-
2
-
-
0031438285
-
A computer perspective of membranes: Molecular dynamics studies of lipid bilayer systems
-
Tieleman D.P., Marrink S.J., Berendsen H.J.C. A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. Biochim Biophys Acta. 1331:1997;235-270.
-
(1997)
Biochim Biophys Acta
, vol.1331
, pp. 235-270
-
-
Tieleman, D.P.1
Marrink, S.J.2
Berendsen, H.J.C.3
-
4
-
-
0032054195
-
Models and simulations of ion channels and related membrane proteins
-
Sansom M.S.P. Models and simulations of ion channels and related membrane proteins. Curr Opin Struct Biol. 8:1998;237-244.
-
(1998)
Curr Opin Struct Biol
, vol.8
, pp. 237-244
-
-
Sansom, M.S.P.1
-
5
-
-
0033066284
-
Interactions of α-helices with lipid bilayers: A review of simulation studies
-
Biggin P.C., Sansom M.S.P. Interactions of α-helices with lipid bilayers: a review of simulation studies. Biophys Chem. 76:1998;161-183.
-
(1998)
Biophys Chem
, vol.76
, pp. 161-183
-
-
Biggin, P.C.1
Sansom, M.S.P.2
-
6
-
-
5244326635
-
United atom force field for phospholipid membranes: Constant pressure molecular dynamics simulation of dipalmitoylphosphatidylcholine/water system
-
Smondyrev A.M., Berkowitz M.L. United atom force field for phospholipid membranes: constant pressure molecular dynamics simulation of dipalmitoylphosphatidylcholine/water system. J Comput Chem. 20:1999;531-545.
-
(1999)
J Comput Chem
, vol.20
, pp. 531-545
-
-
Smondyrev, A.M.1
Berkowitz, M.L.2
-
7
-
-
0000633114
-
Optimization of hydrocarbon chain interaction parameters: Application to the simulation of fluid phase lipid bilayers
-
Chiu S.W., Clark M.M., Jakobsson E., Subramaniam S., Scott H.L. Optimization of hydrocarbon chain interaction parameters: application to the simulation of fluid phase lipid bilayers. J Phys Chem B. 103:1999;6323-6327.
-
(1999)
J Phys Chem B
, vol.103
, pp. 6323-6327
-
-
Chiu, S.W.1
Clark, M.M.2
Jakobsson, E.3
Subramaniam, S.4
Scott, H.L.5
-
8
-
-
0031820877
-
Phospholipid component volumes: Determination and application to bilayer structure calculations
-
Armen R.S., Uitto O.D., Feller S.E. Phospholipid component volumes: determination and application to bilayer structure calculations. Biophys J. 75:1998;734-744.
-
(1998)
Biophys J
, vol.75
, pp. 734-744
-
-
Armen, R.S.1
Uitto, O.D.2
Feller, S.E.3
-
9
-
-
0001455442
-
βI) phase lipid bilayers
-
A study of bilayer simulation methods on gel phase systems that draws some important conclusions regarding the treatment of electrostatics (Ewald summation is preferable to spherical cut-offs). A thorough analysis of acyl chain trans/gauche properties and interface behaviour is used to provide a model for the slow crystallisation of such systems.
-
βI) phase lipid bilayers. J Chem Phys. 112:2000;4822-4832. A study of bilayer simulation methods on gel phase systems that draws some important conclusions regarding the treatment of electrostatics (Ewald summation is preferable to spherical cut-offs). A thorough analysis of acyl chain trans/gauche properties and interface behaviour is used to provide a model for the slow crystallisation of such systems.
-
(2000)
J Chem Phys
, vol.112
, pp. 4822-4832
-
-
Venable, R.M.1
Brooks, B.R.2
Pastor, R.W.3
-
10
-
-
0032614136
-
Constant surface tension simulations of lipid bilayers: The sensitivity of surface areas and compressibilities
-
This paper addresses a key issue of ensemble choice by varying the surface tension in eight 1 ns simulations of 72 DPPC lipids. In addition, the authors have compared several methods for determining the area compressibility modulus of a membrane.
-
Feller S.E., Pastor R.W. Constant surface tension simulations of lipid bilayers: the sensitivity of surface areas and compressibilities. J Chem Phys. 111:1999;1281-1287. This paper addresses a key issue of ensemble choice by varying the surface tension in eight 1 ns simulations of 72 DPPC lipids. In addition, the authors have compared several methods for determining the area compressibility modulus of a membrane.
-
(1999)
J Chem Phys
, vol.111
, pp. 1281-1287
-
-
Feller, S.E.1
Pastor, R.W.2
-
11
-
-
0000112789
-
Molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidycholine bilayer with different macroscopic boundary conditions and parameters
-
Tieleman D.P., Berendsen H.J.C. Molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidycholine bilayer with different macroscopic boundary conditions and parameters. J Chem Phys. 105:1996;4871-4880.
-
(1996)
J Chem Phys
, vol.105
, pp. 4871-4880
-
-
Tieleman, D.P.1
Berendsen, H.J.C.2
-
12
-
-
0033615312
-
Interpretation of NOESY cross relaxation rates from molecular dynamics simulation of a lipid bilayer
-
The authors introduce a novel technique for comparing (existing) NMR data and simulation results, as well as providing an interesting insight into lipid motions.
