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Volumn 90, Issue 1, 2006, Pages 112-123

The influence of amino acid protonation states on molecular dynamics simulations of the bacterial porin OmpF

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; BACTERIAL PROTEIN; OUTER MEMBRANE PROTEIN F;

EID: 33646134384     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.105.059329     Document Type: Article
Times cited : (64)

References (53)
  • 1
    • 0020597554 scopus 로고
    • Porin channels in Escherichia coli: Studies with liposomes reconstituted from purified proteins
    • Nikaido, H., and E. Y. Rosenberg. 1983. Porin channels in Escherichia coli: studies with liposomes reconstituted from purified proteins. J. Bacteriol. 153:241-252.
    • (1983) J. Bacteriol. , vol.153 , pp. 241-252
    • Nikaido, H.1    Rosenberg, E.Y.2
  • 2
    • 0025604614 scopus 로고
    • Biophysics of the structure and function of porins
    • Jap, B. K., and P. J. Walian. 1990. Biophysics of the structure and function of porins. Q. Rev. Biophys. 23:367-403.
    • (1990) Q. Rev. Biophys. , vol.23 , pp. 367-403
    • Jap, B.K.1    Walian, P.J.2
  • 3
    • 0027771708 scopus 로고
    • Transport across the bacterial outer membrane
    • Nikaido, H. 1993. Transport across the bacterial outer membrane. J. Bioenerg. Biomembr. 25:581-589.
    • (1993) J. Bioenerg. Biomembr. , vol.25 , pp. 581-589
    • Nikaido, H.1
  • 4
    • 0030220261 scopus 로고    scopus 로고
    • Porins: General to specific, native to engineered passive pores
    • Schulz, G. E. 1996. Porins: general to specific, native to engineered passive pores. Curr. Opin. Struct. Biol. 6:485-490.
    • (1996) Curr. Opin. Struct. Biol. , vol.6 , pp. 485-490
    • Schulz, G.E.1
  • 5
    • 0030841732 scopus 로고    scopus 로고
    • MiniReview: Function and modulation of bacterial porins: insights from electrophysiology
    • Delcour, A. H. 1997. MiniReview: function and modulation of bacterial porins: insights from electrophysiology. FEMS Microbiol. Lett. 151:115-123.
    • (1997) FEMS Microbiol. Lett. , vol.151 , pp. 115-123
    • Delcour, A.H.1
  • 6
    • 0031857538 scopus 로고    scopus 로고
    • General and specific porins from bacterial outer membranes
    • Schirmer, T. 1998. General and specific porins from bacterial outer membranes. J. Struct. Biol. 121:101-109.
    • (1998) J. Struct. Biol. , vol.121 , pp. 101-109
    • Schirmer, T.1
  • 7
    • 0033942874 scopus 로고    scopus 로고
    • Structure and function of bacterial outer membrane proteins: Barrels in a nutshell
    • Koebnik, R., K. P. Locher, and P. V. Gelder. 2000. Structure and function of bacterial outer membrane proteins: barrels in a nutshell. Mol. Microbiol. 37:239-253.
    • (2000) Mol. Microbiol. , vol.37 , pp. 239-253
    • Koebnik, R.1    Locher, K.P.2    Gelder, P.V.3
  • 8
    • 0347479229 scopus 로고    scopus 로고
    • Molecular basis of bacterial outer membrane permeability revisited
    • Nikaido, H. 2003. Molecular basis of bacterial outer membrane permeability revisited. Microbiol. Mol. Biol. Rev. 67:593-656.
    • (2003) Microbiol. Mol. Biol. Rev. , vol.67 , pp. 593-656
    • Nikaido, H.1
  • 10
    • 0031860932 scopus 로고    scopus 로고
    • A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer
    • see comments
    • Tieleman, D. P., and H. J. Berendsen. 1998. A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer. Biophys. J. 74:2786-2801 [see comments.].
    • (1998) Biophys. J. , vol.74 , pp. 2786-2801
    • Tieleman, D.P.1    Berendsen, H.J.2
  • 11
    • 0036301334 scopus 로고    scopus 로고
    • Ions and counterions in a biological channel: A molecular dynamics simulation of OmpF porin from Escherichia coli in an explicit membrane with 1 M KCl aqueous salt solution
    • Im, W., and B. Roux. 2002. Ions and counterions in a biological channel: a molecular dynamics simulation of OmpF porin from Escherichia coli in an explicit membrane with 1 M KCl aqueous salt solution. J. Mol. Biol. 319:1177-1197.
