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Volumn 2, Issue 14, 2011, Pages 1789-1793

Charge transfer and polarization in solvated proteins from Ab initio molecular dynamics

Author keywords

[No Author keywords available]

Indexed keywords

AB INITIO; AB INITIO MOLECULAR DYNAMICS; BORN-OPPENHEIMER MOLECULAR DYNAMICS; BOVINE PANCREATIC TRYPSIN INHIBITORS; DESKTOP COMPUTER; GASPHASE; GRAPHICAL PROCESSING UNITS; POLAR RESIDUES; POPULATION ANALYSIS; POSITIVE CHARGES; VORONOI; WATER MOLECULE;

EID: 79960742235     PISSN: None     EISSN: 19487185     Source Type: Journal    
DOI: 10.1021/jz200697c     Document Type: Article
Times cited : (126)

References (35)
  • 3
    • 0024287893 scopus 로고
    • The Effect of Water on Enzyme Action in Organic Media
    • Zaks, A.; Klibanov, A. M. The Effect of Water on Enzyme Action in Organic Media J. Biol. Chem. 1988, 263, 8017-8021
    • (1988) J. Biol. Chem. , vol.263 , pp. 8017-8021
    • Zaks, A.1    Klibanov, A.M.2
  • 4
    • 0024094768 scopus 로고
    • Accurate Simulation of Protein Dynamics in Solution
    • Levitt, M.; Sharon, R. Accurate Simulation of Protein Dynamics in Solution Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 7557-7561
    • (1988) Proc. Natl. Acad. Sci. U.S.A. , vol.85 , pp. 7557-7561
    • Levitt, M.1    Sharon, R.2
  • 5
    • 0030038545 scopus 로고    scopus 로고
    • Direct observation of protein solvation and discrete disorder with experimental crystallographic phases
    • Burling, F. T.; Weis, W. I.; Flaherty, K. M.; Brunger, A. T. Direct Observation of Protein Solvation and Discrete Disorder with Experimental Crystallographic Phases Science 1996, 271, 72-77 (Pubitemid 26033279)
    • (1996) Science , vol.271 , Issue.5245 , pp. 72-77
    • Burling, F.T.1    Weis, W.I.2    Flaherty, K.M.3    Brunger, A.T.4
  • 6
    • 24144479792 scopus 로고    scopus 로고
    • Solvation Free Energies of Amino Acid Side Chain Analogs for Common Molecular Mechanics Water Models
    • Shirts, M. R.; Pande, V. S. Solvation Free Energies of Amino Acid Side Chain Analogs for Common Molecular Mechanics Water Models J. Chem. Phys. 2005, 122, 134508
    • (2005) J. Chem. Phys. , vol.122 , pp. 134508
    • Shirts, M.R.1    Pande, V.S.2
  • 7
    • 33947405744 scopus 로고    scopus 로고
    • Solvation free energy of amino acids and side-chain analogues
    • DOI 10.1021/jp0620163
    • Chang, J.; Lenhoff, A. M.; Sandler, S. I. Solvation Free Energy of Amino Acids and Side-Chain Analogues J. Phys. Chem. B 2007, 111, 2098-2106 (Pubitemid 46456207)
    • (2007) Journal of Physical Chemistry B , vol.111 , Issue.8 , pp. 2098-2106
    • Chang, J.1    Lenhoff, A.M.2    Sandler, S.I.3
  • 8
    • 58449090034 scopus 로고    scopus 로고
    • Electron Donation in the Water-Water Hydrogen Bond
    • Khaliullin, R. Z.; Bell, A. T.; Head-Gordon, M. Electron Donation in the Water-Water Hydrogen Bond Chem.?-?Eur. J. 2009, 15, 851-855
    • (2009) Chem.?-?Eur. J. , vol.15 , pp. 851-855
    • Khaliullin, R.Z.1    Bell, A.T.2    Head-Gordon, M.3
  • 10
    • 0032503591 scopus 로고    scopus 로고
    • Charge-Transfer Interactions in Macromolecular Systems: A New View of the Protein/Water interface
    • Nadig, G.; Van Zant, L. C.; Dixon, S. L.; Merz, K. M. Charge-Transfer Interactions in Macromolecular Systems: A New View of the Protein/Water interface J. Am. Chem. Soc. 1998, 120, 5593-5594
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 5593-5594
    • Nadig, G.1    Van Zant, L.C.2    Dixon, S.L.3    Merz, K.M.4
  • 11
    • 0032833998 scopus 로고    scopus 로고
    • The Role of Polarization and Charge Transfer in the Solvation of Biomolecules
    • Van der Vaart, A.; Merz, K. M. The Role of Polarization and Charge Transfer in the Solvation of Biomolecules J. Am. Chem. Soc. 1999, 121, 9182-9190
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 9182-9190
