메뉴 건너뛰기




Volumn 119, Issue 12, 2015, Pages 4371-4381

Exploring reaction pathways for O -GlcNAc transferase catalysis. A string method study

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; FREE ENERGY; MOLECULAR DYNAMICS; MOLECULAR MODELING; MOLECULES; QUANTUM THEORY;

EID: 84925945606     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp511235f     Document Type: Article
Times cited : (27)

References (40)
  • 1
    • 84963958337 scopus 로고    scopus 로고
    • Atomistic Insight into the Catalytic Mechanism of Glycosyltransferases by Combined Quantum Mechanics/molecular Mechanics (QM/MM) Methods
    • Tvaroska, I. Atomistic Insight into the Catalytic Mechanism of Glycosyltransferases by Combined Quantum Mechanics/molecular Mechanics (QM/MM) Methods Carbohydr. Res. 2015, 403, 38-47
    • (2015) Carbohydr. Res. , vol.403 , pp. 38-47
    • Tvaroska, I.1
  • 2
    • 84867747900 scopus 로고    scopus 로고
    • Recent Structures, Evolution and Mechanisms of Glycosyltransferases
    • Breton, C.; Fournel-Gigleux, S.; Palcic, M. M. Recent Structures, Evolution and Mechanisms of Glycosyltransferases Curr. Opin. Struct. Biol. 2012, 22, 540-549
    • (2012) Curr. Opin. Struct. Biol. , vol.22 , pp. 540-549
    • Breton, C.1    Fournel-Gigleux, S.2    Palcic, M.M.3
  • 4
    • 70449590867 scopus 로고    scopus 로고
    • Discovery and Classification of Glycan-Binding Proteins
    • 2 nd ed. Varki, A. Cummings, R. D. Esko, J. D. Freeze, H. H. Stanley, P. Bertozzi, C. R. Hart, G. W. Etzler, M. E. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, New York
    • Varki, A.; Etzler, M. E.; Cummings, R. D.; Esko, J. D. Discovery and Classification of Glycan-Binding Proteins. In Essentials of Glycobiology, 2 nd ed.; Varki, A.; Cummings, R. D.; Esko, J. D.; Freeze, H. H.; Stanley, P.; Bertozzi, C. R.; Hart, G. W.; Etzler, M. E., Eds.; Cold Spring Harbor Laboratory Press: Cold Spring Harbor, New York, 2009.
    • (2009) Essentials of Glycobiology
    • Varki, A.1    Etzler, M.E.2    Cummings, R.D.3    Esko, J.D.4
  • 5
    • 79959381299 scopus 로고    scopus 로고
    • Cross Talk between O-GlcNAcylation and Phosphorylation: Roles in Signaling, Transcription, and Chronic Disease
    • Hart, G. W.; Slawson, C.; Ramirez-Correa, G.; Lagerlof, O. Cross Talk Between O-GlcNAcylation and Phosphorylation: Roles in Signaling, Transcription, and Chronic Disease Annu. Rev. Biochem. 2011, 80, 825-858
    • (2011) Annu. Rev. Biochem. , vol.80 , pp. 825-858
    • Hart, G.W.1    Slawson, C.2    Ramirez-Correa, G.3    Lagerlof, O.4
  • 7
    • 0034705030 scopus 로고    scopus 로고
    • The O-GlcNAc Transferase Gene Resides on the X Chromosome and Is Essential for Embryonic Stem Cell Viability and Mouse Ontogeny
    • Shafi, R.; Lyer, S. P. N.; Ellies, L. G.; ODonnell, N.; Marek, K. W.; Chui, D.; Hart, G. W.; Marth, J. D. The O-GlcNAc Transferase Gene Resides on the X Chromosome and Is Essential for Embryonic Stem Cell Viability and Mouse Ontogeny Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 5735-5739
    • (2000) Proc. Natl. Acad. Sci. U.S.A. , vol.97 , pp. 5735-5739
    • Shafi, R.1    Lyer, S.P.N.2    Ellies, L.G.3    Odonnell, N.4    Marek, K.W.5    Chui, D.6    Hart, G.W.7    Marth, J.D.8
  • 9
    • 34247583996 scopus 로고    scopus 로고
    • Cycling of O-Linked Beta-N-Acetylglucosamine on Nucleocytoplasmic Proteins
