Life at the border: Adaptation of proteins to anisotropic membrane environment
dc.contributor.author | Pogozheva, Irina D. | en_US |
dc.contributor.author | Mosberg, Henry I. | en_US |
dc.contributor.author | Lomize, Andrei L. | en_US |
dc.date.accessioned | 2014-09-03T16:51:45Z | |
dc.date.available | WITHHELD_13_MONTHS | en_US |
dc.date.available | 2014-09-03T16:51:45Z | |
dc.date.issued | 2014-09 | en_US |
dc.identifier.citation | Pogozheva, Irina D.; Mosberg, Henry I.; Lomize, Andrei L. (2014). "Life at the border: Adaptation of proteins to anisotropic membrane environment." Protein Science 23(9): 1165-1196. | en_US |
dc.identifier.issn | 0961-8368 | en_US |
dc.identifier.issn | 1469-896X | en_US |
dc.identifier.uri | https://hdl.handle.net/2027.42/108308 | |
dc.description.abstract | This review discusses main features of transmembrane (TM) proteins which distinguish them from water‐soluble proteins and allow their adaptation to the anisotropic membrane environment. We overview the structural limitations on membrane protein architecture, spatial arrangement of proteins in membranes and their intrinsic hydrophobic thickness, co‐translational and post‐translational folding and insertion into lipid bilayers, topogenesis, high propensity to form oligomers, and large‐scale conformational transitions during membrane insertion and transport function. Special attention is paid to the polarity of TM protein surfaces described by profiles of dipolarity/polarizability and hydrogen‐bonding capacity parameters that match polarity of the lipid environment. Analysis of distributions of Trp resides on surfaces of TM proteins from different biological membranes indicates that interfacial membrane regions with preferential accumulation of Trp indole rings correspond to the outer part of the lipid acyl chain region—between double bonds and carbonyl groups of lipids. These “midpolar” regions are not always symmetric in proteins from natural membranes. We also examined the hydrophobic effect that drives insertion of proteins into lipid bilayer and different free energy contributions to TM protein stability, including attractive van der Waals forces and hydrogen bonds, side‐chain conformational entropy, the hydrophobic mismatch, membrane deformations, and specific protein–lipid binding. | en_US |
dc.publisher | Academic Press | en_US |
dc.publisher | Wiley Periodicals, Inc. | en_US |
dc.subject.other | Hydrophobic Thickness | en_US |
dc.subject.other | Protein–Lipid Interactions | en_US |
dc.subject.other | Polarity | en_US |
dc.subject.other | Database | en_US |
dc.subject.other | Protein Stability | en_US |
dc.subject.other | Protein Folding | en_US |
dc.subject.other | Membrane Protein | en_US |
dc.title | Life at the border: Adaptation of proteins to anisotropic membrane environment | en_US |
dc.type | Article | en_US |
dc.rights.robots | IndexNoFollow | en_US |
dc.subject.hlbsecondlevel | Biological Chemistry | en_US |
dc.subject.hlbtoplevel | Health Sciences | en_US |
dc.description.peerreviewed | Peer Reviewed | en_US |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/108308/1/pro2508.pdf | |
dc.identifier.doi | 10.1002/pro.2508 | en_US |
dc.identifier.source | Protein Science | en_US |
dc.identifier.citedreference | Minetti CA, Remeta DP ( 2006 ) Energetics of membrane protein folding and stability. Arch Biochem Biophys 453: 32 – 53. | en_US |
dc.identifier.citedreference | Findlay HE, Booth PJ ( 2006 ) The biological significance of lipid–protein interactions. J Phys Condens Matter 18: S1281 – S1291. | en_US |
dc.identifier.citedreference | Adamian L, Naveed H, Liang J ( 2011 ) Lipid‐binding surfaces of membrane proteins: evidence from evolutionary and structural analysis. Biochim Biophys Acta 1808: 1092 – 1102. | en_US |
dc.identifier.citedreference | Hite RK, Gonen T, Harrison SC, Walz T ( 2008 ) Interactions of lipids with aquaporin‐0 and other membrane proteins. Pflugers Arch 456: 651 – 661. | en_US |
dc.identifier.citedreference | Hite RK, Li Z, Walz T ( 2010 ) Principles of membrane protein interactions with annular lipids deduced from aquaporin‐0 2D crystals. EMBO J 29: 1652 – 1658. | en_US |
dc.identifier.citedreference | Qin L, Hiser C, Mulichak A, Garavito RM, Ferguson‐Miller S ( 2006 ) Identification of conserved lipid/detergent‐binding sites in a high‐resolution structure of the membrane protein cytochrome c oxidase. Proc Natl Acad Sci USA 103: 16117 – 16122. | en_US |
dc.identifier.citedreference | Horn R, Paulsen H ( 2002 ) Folding in vitro of light‐harvesting chlorophyll a/b protein is coupled with pigment binding. J Mol Biol 318: 547 – 556. | en_US |
dc.identifier.citedreference | Kern J, Guskov A ( 2011 ) Lipids in photosystem II: multifunctional cofactors. J Photochem Photobiol B Biol 104: 19 – 34. | en_US |
dc.identifier.citedreference | Jones MR ( 2007 ) Lipids in photosynthetic reaction centres: structural roles and functional holes. Prog Lipid Res 46: 56 – 87. | en_US |
dc.identifier.citedreference | Krebs MP, Isenbarger TA ( 2000 ) Structural determinants of purple membrane assembly. Biochim Biophys Acta 1460: 15 – 26. | en_US |
dc.identifier.citedreference | Pebay‐Peyroula E, Rosenbusch JP ( 2001 ) High‐resolution structures and dynamics of membrane protein–lipid complexes: a critique. Curr Opin Struct Biol 11: 427 – 432. | en_US |
dc.identifier.citedreference | Shinzawa‐Itoh K, Aoyama H, Muramoto K, Terada H, Kurauchi T, Tadehara Y, Yamasaki A, Sugimura T, Kurono S, Tsujimoto K, Mizushima T, Yamashita E, Tsukihara T, Yoshikawa S ( 2007 ) Structures and physiological roles of 13 integral lipids of bovine heart cytochrome c oxidase. EMBO J 26: 1713 – 1725. | en_US |
dc.identifier.citedreference | Arnarez C, Marrink SJ, Periole X ( 2013 ) Identification of cardiolipin binding sites on cytochrome c oxidase at the entrance of proton channels. Sci Rep 3: 1263. | en_US |
dc.identifier.citedreference | de Kroon AI, Dolis D, Mayer A, Lill R, de Kruijff B ( 1997 ) Phospholipid composition of highly purified mitochondrial outer membranes of rat liver and neurospora crassa. Is cardiolipin present in the mitochondrial outer membrane? Biochim Biophys Acta 1325: 108 – 116. | en_US |
dc.identifier.citedreference | Cosentino K, Garcia‐Saez AJ ( 2014 ) Mitochondrial alterations in apoptosis. Chem Phys Lipids 181: 62 – 75. | en_US |
dc.identifier.citedreference | Zhang M, Mileykovskaya E, Dowhan W ( 2002 ) Gluing the respiratory chain together. Cardiolipin is required for supercomplex formation in the inner mitochondrial membrane. J Biol Chem 277: 43553 – 43556. | en_US |
dc.identifier.citedreference | Schagger H ( 2002 ) Respiratory chain supercomplexes of mitochondria and bacteria. Biochim Biophys Acta 1555: 154 – 159. | en_US |
dc.identifier.citedreference | Schlame M, Rua D, Greenberg ML ( 2000 ) The biosynthesis and functional role of cardiolipin. Prog Lipid Res 39: 257 – 288. | en_US |
dc.identifier.citedreference | Pebay‐Peyroula E, Dahout‐Gonzalez C, Kahn R, Trezeguet V, Lauquin GJ, Brandolin G ( 2003 ) Structure of mitochondrial ADP/ATP carrier in complex with carboxyatractyloside. Nature 426: 39 – 44. | en_US |
dc.identifier.citedreference | Hoffmann B, Stockl A, Schlame M, Beyer K, Klingenberg M ( 1994 ) The reconstituted ADP/ATP carrier activity has an absolute requirement for cardiolipin as shown in cysteine mutants. J Biol Chem 269: 1940 – 1944. | en_US |
dc.identifier.citedreference | Ferguson AD, Welte W, Hofmann E, Lindner B, Holst O, Coulton JW, Diederichs K ( 2000 ) A conserved structural motif for lipopolysaccharide recognition by procaryotic and eucaryotic proteins. Structure 8: 585 – 592. | en_US |
dc.identifier.citedreference | Rapoport TA, Goder V, Heinrich SU, Matlack KE ( 2004 ) Membrane‐protein integration and the role of the translocation channel. Trends Cell Biol 14: 568 – 575. | en_US |
dc.identifier.citedreference | Noinaj N, Kuszak AJ, Gumbart JC, Lukacik P, Chang H, Easley NC, Lithgow T, Buchanan SK ( 2013 ) Structural insight into the biogenesis of beta‐barrel membrane proteins. Nature 501: 385 – 390. | en_US |
dc.identifier.citedreference | Kucerka N, Nagle JF, Sachs JN, Feller SE, Pencer J, Jackson A, Katsaras J ( 2008 ) Lipid bilayer structure determined by the simultaneous analysis of neutron and X‐ray scattering data. Biophys J 95: 2356 – 2367. | en_US |
