-
1
-
-
0031954925
-
Genome-wide analysis of integral membrane proteins from bacterial, archaeal, and eukaryotic organisms
-
E. Wallin, and G. von Heijne Genome-wide analysis of integral membrane proteins from bacterial, archaeal, and eukaryotic organisms Protein Sci. 7 1998 1029 1038
-
(1998)
Protein Sci.
, vol.7
, pp. 1029-1038
-
-
Wallin, E.1
Von Heijne, G.2
-
3
-
-
34249739711
-
The membrane protein universe: What's out there and why bother?
-
G. von Heijne The membrane protein universe: what's out there and why bother? J. Intern. Med. 261 2007 543 557
-
(2007)
J. Intern. Med.
, vol.261
, pp. 543-557
-
-
Von Heijne, G.1
-
5
-
-
0030916841
-
Domain-specific N-glycosylation of the membrane glycoprotein dipeptidylpeptidase IV (CD26) influences its subcellular trafficking, biological stability, enzyme activity and protein folding
-
H. Fan, W.M. Meng, C. Kilian, S. Grams, and W. Reutter Domain-specific N-glycosylation of the membrane glycoprotein dipeptidylpeptidase IV (CD26) influences its subcellular trafficking, biological stability, enzyme activity and protein folding Eur. J. Biochem. 246 1997 243 251
-
(1997)
Eur. J. Biochem.
, vol.246
, pp. 243-251
-
-
Fan, H.1
Meng, W.M.2
Kilian, C.3
Grams, S.4
Reutter, W.5
-
6
-
-
0032560144
-
Three-dimensional map of the plasma membrane H + ATPase in the open conformation
-
M. Auer, G.A. Scarborough, and W. Kuhlbrandt Three-dimensional map of the plasma membrane H + ATPase in the open conformation Nature 392 1998 840 843
-
(1998)
Nature
, vol.392
, pp. 840-843
-
-
Auer, M.1
Scarborough, G.A.2
Kuhlbrandt, W.3
-
9
-
-
0033783032
-
Receptor binding and membrane fusion in virus entry: The influenza hemagglutinin
-
J.J. Skehel, and D.C. Wiley Receptor binding and membrane fusion in virus entry: the influenza hemagglutinin Annu. Rev. Biochem. 69 2000 531 569
-
(2000)
Annu. Rev. Biochem.
, vol.69
, pp. 531-569
-
-
Skehel, J.J.1
Wiley, D.C.2
-
10
-
-
0000063546
-
Lipoprotein receptors: New roles for ancient proteins
-
T.E. Willnow, A. Nykjaer, and J. Herz Lipoprotein receptors: new roles for ancient proteins Nat. Cell Biol. 1 1999 E157 E162
-
(1999)
Nat. Cell Biol.
, vol.1
-
-
Willnow, T.E.1
Nykjaer, A.2
Herz, J.3
-
11
-
-
0037026489
-
The voltage-gated potassium channels and their relatives
-
G. Yellen The voltage-gated potassium channels and their relatives Nature 419 2002 35 42
-
(2002)
Nature
, vol.419
, pp. 35-42
-
-
Yellen, G.1
-
12
-
-
0037198626
-
Crystal structure and mechanism of a calcium-gated potassium channel
-
Y. Jiang, A. Lee, J. Chen, M. Cadene, B.T. Chait, and R. MacKinnon Crystal structure and mechanism of a calcium-gated potassium channel Nature 417 2002 515 522
-
(2002)
Nature
, vol.417
, pp. 515-522
-
-
Jiang, Y.1
Lee, A.2
Chen, J.3
Cadene, M.4
Chait, B.T.5
MacKinnon, R.6
-
13
-
-
0033761347
-
Structure of a glycerol-conducting channel and the basis for its selectivity
-
D. Fu, A. Libson, L.J. Miercke, C. Weitzman, P. Nollert, J. Krucinski, and R.M. Stroud Structure of a glycerol-conducting channel and the basis for its selectivity Science 290 2000 481 486
-
(2000)
Science
, vol.290
, pp. 481-486
-
-
Fu, D.1
Libson, A.2
Miercke, L.J.3
Weitzman, C.4
Nollert, P.5
Krucinski, J.6
Stroud, R.M.7
-
14
-
-
0034609808
-
Structural determinants of water permeation through aquaporin-1
-
K. Murata, K. Mitsuoka, T. Hirai, T. Walz, P. Agre, J.B. Heymann, A. Engel, and Y. Fujiyoshi Structural determinants of water permeation through aquaporin-1 Nature 407 2000 599 605
-
(2000)
Nature
, vol.407
, pp. 599-605
-
-
Murata, K.1
Mitsuoka, K.2
Hirai, T.3
Walz, T.4
Agre, P.5
Heymann, J.B.6
Engel, A.7
Fujiyoshi, Y.8
-
15
-
-
0034614490
-
Signaling - 2000 and beyond
-
T. Hunter Signaling - 2000 and beyond Cell 100 2000 113 127
-
(2000)
Cell
, vol.100
, pp. 113-127
-
-
Hunter, T.1
-
16
-
-
0031740415
-
Hydrophobic mismatch between proteins and lipids in membranes
-
J.A. Killian Hydrophobic mismatch between proteins and lipids in membranes Biochim. Biophys. Acta Rev. Biomembr. 1376 1998 401 416
-
(1998)
Biochim. Biophys. Acta Rev. Biomembr.