-
Feller S.E., Huster D., Gawrisch K. Interpretation of NOESY cross relaxation rates from molecular dynamics simulation of a lipid bilayer. J Am Chem Soc. 121:1999;8963-8964. The authors introduce a novel technique for comparing (existing) NMR data and simulation results, as well as providing an interesting insight into lipid motions.
-
(1999)
J Am Chem Soc
, vol.121
, pp. 8963-8964
-
-
Feller, S.E.1
Huster, D.2
Gawrisch, K.3
-
13
-
-
0033030567
-
Dynamical properties of phospholipid bilayers from computer simulation
-
Essman U., Berkowitz M.L. Dynamical properties of phospholipid bilayers from computer simulation. Biophys J. 76:1999;2081-2089.
-
(1999)
Biophys J
, vol.76
, pp. 2081-2089
-
-
Essman, U.1
Berkowitz, M.L.2
-
14
-
-
0000628431
-
Application of a multiple time step algorithm to biomolecular systems
-
Cheng A., Merz K.M.J. Application of a multiple time step algorithm to biomolecular systems. J Phys Chem B. 103:1999;5396-5405.
-
(1999)
J Phys Chem B
, vol.103
, pp. 5396-5405
-
-
Cheng, A.1
Merz, K.M.J.2
-
15
-
-
0001659533
-
Application of combined Monte Carlo and molecular dynamics method to simulation of dipalmitoyl phosphatidylcholine lipid bilayer
-
This paper provides an introduction to a novel combination of existing techniques that may be helpful in solving the problem of the long timescales of lipid mixing/equilibration in bilayer systems.
-
Chiu S.W., Clark M.M., Jakobsson E., Subramaniam S., Scott H.L. Application of combined Monte Carlo and molecular dynamics method to simulation of dipalmitoyl phosphatidylcholine lipid bilayer. J Comput Chem. 20:1999;1153-1164. This paper provides an introduction to a novel combination of existing techniques that may be helpful in solving the problem of the long timescales of lipid mixing/equilibration in bilayer systems.
-
(1999)
J Comput Chem
, vol.20
, pp. 1153-1164
-
-
Chiu, S.W.1
Clark, M.M.2
Jakobsson, E.3
Subramaniam, S.4
Scott, H.L.5
-
16
-
-
0032706178
-
Combined Monte Carlo and molecular dynamics simulation of fully-hydrated dioleyl and palmitoyl-oleyl phosphatidylcholine lipid bilayers
-
Chiu S.W., Jakobsson E., Subramaniam S., Scott H.L. Combined Monte Carlo and molecular dynamics simulation of fully-hydrated dioleyl and palmitoyl-oleyl phosphatidylcholine lipid bilayers. Biophys J. 77:1999;2462-2469.
-
(1999)
Biophys J
, vol.77
, pp. 2462-2469
-
-
Chiu, S.W.1
Jakobsson, E.2
Subramaniam, S.3
Scott, H.L.4
-
19
-
-
0000826117
-
Molecular dynamics study of Sn-1 and Sn-2 chain conformations in dipalmitoylphosphatidylcholine membranes
-
Smondyrev A.M., Berkowitz M.L. Molecular dynamics study of Sn-1 and Sn-2 chain conformations in dipalmitoylphosphatidylcholine membranes. J Chem Phys. 110:1999;3981-3985.
-
(1999)
J Chem Phys
, vol.110
, pp. 3981-3985
-
-
Smondyrev, A.M.1
Berkowitz, M.L.2
-
20
-
-
0031880829
-
Adhesion forces of lipids in a phospholipid membrane studied by molecular dynamics simulations
-
Marrink S.J., Berger O., Tieleman D.P., Jahnig F. Adhesion forces of lipids in a phospholipid membrane studied by molecular dynamics simulations. Biophys J. 74:1998;931-943.
-
(1998)
Biophys J
, vol.74
, pp. 931-943
-
-
Marrink, S.J.1
Berger, O.2
Tieleman, D.P.3
Jahnig, F.4
-
21
-
-
0032988825
-
Molecular dynamics simulation of DPPC bilayer in DMSO
-
Smondyrev A.M., Berkowitz M.L. Molecular dynamics simulation of DPPC bilayer in DMSO. Biophys J. 76:1999;2472-2478.
-
(1999)
Biophys J
, vol.76
, pp. 2472-2478
-
-
Smondyrev, A.M.1
Berkowitz, M.L.2
-
22
-
-
0032996881
-
Monte Carlo simulation of two-component bilayers: DMPC/DSPC mixtures
-
Sugár I.P., Thompson T.E., Biltonen R.L. Monte Carlo simulation of two-component bilayers: DMPC/DSPC mixtures. Biophys J. 76:1999;2099-2110.
-
(1999)
Biophys J
, vol.76
, pp. 2099-2110
-
-
Sugár, I.P.1
Thompson, T.E.2
Biltonen, R.L.3
-
23
-
-
0031752966
-
Constant-pressure molecular dynamics investigation of cholesterol effects in a dipalmitoylphosphatidyl-choline bilayer
-
Tu K., Klein M.L., Tobias D.J. Constant-pressure molecular dynamics investigation of cholesterol effects in a dipalmitoylphosphatidyl-choline bilayer. Biophys J. 75:1998;2147-2156.
