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Volumn 8, Issue 7, 2012, Pages 2197-2203

Hybrid QM/MM molecular dynamics study of benzocaine in a membrane environment: How does a quantum mechanical treatment of both anesthetic and lipids affect their interaction

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EID: 84863649794     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct300213u     Document Type: Article
Times cited : (16)

References (61)
  • 1
    • 49449114817 scopus 로고    scopus 로고
    • Large-scale molecular dynamics simulations of self-assembling systems
    • Klein, M. L.; Shinoda, W. Large-scale molecular dynamics simulations of self-assembling systems Science 2008, 321, 798-800
    • (2008) Science , vol.321 , pp. 798-800
    • Klein, M.L.1    Shinoda, W.2
  • 2
    • 0036194575 scopus 로고    scopus 로고
    • Molecular modeling and dynamics of the sodium channel inactivation gate
    • Sirota, F. L.; Pascutti, P. G.; Anteneodo, C. Molecular modeling and dynamics of the sodium channel inactivation gate Biophys. J. 2002, 82, 1207-1215
    • (2002) Biophys. J , vol.82 , pp. 1207-1215
    • Sirota, F.L.1    Pascutti, P.G.2    Anteneodo, C.3
  • 3
    • 0000112789 scopus 로고    scopus 로고
    • Molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine bilayer with different macroscopic boundary conditions and parameters
    • Tieleman, D. P.; Berendsen, H. J. C. Molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine bilayer with different macroscopic boundary conditions and parameters J. Chem. Phys. 1996, 105, 4871-4880
    • (1996) J. Chem. Phys , vol.105 , pp. 4871-4880
    • Tieleman, D.P.1    Berendsen, H.J.C.2
  • 4
    • 0028867364 scopus 로고
    • Constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine bilayer
    • Tu, K.; Tobias, D. J.; Klein, M. L. Constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine bilayer Biophys. J. 1995, 69, 2558-2562
    • (1995) Biophys. J , vol.69 , pp. 2558-2562
    • Tu, K.1    Tobias, D.J.2    Klein, M.L.3
  • 5
    • 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.; MacKerell, A. D. Molecular dynamics simulation of unsaturated lipid bilayers at low hydration: parameterization and comparison with diffraction studies Biophys. J. 1997, 73, 2269-2279
    • (1997) Biophys. J , vol.73 , pp. 2269-2279
    • Feller, S.E.1    Yin, D.2    Pastor, R.W.3    MacKerell, A.D.4
  • 6
    • 0036286655 scopus 로고    scopus 로고
    • Computer simulation studies of model biological membranes
    • Saiz, L.; Klein, M. L. Computer simulation studies of model biological membranes Acc. Chem. Res. 2002, 35, 482-489
    • (2002) Acc. Chem. Res , vol.35 , pp. 482-489
    • Saiz, L.1    Klein, M.L.2
  • 7
    • 0021945413 scopus 로고
    • A model for the lateral diffusion of "stiff" chains in a lipid bilayer
    • Nadler, W.; Tavan, P.; Schulten, K. A model for the lateral diffusion of "stiff" chains in a lipid bilayer Eur. Biophys. J. 1985, 12, 25-31
    • (1985) Eur. Biophys. J , vol.12 , pp. 25-31
    • Nadler, W.1    Tavan, P.2    Schulten, K.3
  • 8
    • 0001008704 scopus 로고
    • Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid crystal phase
    • Heller, H.; Schaefer, M.; Schulten, K. Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid crystal phase J. Phys. Chem. 1993, 97, 8343-8360
    • (1993) J. Phys. Chem , vol.97 , pp. 8343-8360
    • Heller, H.1    Schaefer, M.2    Schulten, K.3
  • 9
    • 22544450619 scopus 로고
    • Molecular Dynamics Study of a Membrane-Water Interface
    • Zhou, F.; Schulten, K. Molecular Dynamics Study of a Membrane-Water Interface J. Phys. Chem. 1995, 99, 2194-2207
    • (1995) J. Phys. Chem , vol.99 , pp. 2194-2207
    • Zhou, F.1    Schulten, K.2
