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Volumn , Issue , 2010, Pages 197-205

Reaction path analysis for demethylation process of histone tail lysine residues

Author keywords

Chemical reaction mechanism; Density Functional Theory (DFT); Energy profile; Histone tail; LSD1; Lysine demethylation; Post translational modifications; Quantum mechanical calculations

Indexed keywords

DEMETHYLASE; DEMETHYLATION; DRUG MOLECULES; ENERGY PROFILE; HISTONE PROTEINS; INHIBITOR MOLECULES; LYSINE RESIDUES; POST-TRANSLATIONAL MODIFICATIONS; QUANTUM MECHANICAL METHOD; QUANTUM-MECHANICAL CALCULATION; REACTION MECHANISM; REACTION PATH ANALYSIS; REGULATORY PROCESS; SEMI-EMPIRICAL;

EID: 77954529626     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/HIBIT.2010.5478882     Document Type: Conference Paper
Times cited : (1)

References (38)
  • 1
    • 31944437048 scopus 로고    scopus 로고
    • Catalytic Mechanism, and Product Specifity of the Histone Lysine Methyltransferase SET7/9: Ab inito QM/MM-FE Study with Multiple Initial Structures
    • P. Hu and Y. Zhang, "Catalytic Mechanism, and Product Specifity of the Histone Lysine Methyltransferase SET7/9: Ab inito QM/MM-FE Study with Multiple Initial Structures", J.Am.Chem.Soc. vol. 128, pp. 1272-1278, 2006
    • (2006) J.Am.Chem.Soc. , vol.128 , pp. 1272-1278
    • Hu, P.1    Zhang, Y.2
  • 3
    • 35348812522 scopus 로고    scopus 로고
    • LSDl and the chemistry of histone demethylation
    • Sep.
    • J. C. Culhane and P. A. Cole, "LSDl and the chemistry of histone demethylation", Current Opinion in Chem. Biol., vol. 11, pp. 561-588, Sep. 2007
    • (2007) Current Opinion in Chem. Biol. , vol.11 , pp. 561-588
    • Culhane, J.C.1    Cole, P.A.2
  • 4
    • 33846025127 scopus 로고    scopus 로고
    • Dynamic regulation of histone lysine methylation by demethylases
    • Jan.
    • Y. Shi and J. R. Whetstine, "Dynamic Regulation of Histone Lysine Methylation by Demethylases", Molecular Cell, vol. 25, pp. 1-14, Jan. 2007
    • (2007) Molecular Cell , vol.25 , pp. 1-14
    • Shi, Y.1    Whetstine, J.R.2
  • 5
    • 0015912073 scopus 로고
    • Enzymatic demethylation of calf thymus histones
    • W. K. Paik and S. Kim, "Enzymatic demethylation of calf thymus histones", Biochem, Biophys. Res. Commun., vol. 51, pp.781-788, 1973.
    • (1973) Biochem, Biophys. Res. Commun. , vol.51 , pp. 781-788
    • Paik, W.K.1    Kim, S.2
  • 6
    • 34447338875 scopus 로고    scopus 로고
    • Structural basis for the inhibiton of the LSD1 histone demethylase by the antidepressant trans-2phenylcyclopropylamine
    • May
    • M. Yang, J. C. Culhane, L. M. Szewczuk, P. Jalili, H.L. Ball, M. Machius, P. A. Cole and H. Yu, "Structural Basis for the Inhibiton of the LSD1 Histone Demethylase by the Antidepressant trans-2Phenylcyclopropylamine", Biochemistry, vol. 46, pp. 8058-8065, May 2007.
    • (2007) Biochemistry , vol.46 , pp. 8058-8065
    • Yang, M.1    Culhane, J.C.2    Szewczuk, L.M.3    Jalili, P.4    Ball, H.L.5    Machius, M.6    Cole, P.A.7    Yu, H.8
