-
1
-
-
24644490119
-
Comparative analysis of amino acid distributions in integral membrane proteins from 107 genomes
-
Nilsson, J., B. Persson, and G. von Heijne. 2005. Comparative analysis of amino acid distributions in integral membrane proteins from 107 genomes. Proteins. 60:606-616.
-
(2005)
Proteins
, vol.60
, pp. 606-616
-
-
Nilsson, J.1
Persson, B.2
Von Heijne, G.3
-
3
-
-
0034284386
-
How proteins adapt to a membrane-water interface
-
Killian, J. A., and G. von Heijne. 2000. How proteins adapt to a membrane-water interface. Trends Biochem. Sci. 25:429-434.
-
(2000)
Trends Biochem. Sci.
, vol.25
, pp. 429-434
-
-
Killian, J.A.1
Von Heijne, G.2
-
4
-
-
70849119657
-
Structure and hydration of membranes embedded with voltage-sensing domains
-
Krepkiy, D., M. Mihailescu,..., K. J. Swartz. 2009. Structure and hydration of membranes embedded with voltage-sensing domains. Nature. 462:473-479.
-
(2009)
Nature
, vol.462
, pp. 473-479
-
-
Krepkiy, D.1
Mihailescu, M.2
Swartz, K.J.3
-
5
-
-
57749196006
-
Sensing voltage across lipid membranes
-
Swartz, K. J. 2008. Sensing voltage across lipid membranes. Nature. 456:891-897.
-
(2008)
Nature
, vol.456
, pp. 891-897
-
-
Swartz, K.J.1
-
7
-
-
36248982122
-
+ channel in a lipid membrane-like environment
-
+ channel in a lipid membrane-like environment. Nature. 450:376-382.
-
(2007)
Nature
, vol.450
, pp. 376-382
-
-
Long, S.B.1
Tao, X.2
MacKinnon, R.3
-
8
-
-
0014481138
-
Energy of an ion crossing a low dielectric membrane: Solutions to four relevant electrostatic problems
-
Parsegian, A. 1969. Energy of an ion crossing a low dielectric membrane: solutions to four relevant electrostatic problems. Nature. 221:844-846.
-
(1969)
Nature
, vol.221
, pp. 844-846
-
-
Parsegian, A.1
-
9
-
-
20044389842
-
Membrane insertion of a potassium-channel voltage sensor
-
Hessa, T., S. H. White, and G. von Heijne. 2005. Membrane insertion of a potassium-channel voltage sensor. Science. 307:1427.
-
(2005)
Science
, vol.307
, pp. 1427
-
-
Hessa, T.1
White, S.H.2
Von Heijne, G.3
-
10
-
-
27244444569
-
Interface connections of a transmembrane voltage sensor
-
Freites, J. A., D. J. Tobias,..., S. H. White. 2005. Interface connections of a transmembrane voltage sensor. Proc. Natl. Acad. Sci. USA. 102:15059-15064.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 15059-15064
-
-
Freites, J.A.1
Tobias, D.J.2
White, S.H.3
-
11
-
-
34547622288
-
Modeling charged protein side chains in lipid membranes
-
Allen, T. W. 2007. Modeling charged protein side chains in lipid membranes. J. Gen. Physiol. 130:237-240.
-
(2007)
J. Gen. Physiol.
, vol.130
, pp. 237-240
-
-
Allen, T.W.1
-
12
-
-
34247633528
-
On the thermodynamic stability of a charged arginine side chain in a transmembrane helix
-
Dorairaj, S., and T. W. Allen. 2007. On the thermodynamic stability of a charged arginine side chain in a transmembrane helix. Proc. Natl. Acad. Sci. USA. 104:4943-4948.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 4943-4948
-
-
Dorairaj, S.1
Allen, T.W.2
-
13
-
-
43649094583
-
Distribution of amino acids in a lipid bilayer from computer simulations
-
MacCallum, J. L., W. F. D. Bennett, and D. P. Tieleman. 2008. Distribution of amino acids in a lipid bilayer from computer simulations. Biophys. J. 94:3393-3404.
