Molecular origin of the cation selectivity in OmpF porin: single channel conductances vs. free energy calculation.

[1]  W. Im,et al.  Ion permeation and selectivity of OmpF porin: a theoretical study based on molecular dynamics, Brownian dynamics, and continuum electrodiffusion theory. , 2002, Journal of molecular biology.

[2]  Sergey M. Bezrukov,et al.  Designed to penetrate: Time-resolved interaction of single antibiotic molecules with bacterial pores , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[3]  W. Im,et al.  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. , 2002, Journal of molecular biology.

[4]  Lisen Kullman,et al.  Transport of maltodextrins through maltoporin: a single-channel study. , 2002, Biophysical journal.

[5]  R. Dutzler,et al.  X-ray structure of a ClC chloride channel at 3.0 Å reveals the molecular basis of anion selectivity , 2002, Nature.

[6]  Ronald M. Welch,et al.  Climatic Impact of Tropical Lowland Deforestation on Nearby Montane Cloud Forests , 2001, Science.

[7]  K. Schulten,et al.  Molecular dynamics study of aquaporin‐1 water channel in a lipid bilayer , 2001, FEBS letters.

[8]  B. Hille,et al.  Ionic channels of excitable membranes , 2001 .

[9]  J. Rosenbusch,et al.  Role of charged residues at the OmpF porin channel constriction probed by mutagenesis and simulation. , 2001, Biochemistry.

[10]  W. Im,et al.  Ion channels, permeation, and electrostatics: insight into the function of KcsA. , 2000, Biochemistry.

[11]  Andreas Engel,et al.  Structural determinants of water permeation through aquaporin-1 , 2000, Nature.

[12]  S. Bezrukov,et al.  Probing sugar translocation through maltoporin at the single channel level , 2000, FEBS letters.

[13]  B. Roux,et al.  Molecular dynamics of the KcsA K(+) channel in a bilayer membrane. , 2000, Biophysical journal.

[14]  V. Luzhkov,et al.  Ion permeation mechanism of the potassium channel , 2000, Nature.

[15]  S. Bezrukov,et al.  Ion Channels as Molecular Coulter Counters to Probe Metabolite Transport , 2000, The Journal of Membrane Biology.

[16]  H. Kono,et al.  Stability analysis for the cavity‐filling mutations of the Myb DNA‐binding domain utilizing free‐energy calculations , 2000, Proteins.

[17]  I. Shrivastava,et al.  Simulations of ion permeation through a potassium channel: molecular dynamics of KcsA in a phospholipid bilayer. , 2000, Biophysical journal.

[18]  S. Chung,et al.  Molecular dynamics study of the KcsA potassium channel. , 1999, Biophysical journal.

[19]  V. Torre,et al.  Potassium and sodium binding to the outer mouth of the K+ channel. , 1999, Biochemistry.

[20]  M. Winterhalter Sugar transport through channels reconstituted in planar lipid membranes , 1999 .

[21]  H. Berendsen,et al.  A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer. , 1998, Biophysical journal.

[22]  B. Chait,et al.  The structure of the potassium channel: molecular basis of K+ conduction and selectivity. , 1998, Science.

[23]  A Kitao,et al.  Improved protein free energy calculation by more accurate treatment of nonbonded energy: Application to chymotrypsin inhibitor 2, V57A , 1998, Proteins.

[24]  Y. Komeiji,et al.  Computational Observation of an Ion Permeation Through a Channel Protein , 1998, Bioscience reports.

[25]  Y. Komeiji,et al.  Computational design of a substrate specificity mutant of a protein , 1996, Proteins.

[26]  G. Rummel,et al.  Structural and Functional Characterization of OmpF Porin Mutants Selected for Larger Pore Size , 1996, The Journal of Biological Chemistry.

[27]  N. Saint,et al.  Structural and Functional Characterization of OmpF Porin Mutants Selected for Larger Pore Size , 1996, The Journal of Biological Chemistry.