-
(1998)
Biophys J
, vol.75
, pp. 2147-2156
-
-
Tu, K.1
Klein, M.L.2
Tobias, D.J.3
-
24
-
-
0032863720
-
Structure of dipalmitotylphosphatidyl- choline/cholesterol bilayer at low and high cholesterol concentrations: Molecular dynamics simulation
-
Smondyrev A.M., Berkowitz M.L. Structure of dipalmitotylphosphatidyl- choline/cholesterol bilayer at low and high cholesterol concentrations: molecular dynamics simulation. Biophys J. 77:1999;2075-2089.
-
(1999)
Biophys J
, vol.77
, pp. 2075-2089
-
-
Smondyrev, A.M.1
Berkowitz, M.L.2
-
25
-
-
4243747046
-
Interactions between indole and lipid bilayers studied by molecular dynamics and free energy calculations
-
Grossfield A., Woolf T.B. Interactions between indole and lipid bilayers studied by molecular dynamics and free energy calculations. Biophys J. 78:2000;324A.
-
(2000)
Biophys J
, vol.78
-
-
Grossfield, A.1
Woolf, T.B.2
-
26
-
-
0007461231
-
Indoles at interfaces: Calculations of electrostatic effects with density functional and molecular dynamics methods
-
Grossfield A., Woolf T.B., Pearson J.G. Indoles at interfaces: calculations of electrostatic effects with density functional and molecular dynamics methods. Int J Quant Chem. 25:1999;197-206.
-
(1999)
Int J Quant Chem
, vol.25
, pp. 197-206
-
-
Grossfield, A.1
Woolf, T.B.2
Pearson, J.G.3
-
27
-
-
0032789289
-
Molecular dynamics simulations of supported phospholipid/alkanethiol bilayers on a gold(111) surface
-
Tarek M., Tu K., Klein M.L., Tobias D.J. Molecular dynamics simulations of supported phospholipid/alkanethiol bilayers on a gold(111) surface. Biophys J. 77:1999;964-972.
-
(1999)
Biophys J
, vol.77
, pp. 964-972
-
-
Tarek, M.1
Tu, K.2
Klein, M.L.3
Tobias, D.J.4
-
28
-
-
0001363842
-
Molecular dynamics simulation of fluorination effects on a phospholipid bilayer
-
Smondyrev A.M., Berkowitz M.L. Molecular dynamics simulation of fluorination effects on a phospholipid bilayer. J Chem Phys. 111:1999;9864-9870.
-
(1999)
J Chem Phys
, vol.111
, pp. 9864-9870
-
-
Smondyrev, A.M.1
Berkowitz, M.L.2
-
29
-
-
0025249842
-
Membrane protein folding and oligomerization: The two-state model
-
Popot J.L., Engelman D.M. Membrane protein folding and oligomerization: the two-state model. Biochemistry. 29:1990;4031-4037.
-
(1990)
Biochemistry
, vol.29
, pp. 4031-4037
-
-
Popot, J.L.1
Engelman, D.M.2
-
31
-
-
0033037793
-
Simulation study of a gramicidin/lipid bilayer system in excess water and lipid. II. Rates and mechanisms of water transport
-
•]). The simulations reveal long-lasting hydrogen bonds between tryptophan sidechains and lipid headgroups. Water transport through the channel is analysed in detail.
-
•]). The simulations reveal long-lasting hydrogen bonds between tryptophan sidechains and lipid headgroups. Water transport through the channel is analysed in detail.
-
(1999)
Biophys J
, vol.76
, pp. 1939-1950
-
-
Chiu, S.W.1
Subramaniam, S.2
Jakobsson, E.3
-
32
-
-
0032850757
-
Constructing the suitable initial configuration of the membrane-protein system in molecular dynamics simulations
-
Tang Y.Z., Chen W.Z., Wang C.X., Shi Y.Y. Constructing the suitable initial configuration of the membrane-protein system in molecular dynamics simulations. Eur Biophys J. 28:1999;478-488.
-
(1999)
Eur Biophys J
, vol.28
, pp. 478-488
-
-
Tang, Y.Z.1
Chen, W.Z.2
Wang, C.X.3
Shi, Y.Y.4
-
33
-
-
0030966534
-
Transmembrane helix structure, dynamics, and interactions: Multi-nanosecond molecular dynamics simulations
-
Shen L., Bassolino D., Stouch T. Transmembrane helix structure, dynamics, and interactions: multi-nanosecond molecular dynamics simulations. Biophys J. 73:1997;3-20.
-
(1997)
Biophys J
, vol.73
, pp. 3-20
-
-
Shen, L.1
Bassolino, D.2
Stouch, T.3
-
34
-
-
0030733344
-
Structure and dynamics of an amphiphilic peptide in a lipid bilayer: A molecular dynamics study
-
Belohorcova K., Davis J.H., Woolf T.B., Roux B. Structure and dynamics of an amphiphilic peptide in a lipid bilayer: a molecular dynamics study. Biophys J. 73:1997;3039-3055.
-
(1997)
Biophys J
, vol.73
, pp. 3039-3055
-
-
Belohorcova, K.1
Davis, J.H.2
Woolf, T.B.3
Roux, B.4
-
35
-
-
0030731888
-
Molecular dynamics of individual α-helices of bacteriorhodopsin in dimyristoyl phosphatidylcholine. I. Structure and dynamics
-
Woolf T.B. Molecular dynamics of individual α-helices of bacteriorhodopsin in dimyristoyl phosphatidylcholine. I. Structure and dynamics. Biophys J. 73:1997;2376-2392.