dc.identifier.citedreference | Popot JL, Engelman DM ( 1990 ) Membrane‐protein folding and oligomerization—the 2‐stage model. Biochemistry 29: 4031 – 4037. | en_US |
dc.identifier.citedreference | Bowie JU ( 1997 ) Helix packing in membrane proteins. J Mol Biol 272: 780 – 789. | en_US |
dc.identifier.citedreference | Tan S, Tan HT, Chung MC ( 2008 ) Membrane proteins and membrane proteomics. Proteomics 8: 3924 – 3932. | en_US |
dc.identifier.citedreference | Bill RM, Henderson PJF, Iwata S, Kunji ERS, Michel H, Neutze R, Newstead S, Poolman B, Tate CG, Vogel H ( 2011 ) Overcoming barriers to membrane protein structure determination. Nat Biotechnol 29: 335 – 340. | en_US |
dc.identifier.citedreference | Hedin LE, Illergard K, Elofsson A ( 2011 ) An introduction to membrane proteins. J Proteome Res 10: 3324 – 3331. | en_US |
dc.identifier.citedreference | Johansson LC, Arnlund D, White TA, Katona G, Deponte DP, Weierstall U, Doak RB, Shoeman RL, Lomb L, Malmerberg E, Davidsson J, Nass K, Liang M, Andreasson J, Aquila A, Bajt S, Barthelmess M, Barty A, Bogan MJ, Bostedt C, Bozek JD, Caleman C, Coffee R, Coppola N, Ekeberg T, Epp SW, Erk B, Fleckenstein H, Foucar L, Graafsma H, Gumprecht L, Hajdu J, Hampton CY, Hartmann R, Hartmann A, Hauser G, Hirsemann H, Holl P, Hunter MS, Kassemeyer S, Kimmel N, Kirian RA, Maia FR, Marchesini S, Martin AV, Reich C, Rolles D, Rudek B, Rudenko A, Schlichting I, Schulz J, Seibert MM, Sierra RG, Soltau H, Starodub D, Stellato F, Stern S, Struder L, Timneanu N, Ullrich J, Wahlgren WY, Wang X, Weidenspointner G, Wunderer C, Fromme P, Chapman HN, Spence JC, Neutze R ( 2012 ) Lipidic phase membrane protein serial femtosecond crystallography. Nat Methods 9: 263 – 265. | en_US |
dc.identifier.citedreference | Shahid SA, Bardiaux B, Franks WT, Krabben L, Habeck M, van Rossum BJ, Linke D ( 2012 ) Membrane‐protein structure determination by solid‐state NMR spectroscopy of microcrystals. Nat Methods 9: 1212 – 1217. | en_US |
dc.identifier.citedreference | Hiller S, Garces RG, Malia TJ, Orekhov VY, Colombini M, Wagner G ( 2008 ) Solution structure of the integral human membrane protein VDAC‐1 in detergent micelles. Science 321: 1206 – 1210. | en_US |
dc.identifier.citedreference | Gautier A ( 2014 ) Structure determination of alpha‐helical membrane proteins by solution‐state NMR: emphasis on retinal proteins. Biochim Biophys Acta 1837: 578 – 588. | en_US |
dc.identifier.citedreference | Van Horn WD, Kim HJ, Ellis CD, Hadziselimovic A, Sulistijo ES, Karra MD, Tian C, Sonnichsen FD, Sanders CR ( 2009 ) Solution nuclear magnetic resonance structure of membrane‐integral diacylglycerol kinase. Science 324: 1726 – 1729. | en_US |
dc.identifier.citedreference | Call ME, Chou JJ ( 2010 ) A view into the blind spot: solution NMR provides new insights into signal transduction across the lipid bilayer. Structure 18: 1559 – 1569. | en_US |
dc.identifier.citedreference | Gayen S, Li Q, Kang C ( 2012 ) Solution NMR study of the transmembrane domain of single‐span membrane proteins: opportunities and strategies. Curr Protein Pept Sci 13: 585 – 600. | en_US |
dc.identifier.citedreference | Bocharov EV, Volynsky PE, Pavlov KV, Efremov RG, Arseniev AS ( 2010 ) Structure elucidation of dimeric transmembrane domains of bitopic proteins. Cell Adh Migr 4: 284 – 298. | en_US |
dc.identifier.citedreference | Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Iype L, Jain S, Fagan P, Marvin J, Padolla D, Ravichandran V, Schneider B, Thanki N, Weissig H, Westbrook JD, Zardecki C ( 2002 ) The Protein Data Bank. Acta Crystallogr D Biol Crystallogr 58: 899 – 907. | en_US |
dc.identifier.citedreference | White SH, Snaider C. Database. Available at: http://blanco.biomol.uci.edu/mpstruc White laboratory at UC Irvine. ( 2014 ). | en_US |
dc.identifier.citedreference | Raman P, Cherezov V, Caffrey M ( 2006 ) The membrane Protein Data Bank. Cell Mol Life Sci 63: 36 – 51. | en_US |
dc.identifier.citedreference | Saier MH, Yen MR, Noto K, Tamang DG, Elkan C ( 2009 ) The transporter classification database: recent advances. Nucleic Acids Res 37: D274 – D278. | en_US |
dc.identifier.citedreference | Tusnady GE, Dosztanyi Z, Simon I ( 2005 ) PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank. Nucleic Acids Res 33: D275 – D278. | en_US |
dc.identifier.citedreference | Sansom MSP, Scott KA, Bond PJ ( 2008 ) Coarse‐grained simulation: a high‐throughput computational approach to membrane proteins. Biochem Soc Trans 36: 27 – 32. | en_US |
dc.identifier.citedreference | Chetwynd AP, Scott KA, Mokrab Y, Sansom MSP ( 2008 ) CGDB: a database of membrane protein/lipid interactions by coarse‐grained molecular dynamics simulations. Mol Membr Biol 25: 662 – 669. | en_US |
dc.identifier.citedreference | Lomize MA, Pogozheva ID, Joo H, Mosberg HI, Lomize AL ( 2012 ) OPM database and PPM web server: resources for positioning of proteins in membranes. Nucleic Acids Res 40: 370 – 376. | en_US |
dc.identifier.citedreference | Lomize AL, Pogozheva ID, Mosberg HI ( 2011 ) Anisotropic solvent model of the lipid bilayer. 2. Energetics of insertion of small molecules, peptides, and proteins in membranes. J Chem Inf Model 51: 930 – 946. | en_US |
dc.identifier.citedreference | Pogozheva ID, Tristram‐Nagle S, Mosberg HI, Lomize AL ( 2013 ) Structural adaptations of proteins to different biological membranes. Biochim Biophys Acta 1828: 2592 – 2608. | en_US |
dc.identifier.citedreference | Liu W, Eilers M, Patel AB, Smith SO ( 2004 ) Helix packing moments reveal diversity and conservation in membrane protein structure. J Mol Biol 337: 713 – 729. | en_US |
dc.identifier.citedreference | Oberai A, Ihm Y, Kim S, Bowie JU ( 2006 ) A limited universe of membrane protein families and folds. Protein Sci 15: 1723 – 1734. | en_US |
dc.identifier.citedreference | Almen MS, Nordstrom KJ, Fredriksson R, Schioth HB ( 2009 ) Mapping the human membrane proteome: a majority of the human membrane proteins can be classified according to function and evolutionary origin. BMC Biol 7: 50. | en_US |
dc.identifier.citedreference | Worch R, Bokel C, Hofinger S, Schwille P, Weidemann T ( 2010 ) Focus on composition and interaction potential of single‐pass transmembrane domains. Proteomics 10: 4196 – 4208. | en_US |
dc.identifier.citedreference | Wallin E, von Heijne G ( 1998 ) Genome‐wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci 7: 1029 – 1038. | en_US |
dc.identifier.citedreference | Elofsson A, von Heijne G ( 2007 ) Membrane protein structure: prediction versus reality. Annu Rev Biochem 76: 125 – 140. | en_US |
dc.identifier.citedreference | Vinothkumar KR, Henderson R ( 2010 ) Structures of membrane proteins. Q Rev Biophys 43: 65 – 158. | en_US |
dc.identifier.citedreference | McLuskey K, Roszak AW, Zhu Y, Isaacs NW ( 2010 ) Crystal structures of all‐alpha type membrane proteins. Eur Biophys J 39: 723 – 755. | en_US |
dc.identifier.citedreference | Arce J, Sturgis JN, Duneau J‐P ( 2009 ) Dissecting membrane protein architecture: an annotation of structural complexity. Biopolymers 91: 815 – 829. | en_US |
dc.identifier.citedreference | Gimpelev M, Forrest LR, Murray D, Honig B ( 2004 ) Helical packing patterns in membrane and soluble proteins. Biophys J 87: 4075 – 4086. | en_US |
dc.identifier.citedreference | Eyre TA, Partridge L, Thornton JM ( 2004 ) Computational analysis of alpha‐helical membrane protein structure: implications for the prediction of 3D structural models. Protein Eng Des Sel 17: 613 – 624. | en_US |
dc.identifier.citedreference | Popot JL, Engelman DM ( 2000 ) Helical membrane protein folding, stability, and evolution. Annu Rev Biochem 69: 881 – 922. | en_US |
dc.identifier.citedreference | Yan C, Luo J ( 2010 ) An analysis of reentrant loops. Protein J 29: 350 – 354. | en_US |
dc.identifier.citedreference | Pornillos O, Chang G ( 2006 ) Inverted repeat domains in membrane proteins. FEBS Lett 580: 358 – 362. | en_US |
dc.identifier.citedreference | von Heijne G ( 2006 ) Membrane‐protein topology. Nat Rev Mol Cell Biol 7: 909 – 918. | en_US |
dc.identifier.citedreference | Ojemalm K, Halling KK, Nilsson I, von Heijne G ( 2012 ) Orientational preferences of neighboring helices can drive er insertion of a marginally hydrophobic transmembrane helix. Mol Cell 45: 529 – 540. | en_US |
dc.identifier.citedreference | Zhao G, London E ( 2006 ) An amino acid “transmembrane tendency” scale that approaches the theoretical limit to accuracy for prediction of transmembrane helices: relationship to biological hydrophobicity. Protein Sci 15: 1987 – 2001. | en_US |
