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Volumn 400, Issue , 2007, Pages 89-102

Molecular dynamics simulations as a complement to nuclear magnetic resonance and X-ray diffraction measurements

(1)  Feller, Scott E a  

a NONE

Author keywords

Correlation function; Force field; Lipid bilayer; Modeling; Molecular dynamics; Simulation

Indexed keywords

ARTICLE; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; LIPID BILAYER; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PREDICTION AND FORECASTING; X RAY DIFFRACTION;

EID: 36549015680     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1385/1-59745-519-9:89     Document Type: Article
Times cited : (7)

References (24)
  • 1
    • 22944467757 scopus 로고
    • Computer experiments on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules
    • Verlet, L. (1967) Computer experiments on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules. Phys. Rev. 159, 98-103.
    • (1967) Phys. Rev , vol.159 , pp. 98-103
    • Verlet, L.1
  • 3
    • 36749107785 scopus 로고
    • Molecular dynamics simulations at constant temperature and/or pressure
    • Andersen, H. C. (1980) Molecular dynamics simulations at constant temperature and/or pressure. J. Chem. Phys. 72, 2384-2393.
    • (1980) J. Chem. Phys , vol.72 , pp. 2384-2393
    • Andersen, H.C.1
  • 4
    • 84926811618 scopus 로고
    • Constant pressure molecular dynamics for molecular systems
    • Nose, S. and Klein, M. L. (1983) Constant pressure molecular dynamics for molecular systems. Mol. Phys. 50, 1055-1076.
    • (1983) Mol. Phys , vol.50 , pp. 1055-1076
    • Nose, S.1    Klein, M.L.2
  • 5
    • 0001538909 scopus 로고
    • Canonical dynamics: Equilibrium phase-space distributions
    • Hoover, W. G. (1985) Canonical dynamics: Equilibrium phase-space distributions. Phys. Rev. A 31, 1695-1697.
    • (1985) Phys. Rev. A , vol.31 , pp. 1695-1697
    • Hoover, W.G.1
  • 6
    • 36449007836 scopus 로고
    • Constant pressure molecular dynamics simulation: The Langevin piston method
    • Feller, S. E., Zhang, Y., Pastor, R. W., and Brooks, B. R. (1995) Constant pressure molecular dynamics simulation: The Langevin piston method. J. Chem. Phys. 103, 4613.
    • (1995) J. Chem. Phys , vol.103 , pp. 4613
    • Feller, S.E.1    Zhang, Y.2    Pastor, R.W.3    Brooks, B.R.4
  • 7
    • 0029737564 scopus 로고    scopus 로고
    • What is the surface tension of a bilayer membrane?
    • Jahnig, F. (1996) What is the surface tension of a bilayer membrane? Biophys. J. 71, 1348-1349.
    • (1996) Biophys. J , vol.71 , pp. 1348-1349
    • Jahnig, F.1
  • 8
    • 0029767694 scopus 로고    scopus 로고
    • On simulating lipid bilayers with an applied surface tension: Periodic boundary conditions and undulations
    • Feller, S. E. and Pastor, R. W. (1996) On simulating lipid bilayers with an applied surface tension: periodic boundary conditions and undulations. Biophys. J. 71, 1350-1355.
    • (1996) Biophys. J , vol.71 , pp. 1350-1355
    • Feller, S.E.1    Pastor, R.W.2
  • 9
    • 0033932839 scopus 로고    scopus 로고
    • Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations
    • Lindahl, E. and Edholm, O. (2000) Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations. Biophys. J. 79, 426-433.
    • (2000) Biophys. J , vol.79 , pp. 426-433
    • Lindahl, E.1    Edholm, O.2
  • 10
    • 0031309462 scopus 로고    scopus 로고
    • Length scales of lipid dynamics and molecular dynamics
    • Feller, S. E. and Pastor, R. W. (1997) Length scales of lipid dynamics and molecular dynamics. Pac. Symp. Biocomput. 142-150.
    • (1997) Pac. Symp. Biocomput , pp. 142-150
    • Feller, S.E.1    Pastor, R.W.2
  • 11
    • 2942622288 scopus 로고    scopus 로고
    • Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew
    • Horn, H. W., Swope, W. C., Pitera, J. W., et al. (2004) Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew. J. Chem. Phys. 120, 9665-9679.
    • (2004) J. Chem. Phys , vol.120 , pp. 9665-9679
    • Horn, H.W.1    Swope, W.C.2    Pitera, J.W.3
  • 12
    • 0034271962 scopus 로고    scopus 로고
    • Spatial and energetic-entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations
    • Lindahl, E. and Edholm, O. (2000) Spatial and energetic-entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations. J. Chem. Phys. 113, 3882-3893.
    • (2000) J. Chem. Phys , vol.113 , pp. 3882-3893
