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Volumn 1828, Issue 2, 2013, Pages 851-863

The determinants of hydrophobic mismatch response for transmembrane helices

Author keywords

Free energy; Hydrophobic mismatch; Membrane protein; Molecular dynamics; Protein lipid interactions

Indexed keywords

ALANINE; GRAMICIDIN A; LEUCINE; TRYPTOPHAN;

EID: 84871735658     PISSN: 00052736     EISSN: 18792642     Source Type: Journal    
DOI: 10.1016/j.bbamem.2012.09.012     Document Type: Article
Times cited : (40)

References (94)
  • 1
    • 0031954925 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 4
    • 71749104018 scopus 로고    scopus 로고
    • Computational analysis of membrane proteins: The largest class of drug targets
    • Y. Arinaminpathy, E. Khurana, D.M. Engelman, and M.B. Gerstein Computational analysis of membrane proteins: the largest class of drug targets Drug Discov. Today 14 2009 1130 1135
    • (2009) Drug Discov. Today , vol.14 , pp. 1130-1135
    • Arinaminpathy, Y.1    Khurana, E.2    Engelman, D.M.3    Gerstein, M.B.4
  • 5
    • 0030916841 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 15
    • 0034614490 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 30
    • 22244472946 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 46
    • 0036708458 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 49
    • 67649405180 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 51
    • 0031438285 scopus 로고    scopus 로고
    • A computer perspective of membranes: Molecular dynamics studies of lipid bilayer systems
    • D.P. Tieleman, S.J. Marrink, and H.J.C. Berendsen A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems Biochim. Biophys. Acta Rev. Biomembr. 1331 1997 235 270
    • (1997) Biochim. Biophys. Acta Rev. Biomembr. , vol.1331 , pp. 235-270
    • Tieleman, D.P.1    Marrink, S.J.2    Berendsen, H.J.C.3
  • 52
    • 50549085702 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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
  • 65
    • 0034250744 scopus 로고    scopus 로고
    • 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
  • 67
    • 0000999989 scopus 로고    scopus 로고
    • 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
  • 69
    • 33646940952 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 83
    • 67349266230 scopus 로고    scopus 로고
    • 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
  • 85
    • 0026704101 scopus 로고
    • 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 scopus 로고
    • 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
  • 88
    • 34347262391 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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


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