-
(1997)
Biophys J
, vol.73
, pp. 2376-2392
-
-
Woolf, T.B.1
-
36
-
-
0031961813
-
Molecular dynamics of individual α-helices of bacteriorhodopsin in dimyristoyl phosphatidylcholine. II. Interaction energy analysis
-
A detailed analysis of the interactions of individual helices from bacteriorhodopsin with DMPC bilayers. Aromatic sidechains are seen to interact with the lipid/water interface.
-
Woolf T.B. Molecular dynamics of individual α-helices of bacteriorhodopsin in dimyristoyl phosphatidylcholine. II. Interaction energy analysis. Biophys J. 74:1998;115-131. A detailed analysis of the interactions of individual helices from bacteriorhodopsin with DMPC bilayers. Aromatic sidechains are seen to interact with the lipid/water interface.
-
(1998)
Biophys J
, vol.74
, pp. 115-131
-
-
Woolf, T.B.1
-
37
-
-
0022510143
-
Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins
-
Engelman D.M., Steitz T.A., Goldman A. Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu Rev Biophys Biophys Chem. 15:1986;321-353.
-
(1986)
Annu Rev Biophys Biophys Chem
, vol.15
, pp. 321-353
-
-
Engelman, D.M.1
Steitz, T.A.2
Goldman, A.3
-
38
-
-
0032992048
-
Defining the transmembrane helix of M2 protein from influenza A by molecular dynamics simulations in a lipid bilayer
-
This paper describes the use of multiple molecular dynamics simulations in a POPC bilayer to aid the definition of the transmembrane helix of the M2 channel protein from influenza A.
-
Forrest L.R., Tieleman D.P., Sansom M.S.P. Defining the transmembrane helix of M2 protein from influenza A by molecular dynamics simulations in a lipid bilayer. Biophys J. 76:1999;1886-1896. This paper describes the use of multiple molecular dynamics simulations in a POPC bilayer to aid the definition of the transmembrane helix of the M2 channel protein from influenza A.
-
(1999)
Biophys J
, vol.76
, pp. 1886-1896
-
-
Forrest, L.R.1
Tieleman, D.P.2
Sansom, M.S.P.3
-
39
-
-
0034097318
-
Single transmembrane helices of viral ion channels in a lipid/water environment- A molecular dynamic simulation study
-
in press.
-
Fischer W., Forrest L.R., Smith G.R., Sansom M.S.P. Single transmembrane helices of viral ion channels in a lipid/water environment- a molecular dynamic simulation study. Biopolymers. 53:2000;. in press.
-
(2000)
Biopolymers
, vol.53
-
-
Fischer, W.1
Forrest, L.R.2
Smith, G.R.3
Sansom, M.S.P.4
-
41
-
-
0032925194
-
Isolated transmembrane helices arranged across a membrane: Computational studies
-
Tseitin V.M., Nikiforovich G.V. Isolated transmembrane helices arranged across a membrane: computational studies. Protein Eng. 12:1999;305-311.
-
(1999)
Protein Eng
, vol.12
, pp. 305-311
-
-
Tseitin, V.M.1
Nikiforovich, G.V.2
-
42
-
-
0033412548
-
Peptides in membranes: Assessment of environmental effects via simulations using an implicit solvation model
-
Efremov R.G., Nolde D.E., Vergoten G., Arseniev A.S. Peptides in membranes: assessment of environmental effects via simulations using an implicit solvation model. Theor Chem Accounts. 101:1999;170-174.
-
(1999)
Theor Chem Accounts
, vol.101
, pp. 170-174
-
-
Efremov, R.G.1
Nolde, D.E.2
Vergoten, G.3
Arseniev, A.S.4
-
43
-
-
0032991265
-
A solvent model for simulations of peptides in bilayers. I. Membrane-promoting alpha-helix formation
-
Efremov R.G., Nolde D.E., Vergoten G., Arseniev A.S. A solvent model for simulations of peptides in bilayers. I. Membrane-promoting alpha-helix formation. Biophys J. 76:1999;2448-2459.
-
(1999)
Biophys J
, vol.76
, pp. 2448-2459
-
-
Efremov, R.G.1
Nolde, D.E.2
Vergoten, G.3
Arseniev, A.S.4
-
44
-
-
0032991267
-
A solvent model for simulations of peptides in bilayers. II. Membrane-spanning alpha-helices
-
Efremov R.G., Nolde D.E., Vergoten G., Arseniev A.S. A solvent model for simulations of peptides in bilayers. II. Membrane-spanning alpha-helices. Biophys J. 76:1999;2460-2471.
-
(1999)
Biophys J
, vol.76
, pp. 2460-2471
-
-
Efremov, R.G.1
Nolde, D.E.2
Vergoten, G.3
Arseniev, A.S.4
-
45
-
-
0000011122
-
Mechanism of the unfolding of transmembrane alpha-helical segment (1-36)-bacteriorhodopsin studied by molecular dynamics simulations
-
Korzhnev D.M., Orekhov V.Y., Arseniev A.S., Gratias R., Kessler H. Mechanism of the unfolding of transmembrane alpha-helical segment (1-36)-bacteriorhodopsin studied by molecular dynamics simulations. J Phys Chem B. 103:1999;7036-7043.