dc.identifier.citedreference | Hedin LE, Ojemalm K, Bernsel A, Hennerdal A, Illergard K, Enquist K, Kauko A, Cristobal S, von Heijne G, Lerch‐Bader M, Nilsson I, Elofsson A ( 2010 ) Membrane insertion of marginally hydrophobic transmembrane helices depends on sequence context. J Mol Biol 396: 221 – 229. | en_US |
dc.identifier.citedreference | Rath EM, Tessier D, Campbell AA, Lee HC, Werner T, Salam NK, Lee LK, Church WB ( 2013 ) A benchmark server using high resolution protein structure data, and benchmark results for membrane helix predictions. BMC Bioinform 14: 111. | en_US |
dc.identifier.citedreference | Rath A, Deber CM ( 2012 ) Protein structure in membrane domains. Annu Rev Biophys 41: 135 – 155. | en_US |
dc.identifier.citedreference | Hessa T, Meindl‐Beinker NM, Bernsel A, Kim H, Sato Y, Lerch‐Bader M, Nilsson I, White SH, von Heijne G ( 2007 ) Molecular code for transmembrane‐helix recognition by the Sec61 translocon. Nature 450: 1026 – 1030. | en_US |
dc.identifier.citedreference | von Heijne G ( 2011 ) Membrane proteins: from bench to bits. Biochem Soc Trans 39: 747 – 750. | en_US |
dc.identifier.citedreference | Bano‐Polo M, Baeza‐Delgado C, Orzaez M, Marti‐Renom MA, Abad C, Mingarro I ( 2012 ) Polar/ionizable residues in transmembrane segments: effects on helix–helix packing. PLoS One 7: e44263. | en_US |
dc.identifier.citedreference | Herrmann JR, Fuchs A, Panitz JC, Eckert T, Unterreitmeier S, Frishman D, Langosch D ( 2010 ) Ionic interactions promote transmembrane helix‐helix association depending on sequence context. J Mol Biol 396: 452 – 461. | en_US |
dc.identifier.citedreference | Meindl‐Beinker NM, Lundin C, Nilsson I, White SH, von Heijne G ( 2006 ) Asn‐ and Asp‐mediated interactions between transmembrane helices during translocon‐mediated membrane protein assembly. EMBO Rep 7: 1111 – 1116. | en_US |
dc.identifier.citedreference | Baeza‐Delgado C, Marti‐Renom MA, Mingarro I ( 2013 ) Structure‐based statistical analysis of transmembrane helices. Eur Biophys J 42: 199 – 207. | en_US |
dc.identifier.citedreference | Viklund H, Granseth E, Elofsson A ( 2006 ) Structural classification and prediction of reentrant regions in alpha‐helical transmembrane proteins: application to complete genomes. J Mol Biol 361: 591 – 603. | en_US |
dc.identifier.citedreference | Screpanti E, Hunte C ( 2007 ) Discontinuous membrane helices in transport proteins and their correlation with function. J Struct Biol 159: 261 – 267. | en_US |
dc.identifier.citedreference | Kazi A, Sun JZ, Doi K, Sung SS, Takahashi Y, Yin H, Rodriguez JM, Becerril J, Berndt N, Hamilton AD, Wang HG, Sebti SM ( 2011 ) The BH3 alpha‐helical mimic BH3‐M6 disrupts Bcl‐X(L), Bcl‐2, and MCL‐1 protein‐protein interactions with Bax, Bbak, Bad, or Bim and induces apoptosis in a Bax‐ and Bim‐dependent manner. J Biol Chem 286: 9382 – 9392. | en_US |
dc.identifier.citedreference | Rapp M, Seppala S, Granseth E, von Heijne G ( 2007 ) Emulating membrane protein evolution by rational design. Science 315: 1282 – 1284. | en_US |
dc.identifier.citedreference | Zeth K, Thein M ( 2010 ) Porins in prokaryotes and eukaryotes: common themes and variations. Biochem J 431: 13 – 22. | en_US |
dc.identifier.citedreference | Wimley WC ( 2002 ) Toward genomic identification of beta‐barrel membrane proteins: composition and architecture of known structures. Protein Sci 11: 301 – 312. | en_US |
dc.identifier.citedreference | Zhai YF, Saier MH ( 2002 ) The beta‐barrel finder (BBF) program, allowing identification of outer membrane beta‐barrel proteins encoded within prokaryotic genomes. Protein Sci 11: 2196 – 2207. | en_US |
dc.identifier.citedreference | Buchanan SK ( 1999 ) Beta‐barrel proteins from bacterial outer membranes: structure, function and refolding. Curr Opin Struct Biol 9: 455 – 461. | en_US |
dc.identifier.citedreference | Schulz GE ( 2000 ) Beta‐barrel membrane proteins. Curr Opin Struct Biol 10: 443 – 447. | en_US |
dc.identifier.citedreference | Schulz GE ( 2002 ) The structure of bacterial outer membrane proteins. Biochim Biophys Acta 1565: 308 – 317. | en_US |
dc.identifier.citedreference | Fairman JW, Noinaj N, Buchanan SK ( 2011 ) The structural biology of beta‐barrel membrane proteins: a summary of recent reports. Curr Opin Struct Biol 21: 523 – 531. | en_US |
dc.identifier.citedreference | Buchanan SK, Yamashita Y, Fleming KG. Structure and folding of outer membrane proteins. In: Engelman EH, Tamm LK, Eds. ( 2012 ) Comprehensive biophysics. Oxford: Academic Press, pp 139 – 163. | en_US |
dc.identifier.citedreference | Noinaj N, Guillier M, Barnard TJ, Buchanan SK ( 2010 ) TonB‐dependent transporters: regulation, structure, and function. Annu Rev Microbiol 64: 43 – 60. | en_US |
dc.identifier.citedreference | Bay DC, Hafez M, Young MJ, Court DA ( 2012 ) Phylogenetic and coevolutionary analysis of the beta‐barrel protein family comprised of mitochondrial porin (VDAC) and Tom40. Biochim Biophys Acta 1818: 1502 – 1519. | en_US |
dc.identifier.citedreference | Bayrhuber M, Meins T, Habeck M, Becker S, Giller K, Villinger S, Vonrhein C, Griesinger C, Zweckstetter M, Zeth K ( 2008 ) Structure of the human voltage‐dependent anion channel. Proc Natl Acad Sci USA 105: 15370 – 15375. | en_US |
dc.identifier.citedreference | Ujwal R, Cascio D, Colletier JP, Faham S, Zhang J, Toro L, Ping PP, Abramson J ( 2008 ) The crystal structure of mouse VDAC1 at 2.3 angstrom resolution reveals mechanistic insights into metabolite gating. Proc Natl Acad Sci USA 105: 17742 – 17747. | en_US |
dc.identifier.citedreference | Schredelseker J, Paz A, Lopez CJ, Altenbach C, Leung CS, Drexler MK, Chen JN, Hubbell WL, Abramson J ( 2014 ) High‐resolution structure and double electron‐electron resonance of the zebrafish voltage dependent anion channel 2 reveal an oligomeric population. J Biol Chem 289: 12566 – 12577. | en_US |
dc.identifier.citedreference | Andersen C ( 2003 ) Channel‐tunnels: outer membrane components of type I secretion systems and multidrug efflux pumps of Gram‐negative bacteria. Rev Physiol Biochem Pharmacol 147: 122 – 165. | en_US |
dc.identifier.citedreference | Andersen C, Hughes C, Koronakis V ( 2001 ) Protein export and drug efflux through bacterial channel‐tunnels. Curr Opin Cell Biol 13: 412 – 416. | en_US |
dc.identifier.citedreference | Meng G, Surana NK, St Geme JW, III, Waksman G ( 2006 ) Structure of the outer membrane translocator domain of the haemophilus influenzae Hia trimeric autotransporter. EMBO J 25: 2297 – 2304. | en_US |
dc.identifier.citedreference | Faller M, Niederweis M, Schulz GE ( 2004 ) The structure of a mycobacterial outer‐membrane channel. Science 303: 1189 – 1192. | en_US |
dc.identifier.citedreference | Bischofberger M, Iacovache I, van der Goot FG ( 2012 ) Pathogenic pore‐forming proteins: function and host response. Cell Host Microbe 12: 266 – 275. | en_US |
dc.identifier.citedreference | Iacovache I, Degiacomi MT, van der Goot FG. Pore‐forming toxins. In: Egelman EH, Ed. ( 2012 ) Comprehensive biophysics. Elsevier B.V, Academic Press, New York, v.5, pp 164 – 188. | en_US |
dc.identifier.citedreference | De S, Olson R ( 2011 ) Crystal structure of the vibrio cholerae cytolysin heptamer reveals common features among disparate pore‐forming toxins. Proc Natl Acad Sci USA 108: 7385 – 7390. | en_US |
dc.identifier.citedreference | Song L, Hobaugh MR, Shustak C, Cheley S, Bayley H, Gouaux JE ( 1996 ) Structure of staphylococcal alpha‐hemolysin, a heptameric transmembrane pore. Science 274: 1859 – 1866. | en_US |
dc.identifier.citedreference | Savva CG, Fernandes da Costa SP, Bokori‐Brown M, Naylor CE, Cole AR, Moss DS, Titball RW, Basak AK ( 2013 ) Molecular architecture and functional analysis of NetB, a pore‐forming toxin from clostridium perfringens. J Biol Chem 288: 3512 – 3522. | en_US |
dc.identifier.citedreference | Yamashita K, Kawai Y, Tanaka Y, Hirano N, Kaneko J, Tomita N, Ohta M, Kamio Y, Yao M, Tanaka I ( 2011 ) Crystal structure of the octameric pore of staphylococcal gamma‐hemolysin reveals the beta‐barrel pore formation mechanism by two components. Proc Natl Acad Sci USA 108: 17314 – 17319. | en_US |
dc.identifier.citedreference | Kelkar DA, Chattopadhyay A ( 2007 ) The gramicidin ion channel: a model membrane protein. Biochim Biophys Acta 1768: 2011 – 2025. | en_US |
