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Volumn 114, Issue 40, 2010, Pages 12811-12824

Simulations of a protein crystal with a high resolution X-ray structure: Evaluation of force fields and water models

Author keywords

[No Author keywords available]

Indexed keywords

CRYSTAL ATOMIC STRUCTURE; DIFFRACTION; HYDROGEN BONDS; HYDROPHOBICITY; MOLECULAR DYNAMICS; PROTEINS; THERMODYNAMICS; X RAY DIFFRACTION; X RAYS;

EID: 77957835014     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp105813j     Document Type: Article
Times cited : (72)

References (45)
  • 1
    • 77949359890 scopus 로고    scopus 로고
    • Enhancement of hydrophobic interactions and hydrogen bond strength by cooperativity: Synthesis, modeling, and molecular dynamics simulations of a congeneric series of thrombin inhibitors
    • Muley, L.; Baum, B.; Smolinski, M.; Freindorf, M.; Heine, A.; Klebe, D.; Hangauer, D. G. Enhancement of hydrophobic interactions and hydrogen bond strength by cooperativity: synthesis, modeling, and molecular dynamics simulations of a congeneric series of thrombin inhibitors J. Med. Chem. 2010, 53, 2126-2135
    • (2010) J. Med. Chem. , vol.53 , pp. 2126-2135
    • Muley, L.1    Baum, B.2    Smolinski, M.3    Freindorf, M.4    Heine, A.5    Klebe, D.6    Hangauer, D.G.7
  • 2
    • 58149092426 scopus 로고    scopus 로고
    • Conformational dynamics of the flexible catalytic loop in mycobacterium tuberculosis 1-deoxy-D-xylulose 5-phosphate reductoisomerase
    • Williams, S. L.; McCammon, J. A. Conformational dynamics of the flexible catalytic loop in mycobacterium tuberculosis 1-deoxy-D-xylulose 5-phosphate reductoisomerase Chem. Biol. Drug Des. 2009, 73, 26-38
    • (2009) Chem. Biol. Drug Des. , vol.73 , pp. 26-38
    • Williams, S.L.1    McCammon, J.A.2
  • 3
    • 57049181918 scopus 로고    scopus 로고
    • Computer-based redesign of a β sandwich protein suggests that extensive negative design is not required for de novo β sheet design
    • Hu, X.; Wang, H.; Ke, H.; Kuhlman, B. Computer-based redesign of a β sandwich protein suggests that extensive negative design is not required for de novo β sheet design Structure 2008, 16, 1799-1805
    • (2008) Structure , vol.16 , pp. 1799-1805
    • Hu, X.1    Wang, H.2    Ke, H.3    Kuhlman, B.4
  • 4
    • 33646943202 scopus 로고    scopus 로고
    • Molecular dynamics: Survey of methods for simulating the activity of proteins
    • Adcock, S. A.; McCammon, J. A. Molecular dynamics: survey of methods for simulating the activity of proteins Chem. Rev. 2006, 106, 1589-1615
    • (2006) Chem. Rev. , vol.106 , pp. 1589-1615
    • Adcock, S.A.1    McCammon, J.A.2
  • 6
    • 0037380854 scopus 로고    scopus 로고
    • Gramicidin A channel as a test ground for molecular dynamics force fields
    • Allen, T. W.; Baştuǧ, T.; Kuyucak, S.; Chung, S.-H. Gramicidin A channel as a test ground for molecular dynamics force fields Biophys. J. 2003, 84, 2159-2168
    • (2003) Biophys. J. , vol.84 , pp. 2159-2168
    • Allen, T.W.1    Baştuǧ, T.2    Kuyucak, S.3    Chung, S.-H.4
  • 7
    • 33847254549 scopus 로고    scopus 로고
    • Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: On the structure and possible role of internal water
    • Paschek, D.; Nymeyer, H.; García, A. E. Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water J. Struct. Biol. 2007, 157, 524-533
    • (2007) J. Struct. Biol. , vol.157 , pp. 524-533
    • Paschek, D.1    Nymeyer, H.2    García, A.E.3
