267
8 Molecular Dynamics Simulations of Lipid Bilayers with Incorporated Peptides
studies of the effects of transmembrane α-helical peptides on the organization of phosphatidylcholine bilayers. Biochim Biophys Acta 1511(1):60–73
22. Rybar P, Krivanek R, Samuely T, Lewis RNAH, McElhaney RN, Hianik T (2007) Study
of the interaction of an α-helical transmembrane peptide with phosphatidylcholine bilayer
membranes by means of densimetry and ultrasound velocimetry. Biochim Biophys Acta
1768(6):1466–1478
23. Damodaran KV, Merz KM Jr (1995) Interaction of the fusion inhibiting peptide carbobenzoxy-d-phe-l-phe-gly with n-methyldioleoylphosphatidylethanolamine lipid bilayers. J Am
Chem Soc 117(24):6561–6571
24. Huang P, Loew GH (1995) Interaction of an amphiphilic peptide with a phospholipid bilayer
surface by molecular dynamics simulation study. J Biomol Struct Dyn 12(5):937–956
25. Bernéche S, Nina M, Roux B (1998) Molecular dynamics simulations of melittin in a dimyristoylphosphatidylcholine bilayer membrane. Biophys J 75(4):1603–1618
26. Woolf TB, Roux B (1994) Molecular dynamics simulation of the gramicidin channel in a
phospholipid bilayer. PNAS 91(24):11631–11635
27. Woolf TB, Roux B (1996) Structure, energetics, and dynamics of lipid–protein interactions:
a molecular dynamics study of the gramicidin a channel in DMPC bilayer. Proteins: Struct
Funct Gen 24(1):92–114
28. Woolf TB (1997) Molecular dynamics of individual α-helices of bacteriorhodopsin in dimyristoylphosphatidylcholine. I. Structure and dynamics. Biophys J 73(5):2476–2393
29. Woolf TB (1998) Molecular dynamics simulations of individual α-helices of bacteriorhodopsin in dimyristoylphosphatidylcholine. II. Interaction energy analysis. Biophys J 74(1):115–
131
30. Tieleman DP, Sansom MSP, Berendsen HJC (1999) Alamethicin helices in a bilayer and in
solution: molecular dynamics simulations. Biophys J 76(1):40–49
31. Alter JE, Taylor GT, Sheraga HA (1972) Helix-coil stability constants for the naturally occurring amino acids in water. VI. Leucine parameters from random poly(hydroxypropylglutamineco-l-leucine) and poly(hydroxybutylglutamine-co-l-leucine). Macromolecules 5(6):739–745
32. Chou PY, Fasman GD (1997) β-Turns in proteins. J Mol Biol 115(2):135–175
33. De Planque MRR, Killian JA (2003) Protein lipid interactions studied with designed transmembrane peptides: role of hydrophobic matching and interfacial anchoring. Mol Membr
Biol 20(4):271–284
34. Bloom M, Evans E, Mouritsen OG (1991) Physical properties of the fluid lipid-bilayer component of cell membranes: a perspective. Quart Rev Biophys 24(3):293–397
35. Killian JA, Salemink I, de Planque MRR, Lindblom G, Koeppe II RE, Greathouse DV (1996)
Induction of nonbilayer structures in diacylphosphatidylcholine model membranes by transmembrane α-helical peptides: importance of hydrophobic mismatch and proposed role of
tryptophans. Biochemistry 35(3):1037–1045
36. Demmers JAA, Haverkamp J, Heck AJR, Koeppe II RE, Killian JA (2000) Electrospray
ionization mass spectrometry as a tool to analyze hydrogen/deuterium exchange kinetics of
transmembrane peptides in lipid bilayers. PNAS 97(7):3189–3194
37. Demmers JAA, van Duijn E, Haverkamp J, Greathouse DV, Koeppe II RE, Heck AJR,
Killian JA (2001) Interfacial positioning and stability of transmembrane peptides in lipid
bilayers studied by combining hydrogen/deuterium exchange and mass spectrometry. J Biol
Chem 276(37):34501–34508
38. Liu F, Lewis RNAH, Hodges RS, McElhaney RN (2004) Effect of variations in the structure
of a polyleucine-based α-helical transmembrane peptide on its interaction with phosphatidylethanolamine bilayers. Biophys J 87(4):2470–2482