dc.identifier.citedreference | Wallace BA ( 1990 ) Gramicidin channels and pores. Annu Rev Biophys Biophy Chem 19: 127 – 157. | en_US |
dc.identifier.citedreference | Arseniev AS, Barsukov IL, Bystrov VF, Lomize AL, Ovchinnikov Yu A ( 1985 ) 1 H NMR study of gramicidin a transmembrane ion channel. Head‐to‐head right‐handed, single‐stranded helices. FEBS Lett 186: 168 – 174. | en_US |
dc.identifier.citedreference | Lomize AL, Orekhov V, Arseniev AS ( 1992 ) Refinement of the spatial structure of the gramicidin a ion channel. Bioorg Khim 18: 182 – 200. | en_US |
dc.identifier.citedreference | Ketchem RR, Lee KC, Huo S, Cross TA ( 1996 ) Macromolecular structural elucidation with solid‐state NMR‐derived orientational constraints. J Biomol NMR 8: 1 – 14. | en_US |
dc.identifier.citedreference | Smart OS, Goodfellow JM, Wallace BA ( 1993 ) The pore dimensions of gramicidin a. Biophys J 65: 2455 – 2460. | en_US |
dc.identifier.citedreference | Urry DW, Goodall MC, Glickson JD, Mayers DF ( 1971 ) The gramicidin a transmembrane channel: characteristics of head‐to‐head dimerized (l,d) helices. Proc Natl Acad Sci USA 68: 1907 – 1911. | en_US |
dc.identifier.citedreference | Sun H, Greathouse DV, Andersen OS, Koeppe RE ( 2008 ) The preference of tryptophan for membrane interfaces—insights from N ‐methylation of tryptophans in gramicidin channels. J Biol Chem 283: 22233 – 22243. | en_US |
dc.identifier.citedreference | Koeppe RE, Schmutzer SE, Andersen OS. Gramicidin channels as cation nanotubes. In: Hayden O, Nielsch K, Eds. ( 2011 ) Molecular‐ and nano‐tubes. Berlin: Springer‐Verlag Berlin, pp 11 – 30. | en_US |
dc.identifier.citedreference | Killian JA ( 2003 ) Synthetic peptides as models for intrinsic membrane proteins. FEBS Lett 555: 134 – 138. | en_US |
dc.identifier.citedreference | Deber CM, Liu LP, Wang C ( 1999 ) Perspective: peptides as mimics of transmembrane segments in proteins. J Pept Res 54: 200 – 205. | en_US |
dc.identifier.citedreference | Booth PJ, Curnow P ( 2006 ) Membrane proteins shape up: understanding in vitro folding. Curr Opin Struct Biol 16: 480 – 488. | en_US |
dc.identifier.citedreference | Harris NJ, Booth PJ ( 2012 ) Folding and stability of membrane transport proteins in vitro. Biochim Biophys Acta 1818: 1055 – 1066. | en_US |
dc.identifier.citedreference | DiBartolo ND, Booth PJ. The membrane factor: biophysical studies of alpha helical transmembrane protein folding. In: Egelman EH, Ed. ( 2012 ) Comprehensive biophysics. Elsevier B.V., Academic Press, New York, v.3, pp 290 – 316. | en_US |
dc.identifier.citedreference | Dalbey RE, Kuhn A ( 2000 ) Evolutionarily related insertion pathways of bacterial, mitochondrial, and thylakoid membrane proteins. Annu Rev Cell Dev Biol 16: 51 – 87. | en_US |
dc.identifier.citedreference | Dalbey RE, Wang P, Kuhn A ( 2011 ) Assembly of bacterial inner membrane proteins. Annu Rev Biochem 80: 161 – 187. | en_US |
dc.identifier.citedreference | Zimmer J, Nam Y, Rapoport TA ( 2008 ) Structure of a complex of the ATPase Seca and the protein‐translocation channel. Nature 455: 936 – 943. | en_US |
dc.identifier.citedreference | Van den Berg B, Clemons WM, Jr, Collinson I, Modis Y, Hartmann E, Harrison SC, Rapoport TA ( 2004 ) X‐ray structure of a protein‐conducting channel. Nature 427: 36 – 44. | en_US |
dc.identifier.citedreference | Gogala M, Becker T, Beatrix B, Armache JP, Barrio‐Garcia C, Berninghausen O, Beckmann R ( 2014 ) Structures of the Sec61 complex engaged in nascent peptide translocation or membrane insertion. Nature 506: 107 – 110. | en_US |
dc.identifier.citedreference | White SH, von Heijne G ( 2004 ) The machinery of membrane protein assembly. Curr Opin Struct Biol 14: 397 – 404. | en_US |
dc.identifier.citedreference | Bowie JU ( 2005 ) Solving the membrane protein folding problem. Nature 438: 581 – 589. | en_US |
dc.identifier.citedreference | Park E, Rapoport TA ( 2012 ) Mechanisms of Sec61/SecY‐mediated protein translocation across membranes. Annu Rev Biophys 41: 21 – 40. | en_US |
dc.identifier.citedreference | Zhang L, Paakkarinen V, Suorsa M, Aro EM ( 2001 ) A SecY homologue is involved in chloroplast‐encoded D1 protein biogenesis. J Biol Chem 276: 37809 – 37814. | en_US |
dc.identifier.citedreference | Tsukazaki T, Mori H, Echizen Y, Ishitani R, Fukai S, Tanaka T, Perederina A, Vassylyev DG, Kohno T, Maturana AD, Ito K, Nureki O ( 2011 ) Structure and function of a membrane component SecDF that enhances protein export. Nature 474: 235 – 238. | en_US |
dc.identifier.citedreference | Kol S, Nouwen N, Driessen AJ ( 2008 ) Mechanisms of YidC‐mediated insertion and assembly of multimeric membrane protein complexes. J Biol Chem 283: 31269 – 31273. | en_US |
dc.identifier.citedreference | van der Laan M, Bechtluft P, Kol S, Nouwen N, Driessen AJ ( 2004 ) F1F0 ATP synthase subunit c is a substrate of the novel YidC pathway for membrane protein biogenesis. J Cell Biol 165: 213 – 222. | en_US |
dc.identifier.citedreference | van der Laan M, Nouwen NP, Driessen AJ ( 2005 ) YidC—an evolutionary conserved device for the assembly of energy‐transducing membrane protein complexes. Curr Opin Microbiol 8: 182 – 187. | en_US |
dc.identifier.citedreference | Kiefer D, Kuhn A ( 2007 ) YidC as an essential and multifunctional component in membrane protein assembly. Int Rev Cytol 259: 113 – 138. | en_US |
dc.identifier.citedreference | Kruger V, Deckers M, Hildenbeutel M, van der Laan M, Hellmers M, Dreker C, Preuss M, Herrmann JM, Rehling P, Wagner R, Meinecke M ( 2012 ) The mitochondrial oxidase assembly protein1 (Oxa1) insertase forms a membrane pore in lipid bilayers. J Biol Chem 287: 33314 – 33326. | en_US |
dc.identifier.citedreference | Herrmann JM, Neupert W, Stuart RA ( 1997 ) Insertion into the mitochondrial inner membrane of a polytopic protein, the nuclear‐encoded Oxa1p. EMBO J 16: 2217 – 2226. | en_US |
dc.identifier.citedreference | Jermy A ( 2012 ) Bacterial secretion: Sec and Tat collaborate in a Rieske business. Nat Rev Microbiol 10: 801. | en_US |
dc.identifier.citedreference | Keller R, de Keyzer J, Driessen AJ, Palmer T ( 2012 ) Co‐operation between different targeting pathways during integration of a membrane protein. J Cell Biol 199: 303 – 315. | en_US |
dc.identifier.citedreference | Hagan CL, Silhavy TJ, Kahne D ( 2011 ) Beta‐barrel membrane protein assembly by the Bam complex. Annu Rev Biochem 80: 189 – 210. | en_US |
dc.identifier.citedreference | Rigel NW, Silhavy TJ ( 2012 ) Making a beta‐barrel: assembly of outer membrane proteins in gram‐negative bacteria. Curr Opin Microbiol 15: 189 – 193. | en_US |
dc.identifier.citedreference | Borgese N, Fasana E ( 2011 ) Targeting pathways of c‐tail‐anchored proteins. Biochim Biophys Acta 1808: 937 – 946. | en_US |
dc.identifier.citedreference | Hegde RS, Keenan RJ ( 2011 ) Tail‐anchored membrane protein insertion into the endoplasmic reticulum. Nat Rev Mol Cell Biol 12: 787 – 798. | en_US |
dc.identifier.citedreference | Waizenegger T, Stan T, Neupert W, Rapaport D ( 2003 ) Signal‐anchor domains of proteins of the outer membrane of mitochondria: structural and functional characteristics. J Biol Chem 278: 42064 – 42071. | en_US |
dc.identifier.citedreference | Kanaji S, Iwahashi J, Kida Y, Sakaguchi M, Mihara K ( 2000 ) Characterization of the signal that directs Tom20 to the mitochondrial outer membrane. J Cell Biol 151: 277 – 288. | en_US |
dc.identifier.citedreference | Fox TD ( 2012 ) Mitochondrial protein synthesis, import, and assembly. Genetics 192: 1203 – 1234. | en_US |
dc.identifier.citedreference | von Heijne G, Steppuhn J, Herrmann RG ( 1989 ) Domain structure of mitochondrial and chloroplast targeting peptides. Eur J Biochem 180: 535 – 545. | en_US |
dc.identifier.citedreference | Rehling P, Brandner K, Pfanner N ( 2004 ) Mitochondrial import and the twin‐pore translocase. Nat Rev Mol Cell Biol 5: 519 – 530. | en_US |
dc.identifier.citedreference | Dukanovic J, Rapaport D ( 2011 ) Multiple pathways in the integration of proteins into the mitochondrial outer membrane. Biochim Biophys Acta 1808: 971 – 980. | en_US |
dc.identifier.citedreference | Merklinger E, Gofman Y, Kedrov A, Driessen AJ, Ben‐Tal N, Shai Y, Rapaport D ( 2012 ) Membrane integration of a mitochondrial signal‐anchored protein does not require additional proteinaceous factors. Biochem J 442: 381 – 389. | en_US |