-
(1999)
J Phys Chem B
, vol.103
, pp. 7036-7043
-
-
Korzhnev, D.M.1
Orekhov, V.Y.2
Arseniev, A.S.3
Gratias, R.4
Kessler, H.5
-
46
-
-
0030916534
-
Helix bending in alamethicin: Molecular dynamics simulations and amide hydrogen exchange in methanol
-
Gibbs N., Sessions R.B., Williams P.B., Dempsey C.E. Helix bending in alamethicin: molecular dynamics simulations and amide hydrogen exchange in methanol. Biophys J. 72:1997;2490-2495.
-
(1997)
Biophys J
, vol.72
, pp. 2490-2495
-
-
Gibbs, N.1
Sessions, R.B.2
Williams, P.B.3
Dempsey, C.E.4
-
47
-
-
0032951553
-
Alamethicin helices in a bilayer and in solution: Molecular dynamics simulations
-
Tieleman D.P., Sansom M.S.P., Berendsen H.J.C. Alamethicin helices in a bilayer and in solution: molecular dynamics simulations. Biophys J. 76:1999;40-49.
-
(1999)
Biophys J
, vol.76
, pp. 40-49
-
-
Tieleman, D.P.1
Sansom, M.S.P.2
Berendsen, H.J.C.3
-
48
-
-
0028921479
-
Acetylcholine receptor channel imaged in the open state
-
Unwin N. Acetylcholine receptor channel imaged in the open state. Nature. 373:1995;37-43.
-
(1995)
Nature
, vol.373
, pp. 37-43
-
-
Unwin, N.1
-
49
-
-
0033996292
-
Structure and dynamics of the pore-lining helix of the nicotinic receptor: MD simulations in water, lipid bilayers and transbilayer bundles
-
5 helix bundle in a bilayer suggest the occurrence of hinge-bending motions of the helix that may be related to channel gating.
-
5 helix bundle in a bilayer suggest the occurrence of hinge-bending motions of the helix that may be related to channel gating.
-
(2000)
Proteins
, vol.39
-
-
Law, R.J.1
Forrest, L.R.2
Ranatunga, K.M.3
La Rocca, P.4
Tieleman, D.P.5
Sansom, M.S.P.6
-
50
-
-
0033063884
-
The role of a conserved proline residue in mediating conformational changes associated with voltage gating of Cx32 gap junctions
-
Ri Y., Ballesteros J.A., Abrams C.K., Oh S., Verselis V.K., Weinstein H., Bargiello T.A. The role of a conserved proline residue in mediating conformational changes associated with voltage gating of Cx32 gap junctions. Biophys J. 76:1999;2887-2898.
-
(1999)
Biophys J
, vol.76
, pp. 2887-2898
-
-
Ri, Y.1
Ballesteros, J.A.2
Abrams, C.K.3
Oh, S.4
Verselis, V.K.5
Weinstein, H.6
Bargiello, T.A.7
-
51
-
-
0043206834
-
Molecular dynamics simulation of membranes and a transmembrane helix
-
Simulations of the isolated transmembrane helix 7 of a G-protein-coupled receptor in a DMPC bilayer suggest the occurrence of hinge bending on a nanosecond timescale.
-
Duong T.H., Mehler E.L., Weinstein H. Molecular dynamics simulation of membranes and a transmembrane helix. J Comp Phys. 151:1999;358-387. Simulations of the isolated transmembrane helix 7 of a G-protein-coupled receptor in a DMPC bilayer suggest the occurrence of hinge bending on a nanosecond timescale.
-
(1999)
J Comp Phys
, vol.151
, pp. 358-387
-
-
Duong, T.H.1
Mehler, E.L.2
Weinstein, H.3
-
52
-
-
0033010267
-
Molecular dynamics simulations of the ErbB-2 transmembrane domain within an explicit membrane environment: Comparison with vacuum simulations
-
Simulations of the isolated transmembrane helix from the ErbB-2 tyrosine kinase receptor in DLPE bilayers reveal local formation of π helix. This extends previous work from these authors, who had seen a π helix distortion of transmembrane helices in in vacuo simulations.
-
Duneau J.P., Crouzy S., Garnier N., Chapron Y., Genest M. Molecular dynamics simulations of the ErbB-2 transmembrane domain within an explicit membrane environment: comparison with vacuum simulations. Biophys Chem. 76:1999;35-53. Simulations of the isolated transmembrane helix from the ErbB-2 tyrosine kinase receptor in DLPE bilayers reveal local formation of π helix. This extends previous work from these authors, who had seen a π helix distortion of transmembrane helices in in vacuo simulations.
-
(1999)
Biophys Chem
, vol.76
, pp. 35-53
-
-
Duneau, J.P.1
Crouzy, S.2
Garnier, N.3
Chapron, Y.4
Genest, M.5
-
54
-
-
0033581879
-
Structural changes linked to proton translocation by subunit c of the ATP synthase
-
Rastogi V.K., Girvin M.E. Structural changes linked to proton translocation by subunit c of the ATP synthase. Nature. 402:1999;263-268.
-
(1999)
Nature
, vol.402
, pp. 263-268
-
-
Rastogi, V.K.1
Girvin, M.E.2
-
55
-
-
0011613265
-
Molecular dynamics simulation of melittin in a dimyristoylphosphatidylcholine bilayer membrane
-
Simulations of melittin at the surface of a DMPC bilayer suggest a possible mechanism for membrane destabilisation.