, vol.1376
, pp. 401-416
-
-
Killian, J.A.1
-
18
-
-
0027438092
-
Lipid enrichment and selectivity of integral membrane proteins in two-component lipid bilayers
-
M.M. Sperotto, and O.G. Mouritsen Lipid enrichment and selectivity of integral membrane proteins in two-component lipid bilayers Eur. Biophys. J. 22 1993 323 328
-
(1993)
Eur. Biophys. J.
, vol.22
, pp. 323-328
-
-
Sperotto, M.M.1
Mouritsen, O.G.2
-
19
-
-
0242659352
-
Protein-lipid interactions studied with designed transmembrane peptides: Role of hydrophobic matching and interfacial anchoring (review)
-
M.R.R. de Planque, and J.A. Killian Protein-lipid interactions studied with designed transmembrane peptides: role of hydrophobic matching and interfacial anchoring (review) Mol. Membr. Biol. 20 2003 271 284
-
(2003)
Mol. Membr. Biol.
, vol.20
, pp. 271-284
-
-
De Planque, M.R.R.1
Killian, J.A.2
-
20
-
-
77952093470
-
Orientation and dynamics of transmembrane peptides: The power of simple models
-
A. Holt, and J.A. Killian Orientation and dynamics of transmembrane peptides: the power of simple models Eur. Biophys. J. 39 2010 609 621
-
(2010)
Eur. Biophys. J.
, vol.39
, pp. 609-621
-
-
Holt, A.1
Killian, J.A.2
-
21
-
-
33746647787
-
Peptides in lipid bilayers: The power of simple models
-
J.A. Killian, and T.K.M. Nyholm Peptides in lipid bilayers: the power of simple models Curr. Opin. Struct. Biol. 16 2006 473 479
-
(2006)
Curr. Opin. Struct. Biol.
, vol.16
, pp. 473-479
-
-
Killian, J.A.1
Nyholm, T.K.M.2
-
22
-
-
0001006658
-
Interaction of a synthetic amphiphilic polypeptide and lipids in a bilayer structure
-
J.H. Davis, D.M. Clare, R.S. Hodges, and M. Bloom Interaction of a synthetic amphiphilic polypeptide and lipids in a bilayer structure Biochemistry 22 1983 5298 5305
-
(1983)
Biochemistry
, vol.22
, pp. 5298-5305
-
-
Davis, J.H.1
Clare, D.M.2
Hodges, R.S.3
Bloom, M.4
-
23
-
-
0035895347
-
Peptide models of the helical hydrophobic transmembrane segments of membrane proteins: Interactions of acetyl-K-2-(LA)(12)-K-2-amide with phosphatidylethanolamine bilayer membranes
-
Y.P. Zhang, R. Lewis, R.S. Hodges, and R.N. McElhaney Peptide models of the helical hydrophobic transmembrane segments of membrane proteins: interactions of acetyl-K-2-(LA)(12)-K-2-amide with phosphatidylethanolamine bilayer membranes Biochemistry 40 2001 474 482
-
(2001)
Biochemistry
, vol.40
, pp. 474-482
-
-
Zhang, Y.P.1
Lewis, R.2
Hodges, R.S.3
McElhaney, R.N.4
-
24
-
-
0030029091
-
Induction of nonbilayer structures in diacylphosphatidylcholine model membranes by transmembrane alpha-helical peptides: Importance of hydrophobic mismatch and proposed role of tryptophans
-
J.A. Killian, I. Salemink, M.R. de Planque, G. Lindblom, R.E. Koeppe II, and D.V. Greathouse Induction of nonbilayer structures in diacylphosphatidylcholine model membranes by transmembrane alpha-helical peptides: importance of hydrophobic mismatch and proposed role of tryptophans Biochemistry 35 1996 1037 1045
-
(1996)
Biochemistry
, vol.35
, pp. 1037-1045
-
-
Killian, J.A.1
Salemink, I.2
De Planque, M.R.3
Lindblom, G.4
Koeppe, I.I.R.E.5
Greathouse, D.V.6
-
25
-
-
0027499143
-
Non-random distribution of amino acids in the transmembrane segments of human type i single span membrane proteins
-
C. Landolt-Marticorena, K.A. Williams, C.M. Deber, and R.A.F. Reithmeier Non-random distribution of amino acids in the transmembrane segments of human type I single span membrane proteins J. Mol. Biol. 229 1993 602 608
-
(1993)
J. Mol. Biol.
, vol.229
, pp. 602-608
-
-
Landolt-Marticorena, C.1
Williams, K.A.2
Deber, C.M.3
Reithmeier, R.A.F.4
-
26
-
-
0025292355
-
Model for the structure of bacteriorhodopsin based on high-resolution electron cryomicroscopy
-
R. Henderson, J.M. Baldwin, T.A. Ceska, F. Zemlin, E. Beckmann, and K.H. Downing Model for the structure of bacteriorhodopsin based on high-resolution electron cryomicroscopy J. Mol. Biol. 213 1990 899 929
-
(1990)