    • (2002) J. Mol. Biol. , vol.319 , pp. 1177-1197
    • Im, W.1    Roux, B.2
  • 14
    • 0036216078 scopus 로고    scopus 로고
    • Partitioning of differently sized poly(ethylene glycol)s into OmpF porin
    • Rostovtseva, T. K., E. M. Nestorovich, and S. M. Bezrukov. 2002. Partitioning of differently sized poly(ethylene glycol)s into OmpF porin. Biophys. J. 82:160-169.
    • (2002) Biophys. J. , vol.82 , pp. 160-169
    • Rostovtseva, T.K.1    Nestorovich, E.M.2    Bezrukov, S.M.3
  • 15
    • 1142298543 scopus 로고    scopus 로고
    • Ionization states of residues in OmpF and mutants: Effects of dielectric constant and interactions between residues
    • Varma, S., and E. Jakobsson. 2004. Ionization states of residues in OmpF and mutants: effects of dielectric constant and interactions between residues. Biophys. J. 86:690-704.
    • (2004) Biophys. J. , vol.86 , pp. 690-704
    • Varma, S.1    Jakobsson, E.2
  • 18
    • 0002538230 scopus 로고    scopus 로고
    • Dielectric relaxation in proteins: Microscopic and macroscopic models
    • Simonson, T. 1999. Dielectric relaxation in proteins: microscopic and macroscopic models. Int. J. Quantum Chem. 73:45-57.
    • (1999) Int. J. Quantum Chem. , vol.73 , pp. 45-57
    • Simonson, T.1
  • 19
    • 0035451052 scopus 로고    scopus 로고
    • What are the dielectric "constants" of proteins and how to validate electrostatic models?
    • Schutz, C. N., and A. Warshel. 2001. What are the dielectric "constants" of proteins and how to validate electrostatic models? Proteins. 44:400-417.
    • (2001) Proteins , vol.44 , pp. 400-417
    • Schutz, C.N.1    Warshel, A.2
  • 20
    • 0000000699 scopus 로고    scopus 로고
    • Electrostatic models for computing protonation and redox equilibria in proteins
    • Ullmann, M. G., and E.-W. Knapp. 1999. Electrostatic models for computing protonation and redox equilibria in proteins. Eur. Biophys. J. 28:533-551.
    • (1999) Eur. Biophys. J. , vol.28 , pp. 533-551
    • Ullmann, M.G.1    Knapp, E.-W.2
  • 22
    • 0036099192 scopus 로고    scopus 로고
    • Experimental pKa values of buried residues: Analysis with continuum methods and role of water penetration
    • Fitch, C. A., D. A. Karp, K. K. Lee, W. E. Stites, E. E. Lattman, and E. B. Garcia-Moreno. 2002. Experimental pKa values of buried residues: analysis with continuum methods and role of water penetration. Biophys. J. 82:3289-3304.
    • (2002) Biophys. J. , vol.82 , pp. 3289-3304
    • Fitch, C.A.1    Karp, D.A.2    Lee, K.K.3    Stites, W.E.4    Lattman, E.E.5    Garcia-Moreno, E.B.6
  • 23
    • 10044267947 scopus 로고    scopus 로고
    • Stabilization of internal charges in a protein: Water penetration or conformational change?
    • Denisov, V. P., J. L. Schlessman, E. B. Garcia-Moreno, and B. Halle. 2004. Stabilization of internal charges in a protein: water penetration or conformational change? Biophys. J. 87:3982-3994.
    • (2004) Biophys. J. , vol.87 , pp. 3982-3994
    • Denisov, V.P.1    Schlessman, J.L.2    Garcia-Moreno, E.B.3    Halle, B.4
  • 25
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS: A package for molecular simulation and trajectory analysis
    • Lindahl, E., B. Hess, and D. v. d. Spoel. 2001. GROMACS: a package for molecular simulation and trajectory analysis. J. Mol. Model. 7:306-313.
    • (2001) J. Mol. Model. , vol.7 , pp. 306-313
    • Lindahl, E.1    Hess, B.2    Spoel, D.V.D.3
  • 26
    • 0000388705 scopus 로고    scopus 로고
    • LINCS: A linear constraint solver for molecular simulations
    • Hess, B., H. Bekker, H. J. Berendsen, and G. E. M. Fraaije. 1997. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. 18:1463-1472.
    • (1997) J. Comput. Chem. , vol.18 , pp. 1463-1472
    • Hess, B.1    Bekker, H.2    Berendsen, H.J.3    Fraaije, G.E.M.4
  • 27
    • 84986440341 scopus 로고
    • SETTLE: An analytical version of the SHAKE and RATTLE algorithms for rigid water molecules
    • Miyamoto, S., and P. Kollman. 1992. SETTLE: an analytical version of the SHAKE and RATTLE algorithms for rigid water molecules. J. Comput. Chem. 13:952-962.