dc.identifier.citedreference | Kemper C, Habib SJ, Engl G, Heckmeyer P, Dimmer KS, Rapaport D ( 2008 ) Integration of tail‐anchored proteins into the mitochondrial outer membrane does not require any known import components. J Cell Sci 121: 1990 – 1998. | en_US |
dc.identifier.citedreference | Dimmer KS, Rapaport D ( 2012 ) Unresolved mysteries in the biogenesis of mitochondrial membrane proteins. Biochim Biophys Acta 1818: 1085 – 1090. | en_US |
dc.identifier.citedreference | Kovermann P, Truscott KN, Guiard B, Rehling P, Sepuri NB, Muller H, Jensen RE, Wagner R, Pfanner N ( 2002 ) Tim22, the essential core of the mitochondrial protein insertion complex, forms a voltage‐activated and signal‐gated channel. Mol Cell 9: 363 – 373. | en_US |
dc.identifier.citedreference | Lee DW, Kim JK, Lee S, Choi S, Kim S, Hwang I ( 2008 ) Arabidopsis nuclear‐encoded plastid transit peptides contain multiple sequence subgroups with distinctive chloroplast‐targeting sequence motifs. Plant Cell 20: 1603 – 1622. | en_US |
dc.identifier.citedreference | Wickner W, Schekman R ( 2005 ) Protein translocation across biological membranes. Science 310: 1452 – 1456. | en_US |
dc.identifier.citedreference | Soll J, Schleiff E ( 2004 ) Protein import into chloroplasts. Nat Rev Mol Cell Biol 5: 198 – 208. | en_US |
dc.identifier.citedreference | Robinson C, Thompson SJ, Woolhead C ( 2001 ) Multiple pathways used for the targeting of thylakoid proteins in chloroplasts. Traffic 2: 245 – 251. | en_US |
dc.identifier.citedreference | Skalitzky CA, Martin JR, Harwood JH, Beirne JJ, Adamczyk BJ, Heck GR, Cline K, Fernandez DE ( 2011 ) Plastids contain a second Sec translocase system with essential functions. Plant Physiol 155: 354 – 369. | en_US |
dc.identifier.citedreference | Jaru‐Ampornpan P, Shen K, Lam VQ, Ali M, Doniach S, Jia TZ, Shan SO ( 2010 ) ATP‐independent reversal of a membrane protein aggregate by a chloroplast Srp subunit. Nat Struct Mol Biol 17: 696 – 702. | en_US |
dc.identifier.citedreference | Tu CJ, Schuenemann D, Hoffman NE ( 1999 ) Chloroplast ftsy, chloroplast signal recognition particle, and GTP are required to reconstitute the soluble phase of light‐harvesting chlorophyll protein transport into thylakoid membranes. J Biol Chem 274: 27219 – 27224. | en_US |
dc.identifier.citedreference | Cline K, Dabney‐Smith C ( 2008 ) Plastid protein import and sorting: different paths to the same compartments. Curr Opin Plant Biol 11: 585 – 592. | en_US |
dc.identifier.citedreference | Kapazoglou A, Sagliocco F, Dure L, III ( 1995 ) PSII‐T, a new nuclear encoded lumenal protein from photosystem II. Targeting and processing in isolated chloroplasts. J Biol Chem 270: 12197 – 12202. | en_US |
dc.identifier.citedreference | Lomize AL, Pogozheva ID, Lomize MA, Mosberg HI ( 2006 ) Positioning of proteins in membranes: a computational approach. Protein Sci 15: 1318 – 1333. | en_US |
dc.identifier.citedreference | Mitra K, Ubarretxena‐Belandia T, Taguchi T, Warren G, Engelman DM ( 2004 ) Modulation of the bilayer thickness of exocytic pathway membranes by membrane proteins rather than cholesterol. Proc Natl Acad Sci USA 101: 4083 – 4088. | en_US |
dc.identifier.citedreference | Borgese N, Brambillasca S, Soffientini P, Yabal M, Makarow M ( 2003 ) Biogenesis of tail‐anchored proteins. Biochem Soc Trans 31: 1238 – 1242. | en_US |
dc.identifier.citedreference | Fernandez C, Hilty C, Wider G, Wuthrich K ( 2002 ) Lipid‐protein interactions in DHPC micelles containing the integral membrane protein OmpX investigated by NMR spectroscopy. Proc Natl Acad Sci USA 99: 13533 – 13537. | en_US |
dc.identifier.citedreference | Snijder HJ, Timmins PA, Kalk KH, Dijkstra BW ( 2003 ) Detergent organisation in crystals of monomeric outer membrane phospholipase A. J Struct Biol 141: 122 – 131. | en_US |
dc.identifier.citedreference | Abraham T, Schooling SR, Nieh MP, Kučerka N, Beveridge TJ, Katsaras J ( 2007 ) Neutron diffraction study of pseudomonas aeruginosa lipopolysaccharide bilayers. J Phys Chem B 111: 2477 – 2483. | en_US |
dc.identifier.citedreference | Kucerka N, Papp‐Szabo E, Nieh MP, Harroun TA, Schooling SR, Pencer J, Nicholson EA, Beveridge TJ, Katsaras J ( 2008 ) Effect of cations on the structure of bilayers formed by lipopolysaccharides isolated from pseudomonas aeruginosa PAO1. J Physl Chem B 112: 8057 – 8062. | en_US |
dc.identifier.citedreference | Tamm LK, Hong H, Liang BY ( 2004 ) Folding and assembly of beta‐barrel membrane proteins. Biochim Biophys Acta 1666: 250 – 263. | en_US |
dc.identifier.citedreference | Niederweis M, Danilchanka O, Huff J, Hoffmann C, Engelhardt H ( 2009 ) Mycobacterial outer membranes: in search of proteins. Trends in Microbiol 18: 109 – 116. | en_US |
dc.identifier.citedreference | Fiedler S, Broecker J, Keller S ( 2010 ) Protein folding in membranes. Cell Mol Life Sci 67: 1779 – 1798. | en_US |
dc.identifier.citedreference | Marsh D ( 2007 ) Lateral pressure profile, spontaneous curvature frustration, and the incorporation and conformation of proteins in membranes. Biophys J 93: 3884 – 3899. | en_US |
dc.identifier.citedreference | Cantor RS ( 1997 ) Lateral pressures in cell membranes: a mechanism for modulation of protein function. J Phys Chem B 101: 1723 – 1725. | en_US |
dc.identifier.citedreference | Cantor RS ( 1999 ) Lipid composition and the lateral pressure profile in bilayers. Biophys J 76: 2625 – 2639. | en_US |
dc.identifier.citedreference | Pabst G, Kucerka N, Nieh MP, Rheinstadter MC, Katsaras J ( 2010 ) Applications of neutron and X‐ray scattering to the study of biologically relevant model membranes. Chem Phys Lipids 163: 460 – 479. | en_US |
dc.identifier.citedreference | Raghunathan M, Zubovski Y, Venable RM, Pastor RW, Nagle JF, Tristram‐Nagle S ( 2012 ) Structure and elasticity of lipid membranes with genistein and daidzein bioflavinoids using X‐ray scattering and MD simulations. J Phys Chem B 116: 3918 – 3927. | en_US |
dc.identifier.citedreference | Boscia AL, Treece BW, Mohammadyani D, Klein‐Seetharaman J, Braun AR, Wassenaar TA, Klosgen B, Tristram‐Nagle S ( 2014 ) X‐ray structure, thermodynamics, elastic properties and MD simulations of cardiolipin/dimyristoylphosphatidylcholine mixed membranes. Chem Phys Lipids 178: 1 – 10. | en_US |
dc.identifier.citedreference | Boscia AL, Akabori K, Benamram Z, Michel JA, Jablin MS, Steckbeck JD, Montelaro RC, Nagle JF, Tristram‐Nagle S ( 2013 ) Membrane structure correlates to function of LLP2 on the cytoplasmic tail of HIV‐1 gp41 protein. Biophys J 105: 657 – 666. | en_US |
dc.identifier.citedreference | Lee AG ( 2003 ) Lipid–protein interactions in biological membranes: a structural perspective. Biochim Biophys Acta 1612: 1 – 40. | en_US |
dc.identifier.citedreference | Palsdottir H, Hunte C ( 2004 ) Lipids in membrane protein structures. Biochim Biophys Acta 1666: 2 – 18. | en_US |
dc.identifier.citedreference | Yau WM, Wimley WC, Gawrisch K, White SH ( 1998 ) The preference of tryptophan for membrane interfaces. Biochemistry 37: 14713 – 14718. | en_US |
dc.identifier.citedreference | Hong HD, Park S, Jimenez RHF, Rinehart D, Tamm LK ( 2007 ) Role of aromatic side chains in the folding and thermodynamic stability of integral membrane proteins. J Am Chem Soc 129: 8320 – 8327. | en_US |
dc.identifier.citedreference | Liu W, Caffrey M ( 2006 ) Interactions of tryptophan, tryptophan peptides, and tryptophan alkyl esters at curved membrane interfaces. Biochemistry 45: 11713 – 11726. | en_US |
dc.identifier.citedreference | Sanders CR, Mittendorf KF ( 2011 ) Tolerance to changes in membrane lipid composition as a selected trait of membrane proteins. Biochemistry 50: 7858 – 7867. | en_US |
dc.identifier.citedreference | Hanshaw RG, Stahelin RV, Smith BD ( 2008 ) Noncovalent keystone interactions controlling biomembrane structure. Chemistry 14: 1690 – 1697. | en_US |
dc.identifier.citedreference | Nikaido H. Outer membranes, Gram‐negative bacteria. In: Schaechter M, Ed. ( 2009 ) Encyclopedia of microbiology. Oxford, UK: Academic Press, pp 439 – 452. | en_US |
dc.identifier.citedreference | van Meer G, Voelker DR, Feigenson GW ( 2008 ) Membrane lipids: where they are and how they behave. Nat Rev Mol Cell Biol 9: 112 – 124. | en_US |
dc.identifier.citedreference | Maxfield FR, van Meer G ( 2010 ) Cholesterol, the central lipid of mammalian cells. Curr Opin Cell Biol 22: 422 – 429. | en_US |