J. Mol. Biol.
, vol.213
, pp. 899-929
-
-
Henderson, R.1
Baldwin, J.M.2
Ceska, T.A.3
Zemlin, F.4
Beckmann, E.5
Downing, K.H.6
-
27
-
-
0026331041
-
Molecular architecture and electrostatic properties of a bacterial porin
-
M.S. Weiss, U. Abele, J. Weckesser, W. Welte, E. Schiltz, and G.E. Schulz Molecular architecture and electrostatic properties of a bacterial porin Science 254 1991 1627 1630
-
(1991)
Science
, vol.254
, pp. 1627-1630
-
-
Weiss, M.S.1
Abele, U.2
Weckesser, J.3
Welte, W.4
Schiltz, E.5
Schulz, G.E.6
-
28
-
-
0032581038
-
Influence of lipid/peptide hydrophobic mismatch on the thickness of diacylphosphatidylcholine bilayers. A H-2 NMR and ESR study using designed transmembrane alpha-helical peptides and gramicidin A
-
M.R.R. de Planque, D.V. Greathouse, R.E. Koeppe, H. Schafer, D. Marsh, and J.A. Killian Influence of lipid/peptide hydrophobic mismatch on the thickness of diacylphosphatidylcholine bilayers. A H-2 NMR and ESR study using designed transmembrane alpha-helical peptides and gramicidin A Biochemistry 37 1998 9333 9345
-
(1998)
Biochemistry
, vol.37
, pp. 9333-9345
-
-
De Planque, M.R.R.1
Greathouse, D.V.2
Koeppe, R.E.3
Schafer, H.4
Marsh, D.5
Killian, J.A.6
-
29
-
-
12244255728
-
Hydrophobic mismatch between helices and lipid bilayers
-
T.M. Weiss, P.C.A. van der Wel, J.A. Killian, R.E. Koeppe, and H.W. Huang Hydrophobic mismatch between helices and lipid bilayers Biophys. J. 84 2003 379 385
-
(2003)
Biophys. J.
, vol.84
, pp. 379-385
-
-
Weiss, T.M.1
Van Der Wel, P.C.A.2
Killian, J.A.3
Koeppe, R.E.4
Huang, H.W.5
-
30
-
-
22244472946
-
Lipid bilayer perturbations around a transmembrane nanotube: A coarse grain molecular dynamics study
-
S.O. Nielsen, B. Ensing, V. Ortiz, P.B. Moore, and M.L. Klein Lipid bilayer perturbations around a transmembrane nanotube: a coarse grain molecular dynamics study Biophys. J. 88 2005 3822 3828
-
(2005)
Biophys. J.
, vol.88
, pp. 3822-3828
-
-
Nielsen, S.O.1
Ensing, B.2
Ortiz, V.3
Moore, P.B.4
Klein, M.L.5
-
31
-
-
0025878348
-
Location of ion-binding sites in the gramicidin channel by X-ray-diffraction
-
G.A. Olah, H.W. Huang, W.H. Liu, and Y.L. Wu Location of ion-binding sites in the gramicidin channel by X-ray-diffraction J. Mol. Biol. 218 1991 847 858
-
(1991)
J. Mol. Biol.
, vol.218
, pp. 847-858
-
-
Olah, G.A.1
Huang, H.W.2
Liu, W.H.3
Wu, Y.L.4
-
32
-
-
84871786634
-
The role of tryptophan side chains in membrane protein anchoring and hydrophobic mismatch
-
submitted to
-
A.J. de Jesus, T.W. Allen, The role of tryptophan side chains in membrane protein anchoring and hydrophobic mismatch, submitted to Biochim. Biophys. Acta Rev. Biomembr. (2012).
-
(2012)
Biochim. Biophys. Acta Rev. Biomembr.
-
-
De Jesus, A.J.1
Allen, T.W.2
-
33
-
-
0035942298
-
Sensitivity of single membrane-spanning alpha-helical peptides to hydrophobic mismatch with a lipid bilayer: Effects on backbone structure, orientation, and extent of membrane incorporation
-
M.R.R. de Planque, E. Goormaghtigh, D.V. Greathouse, R.E. Koeppe, J.A.W. Kruijtzer, R.M.J. Liskamp, B. de Kruijff, and J.A. Killian Sensitivity of single membrane-spanning alpha-helical peptides to hydrophobic mismatch with a lipid bilayer: effects on backbone structure, orientation, and extent of membrane incorporation Biochemistry 40 2001 5000 5010
-
(2001)
Biochemistry
, vol.40
, pp. 5000-5010
-
-
De Planque, M.R.R.1
Goormaghtigh, E.2
Greathouse, D.V.3
Koeppe, R.E.4
Kruijtzer, J.A.W.5
Liskamp, R.M.J.6
De Kruijff, B.7
Killian, J.A.8
-
34
-
-
0026442901
-
Interaction of a peptide model of a hydrophobic transmembrane alpha-helical segment of a membrane protein with phosphatidylcholine bilayers: Differential scanning calorimetric and FTIR spectroscopic studies
-
Y.P. Zhang, R.N. Lewis, R.S. Hodges, and R.N. McElhaney Interaction of a peptide model of a hydrophobic transmembrane alpha-helical segment of a membrane protein with phosphatidylcholine bilayers: differential scanning calorimetric and FTIR spectroscopic studies Biochemistry 31 1992 11579 11588
-
(1992)
Biochemistry
, vol.31
, pp. 11579-11588
-
-
Zhang, Y.P.1
Lewis, R.N.2
Hodges, R.S.3
McElhaney, R.N.4
-
35
-
-
0033783447
-
Alignment of lysine-anchored membrane peptides under conditions of hydrophobic mismatch: A CD, 15N and 31P solid-state NMR spectroscopy investigation
-
U. Harzer, and B. Bechinger Alignment of lysine-anchored membrane peptides under conditions of hydrophobic mismatch: a CD, 15N and 31P solid-state NMR spectroscopy investigation Biochemistry 39 2000 13106 13114
-
(2000)
Biochemistry
, vol.39
