Computational investigation of pressure profiles in lipid bilayers with embedded proteins

References

• Marsh , D. 1996 . Lateral pressure in membranes . Biochimica et Biophysica Acta , 1286 ( 3 ) : 183
   PubMed Web of Science ®Google Scholar
• Cantor , R. 1999 . The influence of membrane lateral pressures on simple geometric models of protein conformational equilibria . Chem. Phys. Lipids , 101 ( 1 ) : 45
   PubMed Web of Science ®Google Scholar
• Templer , R.H. , Castle , S.J. , Curran , A.R. , Rumbles , G. and Klug , D.R. 1998 . Sensing isothermal changes in the lateral pressure in model membranes using di-pyrenyl phosphatidylcholine . Faraday Discuss. , 111 : 41
   Google Scholar
• Brannigan , G. , Philips , P.F. and Brown , F.L. 2005 . Flexible lipid bilayers in implicit solvent . Phys. Rev. E Stat. Nonlin. Soft. Matter. Phys. , 72 ( 1 Pt 1 ) : 011915
   PubMedGoogle Scholar
• Goetz , R. and Lipowsky , R. 1998 . Computer simulations of bilayer membranes: self-assembly and interfacial tension . J. Chem. Phys. , 108 ( 17 ) : 7397
   Google Scholar
• Lindahl , E. and Edholm , O. 2000 . Spatial and energetic-entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations . J. Chem. Phys. , 113 ( 9 ) : 3882
   Web of Science ®Google Scholar
• Gullingsrud , J. and Schulten , K. 2004 . Lipid bilayer pressure profiles and mechanosensitive channel gating . Biophys. J. , 86 ( 6 ) : 3496
   PubMed Web of Science ®Google Scholar
• de Planque , M.R. , Rijkers , D.T. , Liskamp , R.M. and Separovic , F. 2004 . The alphaM1 transmembrane segment of the nicotinic acetylcholine receptor interacts strongly with model membranes . Magn. Reson. Chem. , 42 ( 2 ) : 148
   PubMedGoogle Scholar
• Martinez , K.L. , Gohon , Y. , Corringer , P.J. , Tribet , C. , Mžrola , F. , Changeux , J.P. and Popot , J.L. 2002 . Allosteric transitions of torpedo acetylcholine receptor in lipids, detergent and amphipols: molecular interactions vs. physical constraints . FEBS Lett. , 528 ( 1-3 ) : 251
   PubMedGoogle Scholar
• Baenziger , J.E. , Morris , M.L. , Darsaut , T.E. and Ryan , S.E. 2000 . Effect of membrane lipid composition on the conformational equilibria of the nicotinic acetylcholine receptor . J. Biol. Chem. , 275 ( 2 ) : 777
   PubMedGoogle Scholar
• Carrillo-Tripp , M. and Feller , S.E. 2005 . Evidence for a mechanism by which omega-3 polyunsaturated lipids may affect membrane protein function . Biochemistry , 44 ( 30 ) : 10164
   PubMed Web of Science ®Google Scholar
• Patra , M. 2005 . Lateral pressure profiles in cholesterol-dppc bilayers . Eur. Biophys. J. , : 1
   Google Scholar
• Hessa , T. , Kim , H. , Bihlmaier , K. , Lundin , C. , Boekel , J. , Andersson , H. , Nilsson , I. , White , S.H. and von Heijne , G. 2005 . Recognition of transmembrane helices by the endoplasmic reticulum translocon . Nature , 433 : 377
   PubMed Web of Science ®Google Scholar
• Dawson , C.R. , Drake , A.F. , Helliwell , J. and Hider , R.C. 1978 . The interaction of bee melittin with lipid bilayer membranes . Biochimica et Biophysica Acta , 510 ( 1 ) : 75
   PubMed Web of Science ®Google Scholar
• Berneche , S. , Nina , M. and Roux , B. 1998 . Molecular dynamics simulation of melittin in a dimyristoylphosphatidylcholine bilayer membrane . Biophys. J. , 75 ( 4 ) : 1603