[28]  Minoru Saito,et al.  Molecular dynamics/free energy study of a protein in solution with all degrees of freedom and long-range Coulomb interactions , 1995 .

[29]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[30]  J. Rosenbusch,et al.  Structural basis for sugar translocation through maltoporin channels at 3.1 A resolution , 1995, Science.

[31]  S. Bezrukov,et al.  Hofmeister effect in ion transport: reversible binding of halide anions to the roflamycoin channel. , 1994, Biophysical journal.

[32]  Y. Komeiji,et al.  Glycine 85 of the trp-repressor of E. coli is important in forming the hydrophobic tryptophan binding pocket: experimental and computational approaches. , 1994, Protein engineering.

[33]  R. Benz,et al.  Characterization of the channel formed by the mycobacterial porin in lipid bilayer membranes. Demonstration of voltage gating and of negative point charges at the channel mouth. , 1993, The Journal of biological chemistry.

[34]  Y. Komeiji,et al.  Free energy perturbation study on a Trp-binding mutant (Ser88-->Cys) of the trp-repressor. , 1992, Protein engineering.

[35]  G. Rummel,et al.  Crystal structures explain functional properties of two E. coli porins , 1992, Nature.

[36]  D. L. Veenstra,et al.  Probing protein stability with unnatural amino acids. , 1992, Science.

[37]  S J Wodak,et al.  Contribution of the hydrophobic effect to protein stability: analysis based on simulations of the Ile-96----Ala mutation in barnase. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[38]  Peter A. Kollman,et al.  Free energy calculations on protein stability: Thr-157 .fwdarw. Val-157 mutation of T4 lysozyme , 1989 .

[39]  M. Karplus,et al.  Hidden thermodynamics of mutant proteins: a molecular dynamics analysis. , 1989, Science.

[40]  B. Sampson,et al.  Mutations that alter the pore function of the OmpF porin of Escherichia coli K12. , 1988, Journal of molecular biology.

[41]  R. Misra,et al.  Genetic identification of the pore domain of the OmpC porin of Escherichia coli K-12 , 1988, Journal of bacteriology.

[42]  R. Hancock Role of porins in outer membrane permeability , 1987, Journal of bacteriology.

[43]  R. Benz,et al.  Ion selectivity of gram-negative bacterial porins , 1985, Journal of bacteriology.

[44]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[45]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[46]  R. Antolini,et al.  Ion transport through hemocyanin channels in oxidized cholesterol artificial bilayer membranes. , 1981, Biochimica et biophysica acta.

[47]  J. Rosenbusch,et al.  Matrix protein in planar membranes: clusters of channels in a native environment and their functional reassembly. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[48]  R. Benz,et al.  Ionic selectivity of pores formed by the matrix protein (porin) of Escherichia coli. , 1979, Biochimica et biophysica acta.

[49]  R. Benz,et al.  Formation of large, ion-permeable membrane channels by the matrix protein (porin) of Escherichia coli. , 1978, Biochimica et biophysica acta.

[50]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[51]  D. A. Mcquarrie,et al.  The effect of discrete charges on the electrical properties of membranes. II. , 1975, Journal of theoretical biology.

[52]  P. Läuger Ion transport through pores: a rate-theory analysis. , 1973, Biochimica et biophysica acta.

[53]  M Montal,et al.  Formation of bimolecular membranes from lipid monolayers and a study of their electrical properties. , 1972, Proceedings of the National Academy of Sciences of the United States of America.

[54]  A. Hodgkin,et al.  The effect of sodium ions on the electrical activity of the giant axon of the squid , 1949, The Journal of physiology.

[55]  S. Bezrukov,et al.  Partitioning of differently sized poly(ethylene glycol)s into OmpF porin. , 2002, Biophysical journal.

[56]  I. Yamato Ordered Binding Model as a General Tight Coupling Mechanism for Bioenergy Transduction-A Hypothesis. , 1993 .

[57]  J. Rosenbusch,et al.  [25] Isolation and crystallization of bacterial porin , 1986 .