  • 7
    • 11144332565 scopus 로고    scopus 로고
    • Histone demethylation mediated by the nuclear amine oxidase homolog LSD1
    • Dec.
    • Y. Shi, F. Lan, C. Matson, P. Mulligan, J. R. Whetstine, P. A. Cole, R. A. Casero and Y. Shi, "Histone Demethylation Mediated by the Nuclear Amine Oxidase Homolog LSD1", Cell, vol. 119, pp. 941-953, Dec. 2004.
    • (2004) Cell , vol.119 , pp. 941-953
    • Shi, Y.1    Lan, F.2    Matson, C.3    Mulligan, P.4    Whetstine, J.R.5    Cole, P.A.6    Casero, R.A.7    Shi, Y.8
  • 8
    • 0036299092 scopus 로고    scopus 로고
    • The histone variant H3.3 marks active chromatin by replication- independent nucleosome assembly
    • K. Ahmad, S. Henikoff, "The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly", Mol. Cell, vol. 9, pp. 1191-1200, 2002.
    • (2002) Mol. Cell , vol.9 , pp. 1191-1200
    • Ahmad, K.1    Henikoff, S.2
  • 9
    • 0018903045 scopus 로고
    • Proteolytic processing of histone H3 in chromatin: A physiologically regulated event in Tetrahymena micronuclei
    • C. D. Allis, J. K. Bowen, G. N. Abraham, C. V. Glover, and M. A. Gorovsky, "Proteolytic processing of histone H3 in chromatin: a physiologically regulated event in Tetrahymena micronuclei", Cell, vol. 20, pp.55-64, 1980.
    • (1980) Cell , vol.20 , pp. 55-64
    • Allis, C.D.1    Bowen, J.K.2    Abraham, G.N.3    Glover, C.V.4    Gorovsky, M.A.5
  • 10
    • 0035893240 scopus 로고    scopus 로고
    • Histone H3 lysine 4 methylation is mediated by Set1 and required for cell growth and rDNA silencing in Saccharomyces cerevisiae
    • S. D. Briggs, M. Bryk, B. D. Strahl, W. L. Cheung, J. K. Davie, S. Y. Dent, F. Winston and C. D. Allis, "Histone H3 lysine 4 methylation is mediated by Set1 and required for cell growth and rDNA silencing in Saccharomyces cerevisiae", Genes Dev., vol. 15, pp. 3286-3295, 2001.
    • (2001) Genes Dev. , vol.15 , pp. 3286-3295
    • Briggs, S.D.1    Bryk, M.2    Strahl, B.D.3    Cheung, W.L.4    Davie, J.K.5    Dent, S.Y.6    Winston, F.7    Allis, C.D.8
  • 12
    • 0037188911 scopus 로고    scopus 로고
    • Histone methylation: Dynamic or static?
    • Jun.
    • A. J. Bannister, R. Schneider, and T. Kouzarides, "Histone Methylation: Dynamic or Static?", Cell, vol. 109, pp. 801-806, Jun. 2002.
    • (2002) Cell , vol.109 , pp. 801-806
    • Bannister, A.J.1    Schneider, R.2    Kouzarides, T.3
  • 13
    • 0015296118 scopus 로고
    • The distribution of turnover of labelled methyl groups in histone fractions of cultured mammalian cells
    • P. Byvoet, G. R. Shepherd, J. M. Hardin and B. J. Noland,"The distribution of turnover of labelled methyl groups in histone fractions of cultured mammalian cells", Arch. Biochem. Biophys., vol.148, pp. 558-567, 1972.
    • (1972) Arch. Biochem. Biophys. , vol.148 , pp. 558-567
    • Byvoet, P.1    Shepherd, G.R.2    Hardin, J.M.3    Noland, B.J.4
  • 14
    • 0016271161 scopus 로고
    • In vivo öethylation and turnover of rat brain histones