  • 10
    • 49549083949 scopus 로고    scopus 로고
    • Membrane proteins: Molecular dynamics simulations
    • Lindahl, E.; Sansom, M. S. P. Membrane proteins: molecular dynamics simulations Curr. Opin. Struct. Biol. 2008, 18, 425-431
    • (2008) Curr. Opin. Struct. Biol , vol.18 , pp. 425-431
    • Lindahl, E.1    Sansom, M.S.P.2
  • 11
    • 0037325582 scopus 로고    scopus 로고
    • Nonspecific interaction forces at water-membrane interface by forced molecular dynamics simulations
    • Lorenzo, A. C.; Pascutti, P. G.; Bisch, P. M. Nonspecific interaction forces at water-membrane interface by forced molecular dynamics simulations J. Comput. Chem. 2003, 24, 328-39
    • (2003) J. Comput. Chem , vol.24 , pp. 328-339
    • Lorenzo, A.C.1    Pascutti, P.G.2    Bisch, P.M.3
  • 12
    • 84859467021 scopus 로고    scopus 로고
    • Membrane proteins, magic-angle spinning, and in-cell NMR
    • Pielak, G. J.; Tian, F. Membrane proteins, magic-angle spinning, and in-cell NMR Proc. Nat. Acad. Sci. U.S.A. 2012, 109, 4715-4716
    • (2012) Proc. Nat. Acad. Sci. U.S.A , vol.109 , pp. 4715-4716
    • Pielak, G.J.1    Tian, F.2
  • 13
    • 77953297286 scopus 로고    scopus 로고
    • Membrane-mediated effect on ion channels induced by the anesthetic drug ketamine
    • Jerabek, H.; Pabst, G.; Rappolt, M.; Stockner, T. Membrane-mediated effect on ion channels induced by the anesthetic drug ketamine J. Am. Chem. Soc. 2010, 132, 7990-7997
    • (2010) J. Am. Chem. Soc , vol.132 , pp. 7990-7997
    • Jerabek, H.1    Pabst, G.2    Rappolt, M.3    Stockner, T.4
  • 14
    • 0034284386 scopus 로고    scopus 로고
    • How proteins adapt to a membrane-water interface
    • Killian, J. A.; von Heijne, G. How proteins adapt to a membrane-water interface Trends Biochem. Sci. 2000, 25, 429-434
    • (2000) Trends Biochem. Sci , vol.25 , pp. 429-434
    • Killian, J.A.1    Von Heijne, G.2
  • 16
    • 0018982584 scopus 로고
    • Lipid conformation in model membranes and biological membranes
    • Seelig, J.; Seelig, A. Lipid conformation in model membranes and biological membranes Q. Rev. Biophys. 1980, 13, 19-61
    • (1980) Q. Rev. Biophys , vol.13 , pp. 19-61
    • Seelig, J.1    Seelig, A.2
  • 17
    • 0018801591 scopus 로고
    • Physical studies of cell surface and cell membrane structure. Determination of phospholipid head group organization by deuterium and phosphorus nuclear magnetic resonance spectroscopy
    • Skarjune, R.; Oldfield, E. Physical studies of cell surface and cell membrane structure. Determination of phospholipid head group organization by deuterium and phosphorus nuclear magnetic resonance spectroscopy Biochemistry 1979, 18, 5903-5909
    • (1979) Biochemistry , vol.18 , pp. 5903-5909
    • Skarjune, R.1    Oldfield, E.2
  • 18
    • 0017252177 scopus 로고
    • Effects of local anesthetics on cell morphology and membrane-associated cytoskeletal organization in BALB/3T3 cells
    • Nicolson, G. L. Effects of local anesthetics on cell morphology and membrane-associated cytoskeletal organization in BALB/3T3 cells J. Cell Biol. 1976, 68, 395-402
    • (1976) J. Cell Biol , vol.68 , pp. 395-402
    • Nicolson, G.L.1
  • 19
    • 61849153021 scopus 로고    scopus 로고
    • Impact of nanotechnology on drug delivery
    • Farokhzad, O. C.; Langer, R. Impact of nanotechnology on drug delivery ACS Nano 2009, 3, 16-20
    • (2009) ACS Nano , vol.3 , pp. 16-20
    • Farokhzad, O.C.1    Langer, R.2
  • 20
    • 47249159342 scopus 로고    scopus 로고
    • Liposomes and skin: From drug delivery to model membranes
    • El Maghraby, G. M.; Barry, B. W.; Williams, A. C. Liposomes and skin: from drug delivery to model membranes Eur. J. Pharm. Sci. 2008, 34, 203-222