-
(2008)
Biophys. J.
, vol.94
, pp. 3393-3404
-
-
MacCallum, J.L.1
Bennett, W.F.D.2
Tieleman, D.P.3
-
14
-
-
34247098754
-
Multiscale modeling of biomolecular systems: In serial and in parallel
-
Ayton, G. S., W. G. Noid, and G. A. Voth. 2007. Multiscale modeling of biomolecular systems: in serial and in parallel. Curr. Opin. Struct. Biol. 17:192-198.
-
(2007)
Curr. Opin. Struct. Biol.
, vol.17
, pp. 192-198
-
-
Ayton, G.S.1
Noid, W.G.2
Voth, G.A.3
-
15
-
-
53249150686
-
Coarse-grained molecular dynamics simulations of the energetics of helix insertion into a lipid bilayer
-
Bond, P. J., C. L. Wee, and M. S. P. Sansom. 2008. Coarse-grained molecular dynamics simulations of the energetics of helix insertion into a lipid bilayer. Biochemistry. 47:11321-11331.
-
(2008)
Biochemistry
, vol.47
, pp. 11321-11331
-
-
Bond, P.J.1
Wee, C.L.2
Sansom, M.S.P.3
-
16
-
-
1642485164
-
Coarse grained model for semiquantitative lipid simulations
-
Marrink, S. J., A. H. de Vries, and A. E. Mark. 2004. Coarse grained model for semiquantitative lipid simulations. J. Phys. Chem. B. 108:750-760.
-
(2004)
J. Phys. Chem. B.
, vol.108
, pp. 750-760
-
-
Marrink, S.J.1
De Vries, A.H.2
Mark, A.E.3
-
18
-
-
33644893631
-
Coarse grained protein-lipid model with application to lipoprotein particles
-
Shih, A. Y., A. Arkhipov,..., K. Schulten. 2006. Coarse grained protein-lipid model with application to lipoprotein particles. J. Phys. Chem. B. 110:3674-3684.
-
(2006)
J. Phys. Chem. B.
, vol.110
, pp. 3674-3684
-
-
Shih, A.Y.1
Arkhipov, A.2
Schulten, K.3
-
19
-
-
0035902367
-
A coarse grain model for phospholipid simulations
-
Shelley, J. C., M. Y. Shelley,..., M. L. Klein. 2001. A coarse grain model for phospholipid simulations. J. Phys. Chem. B. 105:4464-4470.
-
(2001)
J. Phys. Chem. B.
, vol.105
, pp. 4464-4470
-
-
Shelley, J.C.1
Shelley, M.Y.2
Klein, M.L.3
-
20
-
-
14544291957
-
A multiscale coarse-graining method for biomolecular systems
-
Izvekov, S., and G. A. Voth. 2005. A multiscale coarse-graining method for biomolecular systems. J. Phys. Chem. B. 109:2469-2473.
-
(2005)
J. Phys. Chem. B.
, vol.109
, pp. 2469-2473
-
-
Izvekov, S.1
Voth, G.A.2
-
21
-
-
17044393884
-
Coarse-grained models for proteins
-
Tozzini, V. 2005. Coarse-grained models for proteins. Curr. Opin. Struct. Biol. 15:144-150.
-
(2005)
Curr. Opin. Struct. Biol.
, vol.15
, pp. 144-150
-
-
Tozzini, V.1
-
22
-
-
77950154198
-
Membrane/toxin interaction energetics via serial multi-scale molecular dynamics simulations
-
Wee, C. L., M. B. Ulmschneider, and M. S. P. Sansom. 2010. Membrane/toxin interaction energetics via serial multi-scale molecular dynamics simulations. J. Chem. Theory Comput. 6:966-976.