dc.identifier.citedreference | Chen YJ, Pornillos O, Lieu S, Ma C, Chen AP, Chang G ( 2007 ) X‐ray structure of EmrE supports dual topology model. Proc Natl Acad Sci USA 104: 18999 – 19004. | en_US |
dc.identifier.citedreference | Korkhov VM, Tate CG ( 2009 ) An emerging consensus for the structure of EmrE. Acta Crystallogr D 65: 186 – 192. | en_US |
dc.identifier.citedreference | von Heijne G, Gavel Y ( 1988 ) Topogenic signals in integral membrane proteins. Eur J Biochem 174: 671 – 678. | en_US |
dc.identifier.citedreference | Kauko A, Hedin LE, Thebaud E, Cristobal S, Elofsson A, von Heijne G ( 2010 ) Repositioning of transmembrane alpha‐helices during membrane protein folding. J Mol Biol 397: 190 – 201. | en_US |
dc.identifier.citedreference | Pitonzo D, Skach WR ( 2006 ) Molecular mechanisms of aquaporin biogenesis by the endoplasmic reticulum Sec61 translocon. Biochim Biophys Acta 1758: 976 – 988. | en_US |
dc.identifier.citedreference | Seppala S, Slusky JS, Lloris‐Garcera P, Rapp M, von Heijne G ( 2010 ) Control of membrane protein topology by a single C‐terminal residue. Science 328: 1698 – 1700. | en_US |
dc.identifier.citedreference | Ojemalm K, Watson HR, Roboti P, Cross BC, Warwicker J, von Heijne G, High S ( 2013 ) Positional editing of transmembrane domains during ion channel assembly. J Cell Sci 26: 464 – 472. | en_US |
dc.identifier.citedreference | Lu Y, Turnbull IR, Bragin A, Carveth K, Verkman AS, Skach WR ( 2000 ) Reorientation of aquaporin‐1 topology during maturation in the endoplasmic reticulum. Mol Biol Cell 11: 2973 – 2985. | en_US |
dc.identifier.citedreference | Norholm MH, Cunningham F, Deber CM, von Heijne G ( 2011 ) Converting a marginally hydrophobic soluble protein into a membrane protein. J Mol Biol 407: 171 – 179. | en_US |
dc.identifier.citedreference | Bano‐Polo M, Martinez‐Gil L, Wallner B, Nieva JL, Elofsson A, Mingarro I ( 2013 ) Charge pair interactions in transmembrane helices and turn propensity of the connecting sequence promote helical hairpin insertion. J Mol Biol 425: 830 – 840. | en_US |
dc.identifier.citedreference | Zhang L, Sato Y, Hessa T, von Heijne G, Lee JK, Kodama I, Sakaguchi M, Uozumi N ( 2007 ) Contribution of hydrophobic and electrostatic interactions to the membrane integration of the shaker K+ channel voltage sensor domain. Proc Natl Acad Sci USA 104: 8263 – 8268. | en_US |
dc.identifier.citedreference | Dowhan W, Bogdanov M ( 2009 ) Lipid‐dependent membrane protein topogenesis. Ann Rev Biochem 78: 515 – 540. | en_US |
dc.identifier.citedreference | von Heijne G ( 2007 ) Formation of transmembrane helices in vivo—is hydrophobicity all that matters? J Gen Physiol 129: 353 – 356. | en_US |
dc.identifier.citedreference | van Dalen A, de Kruijff B ( 2004 ) The role of lipids in membrane insertion and translocation of bacterial proteins. Biochim Biophys Acta 1694: 97 – 109. | en_US |
dc.identifier.citedreference | von Heijne G ( 1992 ) Membrane protein structure prediction. Hydrophobicity analysis and the positive‐inside rule. J Mol Biol 225: 487 – 494. | en_US |
dc.identifier.citedreference | Nilsson J, Persson B, von Heijne G ( 2005 ) Comparative analysis of amino acid distributions in integral membrane proteins from 107 genomes. Proteins Struct Funct Bioinform 60: 606 – 616. | en_US |
dc.identifier.citedreference | von Heijne G ( 1989 ) Control of topology and mode of assembly of a polytopic membrane protein by positively charged residues. Nature 341: 456 – 458. | en_US |
dc.identifier.citedreference | von Heijne G ( 1986 ) The distribution of positively charged residues in bacterial inner membrane‐proteins correlates with the trans‐membrane topology. EMBO J 5: 3021 – 3027. | en_US |
dc.identifier.citedreference | Dalbey RE ( 1990 ) Positively charged residues are important determinants of membrane protein topology. Trends Biochem Sci 15: 253 – 257. | en_US |
dc.identifier.citedreference | Sipos L, von Heijne G ( 1993 ) Predicting the topology of eukaryotic membrane proteins. Eur J Biochem 213: 1333 – 1340. | en_US |
dc.identifier.citedreference | Gavel Y, Steppuhn J, Herrmann R, von Heijne G ( 1991 ) The “positive‐inside rule” applies to thylakoid membrane proteins. FEBS Lett 282: 41 – 46. | en_US |
dc.identifier.citedreference | Gavel Y, von Heijne G ( 1992 ) The distribution of charged amino acids in mitochondrial inner‐membrane proteins suggests different modes of membrane integration for nuclearly and mitochondrially encoded proteins. Eur J Biochem 205: 1207 – 1215. | en_US |
dc.identifier.citedreference | Nakashima H, Nishikawa K ( 1992 ) The amino acid composition is different between the cytoplasmic and extracellular sides in membrane proteins. FEBS Lett 303: 141 – 146. | en_US |
dc.identifier.citedreference | Ulmschneider MB, Sansom MSP, Di Nola A ( 2005 ) Properties of integral membrane protein structures: derivation of an implicit membrane potential. Proteins Struct Funct Bioinform 59: 252 – 265. | en_US |
dc.identifier.citedreference | Schramm CA, Hannigan BT, Donald JE, Keasar C, Saven JG, Degrado WF, Samish I ( 2012 ) Knowledge‐based potential for positioning membrane‐associated structures and assessing residue‐specific energetic contributions. Structure 20: 924 – 935. | en_US |
dc.identifier.citedreference | Benning C ( 2009 ) Mechanisms of lipid transport involved in organelle biogenesis in plant cells. Annu Rev Cell Develop Biol 25: 71 – 91. | en_US |
dc.identifier.citedreference | Nilsson I, von Heijne G ( 1990 ) Fine‐tuning the topology of a polytopic membrane protein: role of positively and negatively charged amino acids. Cell 62: 1135 – 1141. | en_US |
dc.identifier.citedreference | Fujita H, Yamagishi M, Kida Y, Sakaguchi M ( 2011 ) Positive charges on the translocating polypeptide chain arrest movement through the translocon. J Cell Sci 124: 4184 – 4193. | en_US |
dc.identifier.citedreference | Johansson M, Nilsson I, von Heijne G ( 1993 ) Positively charged amino acids placed next to a signal sequence block protein translocation more efficiently in Escherichia coli than in mammalian microsomes. Mol Gen Genet 239: 251 – 256. | en_US |
dc.identifier.citedreference | Kiefer D, Hu X, Dalbey R, Kuhn A ( 1997 ) Negatively charged amino acid residues play an active role in orienting the Sec‐independent Pf3 coat protein in the Escherichia coli inner membrane. EMBO J 16: 2197 – 2204. | en_US |
dc.identifier.citedreference | Delgado‐Partin VM, Dalbey RE ( 1998 ) The proton motive force, acting on acidic residues, promotes translocation of amino‐terminal domains of membrane proteins when the hydrophobicity of the translocation signal is low. J Biol Chem 273: 9927 – 9934. | en_US |
dc.identifier.citedreference | Schuenemann TA, Delgado‐Nixon VM, Dalbey RE ( 1999 ) Direct evidence that the proton motive force inhibits membrane translocation of positively charged residues within membrane proteins. J Biol Chem 274: 6855 – 6864. | en_US |
dc.identifier.citedreference | van Klompenburg W, Nilsson I, von Heijne G, de Kruijff B ( 1997 ) Anionic phospholipids are determinants of membrane protein topology. EMBO J 16: 4261 – 4266. | en_US |
dc.identifier.citedreference | Andersson H, von Heijne G ( 1994 ) Membrane‐protein topology—effects of delta‐mu(h)+ on the translocation of charged residues explain the positive inside rule. EMBO J 13: 2267 – 2272. | en_US |
dc.identifier.citedreference | van de Vossenberg JL, Albers SV, van der Does C, Driessen AJ, van Klompenburg W ( 1998 ) The positive inside rule is not determined by the polarity of the delta psi (transmembrane electrical potential). Mol Microbiol 29: 1125 – 1127. | en_US |
dc.identifier.citedreference | Goder V, Junne T, Spiess M ( 2004 ) Sec61p contributes to signal sequence orientation according to the positive‐inside rule. Mol Biol Cell 15: 1470 – 1478. | en_US |
dc.identifier.citedreference | Junne T, Schwede T, Goder V, Spiess M ( 2007 ) Mutations in the Sec61p channel affecting signal sequence recognition and membrane protein topology. J Biol Chem 282: 3201 – 33209. | en_US |
dc.identifier.citedreference | Kumazaki K, Chiba S, Takemoto M, Furukawa A, Nishiyama K‐i, Sugano Y, Mori T, Dohmae N, Hirata K, Nakada‐Nakura Y, Maturana AD, Tanaka Y, Mori H, Sugita Y, Arisaka F, Ito K, Ishitani R, Tsukazaki T, Nureki O ( 2014 ) Structural basis of Sec‐independent membrane protein insertion by YidC. Nature 509: 516 – 520. | en_US |