    • (2008) Eur. J. Pharm. Sci , vol.34 , pp. 203-222
    • El Maghraby, G.M.1    Barry, B.W.2    Williams, A.C.3
  • 21
    • 40549115312 scopus 로고    scopus 로고
    • Monitoring biological membrane-potential changes: A CI QM/MM study
    • Rusu, C. F.; Lanig, H.; Othersen, O. G.; Kryschi, C.; Clark, T. Monitoring biological membrane-potential changes: a CI QM/MM study J. Phys. Chem. B 2008, 112, 2445-2455
    • (2008) J. Phys. Chem. B , vol.112 , pp. 2445-2455
    • Rusu, C.F.1    Lanig, H.2    Othersen, O.G.3    Kryschi, C.4    Clark, T.5
  • 22
    • 56149118705 scopus 로고    scopus 로고
    • Hybrid QM/MM simulation of the hydration phenomena of dipalmitoylphosphatidylcholine headgroup
    • Yin, J.; Zhao, Y.-P. Hybrid QM/MM simulation of the hydration phenomena of dipalmitoylphosphatidylcholine headgroup J. Colloid Interface Sci. 2009, 329, 410-415
    • (2009) J. Colloid Interface Sci , vol.329 , pp. 410-415
    • Yin, J.1    Zhao, Y.-P.2
  • 23
    • 33846327607 scopus 로고    scopus 로고
    • A regularized and renormalized electrostatic coupling Hamiltonian for hybrid quantum-mechanical-molecular-mechanical calculations
    • Biswas, P. K.; Gogonea, V. A regularized and renormalized electrostatic coupling Hamiltonian for hybrid quantum-mechanical-molecular-mechanical calculations J. Chem. Phys. 2005, 123, 164114
    • (2005) J. Chem. Phys , vol.123 , pp. 164114
    • Biswas, P.K.1    Gogonea, V.2
  • 24
    • 4243606192 scopus 로고
    • Unified approach for molecular dynamics and density-functional theory
    • Car, R.; Parrinello, M. Unified approach for molecular dynamics and density-functional theory Phys. Rev. Lett. 1985, 55, 2471-2474
    • (1985) Phys. Rev. Lett , vol.55 , pp. 2471-2474
    • Car, R.1    Parrinello, M.2
  • 27
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • Lindahl, E.; Hess, B.; van der Spoel, D. GROMACS 3.0: a package for molecular simulation and trajectory analysis J. Mol. Model. 2001, 7, 306-317
    • (2001) J. Mol. Model , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    Van Der Spoel, D.3
  • 30
    • 77952334526 scopus 로고    scopus 로고
    • Models and mechanisms of local anesthetic cardiac toxicity: A review
    • Butterworth, J. F. Models and mechanisms of local anesthetic cardiac toxicity: a review Reg. Anesth. Pain Med. 2010, 35, 167-176
    • (2010) Reg. Anesth. Pain Med , vol.35 , pp. 167-176
    • Butterworth, J.F.1
  • 32
    • 16844371631 scopus 로고    scopus 로고
    • Review of local anaesthetic agents
    • McLure, H. A.; Rubin, A. P. Review of local anaesthetic agents Minerva Anestesiol. 2005, 71, 59-74
    • (2005) Minerva Anestesiol , vol.71 , pp. 59-74
    • McLure, H.A.1    Rubin, A.P.2
  • 33
    • 38349011413 scopus 로고    scopus 로고
    • Effect of local anesthetic lidocaine on electrostatic properties of a lipid bilayer
    • Högberg, C.-J.; Lyubartsev, A. P. Effect of local anesthetic lidocaine on electrostatic properties of a lipid bilayer Biophys. J. 2008, 94, 525-531
    • (2008) Biophys. J , vol.94 , pp. 525-531
    • Högberg, C.-J.1    Lyubartsev, A.P.2
  • 34
    • 0029878720 scopus 로고    scopus 로고
    • VMD: Visual molecular dynamics
    • Humphrey, W. VMD: Visual molecular dynamics J. Mol. Graphics 1996, 14, 33-38
    • (1996) J. Mol. Graphics , vol.14 , pp. 33-38
    • Humphrey, W.1
  • 35
    • 0025263891 scopus 로고
    • Molecular mechanisms of local anesthesia: A review
    • Butterworth, J. F.; Strichartz, G. R. Molecular mechanisms of local anesthesia: a review Anesthesiology 1990, 72, 711-734
    • (1990) Anesthesiology , vol.72 , pp. 711-734
    • Butterworth, J.F.1    Strichartz, G.R.2
  • 37
    • 10644250257 scopus 로고
    • Inhomogeneous Electron Gas
    • Hohenberg, P.; Kohn, W. Inhomogeneous Electron Gas Phys. Rev. 1964, 136, B864-B871