  • 8
    • 67649494492 scopus 로고    scopus 로고
    • Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides
    • Best, R. B.; Hummer, G. Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides J. Phys. Chem. B 2009, 113, 9004-9015
    • (2009) J. Phys. Chem. B , vol.113 , pp. 9004-9015
    • Best, R.B.1    Hummer, G.2
  • 9
    • 67650359927 scopus 로고    scopus 로고
    • Force field bias in protein folding simulations
    • Freddolino, P. L.; Park, S.; Roux, B.; Schulten, K. Force field bias in protein folding simulations Biophys. J. 2009, 96, 3772-3780
    • (2009) Biophys. J. , vol.96 , pp. 3772-3780
    • Freddolino, P.L.1    Park, S.2    Roux, B.3    Schulten, K.4
  • 10
    • 33748791718 scopus 로고    scopus 로고
    • Hydration thermodynamic properties of amino acid analogues: A systematic comparison of biomolecular force fields and water models
    • Hess, B.; van der Vegt, N. F. A. Hydration thermodynamic properties of amino acid analogues: a systematic comparison of biomolecular force fields and water models J. Phys. Chem. B. 2006, 110, 17616-17626
    • (2006) J. Phys. Chem. B. , vol.110 , pp. 17616-17626
    • Hess, B.1    Van Der Vegt, N.F.A.2
  • 11
    • 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
  • 13
    • 56249144480 scopus 로고    scopus 로고
    • Simulations of a protein crystal: Explicit treatment of crystallization conditions links theory and experiment in the streptavidin-biotin complex
    • Cerutti, D. S.; Le Trong, I.; Stenkamp, R. E.; Lybrand, T. P. Simulations of a protein crystal: explicit treatment of crystallization conditions links theory and experiment in the streptavidin-biotin complex Biochemistry 2008, 47, 12065-12077
    • (2008) Biochemistry , vol.47 , pp. 12065-12077
    • Cerutti, D.S.1    Le Trong, I.2    Stenkamp, R.E.3    Lybrand, T.P.4
  • 15
    • 28844475404 scopus 로고    scopus 로고
    • Correlated dynamics determining X-ray diffuse scattering from a crystalline protein revealed by molecular dynamics simulation
    • Meinhold, L.; Smith, J. C. Correlated dynamics determining X-ray diffuse scattering from a crystalline protein revealed by molecular dynamics simulation Phys. Rev. Lett. 2005, 95, 218103
    • (2005) Phys. Rev. Lett. , vol.95 , pp. 218103
    • Meinhold, L.1    Smith, J.C.2
  • 16
    • 0001122076 scopus 로고    scopus 로고
    • Simulation of a protein crystal at constant pressure
    • Ceccarelli, M.; Marchi, M. Simulation of a protein crystal at constant pressure J. Phys. Chem. B 1997, 101, 2105-2108
    • (1997) J. Phys. Chem. B , vol.101 , pp. 2105-2108
    • Ceccarelli, M.1    Marchi, M.2
  • 17
    • 10344223464 scopus 로고    scopus 로고
    • Making optimal use of empirical energy functions: Force-field parameterization in crystal space
    • Krieger, E.; Darden, T. A.; Nabuurs, S. B.; Finkelstein, A.; Vriend, G. Making optimal use of empirical energy functions: force-field parameterization in crystal space Proteins 2004, 57, 678-683
    • (2004) Proteins , vol.57 , pp. 678-683
    • Krieger, E.1    Darden, T.A.2    Nabuurs, S.B.3    Finkelstein, A.4    Vriend, G.5
  • 18
    • 1842687872 scopus 로고    scopus 로고
    • Biomolecular cryocyrstallography: Structural changes during flash cooling
    • Halle, B. Biomolecular cryocyrstallography: Structural changes during flash cooling Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 4793-4798
    • (2004) Proc. Natl. Acad. Sci. U.S.A. , vol.101 , pp. 4793-4798
