chem. Soc. 2011, 133, 11103-11305
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 11103-11305
    • Ke, Z.1    Smith, G.K.2    Zhang, Y.3    Guo, H.4
  • 43
    • 78751489563 scopus 로고    scopus 로고
    • Serine Protease Acylation Proceeds with a Subtle Re-Orientation of the Histidine Ring at the Tetrahedral Intermediate
    • Zhou, Y.; Zhang, Y. Serine Protease Acylation Proceeds with a Subtle Re-Orientation of the Histidine Ring at the Tetrahedral Intermediate Chem. Commun. 2011, 47, 1577-1579
    • (2011) Chem. Commun. , vol.47 , pp. 1577-1579
    • Zhou, Y.1    Zhang, Y.2
  • 44
    • 84867519412 scopus 로고    scopus 로고
    • Preferred WMSA Catalytic Mechanism of the Nucleotidyl Transfer Reaction in Human DNA Polymerase Kappa Elucidates Error-Free Bypass of a Bulky DNA Lesion
    • Lior-Hoffmann, L.; Wang, L.; Wang, S.; Geacintov, N. E.; Broyde, S.; Zhang, Y. Preferred WMSA Catalytic Mechanism of the Nucleotidyl Transfer Reaction in Human DNA Polymerase Kappa Elucidates Error-Free Bypass of a Bulky DNA Lesion Nucleic Acids Res. 2012, 40, 9193-9205
    • (2012) Nucleic Acids Res. , vol.40 , pp. 9193-9205
    • Lior-Hoffmann, L.1    Wang, L.2    Wang, S.3    Geacintov, N.E.4    Broyde, S.5    Zhang, Y.6
  • 45
    • 15244355745 scopus 로고    scopus 로고
    • + cosubstrate specificity of a Sir2 enzyme
    • DOI 10.1016/j.molcel.2005.02.022
    • Avalos, J. L.; Bever, K. M.; Wolberger, C. Mechanism of Sirtuin Inhibition by Nicotinamide: Altering the NAD(+) Cosubstrate Specificity of a Sir2 Enzyme Mol. Cell 2005, 17, 855-868 (Pubitemid 40386946)
    • (2005) Molecular Cell , vol.17 , Issue.6 , pp. 855-868
    • Avalos, J.L.1    Bever, K.M.2    Wolberger, C.3
  • 46
    • 3343024449 scopus 로고    scopus 로고
    • +-dependent histone/protein deacetylases
    • DOI 10.1021/bi049592e
    • Borra, M. T.; Langer, M. R.; Slama, J. T.; Denu, J. M. Substrate Specificity and Kinetic Mechanism of the Sir2 Family of NAD(+)-Dependent Histone/Protein Deacetylases Biochemistry 2004, 43, 9877-9887 (Pubitemid 38993837)
    • (2004) Biochemistry , vol.43 , Issue.30 , pp. 9877-9887
    • Borra, M.T.1    Langer, M.R.2    Slama, J.T.3    Denu, J.M.4
  • 47
    • 0035917536 scopus 로고    scopus 로고
    • Crystal structure of a SIR2 homolog-NAD complex
    • DOI 10.1016/S0092-8674(01)00317-8
    • Min, J.; Landry, J.; Sternglanz, R.; Xu, R. M. Crystal Structure of a SIR2 Homolog-NAD Complex Cell 2001, 105, 269-279 (Pubitemid 32429516)
    • (2001) Cell , vol.105 , Issue.2 , pp. 269-279
    • Min, J.1    Landry, J.2    Sternglanz, R.3    Xu, R.-M.4
  • 48
    • 77953289094 scopus 로고    scopus 로고
    • Structural Basis for Sirtuin Function: What We Know and What We Don't
    • Sanders, B. D.; Jackson, B.; Marmorstein, R. Structural Basis for Sirtuin Function: What We Know and What We Don't Biochim. Biophys. Acta 2010, 1804, 1604-1616
    • (2010) Biochim. Biophys. Acta , vol.1804 , pp. 1604-1616
    • Sanders, B.D.1    Jackson, B.2    Marmorstein, R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.