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 966-976
-
-
Wee, C.L.1
Ulmschneider, M.B.2
Sansom, M.S.P.3
-
23
-
-
33846785439
-
How does a voltage sensor interact with a lipid bilayer? Simulations of a potassium channel domain
-
Sands, Z. A., and M. S. P. Sansom. 2007. How does a voltage sensor interact with a lipid bilayer? Simulations of a potassium channel domain. Structure. 15:235-244.
-
(2007)
Structure
, vol.15
, pp. 235-244
-
-
Sands, Z.A.1
Sansom, M.S.P.2
-
24
-
-
77953578254
-
Down-state model of the voltage-sensing domain of a potassium channel
-
Schow, E. V., J. A. Freites,..., D. J. Tobias. 2010. Down-state model of the voltage-sensing domain of a potassium channel. Biophys. J. 98:2857-2866.
-
(2010)
Biophys. J.
, vol.98
, pp. 2857-2866
-
-
Schow, E.V.1
Freites, J.A.2
Tobias, D.J.3
-
26
-
-
0027136282
-
Comparative protein modelling by satisfaction of spatial restraints
-
Sali, A., and T. L. Blundell. 1993. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234:779-815.
-
(1993)
J. Mol. Biol.
, vol.234
, pp. 779-815
-
-
Sali, A.1
Blundell, T.L.2
-
27
-
-
0034567210
-
Comparative protein structure modeling. Introduction and practical examples with modeller
-
Sánchez, R., and A. Sali. 2000. Comparative protein structure modeling. Introduction and practical examples with modeller. Methods Mol. Biol. 143:97-129.
-
(2000)
Methods Mol. Biol.
, vol.143
, pp. 97-129
-
-
Sánchez, R.1
Sali, A.2
-
28
-
-
0003544049
-
-
Biomos & Hochschulverlag AG an der ETH Zurich, Groningen, The Netherlands
-
van Gunsteren, W. F., P. Kruger,..., I. G. Tironi. 1996. Biomolecular Simulation: The GROMOS96 Manual and User Guide. Biomos & Hochschulverlag AG an der ETH Zurich, Groningen, The Netherlands.
-
(1996)
Biomolecular Simulation: The GROMOS96 Manual and User Guide
-
-
Van Gunsteren, W.F.1
Kruger, P.2
Tironi, I.G.3
-
29
-
-
0030999097
-
Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature
-
Berger, O., O. Edholm, and F. Jähnig. 1997. Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophys. J. 72:2002-2013.
-
(1997)
Biophys. J.
, vol.72
, pp. 2002-2013
-
-
Berger, O.1
Edholm, O.2
Jähnig, F.3
-
30
-
-
0031880829
-
Adhesion forces of lipids in a phospholipid membrane studied by molecular dynamics simulations
-
Marrink, S. J., O. Berger,..., F. Jähnig. 1998. Adhesion forces of lipids in a phospholipid membrane studied by molecular dynamics simulations. Biophys. J. 74:931-943.
-
(1998)
Biophys. J.
, vol.74
, pp. 931-943
-
-
Marrink, S.J.1
Berger, O.2
Jähnig, F.3
-
31
-
-
84986519238
-
The weighted histogram analysis method for free-energy calculations on biomolecules. 1. The method
-
Kumar, S., D. Bouzida,..., J. M. Rosenberg. 1992. The weighted histogram analysis method for free-energy calculations on biomolecules. 1. The method. J. Comput. Chem. 13:1011-1021.
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 1011-1021
-
-
Kumar, S.1
Bouzida, D.2
Rosenberg, J.M.3
-
32
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H. J. C., J. P. M. Postma,..., J. R. Haak. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:3684-3690.
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Haak, J.R.3
-
33
-
-
33846823909
-
Particle mesh Ewald: An N.log (N) method for Ewald sums in large systems
-
Darden, T., D. York, and L. Pedersen. 1993. Particle mesh Ewald: an N.log (N) method for Ewald sums in large systems. J. Chem. Phys. 98:10089-10092.