    • Van Der Vaart, A.1    Merz, K.M.2
  • 12
    • 4043072686 scopus 로고    scopus 로고
    • Quantum descriptors for biological macromolecules from linear-scaling electronic structure methods
    • DOI 10.1002/prot.20171
    • Khandogin, J.; York, D. M. Quantum Descriptors for Biological Macromolecules from Linear-Scaling Electronic Structure Methods Proteins 2004, 56, 724-737 (Pubitemid 39063316)
    • (2004) Proteins: Structure, Function and Genetics , vol.56 , Issue.4 , pp. 724-737
    • Khandogin, J.1    York, D.M.2
  • 13
    • 34547317046 scopus 로고    scopus 로고
    • Change in a protein's electronic structure induced by an explicit solvent: An ab initio fragment molecular orbital study of ubiquitin
    • DOI 10.1002/jcc.20686
    • Komeiji, Y.; Ishida, T.; Fedorov, D. G.; Kitaura, K. Change in a Protein's Electronic Structure Induced by an Explicit Solvent: An Ab Initio Fragment Molecular Orbital Study of Ubiquitin J. Comput. Chem. 2007, 28, 1750-1762 (Pubitemid 47146551)
    • (2007) Journal of Computational Chemistry , vol.28 , Issue.10 , pp. 1750-1762
    • Komeiji, Y.1    Ishida, T.2    Fedorov, D.G.3    Kitaura, K.4
  • 14
    • 24944543136 scopus 로고    scopus 로고
    • Solute-solvent charge transfer in aqueous solution
    • DOI 10.1002/cphc.200500039
    • Dal Peraro, M.; Raugei, S.; Carloni, P.; Klein, M. L. Solute-Solvent Charge Transfer in Aqueous Solution ChemPhysChem 2005, 6, 1715-1718 (Pubitemid 41329980)
    • (2005) ChemPhysChem , vol.6 , Issue.9 , pp. 1715-1718
    • Dal Peraro, M.1    Raugei, S.2    Carloni, P.3    Klein, M.L.4
  • 15
    • 72849134374 scopus 로고    scopus 로고
    • Robust Periodic Hartree-Fock Exchange for Large-Scale Simulations Using Gaussian Basis Sets
    • Guidon, M.; Hutter, J.; VandeVondele, J. Robust Periodic Hartree-Fock Exchange for Large-Scale Simulations Using Gaussian Basis Sets J. Chem. Theory Comput. 2009, 5, 3010-3021
    • (2009) J. Chem. Theory Comput. , vol.5 , pp. 3010-3021
    • Guidon, M.1    Hutter, J.2    Vandevondele, J.3
  • 16
    • 51649102178 scopus 로고    scopus 로고
    • Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation
    • Ufimtsev, I. S.; Martinez, T. J. Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation J. Chem. Theory Comput. 2008, 4, 222-231
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 222-231
    • Ufimtsev, I.S.1    Martinez, T.J.2
  • 17
    • 65249137652 scopus 로고    scopus 로고
    • Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field Implementation
    • Ufimtsev, I. S.; Martinez, T. J. Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field Implementation J. Chem. Theory Comput 2009, 5, 1004-1015
    • (2009) J. Chem. Theory Comput , vol.5 , pp. 1004-1015
    • Ufimtsev, I.S.1    Martinez, T.J.2
  • 18
    • 73949083571 scopus 로고    scopus 로고
    • Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics
    • Ufimtsev, I. S.; Martinez, T. J. Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics J. Chem. Theory Comput. 2009, 5, 2619-2628
    • (2009) J. Chem. Theory Comput. , vol.5 , pp. 2619-2628
    • Ufimtsev, I.S.1    Martinez, T.J.2
  • 19
    • 79960706085 scopus 로고    scopus 로고
    • PetaChem. (accessed 6/1/11).
    • PetaChem. http://www.petachem.com (accessed 6/1/11).
  • 20
    • 36749024620 scopus 로고    scopus 로고
    • Polarizable Force Fields: History, Test Cases, and Prospects
    • Warshel, A.; Kato, M.; Pisliakov, A. V. Polarizable Force Fields: History, Test Cases, and Prospects J. Chem. Theory Comput. 2007, 3, 2034-2045
    • (2007) J. Chem. Theory Comput. , vol.3 , pp. 2034-2045
    • Warshel, A.1    Kato, M.2    Pisliakov, A.V.3
  • 22
    • 25844474073 scopus 로고    scopus 로고
    • Accounting for polarization in molecular simulation
    • DOI 10.1016/j.cpc.2005.01.022, PII S0010465505003772