    • A. J. Duerre, and C. T. Lee, "In vivo öethylation and turnover of rat brain histones", J. Neurochem, vol. 23, pp.541-547, 1974.
    • (1974) J. Neurochem , vol.23 , pp. 541-547
    • Duerre, A.J.1    Lee, C.T.2
  • 16
    • 0036168865 scopus 로고    scopus 로고
    • Methylation at arginine 17 of histone H3 is linked to gene activation
    • U. M. Bauer, S. Daujat, S. J. Neilsen, K. Nightingale and T. Kouzarides, "Methylation at arginine 17 of histone H3 is linked to gene activation", EMBO Rep., vol. 3, pp. 3944, 2002.
    • (2002) EMBO Rep. , vol.3 , pp. 3944
    • Bauer, U.M.1    Daujat, S.2    Neilsen, S.J.3    Nightingale, K.4    Kouzarides, T.5
  • 18
    • 59349115177 scopus 로고    scopus 로고
    • Chemical mechanisms of histone lysine and arginine modifications
    • June
    • B. C.: Smith, J. M. Denu, "Chemical mechanisms of histone lysine and arginine modifications", Biochemica et Biophysica Acta, vol. 1789, pp. 45-57, June 2008.
    • (2008) Biochemica et Biophysica Acta , vol.1789 , pp. 45-57
    • Smith, B.C.1    Denu, J.M.2
  • 20
    • 33745862395 scopus 로고    scopus 로고
    • Crystal structure and mechanism of human lysine-specific demethylase-1
    • July
    • P. Stavropoulos, G. Blobel and A. Hoelz, "Crystal structure and mechanism of human lysine-specific demethylase-1", Nature Structural & Molecular Biology, vol. 13, pp. 626-632, July 2006.
    • (2006) Nature Structural & Molecular Biology , vol.13 , pp. 626-632
    • Stavropoulos, P.1    Blobel, G.2    Hoelz, A.3
  • 21
    • 32544432876 scopus 로고    scopus 로고
    • A computational study on the amine-oxidation mechanism of monoamine oxidase: Insight into the polar nucleophilic mechanism
    • Jan.
    • S. Erdem, O. Karahan, I. Yildiz and K. Yelekci, "A computational study on the amine-oxidation mechanism of monoamine oxidase: Insight into the polar nucleophilic mechanism", Organic & Biomolecular Chemistry, vol.4, pp. 646-658, Jan. 2006.
    • (2006) Organic & Biomolecular Chemistry , vol.4 , pp. 646-658
    • Erdem, S.1    Karahan, O.2    Yildiz, I.3    Yelekci, K.4
  • 27
    • 34547132094 scopus 로고    scopus 로고
    • Structural basis of LSD1 -CoREST selectivity in histone H3 recognition
    • July
    • F. Fomeris, C. Binda, A. Adamo, E. Battaglioli and A. Mattevi, "Structural Basis of LSD1 -CoREST Selectivity in Histone H3 Recognition", J. Biol. Chem. vol. 282, pp. 20070-20074, July 2007.
    • (2007) J. Biol. Chem. , vol.282 , pp. 20070-20074
    • Fomeris, F.1    Binda, C.2    Adamo, A.3    Battaglioli, E.4    Mattevi, A.5
  • 28
    • 24944535335 scopus 로고    scopus 로고
    • Regulation of LSD1 histone demethylase activity by its associated factors
    • Sept.
    • Y.-J. Shi, C. Matson, F. Lan, S. Iwase, T. Baba and Y. Shi, "Regulation of LSD1 Histone Demethylase Activity by Its Associated Factors", Molecular Cell, vol. 19, pp. 857-864, Sept. 2005.
    • (2005) Molecular Cell , vol.19 , pp. 857-864
    • Shi, Y.-J.1    Matson, C.2    Lan, F.3    Iwase, S.4    Baba, T.5    Shi, Y.6
  • 29
    • 34250203607 scopus 로고    scopus 로고