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
34
-
-
0000388705
-
LINCS: A linear constraint solver for molecular simulations
-
Hess, B., H. Bekker,..., J. 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
Fraaije, J.G.E.M.3
-
35
-
-
84986440341
-
Settle: An analytical version of the Shake and Rattle algorithm for rigid water models
-
Miyamoto, S., and P. A. Kollman. 1992. Settle: an analytical version of the Shake and Rattle algorithm for rigid water models. J. Comput. Chem. 13:952-962.
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 952-962
-
-
Miyamoto, S.1
Kollman, P.A.2
-
36
-
-
33847258823
-
Bilayer deformation by the Kv channel voltage sensor domain revealed by self-assembly simulations
-
Bond, P. J., and M. S. P. Sansom. 2007. Bilayer deformation by the Kv channel voltage sensor domain revealed by self-assembly simulations. Proc. Natl. Acad. Sci. USA. 104:2631-2636.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 2631-2636
-
-
Bond, P.J.1
Sansom, M.S.P.2
-
37
-
-
33845637597
-
Phospholipids and the origin of cationic gating charges in voltage sensors
-
Schmidt, D., Q. X. Jiang, and R. MacKinnon. 2006. Phospholipids and the origin of cationic gating charges in voltage sensors. Nature. 444:775-779.
-
(2006)
Nature
, vol.444
, pp. 775-779
-
-
Schmidt, D.1
Jiang, Q.X.2
MacKinnon, R.3
-
39
-
-
50549097744
-
Assessing atomistic and coarse-grained force fields for protein-lipid interactions: The formidable challenge of an ionizable side chain in a membrane
-
Vorobyov, I., L. Li, and T. W. Allen. 2008. Assessing atomistic and coarse-grained force fields for protein-lipid interactions: the formidable challenge of an ionizable side chain in a membrane. J. Phys. Chem. B. 112:9588-9602.
-
(2008)
J. Phys. Chem. B.
, vol.112
, pp. 9588-9602
-
-
Vorobyov, I.1
Li, L.2
Allen, T.W.3
-
40
-
-
33646135082
-
Environment of the gating charges in the Kv1.2 Shaker potassium channel
-
Treptow, W., and M. Tarek. 2006. Environment of the gating charges in the Kv1.2 Shaker potassium channel. Biophys. J. 90: L64-L66.
-
(2006)
Biophys. J.
, vol.90
-
-
Treptow, W.1
Tarek, M.2
-
41
-
-
34547628129
-
+ channel in a membrane environment
-
+ channel in a membrane environment. Biophys. J. 93:3070-3082.
-
(2007)
Biophys. J.
, vol.93
, pp. 3070-3082
-
-
Jogini, V.1
Roux, B.2
-
42
-
-
55949123442
-
Double bilayers and transmembrane gradients: A molecular dynamics study of a highly charged peptide
-
Denning, E. J., and T. B. Woolf. 2008. Double bilayers and transmembrane gradients: a molecular dynamics study of a highly charged peptide. Biophys. J. 95:3161-3173.
-
(2008)
Biophys. J.
, vol.95
, pp. 3161-3173
-
-
Denning, E.J.1
Woolf, T.B.2
-
43
-
-
45949109759
-
Gating motions in voltage-gated potassium channels revealed by coarse-grained molecular dynamics simulations
-
Treptow, W., S.-J. Marrink, and M. Tarek. 2008. Gating motions in voltage-gated potassium channels revealed by coarse-grained molecular dynamics simulations. J. Phys. Chem. B. 112:3277-3282.
-
(2008)
J. Phys. Chem. B.
, vol.112
, pp. 3277-3282
-
-
Treptow, W.1
Marrink, S.-J.2
Tarek, M.3
-
44
-
-
13444262028
-
Recognition of transmembrane helices by the endoplasmic reticulum translocon
-
Hessa, T., H. Kim,..., G. von Heijne. 2005. Recognition of transmembrane helices by the endoplasmic reticulum translocon. Nature. 433:377-381.