-
Bernèche S., Nina M., Roux B. Molecular dynamics simulation of melittin in a dimyristoylphosphatidylcholine bilayer membrane. Biophys J. 75:1998;1603-1618. Simulations of melittin at the surface of a DMPC bilayer suggest a possible mechanism for membrane destabilisation.
-
(1998)
Biophys J
, vol.75
, pp. 1603-1618
-
-
Bernèche, S.1
Nina, M.2
Roux, B.3
-
56
-
-
0001183580
-
Melittin at a membrane/water interface: Effects on water orientation and water penetration
-
Bachar M., Becker O.M. Melittin at a membrane/water interface: effects on water orientation and water penetration. J Chem Phys. 111:1999;8672-8685.
-
(1999)
J Chem Phys
, vol.111
, pp. 8672-8685
-
-
Bachar, M.1
Becker, O.M.2
-
57
-
-
0032998180
-
Surface binding of alamethicin stabilises its helical structure: Molecular dynamics simulations
-
Tieleman D.P., Berendsen H.J.C., Sansom M.S.P. Surface binding of alamethicin stabilises its helical structure: molecular dynamics simulations. Biophys J. 76:1999;3186-3191.
-
(1999)
Biophys J
, vol.76
, pp. 3186-3191
-
-
Tieleman, D.P.1
Berendsen, H.J.C.2
Sansom, M.S.P.3
-
58
-
-
0342999428
-
An antimicrobial peptide at the surface of a phospholipid bilayer: Molecular dynamics simulations of dermaseptin B
-
in press
-
La Rocca P., Sansom M.S.P. An antimicrobial peptide at the surface of a phospholipid bilayer: molecular dynamics simulations of dermaseptin B. Eur Biophys J. 2000;. in press.
-
(2000)
Eur Biophys J
-
-
La Rocca, P.1
Sansom, M.S.P.2
-
59
-
-
0032790341
-
Early events in the folding of an amphipathic peptide: A multinanosecond molecular dynamics study
-
Attempts to fold a simple peptide at a water/hydrophobic interface in order to form an amphipathic α helix reveal the long (≥ 100 ns) timescale of this process.
-
Chipot C., Maigret B., Pohorille A. Early events in the folding of an amphipathic peptide: a multinanosecond molecular dynamics study. Proteins. 36:1999;383-399. Attempts to fold a simple peptide at a water/hydrophobic interface in order to form an amphipathic α helix reveal the long (≥ 100 ns) timescale of this process.
-
(1999)
Proteins
, vol.36
, pp. 383-399
-
-
Chipot, C.1
Maigret, B.2
Pohorille, A.3
-
60
-
-
85031644248
-
The secondary structure of dynorphin A (1-17) defines a stable geometry of immersion in phospholipid bilayers
-
Sankararamakrishnan R., Weinstein H. The secondary structure of dynorphin A (1-17) defines a stable geometry of immersion in phospholipid bilayers. Biophys J. 78:2000;321A.
-
(2000)
Biophys J
, vol.78
-
-
Sankararamakrishnan, R.1
Weinstein, H.2
-
61
-
-
0033067113
-
Peptide/bilayer interactions: Simulations of dermaseptin B, an antimicrobial peptide
-
La Rocca P., Shai Y., Sansom M.S.P. Peptide/bilayer interactions: simulations of dermaseptin B, an antimicrobial peptide. Biophys Chem. 76:1999;145-159.
-
(1999)
Biophys Chem
, vol.76
, pp. 145-159
-
-
La Rocca, P.1
Shai, Y.2
Sansom, M.S.P.3
-
62
-
-
0032826793
-
Molecular dynamics simulation of α-melanocyte stimulating hormone in a water-membrane model interface
-
Pascutti P.G., ElJaik L.J., Bisch P.M., Mundim K.C., Ito A.S. Molecular dynamics simulation of α-melanocyte stimulating hormone in a water-membrane model interface. Eur Biophys J. 28:1999;499-509.
-
(1999)
Eur Biophys J
, vol.28
, pp. 499-509
-
-
Pascutti, P.G.1
Eljaik, L.J.2
Bisch, P.M.3
Mundim, K.C.4
Ito, A.S.5
-
63
-
-
0032982468
-
Molecular dynamics study of substance P peptides in a biphasic membrane mimic
-
Wymore T., Wong T.C. Molecular dynamics study of substance P peptides in a biphasic membrane mimic. Biophys J. 76:1999;1199-1212.
-
(1999)
Biophys J
, vol.76
, pp. 1199-1212
-
-
Wymore, T.1
Wong, T.C.2
-
64
-
-
0032874786
-
The alignment of a voltage-sensing peptide in dodecylphosphocholine micelles and in oriented lipid bilayers by nuclear magnetic resonance and molecular modelling
-
Mattila K., Kinder R., Bechinger B. The alignment of a voltage-sensing peptide in dodecylphosphocholine micelles and in oriented lipid bilayers by nuclear magnetic resonance and molecular modelling. Biophys J. 77:1999;2102-2113.
-
(1999)
Biophys J
, vol.77
, pp. 2102-2113
-
-
Mattila, K.1
Kinder, R.2
Bechinger, B.3
-
65
-
-
0033047067
-
Molecular dynamics study of substance P peptides partitioned in a sodium dodecylsulfate micelle
-
Wymore T., Wong T.C. Molecular dynamics study of substance P peptides partitioned in a sodium dodecylsulfate micelle. Biophys J. 76:1999;1213-1227.