    • Mechanistic analysis of a suicide inactivator of histone demethylase LSD1
    • June
    • L. M. Szewczuk, J. C. Culhane, M. Yang, A. Majumdar, H. Yu and P. A. Cole, "Mechanistic Analysis of a Suicide Inactivator of Histone Demethylase LSD1", Biochemistry, vol. 46(23), pp. 6892-6902, June 2007.
    • (2007) Biochemistry , vol.46 , Issue.23 , pp. 6892-6902
    • Szewczuk, L.M.1    Culhane, J.C.2    Yang, M.3    Majumdar, A.4    Yu, H.5    Cole, P.A.6
  • 30
    • 34147173308 scopus 로고    scopus 로고
    • Trans-2phenylcyclopropylamine is a mechanism-based inactivator of the histone demethylase LSD1
    • Jan.
    • D. M. Z. Schmidt and D. G. McCafferty, "trans- 2Phenylcyclopropylamine is a Mechanism-Based Inactivator of the Histone Demethylase LSD1", Biochemistry, vol. 46, pp.4408-4416, Jan. 2007.
    • (2007) Biochemistry , vol.46 , pp. 4408-4416
    • Schmidt, D.M.Z.1    McCafferty, D.G.2
  • 32
    • 34250792398 scopus 로고    scopus 로고
    • Docking of novel reversible monoamine oxidase-B inhibitors: Efficent prediction of ligand binding sites and estimation of inhibitors thermodynamic properties
    • Dec.
    • K. Yelekci, O. Karahan, M. Toprakci, "Docking of novel reversible monoamine oxidase-B inhibitors: Efficent prediction of ligand binding sites and estimation of inhibitors thermodynamic properties", J. Neural Transm, vol. 114, pp. 725-732, Dec. 2006.
    • (2006) J. Neural Transm , vol.114 , pp. 725-732
    • Yelekci, K.1    Karahan, O.2    Toprakci, M.3
  • 33
    • 33748989795 scopus 로고    scopus 로고
    • Crystal structure of human histone lysine-specific demethylase 1 (LSD1)
    • Sept.
    • Y. Chen, Y. Yang, F. Wang, K. Wan, K. Yamane, Y. Zhang and M. Lei, "Crystal structure of human histone lysine-specific demethylase 1 (LSD1)", PNAS, vol. 103, pp. 13956-13961, Sept. 2006.
    • (2006) PNAS , vol.103 , pp. 13956-13961
    • Chen, Y.1    Yang, Y.2    Wang, F.3    Wan, K.4    Yamane, K.5    Zhang, Y.6    Lei, M.7
  • 36
    • 0000189651 scopus 로고
    • B3LYP
    • D. Becke, "B3LYP", J. Chem. Phys., vol. 98, pp. 5648, 1993.
    • (1993) J. Chem. Phys. , vol.98 , pp. 5648
    • Becke, D.1
  • 37
    • 39449102395 scopus 로고    scopus 로고
    • Computational enzymology: Modelling the mechanisms of biological catalysts
    • A. J. Mulholland, "Computational enzymology: modelling the mechanisms of biological catalysts", Biochemical Society Transactions", vol. 36, pp.22-26, 2008.
    • (2008) Biochemical Society Transactions , vol.36 , pp. 22-26
    • Mulholland, A.J.1
  • 38
    • 34547433238 scopus 로고    scopus 로고
    • Mechanism of histone methylation catalyzed by protein lysine methyltransferase SET7/9 and origin of product specificity
    • May
    • H.-B. Guo, and H. Guo, "Mechanism of histone methylation catalyzed by protein lysine methyltransferase SET7/9 and origin of product specificity", PNAS, vol. 104, pp.8797-8802, May 2007.
    • (2007) PNAS , vol.104 , pp. 8797-8802
    • Guo, H.-B.1    Guo, H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.