-
(2005)
Nature
, vol.433
, pp. 377-381
-
-
Hessa, T.1
Kim, H.2
Von Heijne, G.3
-
45
-
-
63649153519
-
Membrane-integration characteristics of two ABC transporters, CFTR and P-glycoprotein
-
Enquist, K., M. Fransson,..., I. Nilsson. 2009. Membrane-integration characteristics of two ABC transporters, CFTR and P-glycoprotein. J. Mol. Biol. 387:1153-1164.
-
(2009)
J. Mol. Biol.
, vol.387
, pp. 1153-1164
-
-
Enquist, K.1
Fransson, M.2
Nilsson, I.3
-
46
-
-
77952569092
-
Changes in transmembrane helix alignment by arginine residues revealed by solid-state NMR experiments and coarse-grained MD simulations
-
Vostrikov, V. V., B. A. Hall,..., M. S. Sansom. 2010. Changes in transmembrane helix alignment by arginine residues revealed by solid-state NMR experiments and coarse-grained MD simulations. J. Am. Chem. Soc. 132:5803-5811.
-
(2010)
J. Am. Chem. Soc.
, vol.132
, pp. 5803-5811
-
-
Vostrikov, V.V.1
Hall, B.A.2
Sansom, M.S.3
-
47
-
-
85031252172
-
Membrane insertion of a S4 potassium channel voltage sensor: An experimental study. 2006 biophysical society meeting abstracts
-
Fernández-Vidal, M., F. Castro-Roman, and S. H. White. 2006. Membrane insertion of a S4 potassium channel voltage sensor: an experimental study. 2006 Biophysical Society Meeting Abstracts. Biophys. J. Suppl. 20 a.: 1164-Pos.
-
(2006)
Biophys. J. Suppl.
, vol.20 A
-
-
Fernández-Vidal, M.1
Castro-Roman, F.2
White, S.H.3
-
49
-
-
48249095616
-
How translocons select transmembrane helices
-
White, S. H., and G. von Heijne. 2008. How translocons select transmembrane helices. Annu. Rev. Biophys. 37:23-42.
-
(2008)
Annu. Rev. Biophys.
, vol.37
, pp. 23-42
-
-
White, S.H.1
Von Heijne, G.2
-
50
-
-
0032987478
-
Membrane protein folding and stability: Physical principles
-
White, S. H., and W. C. Wimley. 1999. Membrane protein folding and stability: physical principles. Annu. Rev. Biophys. Biomol. Struct. 28:319-365.
-
(1999)
Annu. Rev. Biophys. Biomol. Struct
, vol.28
, pp. 319-365
-
-
White, S.H.1
Wimley, W.C.2
-
51
-
-
0033609809
-
A calorimetric study of the folding-unfolding of an a-helix with covalently closed N and C-terminal loops
-
Taylor, J. W., N. J. Greenfield,..., P. L. Privalov. 1999. A calorimetric study of the folding-unfolding of an a-helix with covalently closed N and C-terminal loops. J. Mol. Biol. 291:965-976.
-
(1999)
J. Mol. Biol.
, vol.291
, pp. 965-976
-
-
Taylor, J.W.1
Greenfield, N.J.2
Privalov, P.L.3
-
52
-
-
18844361915
-
Helix-coil transition of alanine peptides in water: Force field dependence on the folded and unfolded structures
-
Gnanakaran, S., and A. E. Garćia. 2005. Helix-coil transition of alanine peptides in water: force field dependence on the folded and unfolded structures. Proteins. 59:773-782.
-
(2005)
Proteins
, vol.59
, pp. 773-782
-
-
Gnanakaran, S.1
Garćia, A.E.2
-
53
-
-
0032874786
-
The alignment of a voltage-sensing peptide in dodecylphosphocholine micelles and in oriented lipid bilayers by nuclear magnetic resonance and molecular modeling
-
Mattila, K., R. Kinder, and B. Bechinger. 1999. The alignment of a voltage-sensing peptide in dodecylphosphocholine micelles and in oriented lipid bilayers by nuclear magnetic resonance and molecular modeling. Biophys. J. 77:2102-2113.