    • (1992) J. Comput. Chem. , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.2
  • 28
    • 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
  • 29
    • 0019707626 scopus 로고
    • Polymorphic transition in single crystals: A new molecular dynamics method
    • Parrinello, M., and A. Rahman. 1981. Polymorphic transition in single crystals: a new molecular dynamics method. J. Appl. Phys. 52:7128-7190.
    • (1981) J. Appl. Phys. , vol.52 , pp. 7128-7190
    • Parrinello, M.1    Rahman, A.2
  • 31
    • 85030600642 scopus 로고    scopus 로고
    • Reference deleted in proof
    • Reference deleted in proof.
  • 33
    • 0030404988 scopus 로고    scopus 로고
    • HOLE: A program for the analysis of the pore dimensions of ion channel structural models
    • Smart, O. S., J. G. Neduvelila, X. Wanga, B. A. Wallacea, and M. S. Sansom. 1996. HOLE: a program for the analysis of the pore dimensions of ion channel structural models. J. Mol. Graph. 14:354-360.
    • (1996) J. Mol. Graph. , vol.14 , pp. 354-360
    • Smart, O.S.1    Neduvelila, J.G.2    Wanga, X.3    Wallacea, B.A.4    Sansom, M.S.5
  • 35
    • 0025914739 scopus 로고
    • The bacterial porin superfamily: Sequence alignment and structure prediction
    • Jeanteur, D., J. H. Lakey, and F. Pattus. 1991. The bacterial porin superfamily: sequence alignment and structure prediction. Mol. Microbiol. 5:2153-2164.
    • (1991) Mol. Microbiol. , vol.5 , pp. 2153-2164
    • Jeanteur, D.1    Lakey, J.H.2    Pattus, F.3
  • 36
    • 0031668883 scopus 로고    scopus 로고
    • The spontaneous gating activity of OmpC porin is affected by mutations of a putative hydrogen bond network or of a salt bridge between the L3 loop and the barrel
    • Liu, N., and A. H. Delcour. 1998. The spontaneous gating activity of OmpC porin is affected by mutations of a putative hydrogen bond network or of a salt bridge between the L3 loop and the barrel. Protein Eng. 11:797-802.
    • (1998) Protein Eng. , vol.11 , pp. 797-802
    • Liu, N.1    Delcour, A.H.2
  • 37
    • 0032536195 scopus 로고    scopus 로고
    • Voltage-gating of Escherichia coli porin: A cystine-scanning mutagenesis study of loop 3
    • Bainbridge, G., H. Mobasheri, G. A. Armstrong, E. J. A. Lea, and J. H. Lakey. 1998. Voltage-gating of Escherichia coli porin: a cystine-scanning mutagenesis study of loop 3. J. Mol. Biol. 275:171-176.
    • (1998) J. Mol. Biol. , vol.275 , pp. 171-176
    • Bainbridge, G.1    Mobasheri, H.2    Armstrong, G.A.3    Lea, E.J.A.4    Lakey, J.H.5
  • 39
    • 0033579482 scopus 로고    scopus 로고
    • Brownian dynamics simulation of ion flow through porin channels
    • Schirmer, T., and P. S. Phale. 1999. Brownian dynamics simulation of ion flow through porin channels. J. Mol. Biol. 294:1159-1167.
    • (1999) J. Mol. Biol. , vol.294 , pp. 1159-1167
    • Schirmer, T.1    Phale, P.S.2
  • 40
    • 0035967529 scopus 로고    scopus 로고
    • Role of charged residues at the OmpF porin channel constriction probed by mutagenesis and simulation
    • Phale, P. S., A. Philippsen, C. Widmer, V. P. Phale, J. P. Rosenbusch, and T. Schirmer. 2001. Role of charged residues at the OmpF porin channel constriction probed by mutagenesis and simulation. Biochemistry. 40:6319-6325.
    • (2001) Biochemistry , vol.40 , pp. 6319-6325
    • Phale, P.S.1    Philippsen, A.2    Widmer, C.3    Phale, V.P.4    Rosenbusch, J.P.5    Schirmer, T.6
  • 42
    • 0033006203 scopus 로고    scopus 로고
    • Distinct sensitivities of OmpF and PhoE porins to charged modulators
    • Samartzidou, H., and A. H. Delcour. 1999. Distinct sensitivities of OmpF and PhoE porins to charged modulators. FEBS Lett. 444:65-70.
    • (1999) FEBS Lett. , vol.444 , pp. 65-70
    • Samartzidou, H.1    Delcour, A.H.2
  • 43
    • 0036566425 scopus 로고    scopus 로고
    • Alteration of pore properties of Escherichia coli OmpF induced by mutation of key residues in anti-loop 3 region
    • Bredin, J., N. Saint, M. Mallea, E. D. G. Molle, J. M. Pages, and V. Simonet. 2002. Alteration of pore properties of Escherichia coli OmpF induced by mutation of key residues in anti-loop 3 region. Biochem. J. 363:521-528.