, pp. 13106-13114
-
-
Harzer, U.1
Bechinger, B.2
-
36
-
-
0033522486
-
Control of the transmembrane orientation and interhelical interactions within membranes by hydrophobic helix length
-
J. Ren, S. Lew, J. Wang, and E. London Control of the transmembrane orientation and interhelical interactions within membranes by hydrophobic helix length Biochemistry 38 1999 5905 5912
-
(1999)
Biochemistry
, vol.38
, pp. 5905-5912
-
-
Ren, J.1
Lew, S.2
Wang, J.3
London, E.4
-
37
-
-
0030738720
-
Transmembrane orientation of hydrophobic alpha-helices is regulated both by the relationship of helix length to bilayer thickness and by the cholesterol concentration
-
J. Ren, S. Lew, Z. Wang, and E. London Transmembrane orientation of hydrophobic alpha-helices is regulated both by the relationship of helix length to bilayer thickness and by the cholesterol concentration Biochemistry 36 1997 10213 10220
-
(1997)
Biochemistry
, vol.36
, pp. 10213-10220
-
-
Ren, J.1
Lew, S.2
Wang, Z.3
London, E.4
-
38
-
-
0032512417
-
Hydrophobic mismatch and the incorporation of peptides into lipid bilayers: A possible mechanism for retention in the Golgi
-
R.J. Webb, J.M. East, R.P. Sharma, and A.G. Lee Hydrophobic mismatch and the incorporation of peptides into lipid bilayers: a possible mechanism for retention in the Golgi Biochemistry 37 1998 673 679
-
(1998)
Biochemistry
, vol.37
, pp. 673-679
-
-
Webb, R.J.1
East, J.M.2
Sharma, R.P.3
Lee, A.G.4
-
39
-
-
0032909033
-
Membrane helix orientation from linear dichroism of infrared attenuated total reflection spectra
-
B. Bechinger, J.M. Ruysschaert, and E. Goormaghtigh Membrane helix orientation from linear dichroism of infrared attenuated total reflection spectra Biophys. J. 76 1999 552 563
-
(1999)
Biophys. J.
, vol.76
, pp. 552-563
-
-
Bechinger, B.1
Ruysschaert, J.M.2
Goormaghtigh, E.3
-
40
-
-
0036284109
-
Organization of model helical peptides in lipid bilayers: Insight into the behavior of single-span protein transmembrane domains
-
S. Sharpe, K.R. Barber, C.W. Grant, D. Goodyear, and M.R. Morrow Organization of model helical peptides in lipid bilayers: insight into the behavior of single-span protein transmembrane domains Biophys. J. 83 2002 345 358
-
(2002)
Biophys. J.
, vol.83
, pp. 345-358
-
-
Sharpe, S.1
Barber, K.R.2
Grant, C.W.3
Goodyear, D.4
Morrow, M.R.5
-
41
-
-
0037062590
-
Lipid dependence of membrane anchoring properties and snorkeling behavior of aromatic and charged residues in transmembrane peptides
-
E. Strandberg, S. Morein, D.T.S. Rijkers, R.M.J. Liskamp, P.C.A. van der Wel, and J.A. Killian Lipid dependence of membrane anchoring properties and snorkeling behavior of aromatic and charged residues in transmembrane peptides Biochemistry 41 2002 7190 7198
-
(2002)
Biochemistry
, vol.41
, pp. 7190-7198
-
-
Strandberg, E.1
Morein, S.2
Rijkers, D.T.S.3
Liskamp, R.M.J.4
Van Der Wel, P.C.A.5
Killian, J.A.6
-
42
-
-
37049023237
-
On the orientation of a designed transmembrane peptide: Toward the right tilt angle?
-
S. Ozdirekcan, C. Etchebest, J.A. Killian, and P.F.J. Fuchs On the orientation of a designed transmembrane peptide: toward the right tilt angle? J. Am. Chem. Soc. 129 2007 15174 15181
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 15174-15181
-
-
Ozdirekcan, S.1
Etchebest, C.2
Killian, J.A.3
Fuchs, P.F.J.4
-
43
-
-
33646198955
-
Molecular dynamics simulations of model trans-membrane peptides in lipid bilayers: A systematic investigation of hydrophobic mismatch
-
S.K. Kandasamy, and R.G. Larson Molecular dynamics simulations of model trans-membrane peptides in lipid bilayers: a systematic investigation of hydrophobic mismatch Biophys. J. 90 2006 2326 2343
-
(2006)
Biophys. J.
, vol.90
, pp. 2326-2343
-
-
Kandasamy, S.K.1
Larson, R.G.2
-
44
-
-
37349011230
-
The dynamic orientation of membrane-bound peptides: Bridging simulations and experiments
-
S. Esteban-Martin, and J. Salgado The dynamic orientation of membrane-bound peptides: bridging simulations and experiments Biophys. J. 93 2007 4278 4288
-
(2007)
Biophys. J.
, vol.93
, pp. 4278-4288
-
-
Esteban-Martin, S.1
Salgado, J.2
-
45
-
-
2942662220
-
Tilt angles of transmembrane model peptides in oriented and non-oriented lipid bilayers as determined by H-2 solid-state NMR
-
E. Strandberg, S. Ozdirekcan, D.T.S. Rijkers, P.C.A. van der Wel, R.E. Koeppe, R.M.J. Liskamp, and J.A. Killian Tilt angles of transmembrane model peptides in oriented and non-oriented lipid bilayers as determined by H-2 solid-state NMR Biophys. J. 86 2004 3709 3721
-
(2004)
Biophys. J.