dc.identifier.citedreference | Jackups R, Liang J ( 2005 ) Interstrand pairing patterns in beta‐barrel membrane proteins: the positive‐outside rule, aromatic rescue, and strand registration prediction. J Mol Biol 354: 979 – 993. | en_US |
dc.identifier.citedreference | Qu J, Behrens‐Kneip S, Holst O, Kleinschmidt JH ( 2009 ) Binding regions of outer membrane protein a in complexes with the periplasmic chaperone Skp. A site‐directed fluorescence study. Biochemistry 48: 4926 – 4936. | en_US |
dc.identifier.citedreference | Cymer F, Schneider D ( 2012 ) Oligomerization of polytopic alpha‐helical membrane proteins: causes and consequences. Biol Chem 393: 1215 – 1230. | en_US |
dc.identifier.citedreference | Pereira‐Leal JB, Levy ED, Teichmann SA ( 2006 ) The origins and evolution of functional modules: lessons from protein complexes. Philos Trans R Soc Lond B Biol Sci 361: 507 – 517. | en_US |
dc.identifier.citedreference | Venkatakrishnan AJ, Levy ED, Teichmann SA ( 2010 ) Homomeric protein complexes: evolution and assembly. Biochem Soc Trans 38: 879 – 882. | en_US |
dc.identifier.citedreference | Nishi H, Hashimoto K, Madej T, Panchenko AR ( 2013 ) Evolutionary, physicochemical, and functional mechanisms of protein homooligomerization. Prog Mol Biol Transl Sci 117: 3 – 24. | en_US |
dc.identifier.citedreference | Marianayagam NJ, Sunde M, Matthews JM ( 2004 ) The power of two: protein dimerization in biology. Trends Biochem Sci 29: 618 – 625. | en_US |
dc.identifier.citedreference | Ridder A, Langosch D Transmembrane domains in membrane protein folding, oligomerization, and function. In: Buchner J, Kiefhaber T, Eds. ( 2008 ) Protein Folding Handbook. Wiley‐VCH Verlag GmbH, Weinheim, Germany, pp 876 – 918. | en_US |
dc.identifier.citedreference | Langosch D, Arkin IT ( 2009 ) Interaction and conformational dynamics of membrane‐spanning protein helices. Protein Sci 18: 1343 – 1358. | en_US |
dc.identifier.citedreference | Schneider D, Finger C, Prodohl A, Volkmer T ( 2007 ) From interactions of single transmembrane helices to folding of alpha‐helical membrane proteins: analyzing transmembrane helix–helix interactions in bacteria. Curr Protein Pept Sci 8: 45 – 61. | en_US |
dc.identifier.citedreference | Senes A, Engel DE, DeGrado WF ( 2004 ) Folding of helical membrane proteins: the role of polar, gxxxg‐like and proline motifs. Curr Opin Struct Biol 14: 465 – 479. | en_US |
dc.identifier.citedreference | Curran AR, Engelman DM ( 2003 ) Sequence motifs, polar interactions and conformational changes in helical membrane proteins. Curr Opin Struct Biol 13: 412 – 417. | en_US |
dc.identifier.citedreference | Cymer F, Veerappan A, Schneider D ( 2012 ) Transmembrane helix–helix interactions are modulated by the sequence context and by lipid bilayer properties. Biochim Biophys Acta 1818: 963 – 973. | en_US |
dc.identifier.citedreference | Melnyk RA, Kim S, Curran AR, Engelman DM, Bowie JU, Deber CM ( 2004 ) The affinity of GxxxG motifs in transmembrane helix–helix interactions is modulated by long‐range communication. J Biol Chem 279: 16591 – 16597. | en_US |
dc.identifier.citedreference | Li E, Wimley WC, Hristova K ( 2012 ) Transmembrane helix dimerization: beyond the search for sequence motifs. Biochim Biophys Acta 1818: 183 – 193. | en_US |
dc.identifier.citedreference | Parton DL, Klingelhoefer JW, Sansom MS ( 2011 ) Aggregation of model membrane proteins, modulated by hydrophobic mismatch, membrane curvature, and protein class. Biophys J 101: 691 – 699. | en_US |
dc.identifier.citedreference | Hong H, Bowie JU ( 2011 ) Dramatic destabilization of transmembrane helix interactions by features of natural membrane environments. J Am Chem Soc 133: 11389 – 11398. | en_US |
dc.identifier.citedreference | Cross TA, Sharma M, Yi M, Zhou HX ( 2011 ) Influence of solubilizing environments on membrane protein structures. Trends Biochem Sci 36: 117 – 125. | en_US |
dc.identifier.citedreference | Grigoryan G, Moore DT, DeGrado WF ( 2011 ) Transmembrane communication: general principles and lessons from the structure and function of the M2 proton channel, K(+) channels, and integrin receptors. Annu Rev Biochem 80: 211 – 237. | en_US |
dc.identifier.citedreference | Ubarretxena‐Belandia I, Stokes DL ( 2012 ) Membrane protein structure determination by electron crystallography. Curr Opin Struct Biol 22: 520 – 528. | en_US |
dc.identifier.citedreference | Gurevich VV, Gurevich EV ( 2008 ) How and why do GPCRs dimerize? Trends Pharmacol Sci 29: 234 – 240. | en_US |
dc.identifier.citedreference | Meng GY, Fronzes R, Chandran V, Remaut H, Waksman G ( 2009 ) Protein oligomerization in the bacterial outer membrane. Mol Membr Biol 26: 136 – 145. | en_US |
dc.identifier.citedreference | Bechinger B ( 2008 ) A dynamic view of peptides and proteins in membranes. Cell Mol Life Sci 65: 3028 – 3039. | en_US |
dc.identifier.citedreference | Song C, Weichbrodt C, Salnikov ES, Dynowski M, Forsberg BO, Bechinger B, Steinem C, de Groot BL, Zachariae U, Zeth K ( 2013 ) Crystal structure and functional mechanism of a human antimicrobial membrane channel. Proc Natl Acad Sci USA 110: 4586 – 4591. | en_US |
dc.identifier.citedreference | Bechinger B, Resende JM, Aisenbrey C ( 2011 ) The structural and topological analysis of membrane‐associated polypeptides by oriented solid‐state nmr spectroscopy: established concepts and novel developments. Biophys Chem 153: 115 – 125. | en_US |
dc.identifier.citedreference | Poschner BC, Fischer K, Herrmann JR, Hofmann MW, Langosch D ( 2011 ) Structural features of fusogenic model transmembrane domains that differentially regulate inner and outer leaflet mixing in membrane fusion. Mol Membr Biol 27: 1 – 10. | en_US |
dc.identifier.citedreference | Iacovache I, van der Goot FG, Pernot L ( 2008 ) Pore formation: an ancient yet complex form of attack. Biochim Biophys Acta 1778: 1611 – 1623. | en_US |
dc.identifier.citedreference | White SH, Wimley WC, Ladokhin AS, Hristova K ( 1998 ) Protein folding in membranes: determining energetics of peptide‐bilayer interactions. Energ Biol Macromol B 295: 62 – 87. | en_US |
dc.identifier.citedreference | Wimley WC, White SH ( 1996 ) Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nat Struct Biol 3: 842 – 848. | en_US |
dc.identifier.citedreference | Marcoux J, Wang SC, Politis A, Reading E, Ma J, Biggin PC, Zhou M, Tao H, Zhang Q, Chang G, Morgner N, Robinson CV ( 2013 ) Mass spectrometry reveals synergistic effects of nucleotides, lipids, and drugs binding to a multidrug resistance efflux pump. Proc Natl Acad Sci USA 110: 9704 – 9709. | en_US |
dc.identifier.citedreference | Thogersen L, Nissen P ( 2012 ) Flexible P‐type ATPases interacting with the membrane. Curr Opin Struct Biol 22: 491 – 499. | en_US |
dc.identifier.citedreference | Rollauer SE, Tarry MJ, Graham JE, Jaaskelainen M, Jager F, Johnson S, Krehenbrink M, Liu SM, Lukey MJ, Marcoux J, McDowell MA, Rodriguez F, Roversi P, Stansfeld PJ, Robinson CV, Sansom MS, Palmer T, Högbom M, Berks BC, Lea SM ( 2012 ) Structure of the TatC core of the twin‐arginine protein transport system. Nature 492: 210 – 214. | en_US |
dc.identifier.citedreference | Shi Y ( 2013 ) Common folds and transport mechanisms of secondary active transporters. Annu Rev Biophys 42: 51 – 72. | en_US |
dc.identifier.citedreference | Matthews EE, Zoonens M, Engelman DM ( 2006 ) Dynamic helix interactions in transmembrane signaling. Cell 127: 447 – 450. | en_US |
dc.identifier.citedreference | Wang T, Fu G, Pan X, Wu J, Gong X, Wang J, Shi Y ( 2013 ) Structure of a bacterial energy‐coupling factor transporter. Nature 497: 272 – 276. | en_US |
dc.identifier.citedreference | Xu K, Zhang M, Zhao Q, Yu F, Guo H, Wang C, He F, Ding J, Zhang P ( 2013 ) Crystal structure of a folate energy‐coupling factor transporter from Lactobacillus brevis. Nature 497: 268 – 271. | en_US |
dc.identifier.citedreference | Palmer T, Berks BC ( 2012 ) The twin‐arginine translocation (Tat) protein export pathway. Nat Rev Microbiol 10: 483 – 496. | en_US |
dc.identifier.citedreference | Frobel J, Rose P, Muller M ( 2012 ) Twin‐arginine‐dependent translocation of folded proteins. Philos Trans R Soc Lond B Biol Sci 367: 1029 – 1046. | en_US |
dc.identifier.citedreference | Johansson ACV, Lindahl E ( 2008 ) Position‐resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations. Proteins Struct Funct Bioinform 70: 1332 – 1344. | en_US |