    • (2002) Biochem. J. , vol.363 , pp. 521-528
    • Bredin, J.1    Saint, N.2    Mallea, M.3    Molle, E.D.G.4    Pages, J.M.5    Simonet, V.6
  • 44
    • 0345413270 scopus 로고    scopus 로고
    • Residue ionization and ion transport through OmpF channels
    • Nestorovich, E. M., T. K. Rostovtseva, and S. M. Bezrukov. 2003. Residue ionization and ion transport through OmpF channels. Biophys. J. 85:3718-3729.
    • (2003) Biophys. J. , vol.85 , pp. 3718-3729
    • Nestorovich, E.M.1    Rostovtseva, T.K.2    Bezrukov, S.M.3
  • 45
    • 0347720653 scopus 로고    scopus 로고
    • Ab initio molecular dynamics study of formate ion hydration
    • Leung, K., and S. B. Rempe. 2004. Ab initio molecular dynamics study of formate ion hydration. J. Am. Chem. Soc. 126:344-351.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 344-351
    • Leung, K.1    Rempe, S.B.2
  • 46
    • 10344245541 scopus 로고    scopus 로고
    • On the importance of atomic fluctuations, protein flexibility, and solvent in ion permeation
    • Allen, T. W., O. S. Andersen, and B. Roux. 2004. On the importance of atomic fluctuations, protein flexibility, and solvent in ion permeation. J. Gen. Physiol. 124:679-690.
    • (2004) J. Gen. Physiol. , vol.124 , pp. 679-690
    • Allen, T.W.1    Andersen, O.S.2    Roux, B.3
  • 47
    • 0034516442 scopus 로고    scopus 로고
    • A dynamic lattice Monte Carlo model of ion transport in inhomogeneous dielectric environments. Method and Implementation
    • Graf, P., A. Nitzan, M. G. Kurnikova, and R. D. Coalson. 2000. A dynamic lattice Monte Carlo model of ion transport in inhomogeneous dielectric environments. Method and Implementation. J. Phys. Chem. B. 104:12324-12338.
    • (2000) J. Phys. Chem. B , vol.104 , pp. 12324-12338
    • Graf, P.1    Nitzan, A.2    Kurnikova, M.G.3    Coalson, R.D.4
  • 48
    • 85071084137 scopus 로고    scopus 로고
    • Simulating ion permeation through the ompF porin ion channel using three-dimensional drift-diffusion theory
    • van der Straaten, T., J. M. Tang, U. Ravaioli, R. S. Eisenberg, and N. R. Aluru. 2003. Simulating ion permeation through the ompF porin ion channel using three-dimensional drift-diffusion theory. J. Comput. Electronics. 2:29-47.
    • (2003) J. Comput. Electronics , vol.2 , pp. 29-47
    • Van Der Straaten, T.1    Tang, J.M.2    Ravaioli, U.3    Eisenberg, R.S.4    Aluru, N.R.5
  • 50
    • 0033884302 scopus 로고    scopus 로고
    • A grand canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels
    • Im, W., S. Seefeld, and B. Roux. 2000. A grand canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels. Biophys. J. 79:788-801.
    • (2000) Biophys. J. , vol.79 , pp. 788-801
    • Im, W.1    Seefeld, S.2    Roux, B.3
  • 51
    • 0034763324 scopus 로고    scopus 로고
    • Hierarchical approach to predicting permeation in ion channels
    • Mashl, R. J., Y. Tang, J. Schnitzer, and E. Jakobsson. 2001. Hierarchical approach to predicting permeation in ion channels. Biophys. J. 81:2473-2483.
    • (2001) Biophys. J. , vol.81 , pp. 2473-2483
    • Mashl, R.J.1    Tang, Y.2    Schnitzer, J.3    Jakobsson, E.4
  • 52
    • 0031870447 scopus 로고    scopus 로고
    • Study of ionic currents across a model membrane channel using Brownian dynamics
    • Chung, S. H., M. Hoyles, T. Allen, and S. Kuyucak. 1998. Study of ionic currents across a model membrane channel using Brownian dynamics. Biophys. J. 75:793-809.
    • (1998) Biophys. J. , vol.75 , pp. 793-809
    • Chung, S.H.1    Hoyles, M.2    Allen, T.3    Kuyucak, S.4
  • 53
    • 4444247468 scopus 로고    scopus 로고
    • Functional engineered channels and pores
    • Bayley, H., and L. Jayasinghe. 2004. Functional engineered channels and pores (Review). Mol. Membr. Biol. 21:209-220.
    • (2004) Mol. Membr. Biol. , vol.21 , pp. 209-220
    • Bayley, H.1    Jayasinghe, L.2


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