39. Killian JA (2003) Synthetic peptides as models for intrinsic membrane proteins. FEBS Lett
555(1):134–138
40. Lee AG (2003) Lipid–protein interactions in biological membranes: a structural perspective.
Biochim Biophys Acta 1612(1):1–40
41. De Planque MMR, Bonev BB, Demmers JAA, Greathouse DV, Koeppe II RE, Separovic F,
Watts A, Killian JA (2003) Interfacial anchor properties of tryptophan residues in transmem-
8 Molecular Dynamics Simulations of Lipid Bilayers with Incorporated Peptides
studies of the effects of transmembrane α-helical peptides on the organization of phosphatidylcholine bilayers. Biochim Biophys Acta 1511(1):60–73
22. Rybar P, Krivanek R, Samuely T, Lewis RNAH, McElhaney RN, Hianik T (2007) Study
of the interaction of an α-helical transmembrane peptide with phosphatidylcholine bilayer
membranes by means of densimetry and ultrasound velocimetry. Biochim Biophys Acta
1768(6):1466–1478
23. Damodaran KV, Merz KM Jr (1995) Interaction of the fusion inhibiting peptide carbobenzoxy-d-phe-l-phe-gly with n-methyldioleoylphosphatidylethanolamine lipid bilayers. J Am
Chem Soc 117(24):6561–6571
24. Huang P, Loew GH (1995) Interaction of an amphiphilic peptide with a phospholipid bilayer
surface by molecular dynamics simulation study. J Biomol Struct Dyn 12(5):937–956
25. Bernéche S, Nina M, Roux B (1998) Molecular dynamics simulations of melittin in a dimyristoylphosphatidylcholine bilayer membrane. Biophys J 75(4):1603–1618
26. Woolf TB, Roux B (1994) Molecular dynamics simulation of the gramicidin channel in a
phospholipid bilayer. PNAS 91(24):11631–11635
27. Woolf TB, Roux B (1996) Structure, energetics, and dynamics of lipid–protein interactions:
a molecular dynamics study of the gramicidin a channel in DMPC bilayer. Proteins: Struct
Funct Gen 24(1):92–114
28. Woolf TB (1997) Molecular dynamics of individual α-helices of bacteriorhodopsin in dimyristoylphosphatidylcholine. I. Structure and dynamics. Biophys J 73(5):2476–2393
29. Woolf TB (1998) Molecular dynamics simulations of individual α-helices of bacteriorhodopsin in dimyristoylphosphatidylcholine. II. Interaction energy analysis. Biophys J 74(1):115–
131
30. Tieleman DP, Sansom MSP, Berendsen HJC (1999) Alamethicin helices in a bilayer and in
solution: molecular dynamics simulations. Biophys J 76(1):40–49
31. Alter JE, Taylor GT, Sheraga HA (1972) Helix-coil stability constants for the naturally occurring amino acids in water. VI. Leucine parameters from random poly(hydroxypropylglutamineco-l-leucine) and poly(hydroxybutylglutamine-co-l-leucine). Macromolecules 5(6):739–745
32. Chou PY, Fasman GD (1997) β-Turns in proteins. J Mol Biol 115(2):135–175
33. De Planque MRR, Killian JA (2003) Protein lipid interactions studied with designed transmembrane peptides: role of hydrophobic matching and interfacial anchoring. Mol Membr
Biol 20(4):271–284
34. Bloom M, Evans E, Mouritsen OG (1991) Physical properties of the fluid lipid-bilayer component of cell membranes: a perspective. Quart Rev Biophys 24(3):293–397
35. Killian JA, Salemink I, de Planque MRR, Lindblom G, Koeppe II RE, Greathouse DV (1996)
Induction of nonbilayer structures in diacylphosphatidylcholine model membranes by transmembrane α-helical peptides: importance of hydrophobic mismatch and proposed role of
tryptophans. Biochemistry 35(3):1037–1045
36. Demmers JAA, Haverkamp J, Heck AJR, Koeppe II RE, Killian JA (2000) Electrospray
ionization mass spectrometry as a tool to analyze hydrogen/deuterium exchange kinetics of
transmembrane peptides in lipid bilayers. PNAS 97(7):3189–3194
37. Demmers JAA, van Duijn E, Haverkamp J, Greathouse DV, Koeppe II RE, Heck AJR,
Killian JA (2001) Interfacial positioning and stability of transmembrane peptides in lipid
bilayers studied by combining hydrogen/deuterium exchange and mass spectrometry. J Biol
Chem 276(37):34501–34508
38. Liu F, Lewis RNAH, Hodges RS, McElhaney RN (2004) Effect of variations in the structure
of a polyleucine-based α-helical transmembrane peptide on its interaction with phosphatidylethanolamine bilayers. Biophys J 87(4):2470–2482
39. Killian JA (2003) Synthetic peptides as models for intrinsic membrane proteins. FEBS Lett
555(1):134–138
40. Lee AG (2003) Lipid–protein interactions in biological membranes: a structural perspective.
Biochim Biophys Acta 1612(1):1–40
41. De Planque MMR, Bonev BB, Demmers JAA, Greathouse DV, Koeppe II RE, Separovic F,
Watts A, Killian JA (2003) Interfacial anchor properties of tryptophan residues in transmem-