    • Hart, G. W.; Housley, M. P.; Slawson, C. Cycling of O-Linked Beta-N-Acetylglucosamine on Nucleocytoplasmic Proteins Nature 2007, 446, 1017-1022
    • (2007) Nature , vol.446 , pp. 1017-1022
    • Hart, G.W.1    Housley, M.P.2    Slawson, C.3
  • 10
    • 84858630824 scopus 로고    scopus 로고
    • Neurodegeneration: Recall Sugars, Forget Alzheimers
    • Lefebvre, T. Neurodegeneration: Recall Sugars, Forget Alzheimers Nat. Chem. Biol. 2012, 8, 325-326
    • (2012) Nat. Chem. Biol. , vol.8 , pp. 325-326
    • Lefebvre, T.1
  • 12
    • 0035171364 scopus 로고    scopus 로고
    • Carbohydrate Mimetics-Based Glycosyltransferase Inhibitors
    • Compain, P.; Martin, O. R. Carbohydrate Mimetics-Based Glycosyltransferase Inhibitors Bioorg. Med. Chem. 2001, 9, 3077-3092
    • (2001) Bioorg. Med. Chem. , vol.9 , pp. 3077-3092
    • Compain, P.1    Martin, O.R.2
  • 13
    • 79251611901 scopus 로고    scopus 로고
    • Structure of Human O-GlcNAc Transferase and Its Complex with a Peptide Substrate
    • Lazarus, M. B.; Nam, Y.; Jiang, J.; Sliz, P.; Walker, S. Structure of Human O-GlcNAc Transferase and Its Complex with a Peptide Substrate Nature 2011, 469, 564-U168
    • (2011) Nature , vol.469 , pp. 564-U168
    • Lazarus, M.B.1    Nam, Y.2    Jiang, J.3    Sliz, P.4    Walker, S.5
  • 16
    • 84866522320 scopus 로고    scopus 로고
    • Substrate-Assisted Catalytic Mechanism of O-GIcNAc Transferase Discovered by Quantum Mechanics/Molecular Mechanics Investigation
    • Tvaroska, I.; Kozmon, S.; Wimmerova, M.; Koca, J. Substrate-Assisted Catalytic Mechanism of O-GIcNAc Transferase Discovered by Quantum Mechanics/Molecular Mechanics Investigation J. Am. Chem. Soc. 2012, 134, 15563-15571
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 15563-15571
    • Tvaroska, I.1    Kozmon, S.2    Wimmerova, M.3    Koca, J.4
  • 17
    • 0036696910 scopus 로고    scopus 로고
    • String Method for the Study of Rare Events
    • Weinan, E.; Ren, W. Q.; Vanden-Eijnden, E. String Method for the Study of Rare Events Phys. Rev. B 2002, 66, 052301
    • (2002) Phys. Rev. B , vol.66 , pp. 052301
    • Weinan, E.1    Ren, W.Q.2    Vanden-Eijnden, E.3
  • 18
    • 33746255471 scopus 로고    scopus 로고
    • String Method in Collective Variables: Minimum Free Energy Paths and Isocommittor Surfaces
    • Maragliano, L.; Fischer, A.; Vanden-Eijnden, E.; Ciccotti, G. String Method in Collective Variables: Minimum Free Energy Paths and Isocommittor Surfaces J. Chem. Phys. 2006, 125, 024106
    • (2006) J. Chem. Phys. , vol.125 , pp. 024106
    • Maragliano, L.1    Fischer, A.2    Vanden-Eijnden, E.3    Ciccotti, G.4
  • 19
    • 17544365232 scopus 로고    scopus 로고
    • Finite Temperature String Method for the Study of Rare Events
    • Weinan, E.; Ren, W. Q.; Vanden-Eijnden, E. Finite Temperature String Method for the Study of Rare Events J. Phys. Chem. B 2005, 109, 6688-6693
    • (2005) J. Phys. Chem. B , vol.109 , pp. 6688-6693
    • Weinan, E.1    Ren, W.Q.2    Vanden-Eijnden, E.3
  • 20
    • 84871387422 scopus 로고    scopus 로고
    • Theoretical Study of the Mechanism of the Hydride Transfer between Ferredoxin-NADP(+) Reductase and NADP(+): The Role of Tyr303