    • Halle, B.1
  • 19
    • 0024094439 scopus 로고
    • Orthorhombic crystals and three-dimensional structure of the potent toxin II from the scorpion Androctonus australis Hector
    • Fontecilla-Camps, J. C.; Habersetzer-Rochat, C.; Rochat, H. Orthorhombic crystals and three-dimensional structure of the potent toxin II from the scorpion Androctonus australis Hector Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 7443-7447
    • (1988) Proc. Natl. Acad. Sci. U.S.A. , vol.85 , pp. 7443-7447
    • Fontecilla-Camps, J.C.1    Habersetzer-Rochat, C.2    Rochat, H.3
  • 21
    • 0028233375 scopus 로고
    • Crystal structure of toxin II from the scorpion Androctonus australis Hector refined at 1.3Å resolution
    • Housset, D.; Habersetzer-Rochat, C.; Astier, J.; Fontecilla-Camps, J. C. Crystal structure of toxin II from the scorpion Androctonus australis Hector refined at 1.3Å resolution J. Mol. Biol. 1994, 238, 88-103
    • (1994) J. Mol. Biol. , vol.238 , pp. 88-103
    • Housset, D.1    Habersetzer-Rochat, C.2    Astier, J.3    Fontecilla-Camps, J.C.4
  • 22
    • 33748518255 scopus 로고    scopus 로고
    • Comparison of multiple Amber force fields and development of improved protein backbone parameters
    • Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of multiple Amber force fields and development of improved protein backbone parameters Proteins 2006, 65, 712-725
    • (2006) Proteins , vol.65 , pp. 712-725
    • Hornak, V.1    Abel, R.2    Okur, A.3    Strockbine, B.4    Roitberg, A.5    Simmerling, C.6
  • 23
    • 3142714765 scopus 로고    scopus 로고
    • Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
    • MacKerrel, A. D.; Feig, M.; Brooks, C. L., III. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations J. Comput. Chem. 2004, 25, 1400-1415
    • (2004) J. Comput. Chem. , vol.25 , pp. 1400-1415
    • MacKerrel, A.D.1    Feig, M.2    Brooks III, C.L.3
  • 26
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids J. Am. Chem. Soc. 1996, 118, 11225-11236
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 29
    • 10844247921 scopus 로고    scopus 로고
    • A modified TIP3P water potential for simulation with Ewald summation
    • Price, D. J.; Brooks, C. L. A modified TIP3P water potential for simulation with Ewald summation J. Chem. Phys. 2004, 121, 10096-10103
    • (2004) J. Chem. Phys. , vol.121 , pp. 10096-10103
    • Price, D.J.1    Brooks, C.L.2
  • 30
    • 29244471731 scopus 로고    scopus 로고
    • A general purpose model for the condensed phases of water: TIP4P/2005
    • Abascal, J. L. F.; Vega, C. A general purpose model for the condensed phases of water: TIP4P/2005 J. Chem. Phys. 2005, 123, 234505
    • (2005) J. Chem. Phys. , vol.123 , pp. 234505
    • Abascal, J.L.F.1    Vega, C.2
  • 33
    • 0031080431 scopus 로고    scopus 로고
    • Monte Carlo simulations of guanidinium acetate and methylammonium acetate ion pairs in water
    • Saigal, S.; Pranata, J. Monte Carlo simulations of guanidinium acetate and methylammonium acetate ion pairs in water Bioorg. Chem. 1997, 25, 11-21
    • (1997) Bioorg. Chem. , vol.25 , pp. 11-21
    • Saigal, S.1    Pranata, J.2
  • 34
    • 33845461593 scopus 로고    scopus 로고
    • Ammonium Recruitment and Ammonia Transport by E. coli Ammonia Channel AmtB
    • Nygaard, T. P.; Rovira, C.; Peters, G. H.; Jensen, M. Ø. Ammonium Recruitment and Ammonia Transport by E. coli Ammonia Channel AmtB Biophys. J. 2006, 91, 4401-4412