, vol.86
, pp. 3709-3721
-
-
Strandberg, E.1
Ozdirekcan, S.2
Rijkers, D.T.S.3
Van Der Wel, P.C.A.4
Koeppe, R.E.5
Liskamp, R.M.J.6
Killian, J.A.7
-
46
-
-
0036708458
-
Geometry and intrinsic tilt of a tryptophan-anchored transmembrane alpha-helix determined by H-2 NMR
-
P.C.A. van der Wel, E. Strandberg, J.A. Killian, and R.E. Koeppe Geometry and intrinsic tilt of a tryptophan-anchored transmembrane alpha-helix determined by H-2 NMR Biophys. J. 83 2002 1479 1488
-
(2002)
Biophys. J.
, vol.83
, pp. 1479-1488
-
-
Van Der Wel, P.C.A.1
Strandberg, E.2
Killian, J.A.3
Koeppe, R.E.4
-
47
-
-
0042626159
-
The structure of gramicidin A in a lipid bilayer environment determined using molecular dynamics simulations and solid-state NMR data
-
T.W. Allen, O.S. Andersen, and B. Roux The structure of gramicidin A in a lipid bilayer environment determined using molecular dynamics simulations and solid-state NMR data J. Am. Chem. Soc. 125 2003 9868 9877
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 9868-9877
-
-
Allen, T.W.1
Andersen, O.S.2
Roux, B.3
-
48
-
-
77952257688
-
Order parameters of a transmembrane helix in a fluid bilayer: Case study of a WALP peptide
-
A. Holt, L. Rougier, V. Reat, F. Jolibois, O. Saurel, J. Czaplicki, J.A. Killian, and A. Milon Order parameters of a transmembrane helix in a fluid bilayer: case study of a WALP peptide Biophys. J. 98 2010 1864 1872
-
(2010)
Biophys. J.
, vol.98
, pp. 1864-1872
-
-
Holt, A.1
Rougier, L.2
Reat, V.3
Jolibois, F.4
Saurel, O.5
Czaplicki, J.6
Killian, J.A.7
Milon, A.8
-
49
-
-
67649405180
-
Orientation and dynamics of peptides in membranes calculated from 2H-NMR data
-
E. Strandberg, S. Esteban-Martin, J. Salgado, and A.S. Ulrich Orientation and dynamics of peptides in membranes calculated from 2H-NMR data Biophys. J. 96 2009 3223 3232
-
(2009)
Biophys. J.
, vol.96
, pp. 3223-3232
-
-
Strandberg, E.1
Esteban-Martin, S.2
Salgado, J.3
Ulrich, A.S.4
-
50
-
-
0001659533
-
Application of combined Monte Carlo and molecular dynamics method to simulation of dipalmitoyl phosphatidylcholine lipid bilayer
-
S.W. Chiu, M.M. Clark, E. Jakobsson, S. Subramaniam, and H.L. Scott Application of combined Monte Carlo and molecular dynamics method to simulation of dipalmitoyl phosphatidylcholine lipid bilayer J. Comput. Chem. 20 1999 1153 1164
-
(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
-
52
-
-
50549085702
-
Potential of mean force and pK(a) profile calculation for a lipid membrane-exposed arginine side chain
-
L.B. Li, I. Vorobyov, and T.W. Allen Potential of mean force and pK(a) profile calculation for a lipid membrane-exposed arginine side chain J. Phys. Chem. B 112 2008 9574 9587
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 9574-9587
-
-
Li, L.B.1
Vorobyov, I.2
Allen, T.W.3
-
53
-
-
34247633528
-
On the thermodynamic stability of a charged arginine side chain in a transmembrane helix
-
S. Dorairaj, and T.W. Allen On the thermodynamic stability of a charged arginine side chain in a transmembrane helix Proc. Natl. Acad. Sci. U. S. A. 104 2007 4943 4948
-
(2007)
Proc. Natl. Acad. Sci. U. S. A.
, vol.104
, pp. 4943-4948
-
-
Dorairaj, S.1
Allen, T.W.2
-
54
-
-
77953589882
-
Electrostatics of deformable lipid membranes
-
I. Vorobyov, B. Bekker, and T.W. Allen Electrostatics of deformable lipid membranes Biophys. J. 98 2010 2904 2913
-
(2010)
Biophys. J.
, vol.98
, pp. 2904-2913
-
-
Vorobyov, I.1
Bekker, B.2
Allen, T.W.3
-
56
-
-
28444469286
-
Interfacial tryptophan residues: A role for the cation-pi effect?
-
F.N.R. Petersen, M.O. Jensen, and C.H. Nielsen Interfacial tryptophan residues: a role for the cation-pi effect? Biophys. J. 89 2005 3985 3996
-
(2005)
Biophys. J.
, vol.89
, pp. 3985-3996
-
-
Petersen, F.N.R.1
Jensen, M.O.2
Nielsen, C.H.3
-
57
-
-
0030038849
-
Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer
-
T.B. Woolf, and B. Roux Structure, energetics, and dynamics of lipid-protein interactions: a molecular dynamics study of the gramicidin A channel in a DMPC bilayer Proteins 24 1996 92 114
-
(1996)
Proteins
, vol.24
, pp. 92-114
-
-
Woolf, T.B.1
Roux, B.2
-
58
-
-
0028020035
-
Molecular-dynamics simulation of the gramicidin channel in a phospholipid-bilayer
-
T.B. Woolf, and B. Roux Molecular-dynamics simulation of the gramicidin channel in a phospholipid-bilayer Proc. Natl. Acad. Sci. U. S. A. 91 1994 11631 11635
-
(1994)
Proc. Natl. Acad. Sci. U. S. A.