    • Lans, I.; Medina, M.; Rosta, E.; Hummer, G.; Garcia-Viloca, M.; Lluch, J. M.; Gonzalez-Lafont, A. Theoretical Study of the Mechanism of the Hydride Transfer between Ferredoxin-NADP(+) Reductase and NADP(+): The Role of Tyr303 J. Am. Chem. Soc. 2012, 134, 20544-20553
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 20544-20553
    • Lans, I.1    Medina, M.2    Rosta, E.3    Hummer, G.4    Garcia-Viloca, M.5    Lluch, J.M.6    Gonzalez-Lafont, A.7
  • 21
    • 79958776843 scopus 로고    scopus 로고
    • Catalytic Mechanism of RNA Backbone Cleavage by Ribonuclease H from Quantum Mechanics/Molecular Mechanics Simulations
    • Rosta, E.; Nowotny, M.; Yang, W.; Hummer, G. Catalytic Mechanism of RNA Backbone Cleavage by Ribonuclease H from Quantum Mechanics/Molecular Mechanics Simulations J. Am. Chem. Soc. 2011, 133, 8934-8941
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 8934-8941
    • Rosta, E.1    Nowotny, M.2    Yang, W.3    Hummer, G.4
  • 22
    • 84893445982 scopus 로고    scopus 로고
    • Quantum Mechanical/Molecular Mechanical Free Energy Simulations of the Self-Cleavage Reaction in the Hepatitis Delta Virus Ribozyme
    • Ganguly, A.; Thaplyal, P.; Rosta, E.; Bevilacqua, P. C.; Hammes-Schiffer, S. Quantum Mechanical/Molecular Mechanical Free Energy Simulations of the Self-Cleavage Reaction in the Hepatitis Delta Virus Ribozyme J. Am. Chem. Soc. 2014, 136, 1483-1496
    • (2014) J. Am. Chem. Soc. , vol.136 , pp. 1483-1496
    • Ganguly, A.1    Thaplyal, P.2    Rosta, E.3    Bevilacqua, P.C.4    Hammes-Schiffer, S.5
  • 23
    • 1242329035 scopus 로고    scopus 로고
    • Improved Tangent Estimate in the Nudged Elastic Band Method for Finding Minimum Energy Paths and Saddle Points
    • Henkelman, G.; Jonsson, H. Improved Tangent Estimate in the Nudged Elastic Band Method for Finding Minimum Energy Paths and Saddle Points J. Chem. Phys. 2000, 113, 9978-9985
    • (2000) J. Chem. Phys. , vol.113 , pp. 9978-9985
    • Henkelman, G.1    Jonsson, H.2
  • 24
    • 83655163673 scopus 로고    scopus 로고
    • A Neutral Diphosphate Mimic Crosslinks the Active Site of Human O-GlcNAc Transferase
    • Jiang, J.; Lazarus, M. B.; Pasquina, L.; Sliz, P.; Walker, S. A Neutral Diphosphate Mimic Crosslinks the Active Site of Human O-GlcNAc Transferase Nat. Chem. Biol. 2012, 8, 72-77
    • (2012) Nat. Chem. Biol. , vol.8 , pp. 72-77
    • Jiang, J.1    Lazarus, M.B.2    Pasquina, L.3    Sliz, P.4    Walker, S.5
  • 25
    • 0027136282 scopus 로고
    • Comparative Protein Modeling by Satisfaction of Spatial Restraints
    • Sali, A.; Blundell, T. Comparative Protein Modeling by Satisfaction of Spatial Restraints J. Mol. Biol. 1993, 234, 779-815
    • (1993) J. Mol. Biol. , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.2
  • 26
    • 84880529288 scopus 로고    scopus 로고
    • Protein and Ligand Preparation: Parameters, Protocols, and Influence on Virtual Screening Enrichments
    • Sastry, G. M.; Adzhigirey, M.; Day, T.; Annabhimoju, R.; Sherman, W. Protein and Ligand Preparation: Parameters, Protocols, and Influence on Virtual Screening Enrichments J. Comput. Aided Mol. Des. 2013, 27, 221-234
    • (2013) J. Comput. Aided Mol. Des. , vol.27 , pp. 221-234
    • Sastry, G.M.1    Adzhigirey, M.2    Day, T.3    Annabhimoju, R.4    Sherman, W.5
  • 28
    • 84925969237 scopus 로고    scopus 로고
    • Schrodinger, LLC: New York, NY
    • Epik; Schrodinger, LLC: New York, NY, 2013.