    • Yu, H. B.; van Gunsteren, W. F. Accounting for Polarization in Molecular Simulation Comput. Phys. Commun. 2005, 172, 69-85 (Pubitemid 41400670)
    • (2005) Computer Physics Communications , vol.172 , Issue.2 , pp. 69-85
    • Yu, H.1    Van Gunsteren, W.F.2
  • 23
    • 0016610491 scopus 로고
    • Computer Simulations of Protein Folding
    • Levitt, M.; Warshel, A. Computer Simulations of Protein Folding Nature 1975, 253, 694-698
    • (1975) Nature , vol.253 , pp. 694-698
    • Levitt, M.1    Warshel, A.2
  • 24
  • 25
    • 0017100947 scopus 로고
    • Theoretical Studies of Enzymic Reactions
    • Warshel, A.; Levitt, M. Theoretical Studies of Enzymic Reactions J. Mol. Biol. 1976, 103, 227-249
    • (1976) J. Mol. Biol. , vol.103 , pp. 227-249
    • Warshel, A.1    Levitt, M.2
  • 26
    • 21244497608 scopus 로고    scopus 로고
    • Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis
    • DOI 10.1146/annurev.physchem.55.091602.094410
    • Friesner, R. A.; Guallar, V. Ab Initio Quantum Chemical and Mixed Quantum Mechanics/Molecular Mechanics (QM/MM) Methods for Studying Enzymic Catalysis Annu. Rev. Phys. Chem. 2005, 56, 389-427 (Pubitemid 41156883)
    • (2005) Annual Review of Physical Chemistry , vol.56 , pp. 389-427
    • Friesner, R.A.1    Guallar, V.2
  • 27
    • 0033654137 scopus 로고    scopus 로고
    • Peptide and Proteins in the Vapor Phase
    • Jarrold, M. F. Peptide and Proteins in the Vapor Phase Annu. Rev. Phys. Chem. 2000, 51, 179-207
    • (2000) Annu. Rev. Phys. Chem. , vol.51 , pp. 179-207
    • Jarrold, M.F.1
  • 28
    • 0031568682 scopus 로고    scopus 로고
    • Using Protein Charge Ladders to Estimate the Effective Charges and Molecular Weights of Proteins in Solution
    • Gao, J.; Whitesides, G. M. Using Protein Charge Ladders to Estimate the Effective Charges and Molecular Weights of Proteins in Solution Anal. Chem. 1997, 69, 575-580
    • (1997) Anal. Chem. , vol.69 , pp. 575-580
    • Gao, J.1    Whitesides, G.M.2
  • 31
    • 49449097052 scopus 로고    scopus 로고
    • Insights into Current Limitations of Density Functional theory
    • Cohen, A. J.; Mori-Sanchez, P.; Yang, W. T. Insights into Current Limitations of Density Functional theory Science 2008, 321, 792-794
    • (2008) Science , vol.321 , pp. 792-794
    • Cohen, A.J.1    Mori-Sanchez, P.2    Yang, W.T.3
  • 33
    • 0346341238 scopus 로고    scopus 로고
    • Voronoi Deformation Density (VDD) Charges: Assessment of the Mulliken, Bader, Hirshfeld, Weinhold, and VDD Methods for Charge Analysis
    • Guerra, C. F.; Handgraaf, J. W.; Baerends, E. J.; Bickelhaupt, F. M. Voronoi Deformation Density (VDD) Charges: Assessment of the Mulliken, Bader, Hirshfeld, Weinhold, And VDD Methods for Charge Analysis J. Comput. Chem. 2004, 25, 210
    • (2004) J. Comput. Chem. , vol.25 , pp. 210
    • Guerra, C.F.1    Handgraaf, J.W.2    Baerends, E.J.3    Bickelhaupt, F.M.4
  • 34
    • 47249085107 scopus 로고    scopus 로고
    • The Variational Explicit Polarization Potential and Analytical First Derivative of Energy: Towards a Next Generation Force Field
    • Xie, W. S.; Song, L. C.; Truhlar, D. G.; Gao, J. L. The Variational Explicit Polarization Potential and Analytical First Derivative of Energy: Towards a Next Generation Force Field J. Chem. Phys. 2008, 128, 234108
    • (2008) J. Chem. Phys. , vol.128 , pp. 234108
    • Xie, W.S.1    Song, L.C.2    Truhlar, D.G.3    Gao, J.L.4
  • 35
    • 77449118147 scopus 로고    scopus 로고
    • Quantum Mechanical Dynamics of Charge Transfer in Ubiquitin in Aqueous Solution
    • Anisimov, V. M.; Bugaenko, V. L.; Cavasotto, C. N. Quantum Mechanical Dynamics of Charge Transfer in Ubiquitin in Aqueous Solution ChemPhysChem 2009, 10, 3194-3196
    • (2009) ChemPhysChem , vol.10 , pp. 3194-3196
    • Anisimov, V.M.1    Bugaenko, V.L.2    Cavasotto, C.N.3


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