, vol.91
, pp. 11631-11635
-
-
Woolf, T.B.1
Roux, B.2
-
59
-
-
0004122931
-
-
Updated Third edition Thomson Brooks/Cole
-
R. Garrett, and C. Grisham Biochemistry Updated Third edition 2007 Thomson Brooks/Cole
-
(2007)
Biochemistry
-
-
Garrett, R.1
Grisham, C.2
-
60
-
-
0037881905
-
Interfacial anchor properties of tryptophan residues in transmembrane peptides can dominate over hydrophobic matching effects in peptide-lipid interactions
-
M.R.R. de Planque, B.B. Bonev, J.A.A. Demmers, D.V. Greathouse, R.E. Koeppe, F. Separovic, A. Watts, and J.A. Killian Interfacial anchor properties of tryptophan residues in transmembrane peptides can dominate over hydrophobic matching effects in peptide-lipid interactions Biochemistry 42 2003 5341 5348
-
(2003)
Biochemistry
, vol.42
, pp. 5341-5348
-
-
De Planque, M.R.R.1
Bonev, B.B.2
Demmers, J.A.A.3
Greathouse, D.V.4
Koeppe, R.E.5
Separovic, F.6
Watts, A.7
Killian, J.A.8
-
61
-
-
0027251833
-
Area/lipid of bilayers from NMR
-
J.F. Nagle Area/lipid of bilayers from NMR Biophys. J. 64 1993 1476 1481
-
(1993)
Biophys. J.
, vol.64
, pp. 1476-1481
-
-
Nagle, J.F.1
-
62
-
-
34250872768
-
Orientation and motion of tryptophan interfacial anchors in membrane-spanning peptides
-
P.C.A. van der Wel, N.D. Reed, D.V. Greathouse, and R.E. Koeppe Orientation and motion of tryptophan interfacial anchors in membrane-spanning peptides Biochemistry 46 2007 7514 7524
-
(2007)
Biochemistry
, vol.46
, pp. 7514-7524
-
-
Van Der Wel, P.C.A.1
Reed, N.D.2
Greathouse, D.V.3
Koeppe, R.E.4
-
63
-
-
0027160197
-
Backbone-dependent rotamer library for proteins - Application to side-chain prediction
-
R.L. Dunbrack, and M. Karplus Backbone-dependent rotamer library for proteins - application to side-chain prediction J. Mol. Biol. 230 1993 543 574
-
(1993)
J. Mol. Biol.
, vol.230
, pp. 543-574
-
-
Dunbrack, R.L.1
Karplus, M.2
-
64
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan, and M. Karplus CHARMM: a program for macromolecular energy, minimization, and dynamics calculations J. Comput. Chem. 4 1983 187 217
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
65
-
-
0034250744
-
An improved empirical potential energy function for molecular simulations of phospholipids
-
S.E. Feller, and A.D. MacKerell An improved empirical potential energy function for molecular simulations of phospholipids J. Phys. Chem. B 104 2000 7510 7515
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 7510-7515
-
-
Feller, S.E.1
MacKerell, A.D.2
-
66
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
A.D. MacKerell, D. Bashford, Bellott, R.L. Dunbrack, J.D. Evanseck, M.J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F.T.K. Lau, C. Mattos, S. Michnick, T. Ngo, D.T. Nguyen, B. Prodhom, W.E. Reiher, B. Roux, M. Schlenkrich, J.C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 102 1998 3586 3616
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
MacKerell, A.D.1
Bashford, D.2
Bellott3
Dunbrack, R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-Mccarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
67
-
-
0000999989
-
Combined ab initio/empirical approach for optimization of Lennard-Jones parameters
-
D. Yin, and A.D. MacKerell Combined ab initio/empirical approach for optimization of Lennard-Jones parameters J. Comput. Chem. 19 1998 334 348
-
(1998)
J. Comput. Chem.
, vol.19
, pp. 334-348
-
-
Yin, D.1
MacKerell, A.D.2
-
68
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, and M.L. Klein Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 926 935
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
69
-
-
33646940952
-
Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
J.-P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comput. Phys. 23 1977 327 341
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.-P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
70
-
-
33846823909
-
Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems
-
T. Darden, D. York, and L. Pedersen Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems J. Chem. Phys. 98 1993 10089 10092
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
71
-
-
36449007836
-
Constant-pressure molecular-dynamics simulation - The Langevin Piston method
-
S.E. Feller, Y.H. Zhang, R.W. Pastor, and B.R. Brooks Constant-pressure molecular-dynamics simulation - the Langevin Piston method J. Chem. Phys. 103 1995 4613 4621
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 4613-4621
-
-
Feller, S.E.1
Zhang, Y.H.2
Pastor, R.W.3
Brooks, B.R.4
-
72
-
-
84943502952
-
A molecular-dynamics method for simulations in the canonical ensemble
-
S. Nose A molecular-dynamics method for simulations in the canonical ensemble Mol. Phys. 52 1984 255 268
-
(1984)
Mol. Phys.