    • (1964) Phys. Rev , vol.136
    • Hohenberg, P.1    Kohn, W.2
  • 38
    • 0042113153 scopus 로고
    • Self-Consistent Equations Including Exchange and Correlation Effects
    • Kohn, W.; Sham, L. J. Self-Consistent Equations Including Exchange and Correlation Effects Phys. Rev. 1965, 140, A1133-A1138
    • (1965) Phys. Rev , vol.140
    • Kohn, W.1    Sham, L.J.2
  • 39
    • 4243553426 scopus 로고
    • Density-functional exchange-energy approximation with correct asymptotic behavior
    • Becke, A. D. Density-functional exchange-energy approximation with correct asymptotic behavior Phys. Rev. A 1988, 38, 3098-3100
    • (1988) Phys. Rev. A , vol.38 , pp. 3098-3100
    • Becke, A.D.1
  • 40
    • 0000189651 scopus 로고
    • Density-functional thermochemistry. III. The role of exact exchange
    • Becke, A. D. Density-functional thermochemistry. III. The role of exact exchange J. Chem. Phys. 1993, 98, 5648-5652
    • (1993) J. Chem. Phys , vol.98 , pp. 5648-5652
    • Becke, A.D.1
  • 41
    • 0345491105 scopus 로고
    • Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
    • Lee, C.; Yang, W.; Parr, R. G. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density Phys. Rev. B 1988, 37, 785-789
    • (1988) Phys. Rev. B , vol.37 , pp. 785-789
    • Lee, C.1    Yang, W.2    Parr, R.G.3
  • 42
    • 33751157732 scopus 로고
    • Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields
    • Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J. Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields J. Phys. Chem. 1994, 98, 11623-11627
    • (1994) J. Phys. Chem , vol.98 , pp. 11623-11627
    • Stephens, P.J.1    Devlin, F.J.2    Chabalowski, C.F.3    Frisch, M.J.4
  • 43
    • 36549091806 scopus 로고
    • A complete basis set model chemistry. I. The total energies of closed-shell atoms and hydrides of the first-row elements
    • Petersson, G. A.; Bennett, A.; Tensfeldt, T. G.; Al-Laham, M. A.; Shirley, W. A.; Mantzaris, J. A complete basis set model chemistry. I. The total energies of closed-shell atoms and hydrides of the first-row elements J. Phys. Chem. 1988, 89, 2193-2218
    • (1988) J. Phys. Chem , vol.89 , pp. 2193-2218
    • Petersson, G.A.1    Bennett, A.2    Tensfeldt, T.G.3    Al-Laham, M.A.4    Shirley, W.A.5    Mantzaris, J.6
  • 44
    • 0038035472 scopus 로고
    • A complete basis set model chemistry. II. Open-shell systems and the total energies of the first-row atoms
    • Petersson, G. A.; Al-Laham, M. A. A complete basis set model chemistry. II. Open-shell systems and the total energies of the first-row atoms J. Chem. Phys. 1991, 94, 6081-6090
    • (1991) J. Chem. Phys , vol.94 , pp. 6081-6090
    • Petersson, G.A.1    Al-Laham, M.A.2
  • 45
    • 84986513567 scopus 로고
    • Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis
    • Breneman, C. M.; Wiberg, K. B. Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis J. Comput. Chem. 1990, 11, 361-373
    • (1990) J. Comput. Chem , vol.11 , pp. 361-373
    • Breneman, C.M.1    Wiberg, K.B.2
  • 48
    • 84863655347 scopus 로고    scopus 로고
    • Methods and Parameters for Membrane Simulation
    • 1st ed. Sansom, M. S. P. Biggin, P. C. The Royal Society of Chemistry: London
    • Tieleman, P. Methods and Parameters for Membrane Simulation. In Molecular Simulations and Biomembranes: From Biophysics to Function, 1st ed.; Sansom, M. S. P.; Biggin, P. C., Eds.; The Royal Society of Chemistry: London, 2010; pp 1-25
    • (2010) Molecular Simulations and Biomembranes: From Biophysics to Function , pp. 1-25
    • Tieleman, P.1
  • 50
    • 84926811618 scopus 로고
    • Constant pressure molecular dynamics for molecular systems