    • Lindahl, E.1    Edholm, O.2
  • 13
    • 2942675244 scopus 로고    scopus 로고
    • Lipid bilayer pressure profiles and mechanosensitive channel gating
    • Gullingsrud, J. and Schulten, K. (2004) Lipid bilayer pressure profiles and mechanosensitive channel gating. Biophys. J. 86, 3496-3509.
    • (2004) Biophys. J , vol.86 , pp. 3496-3509
    • Gullingsrud, J.1    Schulten, K.2
  • 14
    • 23044495981 scopus 로고    scopus 로고
    • Evidence for a Mechanism by Which Omega-3 Polyunsaturated Lipids May Affect Membrane Protein Function
    • 10, 169
    • Carrillo-Tripp, M. and Feller, S. E. (2005) Evidence for a Mechanism by Which Omega-3 Polyunsaturated Lipids May Affect Membrane Protein Function. Biochemistry 44, 10, 164-10, 169.
    • (2005) Biochemistry , vol.44 , pp. 164-110
    • Carrillo-Tripp, M.1    Feller, S.E.2
  • 17
    • 0034250744 scopus 로고    scopus 로고
    • An improved empirical potential energy function for molecular simulations of phospholipids
    • Feller, S. E. and MacKerell, A. D., Jr. (2000) An improved empirical potential energy function for molecular simulations of phospholipids. J. Phys. Chem. B 104, 7510-7515.
    • (2000) J. Phys. Chem. B , vol.104 , pp. 7510-7515
    • Feller, S.E.1    MacKerell Jr., A.D.2
  • 18
    • 24944554872 scopus 로고    scopus 로고
    • Adjacent gauche stabilization in linear alkanes: Implications for polymer models and conformational analysis
    • 15, 686
    • Klauda, J. B., Brooks, B. R., and Pastor, R. W. (2005) Adjacent gauche stabilization in linear alkanes: implications for polymer models and conformational analysis. J. Phys. Chem. B 109, 15, 684-15, 686.
    • (2005) J. Phys. Chem. B , vol.109 , pp. 684-615
    • Klauda, J.B.1    Brooks, B.R.2    Pastor, R.W.3
  • 19
    • 15744368593 scopus 로고    scopus 로고
    • An ab Initio Study on the Torsional Surface of Alkanes and Its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer
    • Klauda, J. B., Brooks, B. R., MacKerell, A. D., Jr., Venable, R. M., and Pastor, R. W. (2005) An ab Initio Study on the Torsional Surface of Alkanes and Its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer. J. Phys. Chem. B 109, 5300-5311.
    • (2005) J. Phys. Chem. B , vol.109 , pp. 5300-5311
    • Klauda, J.B.1    Brooks, B.R.2    MacKerell Jr., A.D.3    Venable, R.M.4    Pastor, R.W.5
  • 20
    • 1642455952 scopus 로고    scopus 로고
    • Pressure-Based Long-Range Correction for Lennard-Jones Interactions in Molecular Dynamics Simulations: Application to Alkanes and Interfaces
    • Laguee, P., Pastor, R. W., and Brooks, B. R. (2004) Pressure-Based Long-Range Correction for Lennard-Jones Interactions in Molecular Dynamics Simulations: Application to Alkanes and Interfaces. J. Phys. Chem. B 108, 363-368.
    • (2004) J. Phys. Chem. B , vol.108 , pp. 363-368
    • Laguee, P.1    Pastor, R.W.2    Brooks, B.R.3
  • 21
    • 0030844208 scopus 로고    scopus 로고
    • Molecular dynamics simulation of unsaturated lipid bilayers at low hydration: Parameterization and comparison with diffraction studies
    • Feller, S. E., Yin, D., Pastor, R. W., and MacKerell, A. D., Jr. (1997) Molecular dynamics simulation of unsaturated lipid bilayers at low hydration: parameterization and comparison with diffraction studies. Biophys. J. 73, 2269-2279.
    • (1997) Biophys. J , vol.73 , pp. 2269-2279
    • Feller, S.E.1    Yin, D.2    Pastor, R.W.3    MacKerell Jr., A.D.4
  • 22
    • 0000951252 scopus 로고    scopus 로고
    • Feller, S. E., Pastor, R. W., Rojnuckarin, A., Bogusz, S., and Brooks, B. R. (1996) Effect of Electrostatic Force Truncation on Interfacial and Transport Properties of Water. J. Phys. Chem. 100, 17, 011-17, 020.
    • Feller, S. E., Pastor, R. W., Rojnuckarin, A., Bogusz, S., and Brooks, B. R. (1996) Effect of Electrostatic Force Truncation on Interfacial and Transport Properties of Water. J. Phys. Chem. 100, 17, 011-17, 020.
  • 23
    • 0038440700 scopus 로고    scopus 로고
    • Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions
    • Patra, M., Karttunen, M., Hyvonen, M. T., Falck, E., Lindqvist, P., and Vattulainen, I. (2003) Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions. Biophys. J. 84, 3636-3645.
    • (2003) Biophys. J , vol.84 , pp. 3636-3645
    • Patra, M.1    Karttunen, M.2    Hyvonen, M.T.3    Falck, E.4    Lindqvist, P.5    Vattulainen, I.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.