   PubMedGoogle Scholar
• Terwilliger , T.C. and Eisenberg , D. 1982 . The structure of melittin: structure determination and partial refinement . J. Biol. Chem. , 257 ( 11 ) : 6010
   PubMed Web of Science ®Google Scholar
• Humphrey , W. , Dalke , A. and Schulten , K. 1996 . Vmd—visual molecular dynamics . J. Mol. Graphics , 14 ( 1 ) : 33
   PubMedGoogle Scholar
• Bachar , M. and Becker , O.M. 2000 . Protein-induced membrane disorder: a molecular dynamics study of melittin in a dipalmitoylphosphatidylcholine bilayer . Biophys. J. , 78 : 1359
   PubMed Web of Science ®Google Scholar
• Kal , L. , Skeel , R. , Bhandarkar , M. , Brunner , R. , Gursoy , A. , Krawetz , N. , Phillips , J. , Shinozaki , A. , Varadarajan , K. and Schulten , K. 1999 . Namd2: greater scalability for parallel molecular dynamics . J. Comp. Phys. , 151 ( 1 ) : 283
   Google Scholar
• MacKerell , A.D. , Bashford , D. , Bellott , M. , Dunbrack , R.L. , Evanseck , J.D. , Field , M.J. , Fischer , S. , Gao , J. , Guo , H. , Ha , S. , Joseph-McCarthy , D. , Kuchnir , L. , Kuczera , K. , Lau , F.T.K. , Mattos , C. , Michnick , S. , Ngo , T. , Nguyen , D.T. , Prodhom , B. , Reiher , W.E. , Roux , B. , Schlenkrich , M. , Smith , J.C. , Stote , R. , Straub , J. , Watanabe , M. , Wiorkiewicz-Kuczera , J. , Yin , D. and Karplus , M. 1998 . All-atom empirical potential for molecular modeling and dynamics studies of proteins . J. Phys. Chem. B , 102 ( 18 ) : 3586
   PubMed Web of Science ®Google Scholar
• Feller , S.E. , Zhang , Y.H. , Pastor , R.W. and Brooks , B.R. 1995 . Constant pressure molecular dynamics simulation—the Langevin piston method . J. Chem. Phys. , 103 ( 11 ) : 4613
   Web of Science ®Google Scholar
• Essmann , U. , Perera , L. , Berkowitz , M.L. , Darden , T. , Lee , H. and Pedersen , L.G. 1995 . A smooth particle mesh Ewald method . J. Chem. Phys. , 103 : 8577
   Web of Science ®Google Scholar
• Irving , J.H. and Kirkwood , J.G. 1950 . The statistical mechanical theory of transport processes. iv. The equations of hydrodynamics . J. Chem. Phys. , 18 ( 6 ) : 817
   Web of Science ®Google Scholar
• Sonne , J. , Hansen , F.Y. and Peters , GH . 2005 . Methodological problems in pressure profile calculations for lipid bilayers . J. Chem. Phys. , 122 ( 12 ) : 124903
   PubMedGoogle Scholar
• Harasima , A. 1958 . Molecular theory of surface tension . Adv. Chem. Phys. , : 203
   Google Scholar
• Kaszycki , P. and Wasylewski , Z. 1990 . Fluorescence-quenching-resolved spectra of melittin in lipid bilayers . Biochimica et Biophysica Acta: Protein Structure and Molecular Enzymology , 1040 : 337
   PubMedGoogle Scholar
• Seelig , J. and Browning , J.L. 1978 . General features of phospholipid conformation in membranes . FEBS Lett. , 92 ( 1 ) : 41
   Google Scholar
• Feller , S.E. and Pastor , R.W. 1999 . Constant surface tension simulations of lipid bilayers: the sensitivity of surface areas and compressibilities . J. Chem. Phys. , 111 ( 3 ) : 1281
   Google Scholar
• Skibinsky , A. , Venable , R.M. and Pastor , R.W. 2005 . A molecular dynamics study of the response of lipid bilayers and monolayers to trehalose . Biophys. J. , 89 ( 6 ) : 4111
   PubMed Web of Science ®Google Scholar