, vol.52
, pp. 255-268
-
-
Nose, S.1
-
73
-
-
0001538909
-
Canonical dynamics - Equilibrium phase-space distributions
-
W.G. Hoover Canonical dynamics - equilibrium phase-space distributions Phys. Rev. A 31 1985 1695 1697
-
(1985)
Phys. Rev. A
, vol.31
, pp. 1695-1697
-
-
Hoover, W.G.1
-
74
-
-
0022583145
-
A simple way to calculate the axis of an alpha-helix
-
J. Aqvist A simple way to calculate the axis of an alpha-helix Comput. Chem. 10 1986 97 99
-
(1986)
Comput. Chem.
, vol.10
, pp. 97-99
-
-
Aqvist, J.1
-
75
-
-
40749090459
-
Transmembrane helix tilting: Insights from calculating the potential of mean force
-
J. Lee, and W. Im Transmembrane helix tilting: insights from calculating the potential of mean force Phys. Rev. Lett. 100 2008
-
(2008)
Phys. Rev. Lett.
, vol.100
-
-
Lee, J.1
Im, W.2
-
76
-
-
0023018907
-
Deformation free-energy of bilayer-membrane and its effect on gramicidin channel lifetime
-
H.W. Huang Deformation free-energy of bilayer-membrane and its effect on gramicidin channel lifetime Biophys. J. 50 1986 1061 1070
-
(1986)
Biophys. J.
, vol.50
, pp. 1061-1070
-
-
Huang, H.W.1
-
77
-
-
12344266698
-
Influence of flanking residues on tilt and rotation angles of transmembrane peptides in lipid bilayers. A solid-state H-2 NMR study
-
S. Ozdirekcan, D.T.S. Rijkers, R.M.J. Liskamp, and J.A. Killian Influence of flanking residues on tilt and rotation angles of transmembrane peptides in lipid bilayers. A solid-state H-2 NMR study Biochemistry 44 2005 1004 1012
-
(2005)
Biochemistry
, vol.44
, pp. 1004-1012
-
-
Ozdirekcan, S.1
Rijkers, D.T.S.2
Liskamp, R.M.J.3
Killian, J.A.4
-
78
-
-
77954371031
-
Revisiting hydrophobic mismatch with free energy simulation studies of transmembrane helix tilt and rotation
-
T. Kim, and W. Im Revisiting hydrophobic mismatch with free energy simulation studies of transmembrane helix tilt and rotation Biophys. J. 99 2010 175 183
-
(2010)
Biophys. J.
, vol.99
, pp. 175-183
-
-
Kim, T.1
Im, W.2
-
79
-
-
33847058118
-
Transmembrane helices of membrane proteins may flex to satisfy hydrophobic mismatch
-
P.L. Yeagle, M. Bennett, V. Lemaitre, and A. Watts Transmembrane helices of membrane proteins may flex to satisfy hydrophobic mismatch Biochim. Biophys. Acta 1768 2007 530 537
-
(2007)
Biochim. Biophys. Acta
, vol.1768
, pp. 530-537
-
-
Yeagle, P.L.1
Bennett, M.2
Lemaitre, V.3
Watts, A.4
-
80
-
-
0041320859
-
Investigating lipid composition effects on the mechanosensitive channel of large conductance (MscL) using molecular dynamics simulations
-
D.E. Elmore, and D.A. Dougherty Investigating lipid composition effects on the mechanosensitive channel of large conductance (MscL) using molecular dynamics simulations Biophys. J. 85 2003 1512 1524
-
(2003)
Biophys. J.
, vol.85
, pp. 1512-1524
-
-
Elmore, D.E.1
Dougherty, D.A.2
-
81
-
-
65249115932
-
Solid-state NMR and molecular dynamics characterization of cannabinoid receptor-1 (CB1) helix 7 conformational plasticity in model membranes
-
E.K. Tiburu, A.L. Bowman, J.O. Struppe, D.R. Janero, H.K. Avraham, and A. Makriyannis Solid-state NMR and molecular dynamics characterization of cannabinoid receptor-1 (CB1) helix 7 conformational plasticity in model membranes Biochim. Biophys. Acta Biomembr. 1788 2009 1159 1167
-
(2009)
Biochim. Biophys. Acta Biomembr.
, vol.1788
, pp. 1159-1167
-
-
Tiburu, E.K.1
Bowman, A.L.2
Struppe, J.O.3
Janero, D.R.4
Avraham, H.K.5
Makriyannis, A.6
-
82
-
-
0003422388
-
-
W. H. Freeman
-
H. Lodish, A. Berk, C. Kaiser, M. Krieger, M. Scott, A. Bretscher, H. Ploegh, and P. Matsudaira Molecular Cell Biology (Lodish, Molecular Cell Biology) 2007 W. H. Freeman
-
(2007)
Molecular Cell Biology (Lodish, Molecular Cell Biology)
-
-
Lodish, H.1
Berk, A.2
Kaiser, C.3
Krieger, M.4
Scott, M.5
Bretscher, A.6
Ploegh, H.7
Matsudaira, P.8
-
83
-
-
67349266230
-
Position of helical kinks in membrane protein crystal structures and the accuracy of computational prediction
-
S.E. Hall, K. Roberts, and N. Vaidehi Position of helical kinks in membrane protein crystal structures and the accuracy of computational prediction J. Mol. Graph. Model. 27 2009 944 950
-
(2009)