    • (2013) Epik
  • 29
    • 84925947110 scopus 로고    scopus 로고
    • Schrodinger, LLC: New York, NY
    • Impact; Schrodinger, LLC: New York, NY, 2013.
    • (2013) Impact
  • 30
    • 84925941050 scopus 로고    scopus 로고
    • Schrodinger, LLC: New York, NY
    • Prime; Schrodinger, LLC: New York, NY, 2013.
    • (2013) Prime
  • 31
    • 84925946752 scopus 로고    scopus 로고
    • Schrodinger, LLC: New York, NY
    • Maestro; Schrodinger, LLC: New York, NY, 2013.
    • (2013) Maestro
  • 32
    • 84922370903 scopus 로고    scopus 로고
    • Schrodinger, LLC: New York, NY
    • Schrodinger Suite; Schrodinger, LLC: New York, NY, 2013.
    • (2013) Schrodinger Suite
  • 33
    • 79960258119 scopus 로고    scopus 로고
    • Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pK(a) Values
    • Sondergaard, C. R.; Olsson, M. H. M.; Rostkowski, M.; Jensen, J. H. Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pK(a) Values J. Chem. Theory Comput. 2011, 7, 2284-2295
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 2284-2295
    • Sondergaard, C.R.1    Olsson, M.H.M.2    Rostkowski, M.3    Jensen, J.H.4
  • 34
    • 28644432877 scopus 로고    scopus 로고
    • Very Fast Empirical Prediction and Rationalization of Protein pKa Values
    • Li, H.; Robertson, A. D.; Jensen, J. H. Very Fast Empirical Prediction and Rationalization of Protein pKa Values Proteins 2005, 61, 704-721
    • (2005) Proteins , vol.61 , pp. 704-721
    • Li, H.1    Robertson, A.D.2    Jensen, J.H.3
  • 36
    • 84925943516 scopus 로고    scopus 로고
    • Copyright IBM Corp 1990-2008, Copyright MPI fur Festkorperforschung Stuttgart
    • CPMD; Copyright IBM Corp 1990-2008, Copyright MPI fur Festkorperforschung Stuttgart 1997-2001.
    • (1997) CPMD
  • 37
    • 0037156101 scopus 로고    scopus 로고
    • A Hamiltonian Electrostatic Coupling Scheme for Hybrid Car-Parrinello Molecular Dynamics Simulations
    • Laio, A.; VandeVondele, J.; Rothlisberger, U. A Hamiltonian Electrostatic Coupling Scheme for Hybrid Car-Parrinello Molecular Dynamics Simulations J. Chem. Phys. 2002, 116, 6941-6947
    • (2002) J. Chem. Phys. , vol.116 , pp. 6941-6947
    • Laio, A.1    Vandevondele, J.2    Rothlisberger, U.3
  • 38
    • 4243943295 scopus 로고    scopus 로고
    • Generalized Gradient Approximation Made Simple
    • Perdew, J. P.; Burke, K.; Ernzerhof, M. Generalized Gradient Approximation Made Simple Phys. Rev. Lett. 1996, 77, 3865-3868
    • (1996) Phys. Rev. Lett. , vol.77 , pp. 3865-3868
    • Perdew, J.P.1    Burke, K.2    Ernzerhof, M.3
  • 40
    • 1842692143 scopus 로고
    • General Definition of Ring Puckering Coordinates
    • Cremer, D.; Pople, J. General Definition of Ring Puckering Coordinates J. Am. Chem. Soc. 1975, 97, 1354-1358
    • (1975) J. Am. Chem. Soc. , vol.97 , pp. 1354-1358
    • Cremer, D.1    Pople, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.