Computational studies of the gramicidin channel

Accounts of Chemical Research

Volumn 35, Issue 6, 2002, Pages 366-375

  Roux, Benoît ^a  

^a WEILL CORNELL MEDICAL COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GRAMICIDIN; GRAMICIDIN A; MEMBRANE LIPID; MEMBRANE PROTEIN; ION CHANNEL;

ARTICLE; BINDING SITE; CHANNEL GATING; ION CHANNEL; ION PERMEABILITY; MEMBRANE POTENTIAL; MOLECULAR DYNAMICS; MOLECULAR MODEL; NUCLEAR MAGNETIC RESONANCE; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN STRUCTURE; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; REVIEW;

COMPUTER SIMULATION; GRAMICIDIN; ION CHANNELS; MODELS, CHEMICAL; PROTEIN CONFORMATION;

EID: 0036280795     PISSN: 00014842     EISSN: None     Source Type: Journal    
DOI: 10.1021/ar010028v     Document Type: Article

References (70)

1. Molecular determinants of channel function
2. Molecular dynamics simulations of the gramicidin channel
3. 1H-NMR study of gramicidin A transmembrane ion channel. Head-to-head, right-handed, single-stranded helices
4. High-resolution conformation of gramicidin A in lipid bilayer by solid-state NMR
5. High-resolution refinement of a solic-state NMR-derived structure of gramicidin A in a lipid bilayer environment
6. Structures of gramicidins A, B, and C incorporated into sodium dodecyl sulfate micelles
7. Structure and dynamics of ion transport through gramicidin A
8. Dynamics of folded proteins
9. 2O)n
10. Reaction enthalpies for M(+)L = M(+) + L, where M(+) = Na+ and K+ and L equals acetamide, N-methylacetamide, N,N-dimethyl-acetamide, glycine, and glycylglycine, from determinations of the collision-induced dissociation thresholds
11. Potential energy function for cations-peptides interactions: An Ab initio study
12. Ion water interaction potential derived from free energy perturbation simulations
13. Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations
14. The proton's absolute aqueous enthalpy and gibbs free energy of solvation from cluster ion solvation data
15. + in the gramicidin channel
16. Ion transport in the gramicidin channel: Molecular dynamics study of single and double occupancy
17. The binding site of sodium in the gramicidin A channel: A comparison of molecular dynamics simulations with solid state NMR data
18. High-temperature equation of state by a perturbation method
19. Monte Carlo free energy estimates using non-Boltzmann sampling: Application to the sub-critical Lennard-Jones fluid
20. Ion transport in the gramicidin channel: Free energy of the solvated right-handed dimer in a model membrane
21. Statistical mechanics of isomerization dynamics in liquids and the transition state approximation
22. Classical and modern methods in reaction rate theory
23. A molecular dynamics study of gating in dioxolane-linked gramicidin A channels
24. Free energy calculations: Applications to chemical and biochemical phenomena
25. Valence selectivity of the gramicidin channel: A molecular dynamics free energy perturbation study
26. Exploiting the isomorphism between quantum theory and classical statistical mechanics of polyatomic fluids
27. Structure and dynamics of a proton wire: A theoretical study of H+ translocation along the single-file water chain in the gramicidin A channel
28. The influence of the membrane potential on the free energy of an intrinsic protein
29. Statistical mechanical equilibrium theory of selective ion channels
30. Ion channels, permeation and electrostatics: Insight into the function of KcsA
31. CHARMM: A program for macromolecular energy minimization and dynamics calculations
32. Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer
33. Structure, energetics and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer
34. Molecular dynamics simulations of a lipid bilayer and of hexadecane: An investigation of membrane fluidity
35. 15N chemical shift tensor of the gramicidin channel: A molecular dynamics and density functional study
36. Amino acid sequence modulation of gramicidin channel function: Effetcs of tryptophane-to-phenylalanine substitutions on the single-channel conductance and duration
37. Lipid properties and the orientation of aromatic residues in OmpF, influenza M2, and alamethicin systems: Molecular dynamics simulations
38. Deuterium nuclear magnetic resonance studies of the interaction between dimyristoylphosphatidylcholine and gramicidin a
39. Simulation study of a gramicidin/lipid bilayer system in excess water and lipid. I. Structure of the molecular complex
40. Simulation study of a gramicidin/lipid bilayer system in excess water and lipid. II. Rates and mechanisms of water transport
41. Solid-state 13c-nmr studies of the effects of sodium ions on the gramicidin a ion channel
42. Monovalent cation transport: Lack of structural deformation upon cation binding
43. The thallium ion distribution in the gramicidin channel by x-ray diffraction
44. Continuum solvation model: Electrostatic forces from numerical solutions to the Poisson-Bolztmann equation
45. Transmembrane channels based on tartaric acid-gramicidin A hybrid
46. Molecular mechanisms for proton transport in membranes
47. The formation and dynamics of proton wires in channel environments
48. B
49. Polarization model for water and its ionic dissociation products
50. Theoretical study of H+ translocation along a model proton wire
51. A combined molecular dynamics and diffusion model of single proton conduction through gramicidin
52. Framework model for single proton conduction through gramicidin
53. Free energy profiles for H+ conduction along hydrogen-bonded chains of water molecules
54. A molecular dynamics study of the pores formed by E. coli OmpF porin in a fully hydrated POPE bilayer
55. Structural determinants of MscL gating studied by molecular dynamics simulations
56. Molecular dynamics simulations of wild-type and mutant forms of the Mycobacterium tuberculosis MscL channel
57. Potassium and sodium binding to the outer mouth of the K+ channel
58. Simulations of ion permeation through a potassium channel: Molecular dynamics of KcsA in a phospholipid bilayer
59. Molecular dynamics of the KcsA K(+) channel in a bilayer membrane
60. + channels by TEA: Results from molecular dynamics simulations of the KcsA channel
61. Energetics of ion conduction through the k+ channel
62. The cavity and pore helices in the KcsA K+ channel: Electrostatic stabilization of monovalent cations
63. Boundary conditions for single-ion diffusion
64. A lattice relaxation algorithm for three-dimensional Poisson-Nernst-Planck theory with application to ion transport through the gramicidin A channel
65. Stochastic theory of ion movement in channels with single-ion occupancy. Application to sodium permeation of gramicidin channels
66. Permeation of ions across the potassium channel: Brownian dynamics studies
67. Grand canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels
68. Brownian dynamics solutions of ions channels: A general treatment of electrostatic reaction fields for molecular pores of arbitrary geometry