-
(1999)
Biophys J
, vol.76
, pp. 1213-1227
-
-
Wymore, T.1
Wong, T.C.2
-
67
-
-
0033035249
-
An alamethicin channel in a lipid bilayer:- molecular dynamics simulations
-
•]) reveal the complex dynamic properties of water molecules within transbilayer pores.
-
•]) reveal the complex dynamic properties of water molecules within transbilayer pores.
-
(1999)
Biophys J
, vol.76
, pp. 1757-1769
-
-
Tieleman, D.P.1
Berendsen, H.J.C.2
Sansom, M.S.P.3
-
69
-
-
0023907575
-
Synthetic amphiphilic peptide models for protein ion channels
-
Lear J.D., Wasserman Z.R., DeGrado W.F. Synthetic amphiphilic peptide models for protein ion channels. Science. 240:1988;1177-1181.
-
(1988)
Science
, vol.240
, pp. 1177-1181
-
-
Lear, J.D.1
Wasserman, Z.R.2
DeGrado, W.F.3
-
70
-
-
0032989631
-
Exploration of the structural features defining the conduction properties of a synthetic ion channel
-
Dieckmann G.R., Lear J.D., Zhong Q., Klein M.L., DeGrado W.F., Sharp K.A. Exploration of the structural features defining the conduction properties of a synthetic ion channel. Biophys J. 76:1999;618-630.
-
(1999)
Biophys J
, vol.76
, pp. 618-630
-
-
Dieckmann, G.R.1
Lear, J.D.2
Zhong, Q.3
Klein, M.L.4
DeGrado, W.F.5
Sharp, K.A.6
-
71
-
-
0032496397
-
Molecular dynamics study of the LS3 voltage-gated ion channel
-
Zhong Q., Moore P.B., Newns D.M., Klein M.L. Molecular dynamics study of the LS3 voltage-gated ion channel. FEBS Lett. 427:1998;267-270.
-
(1998)
FEBS Lett
, vol.427
, pp. 267-270
-
-
Zhong, Q.1
Moore, P.B.2
Newns, D.M.3
Klein, M.L.4
-
72
-
-
0032705715
-
Molecular dynamics of synthetic leucine-serine ion channels in a phospholipid membrane
-
Simulations of ion channels formed by bundles of synthetic α helices suggest that differences in the behaviour of water within two channels correlate with differences in their ion transport properties.
-
Randa H.S., Forrest L.R., Voth G.A., Sansom M.S.P. Molecular dynamics of synthetic leucine-serine ion channels in a phospholipid membrane. Biophys J. 77:1999;2400-2410. Simulations of ion channels formed by bundles of synthetic α helices suggest that differences in the behaviour of water within two channels correlate with differences in their ion transport properties.
-
(1999)
Biophys J
, vol.77
, pp. 2400-2410
-
-
Randa, H.S.1
Forrest, L.R.2
Voth, G.A.3
Sansom, M.S.P.4
-
73
-
-
0032410913
-
Two models of the influenza A M2 channel domain: Verification by comparison
-
Forrest L.R., DeGrado W.F., Dieckmann G.R., Sansom M.S.P. Two models of the influenza A M2 channel domain: verification by comparison. Fold Des. 3:1998;443-448.
-
(1998)
Fold des
, vol.3
, pp. 443-448
-
-
Forrest, L.R.1
DeGrado, W.F.2
Dieckmann, G.R.3
Sansom, M.S.P.4
-
74
-
-
0032434323
-
The M2 channel of influenza A virus: A molecular dynamics study
-
Zhong Q., Husslein T., Moore P.B., Newns D.M., Pattnaik P., Klein M.L. The M2 channel of influenza A virus: a molecular dynamics study. FEBS Lett. 434:1998;265-271.
-
(1998)
FEBS Lett
, vol.434
, pp. 265-271
-
-
Zhong, Q.1
Husslein, T.2
Moore, P.B.3
Newns, D.M.4
Pattnaik, P.5
Klein, M.L.6
-
75
-
-
0342564998
-
Molecular dynamics study of structure and gating of low molecular weight ion channels
-
in press
-
Newns D.M., Zhong Q., Moore P.B., Husslein T., Pattnaik P., Klein M.L. Molecular dynamics study of structure and gating of low molecular weight ion channels. J Comput Chem. 2000;. in press.
-
(2000)
J Comput Chem
-
-
Newns, D.M.1
Zhong, Q.2
Moore, P.B.3
Husslein, T.4
Pattnaik, P.5
Klein, M.L.6
-
76
-
-
0034030929
-
Exploring models of the influenza A M2 channel: MD simulations in a lipid bilayer
-
Forrest L.R., Kukol A., Arkin I.T., Tieleman D.P., Sansom M.S.P. Exploring models of the influenza A M2 channel: MD simulations in a lipid bilayer. Biophys J. 78:2000;55-69.
-
(2000)
Biophys J
, vol.78
, pp. 55-69
-
-
Forrest, L.R.1
Kukol, A.2
Arkin, I.T.3
Tieleman, D.P.4
Sansom, M.S.P.5
-
77
-
-
0032442211
-
Viral ion channels: Molecular modelling and simulation
-
Sansom M.S.P., Forrest L.R., Bull R. Viral ion channels: molecular modelling and simulation. Bioessays. 20:1998;992-1000.