-
(1999)
Biophys. J.
, vol.77
, pp. 2102-2113
-
-
Mattila, K.1
Kinder, R.2
Bechinger, B.3
-
54
-
-
40749090459
-
Transmembrane helix tilting: Insights from calculating the potential of mean force
-
Lee, J., and W. Im. 2008. Transmembrane helix tilting: insights from calculating the potential of mean force. Phys. Rev. Lett. 100:018103.
-
(2008)
Phys. Rev. Lett.
, vol.100
, pp. 018103
-
-
Lee, J.1
Im, W.2
-
55
-
-
70349436810
-
Protein contents in biological membranes can explain abnormal solvation of charged and polar residues
-
Johansson, A. C. V., and E. Lindahl. 2009. Protein contents in biological membranes can explain abnormal solvation of charged and polar residues. Proc. Natl. Acad. Sci. USA. 106:15684-15689.
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 15684-15689
-
-
Johansson, A.C.V.1
Lindahl, E.2
-
56
-
-
50349088433
-
Molecular dynamics simulation of Kv channel voltage sensor helix in a lipid membrane with applied electric field
-
Nishizawa, M., and K. Nishizawa. 2008. Molecular dynamics simulation of Kv channel voltage sensor helix in a lipid membrane with applied electric field. Biophys. J. 95:1729-1744.
-
(2008)
Biophys. J.
, vol.95
, pp. 1729-1744
-
-
Nishizawa, M.1
Nishizawa, K.2
-
59
-
-
36549041108
-
Proton transport behavior through the influenza A M2 channel: Insights from molecular simulation
-
Chen, H. N., Y. J. Wu, and G. A. Voth. 2007. Proton transport behavior through the influenza A M2 channel: insights from molecular simulation. Biophys. J. 93:3470-3479.
-
(2007)
Biophys. J.
, vol.93
, pp. 3470-3479
-
-
Chen, H.N.1
Wu, Y.J.2
Voth, G.A.3
-
61
-
-
67849095786
-
Initial response of the potassium channel voltage sensor to a transmembrane potential
-
Treptow, W., M. Tarek, and M. L. Klein. 2009. Initial response of the potassium channel voltage sensor to a transmembrane potential. J. Am. Chem. Soc. 131:2107-2109.
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 2107-2109
-
-
Treptow, W.1
Tarek, M.2
Klein, M.L.3
-
62
-
-
75649151376
-
Interactions of phospholipid bilayers with several classes of amphiphilic a-helical peptides: Insights from coarse-grained molecular dynamics simulations
-
Gkeka, P., and L. Sarkisov. 2010. Interactions of phospholipid bilayers with several classes of amphiphilic a-helical peptides: insights from coarse-grained molecular dynamics simulations. J. Phys. Chem. B. 114:826-839.
-
(2010)
J. Phys. Chem. B.
, vol.114
, pp. 826-839
-
-
Gkeka, P.1
Sarkisov, L.2
-
63
-
-
77953598334
-
Peptide partitioning properties from direct insertion studies
-
Ulmschneider, M. B., J. C. Smith, and J. P. Ulmschneider. 2010. Peptide partitioning properties from direct insertion studies. Biophys. J. 98: L60-L62.
-
(2010)
Biophys. J.
, vol.98
-
-
Ulmschneider, M.B.1
Smith, J.C.2
Ulmschneider, J.P.3
-
64
-
-
58049194119
-
+ channel gating and voltage sensor toxin sensitivity depend on the mechanical state of the lipid membrane
-
+ channel gating and voltage sensor toxin sensitivity depend on the mechanical state of the lipid membrane. Proc. Natl. Acad. Sci. USA. 105:19276-19281.
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 19276-19281
-
-
Schmidt, D.1
MacKinnon, R.2
|