J. Mol. Graph. Model.
, vol.27
, pp. 944-950
-
-
Hall, S.E.1
Roberts, K.2
Vaidehi, N.3
-
84
-
-
0037441653
-
Structure validation by C alpha geometry: Phi, psi and C beta deviation
-
S.C. Lovell, I.W. Davis, W.B. Adrendall, P.I.W. de Bakker, J.M. Word, M.G. Prisant, J.S. Richardson, and D.C. Richardson Structure validation by C alpha geometry: phi, psi and C beta deviation Proteins 50 2003 437 450
-
(2003)
Proteins
, vol.50
, pp. 437-450
-
-
Lovell, S.C.1
Davis, I.W.2
Adrendall, W.B.3
De Bakker, P.I.W.4
Word, J.M.5
Prisant, M.G.6
Richardson, J.S.7
Richardson, D.C.8
-
85
-
-
0026704101
-
Combined influence of cholesterol and synthetic amphiphillic peptides upon bilayer thickness in model membranes
-
F.A. Nezil, and M. Bloom Combined influence of cholesterol and synthetic amphiphillic peptides upon bilayer thickness in model membranes Biophys. J. 61 1992 1176 1183
-
(1992)
Biophys. J.
, vol.61
, pp. 1176-1183
-
-
Nezil, F.A.1
Bloom, M.2
-
86
-
-
0026594687
-
Constant helical pitch of the gramicidin channel in phospholipid-bilayers
-
J. Katsaras, R.S. Prosser, R.H. Stinson, and J.H. Davis Constant helical pitch of the gramicidin channel in phospholipid-bilayers Biophys. J. 61 1992 827 830
-
(1992)
Biophys. J.
, vol.61
, pp. 827-830
-
-
Katsaras, J.1
Prosser, R.S.2
Stinson, R.H.3
Davis, J.H.4
-
87
-
-
34249685982
-
An electrostatic/hydrogen bond switch as the basis for the specific interaction of phosphatidic acid with proteins
-
E.E. Kooijman, D.P. Tieleman, C. Testerink, T. Munnik, D.T.S. Rijkers, K.N.J. Burger, and B. de Kruijff An electrostatic/hydrogen bond switch as the basis for the specific interaction of phosphatidic acid with proteins J. Biol. Chem. 282 2007 11356 11364
-
(2007)
J. Biol. Chem.
, vol.282
, pp. 11356-11364
-
-
Kooijman, E.E.1
Tieleman, D.P.2
Testerink, C.3
Munnik, T.4
Rijkers, D.T.S.5
Burger, K.N.J.6
De Kruijff, B.7
-
88
-
-
34347262391
-
Bilayer thickness and membrane protein function: An energetic perspective
-
O.S. Andersen, and R.E. Koeppe Bilayer thickness and membrane protein function: an energetic perspective Annu. Rev. Biophys. Biomol. Struct. 36 2007 107 130
-
(2007)
Annu. Rev. Biophys. Biomol. Struct.
, vol.36
, pp. 107-130
-
-
Andersen, O.S.1
Koeppe, R.E.2
-
89
-
-
0031895461
-
Energetics of inclusion-induced bilayer deformations
-
C. Nielsen, M. Goulian, and O.S. Andersen Energetics of inclusion-induced bilayer deformations Biophys. J. 74 1998 1966 1983
-
(1998)
Biophys. J.
, vol.74
, pp. 1966-1983
-
-
Nielsen, C.1
Goulian, M.2
Andersen, O.S.3
-
90
-
-
45249103058
-
Limitations and strengths of uniformly charged double-layer theory: Physical significance of capacitance anomalies
-
M.B. Partenskii, and P.C. Jordan Limitations and strengths of uniformly charged double-layer theory: physical significance of capacitance anomalies Phys. Rev. E 77 2008
-
(2008)
Phys. Rev. e
, vol.77
-
-
Partenskii, M.B.1
Jordan, P.C.2
-
91
-
-
0033737385
-
Inclusion-induced bilayer deformations: Effects of monolayer equilibrium curvature
-
C. Nielsen, and O.S. Andersen Inclusion-induced bilayer deformations: effects of monolayer equilibrium curvature Biophys. J. 79 2000 2583 2604
-
(2000)
Biophys. J.
, vol.79
, pp. 2583-2604
-
-
Nielsen, C.1
Andersen, O.S.2
-
92
-
-
44349099863
-
A continuum method for determining membrane protein insertion energies and the problem of charged residues
-
S. Choe, K.A. Hecht, and M. Grabe A continuum method for determining membrane protein insertion energies and the problem of charged residues J. Gen. Physiol. 131 2008 563 573
-
(2008)
J. Gen. Physiol.
, vol.131
, pp. 563-573
-
-
Choe, S.1
Hecht, K.A.2
Grabe, M.3
-
93
-
-
0030992795
-
Lipid bilayer electrostatic energy, curvature stress, and assembly of gramicidin channels
-
J.A. Lundbaek, A.M. Maer, and O.S. Andersen Lipid bilayer electrostatic energy, curvature stress, and assembly of gramicidin channels Biochemistry 36 1997 5695 5701
-
(1997)
Biochemistry
, vol.36
, pp. 5695-5701
-
-
Lundbaek, J.A.1
Maer, A.M.2
Andersen, O.S.3
-
94
-
-
77956595226
-
Lateral diffusion of membrane proteins: Consequences of hydrophobic mismatch and lipid composition
-
S. Ramadurai, R. Duurkens, V.V. Krasnikov, and B. Poolman Lateral diffusion of membrane proteins: consequences of hydrophobic mismatch and lipid composition Biophys. J. 99 2010 1482 1489
-
(2010)
Biophys. J.
, vol.99
, pp. 1482-1489
-
-
Ramadurai, S.1
Duurkens, R.2
Krasnikov, V.V.3
Poolman, B.4
|