    • Nosé, S.; Klein, M. L. Constant pressure molecular dynamics for molecular systems Mol. Phys. 1983, 50, 1055-1076
    • (1983) Mol. Phys , vol.50 , pp. 1055-1076
    • Nosé, S.1    Klein, M.L.2
  • 51
    • 0001538909 scopus 로고
    • Canonical dynamics: Equilibrium phase-space distributions
    • Hoover, W. G. Canonical dynamics: Equilibrium phase-space distributions Phys. Rev. A 1985, 31, 1695-1697
    • (1985) Phys. Rev. A , vol.31 , pp. 1695-1697
    • Hoover, W.G.1
  • 52
    • 0019707626 scopus 로고
    • Polymorphic transitions in single crystals: A new molecular dynamics method
    • Parrinello, M.; Rahman, A. Polymorphic transitions in single crystals: A new molecular dynamics method J. Appl. Phys. 1981, 52, 7182-7190
    • (1981) J. Appl. Phys , vol.52 , pp. 7182-7190
    • Parrinello, M.1    Rahman, A.2
  • 53
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An Nlog(N) method for Ewald sums in large systems
    • Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: An Nlog(N) method for Ewald sums in large systems J. Chem. Phys. 1993, 98, 10089
    • (1993) J. Chem. Phys , vol.98 , pp. 10089
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 54
  • 55
    • 84986440341 scopus 로고
    • Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
    • Miyamoto, S.; Kollman, P. A. Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models J. Comput. Chem. 1992, 13, 952-962
    • (1992) J. Comput. Chem , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 56
    • 34547507515 scopus 로고    scopus 로고
    • QM/MM methods for biological systems
    • Senn, H. M.; Thiel, W. QM/MM methods for biological systems Top. Curr. Chem. 2007, 268, 173-290
    • (2007) Top. Curr. Chem , vol.268 , pp. 173-290
    • Senn, H.M.1    Thiel, W.2
  • 57
    • 33846570818 scopus 로고    scopus 로고
    • QM/MM: What have we learned, where are we, and where do we go from here?
    • Lin, H.; Truhlar, D. G. QM/MM: what have we learned, where are we, and where do we go from here? Theor. Chem. Acc. 2006, 117, 185-199
    • (2006) Theor. Chem. Acc , vol.117 , pp. 185-199
    • Lin, H.1    Truhlar, D.G.2
  • 58
    • 20144363830 scopus 로고    scopus 로고
    • CPMD: Car-Parrinello molecular dynamics
    • Hutter, J.; Iannuzzi, M. CPMD: Car-Parrinello molecular dynamics Z. Kristallogr. 2005, 220, 549-551
    • (2005) Z. Kristallogr , vol.220 , pp. 549-551
    • Hutter, J.1    Iannuzzi, M.2
  • 59
    • 20544463457 scopus 로고
    • Soft self-consistent pseudopotentials in a generalized eigenvalue formalism
    • Vanderbilt, D. Soft self-consistent pseudopotentials in a generalized eigenvalue formalism Phys. Rev. B 1990, 41, 7892-7895
    • (1990) Phys. Rev. B , vol.41 , pp. 7892-7895
    • Vanderbilt, D.1
  • 60
    • 34147185256 scopus 로고    scopus 로고
    • Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations
    • Dal Peraro, M.; Ruggerone, P.; Raugei, S.; Gervasio, F. L.; Carloni, P. Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations Curr. Opin. Struct. Biol. 2007, 17, 149-156
    • (2007) Curr. Opin. Struct. Biol , vol.17 , pp. 149-156
    • Dal Peraro, M.1    Ruggerone, P.2    Raugei, S.3    Gervasio, F.L.4    Carloni, P.5
  • 61
    • 0032826793 scopus 로고    scopus 로고
    • Molecular dynamics simulation of alpha-melanocyte stimulating hormone in a water-membrane model interface
    • Pascutti, P. G.; El-Jaik, L. J.; Bisch, P. M.; Mundim, K. C.; Ito, A. S. Molecular dynamics simulation of alpha-melanocyte stimulating hormone in a water-membrane model interface Eur. Biophys. J. 1999, 28, 499-509
    • (1999) Eur. Biophys. J , vol.28 , pp. 499-509
    • Pascutti, P.G.1    El-Jaik, L.J.2    Bisch, P.M.3    Mundim, K.C.4    Ito, A.S.5


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