    • (2006) Biophys. J. , vol.91 , pp. 4401-4412
    • Nygaard, T.P.1    Rovira, C.2    Peters, G.H.3    Jensen M.Ø4
  • 35
    • 67650070516 scopus 로고    scopus 로고
    • Dynamics of the streptavidin-biotin complex in solution and in its crystal lattice: Distinct behavior revealed by molecular simulations
    • Cerutti, D. S.; Le Trong, I.; Stenkamp, R. E.; Lybrand, T. P. Dynamics of the streptavidin-biotin complex in solution and in its crystal lattice: distinct behavior revealed by molecular simulations J. Phys. Chem. B 2009, 113, 6971-6985
    • (2009) J. Phys. Chem. B , vol.113 , pp. 6971-6985
    • Cerutti, D.S.1    Le Trong, I.2    Stenkamp, R.E.3    Lybrand, T.P.4
  • 38
    • 30744437399 scopus 로고    scopus 로고
    • Flexible simple point-charge water model with improved liquid-state properties
    • 024503
    • Wu, Y.; Tepper, H. L.; Voth, G. A. Flexible simple point-charge water model with improved liquid-state properties J. Chem. Phys. 2006, 124 024503
    • (2006) J. Chem. Phys. , vol.124
    • Wu, Y.1    Tepper, H.L.2    Voth, G.A.3
  • 39
    • 58149163268 scopus 로고    scopus 로고
    • A vulnerability in several popular molecular dynamics packages concerning Langevin and Andersen dynamics
    • Cerutti, D. S.; Duke, R. E.; Freddolino, P. L.; Fan, H.; Lybrand, T. P. A vulnerability in several popular molecular dynamics packages concerning Langevin and Andersen dynamics J. Chem. Theory Comput. 2008, 4, 1669-1680
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 1669-1680
    • Cerutti, D.S.1    Duke, R.E.2    Freddolino, P.L.3    Fan, H.4    Lybrand, T.P.5
  • 40
    • 0000885331 scopus 로고
    • Harmonic analysis of large systems. I. Methodology
    • Brooks, B. R.; Janežič, D.; Karplus, M. Harmonic analysis of large systems. I. Methodology J. Comput. Chem. 1995, 16, 1522-1542
    • (1995) J. Comput. Chem. , vol.16 , pp. 1522-1542
    • Brooks, B.R.1    Janežič, D.2    Karplus, M.3
  • 41
    • 84986469420 scopus 로고
    • Harmonic analysis of large systems. II. Comparison of different protein models
    • Janežič, D.; Brooks, B. R. Harmonic analysis of large systems. II. Comparison of different protein models J. Comput. Chem. 1995, 16, 1543-1553
    • (1995) J. Comput. Chem. , vol.16 , pp. 1543-1553
    • Janežič, D.1    Brooks, B.R.2
  • 43
    • 0037025230 scopus 로고    scopus 로고
    • Cation- π interactions between ammonium ion and aromatic rings: An energy decomposition study
    • Aschi, M.; Mazza, F.; Di Nola, A. Cation- π interactions between ammonium ion and aromatic rings: an energy decomposition study THEOCHEM 2002, 587, 177-188
    • (2002) THEOCHEM , vol.587 , pp. 177-188
    • Aschi, M.1    Mazza, F.2    Di Nola, A.3
  • 44
    • 46749127364 scopus 로고    scopus 로고
    • Are current molecular dynamics force fields too helical
    • Best, R. B.; Buchete, N.; Hummer, G. Are current molecular dynamics force fields too helical Biophys. J. 2008, 95, L07-09
    • (2008) Biophys. J. , vol.95 , pp. 07-09
    • Best, R.B.1    Buchete, N.2    Hummer, G.3
  • 45
    • 43849093505 scopus 로고    scopus 로고
    • Ten-microsecond MD simulation of a fast-folding WW domain
    • Freddolino, P. L.; Liu, F.; Gruebele, M.; Schulten, K. Ten-microsecond MD simulation of a fast-folding WW domain Biophys. J. 2008, 94, L75-77
    • (2008) Biophys. J. , vol.94 , pp. 75-77
    • Freddolino, P.L.1    Liu, F.2    Gruebele, M.3    Schulten, K.4


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