-
(1998)
Bioessays
, vol.20
, pp. 992-1000
-
-
Sansom, M.S.P.1
Forrest, L.R.2
Bull, R.3
-
78
-
-
0032540881
-
Simulation of the HIV-1 Vpu transmembrane domain as a pentameric bundle
-
Moore P.B., Zhong Q., Husslein T., Klein M.L. Simulation of the HIV-1 Vpu transmembrane domain as a pentameric bundle. FEBS Lett. 431:1998;143-148.
-
(1998)
FEBS Lett
, vol.431
, pp. 143-148
-
-
Moore, P.B.1
Zhong, Q.2
Husslein, T.3
Klein, M.L.4
-
79
-
-
0342999422
-
The use of molecular dynamics in de novo design: Application to a transmembrane four-helix coiled coil
-
Tieleman D.P., Choma C.T., Berendsen H.J.C. The use of molecular dynamics in de novo design: application to a transmembrane four-helix coiled coil. Biophys J. 76:1999;A426.
-
(1999)
Biophys J
, vol.76
, pp. 426
-
-
Tieleman, D.P.1
Choma, C.T.2
Berendsen, H.J.C.3
-
80
-
-
0031860932
-
A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer
-
A landmark simulation of a large and complex membrane protein that demonstrated the feasibility of such studies.
-
Tieleman D.P., Berendsen H.J.C. A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer. Biophys J. 74:1998;2786-2801. A landmark simulation of a large and complex membrane protein that demonstrated the feasibility of such studies.
-
(1998)
Biophys J
, vol.74
, pp. 2786-2801
-
-
Tieleman, D.P.1
Berendsen, H.J.C.2
-
82
-
-
0034036372
-
Simulations of ion permeation through a K channel: Molecular dynamics of KcsA in a phospholipid bilayer
-
•], describes the use of molecular dynamics simulations to relate the recently determined structure of a bacterial potassium channel to its physiological function.
-
•], describes the use of molecular dynamics simulations to relate the recently determined structure of a bacterial potassium channel to its physiological function.
-
(2000)
Biophys J
, vol.78
, pp. 557-570
-
-
Shrivastava, I.H.1
Sansom, M.S.P.2
-
83
-
-
0034123344
-
Homology modelling and molecular dynamics simulation studies of an inward rectifier potassium channel
-
in press
-
Capener C.E., Shrivastava I.H., Ranatunga K.M., Forrest L.R., Smith G.R., Sansom M.S.P. Homology modelling and molecular dynamics simulation studies of an inward rectifier potassium channel. Biophys J. 78:2000;. in press.
-
(2000)
Biophys J
, vol.78
-
-
Capener, C.E.1
Shrivastava, I.H.2
Ranatunga, K.M.3
Forrest, L.R.4
Smith, G.R.5
Sansom, M.S.P.6
-
84
-
-
0032750783
-
Molecular dynamics study of the KcsA potassium channel
-
Allen T.W., Kuyucak S., Chung S.H. Molecular dynamics study of the KcsA potassium channel. Biophys J. 77:1999;2502-2516.
-
(1999)
Biophys J
, vol.77
, pp. 2502-2516
-
-
Allen, T.W.1
Kuyucak, S.2
Chung, S.H.3
-
85
-
-
0032534843
-
Lipid properties and the orientation of aromatic residues in OmpF, influenza M2 and alamethicin systems: Molecular dynamics simulations
-
Tieleman D.P., Forrest L.R., Berendsen H.J.C., Sansom M.S.P. Lipid properties and the orientation of aromatic residues in OmpF, influenza M2 and alamethicin systems: molecular dynamics simulations. Biochemistry. 37:1999;17554-17561.
-
(1999)
Biochemistry
, vol.37
, pp. 17554-17561
-
-
Tieleman, D.P.1
Forrest, L.R.2
Berendsen, H.J.C.3
Sansom, M.S.P.4
-
86
-
-
2542637112
-
Molecular dynamics simulation of a hydrated diphytanol phosphatidylcholine lipid bilayer containing an alpha-helical bundle of four transmembrane domains of the influenza A virus M2 protein
-
Husslein T., Moore P.B., Zhong Q.F., Newns D.M., Pattnaik P.C., Klein M.L. Molecular dynamics simulation of a hydrated diphytanol phosphatidylcholine lipid bilayer containing an alpha-helical bundle of four transmembrane domains of the influenza A virus M2 protein. Faraday Disc. 111:1998;201-208.
-
(1998)
Faraday Disc
, vol.111
, pp. 201-208
-
-
Husslein, T.1
Moore, P.B.2
Zhong, Q.F.3
Newns, D.M.4
Pattnaik, P.C.5
Klein, M.L.6
-
87
-
-
0034039757
-
Computer simulations of ion channel gating: The M2 channel of influenza A virus in a lipid bilayer
-
Schweighofer K.J., Pohorille A. Computer simulations of ion channel gating: the M2 channel of influenza A virus in a lipid bilayer. Biophys J. 78:2000;150-163.
-
(2000)
Biophys J
, vol.78
, pp. 150-163
-
-
Schweighofer, K.J.1
Pohorille, A.2
-
88
-
-
0034068919
-
Stability of a melittin pore in a lipid bilayer: A molecular dynamics study
-
in press
-
Lin J-S., Baumgaertner A. Stability of a melittin pore in a lipid bilayer: a molecular dynamics study. Biophys J. 78:2000;. in press.
-
(2000)
Biophys J
, vol.78
-
-
Lin, J.-S.1
Baumgaertner, A.2
|