dc.identifier.citedreference | Gohlke U, Pullan L, McDevitt CA, Porcelli I, de Leeuw E, Palmer T, Saibil HR, Berks BC ( 2005 ) The tata component of the twin‐arginine protein transport system forms channel complexes of variable diameter. Proc Natl Acad Sci USA 102: 10482 – 10486. | en_US |
dc.identifier.citedreference | White SH ( 2003 ) Translocons, thermodynamics, and the folding of membrane proteins. FEBS Lett 555: 116 – 121. | en_US |
dc.identifier.citedreference | Haltia T, Freire E ( 1995 ) Forces and factors that contribute to the structural stability of membrane proteins. Biochim Biophys Acta 1241: 295 – 322. | en_US |
dc.identifier.citedreference | White SH, Wimley WC ( 1999 ) Membrane protein folding and stability: physical principles. Annu Rev Biophys Biomol Struct 28: 319 – 365. | en_US |
dc.identifier.citedreference | Booth PJ, Templer RH, Meijberg W, Allen SJ, Curran AR, Lorch M ( 2001 ) In vitro studies of membrane protein folding. Crit Rev Biochem Mol Biol 36: 501 – 603. | en_US |
dc.identifier.citedreference | Killian JA, von Heijne G ( 2000 ) How proteins adapt to a membrane‐water interface. Trends Biochem Sci 25: 429 – 434. | en_US |
dc.identifier.citedreference | MacKenzie KR ( 2006 ) Folding and stability of alpha‐helical integral membrane proteins. Chem Rev 106: 1931 – 1977. | en_US |
dc.identifier.citedreference | Stanley AM, Fleming KG ( 2008 ) The process of folding proteins into membranes: challenges and progress. Arch Biochem Biophys 469: 46 – 66. | en_US |
dc.identifier.citedreference | Bowie JU ( 2011 ) Membrane protein folding: how important are hydrogen bonds? Curr Opin Struct Biol 21: 42 – 49. | en_US |
dc.identifier.citedreference | Chakrabartty A, Baldwin RL ( 1995 ) Stability of alpha‐helices. Adv Protein Chem 46: 141 – 176. | en_US |
dc.identifier.citedreference | Lomize AL, Mosberg HI ( 1997 ) Thermodynamic model of secondary structure for alpha‐helical peptides and proteins. Biopolymers 42: 239 – 269. | en_US |
dc.identifier.citedreference | Makhatadze GI ( 2005 ) Thermodynamics of alpha‐helix formation. Adv Protein Chem 72: 199 – 226. | en_US |
dc.identifier.citedreference | Ladokhin AS, White SH ( 2001 ) Protein chemistry at membrane interfaces: non‐additivity of electrostatic and hydrophobic interactions. J Mol Biol 309: 543 – 552. | en_US |
dc.identifier.citedreference | Seelig J ( 2004 ) Thermodynamics of lipid‐peptide interactions. Biochim Biophys Acta 1666: 40 – 50. | en_US |
dc.identifier.citedreference | Ziegler A ( 2008 ) Thermodynamic studies and binding mechanisms of cell‐penetrating peptides with lipids and glycosaminoglycans. Adv Drug Deliv Rev 60: 580 – 597. | en_US |
dc.identifier.citedreference | Reshetnyak YK, Andreev OA, Segala M, Markin VS, Engelman DM ( 2008 ) Energetics of peptide (PHLIP) binding to and folding across a lipid bilayer membrane. Proc Natl Acad Sci USA 105: 15340 – 15345. | en_US |
dc.identifier.citedreference | Wimley WC, White SH ( 2000 ) Designing transmembrane alpha‐helices that insert spontaneously. Biochemistry 39: 4432 – 4442. | en_US |
dc.identifier.citedreference | Kyrychenko A, Rodnin MV, Posokhov YO, Holt A, Pucci B, Killian JA, Ladokhin AS ( 2012 ) Thermodynamic measurements of bilayer insertion of a single transmembrane helix chaperoned by fluorinated surfactants. J Mol Biol 416: 328 – 334. | en_US |
dc.identifier.citedreference | Lomize AL, Pogozheva ID, Lomize MA, Mosberg HI ( 2007 ) The role of hydrophobic interactions in positioning of peripheral proteins in membranes. BMC Struct Biol 7: 44. | en_US |
dc.identifier.citedreference | MacKenzie KR, Fleming KG ( 2008 ) Association energetics of membrane spanning alpha‐helices. Curr Opin Struct Biol 18: 412 – 419. | en_US |
dc.identifier.citedreference | Booth PJ, Curnow P ( 2009 ) Folding scene investigation: membrane proteins. Curr Opin Struct Biol 19: 8 – 13. | en_US |
dc.identifier.citedreference | Lomize AL, Pogozheva ID, Mosberg HI ( 2011 ) Anisotropic solvent model of the lipid bilayer. 1. Parameterization of long‐range electrostatics and first solvation shell effects. J Chem Inf Model 51: 918 – 929. | en_US |
dc.identifier.citedreference | Lomize AL, Pogozheva ID, Mosberg HI ( 2004 ) Quantification of helix‐helix binding affinities in micelles and lipid bilayers. Protein Sci 13: 2600 – 2612. | en_US |
dc.identifier.citedreference | White SH, Wimley WC ( 1998 ) Hydrophobic interactions of peptides with membrane interfaces. Biochim Biophys Acta 1376: 339 – 352. | en_US |
dc.identifier.citedreference | Moon CP, Fleming KG ( 2011 ) Side‐chain hydrophobicity scale derived from transmembrane protein folding into lipid bilayers. Proc Natl Acad Sci USA 108: 10174 – 10177. | en_US |
dc.identifier.citedreference | Adamian L, Nanda V, DeGrado WF, Liang J ( 2005 ) Empirical lipid propensities of amino acid residues in multispan alpha helical membrane proteins. Proteins Struct Funct Bioinform 59: 496 – 509. | en_US |
dc.identifier.citedreference | Koehler J, Woetzel N, Staritzbichler R, Sanders CR, Meiler J ( 2009 ) A unified hydrophobicity scale for multispan membrane proteins. Proteins Struct Funct Bioinform 76: 13 – 29. | en_US |
dc.identifier.citedreference | Senes A, Chadi DC, Law PB, Walters RFS, Nanda V, DeGrado WF ( 2007 ) E‐z, a depth‐dependent potential for assessing the energies of insertion of amino acid side‐chains into membranes: derivation and applications to determining the orientation of transmembrane and interfacial helices. J Mol Biol 366: 436 – 448. | en_US |
dc.identifier.citedreference | Hsieh D, Davis A, Nanda V ( 2012 ) A knowledge‐based potential highlights unique features of membrane alpha‐helical and beta‐barrel protein insertion and folding. Protein Sci 21: 50 – 62. | en_US |
dc.identifier.citedreference | Schow EV, Freites JA, Cheng P, Bernsel A, von Heijne G, White SH, Tobias DJ ( 2011 ) Arginine in membranes: the connection between molecular dynamics simulations and translocon‐mediated insertion experiments. J Membr Biol 239: 35 – 48. | en_US |
dc.identifier.citedreference | MacCallum JL, Bennett WFD, Tieleman DP ( 2007 ) Partitioning of amino acid side chains into lipid bilayers: results from computer simulations and comparison to experiment. J Gen Physiol 129: 371 – 377. | en_US |
dc.identifier.citedreference | MacCallum JL, Bennett WF, Tieleman DP ( 2008 ) Distribution of amino acids in a lipid bilayer from computer simulations. Biophys J 94: 3393 – 3404. | en_US |
dc.identifier.citedreference | Zhao G, London E ( 2009 ) Strong correlation between statistical transmembrane tendency and experimental hydrophobicity scales for identification of transmembrane helices. J Membr Biol 229: 165 – 168. | en_US |
dc.identifier.citedreference | MacCallum JL, Tieleman DP ( 2011 ) Hydrophobicity scales: a thermodynamic looking glass into lipid–protein interactions. Trends Biochem Sci 36: 653 – 662. | en_US |
dc.identifier.citedreference | Hessa T, Kim H, Bihlmaier K, Lundin C, Boekel J, Andersson H, Nilsson I, White SH, von Heijne G ( 2005 ) Recognition of transmembrane helices by the endoplasmic reticulum translocon. Nature 433: 377 – 381. | en_US |
dc.identifier.citedreference | Hessa T, Reithinger JH, von Heijne G, Kim H ( 2009 ) Analysis of transmembrane helix integration in the endoplasmic reticulum in S. cerevisiae. J Mol Biol 386: 1222 – 1228. | en_US |
dc.identifier.citedreference | Xie K, Hessa T, Seppala S, Rapp M, von Heijne G, Dalbey RE ( 2007 ) Features of transmembrane segments that promote the lateral release from the translocase into the lipid phase. Biochemistry 46: 15153 – 15161. | en_US |
dc.identifier.citedreference | Botelho SC, Osterberg M, Reichert AS, Yamano K, Bjorkholm P, Endo T, von Heijne G, Kim H ( 2011 ) Tim23‐mediated insertion of transmembrane alpha‐helices into the mitochondrial inner membrane. EMBO J 30: 1003 – 1011. | en_US |
dc.identifier.citedreference | White SH, von Heijne G ( 2008 ) How translocons select transmembrane helices. Annu Rev Biophys 37: 23 – 42. | en_US |
dc.identifier.citedreference | Fagerberg L, Jonasson K, von Heijne G, Uhlen M, Berglund L ( 2010 ) Prediction of the human membrane proteome. Proteomics 10: 1141 – 1149. | en_US |
dc.identifier.citedreference | Bernsel A, Viklund H, Falk J, Lindahl E, von Heijne G, Elofsson A ( 2008 ) Prediction of membrane‐protein topology from first principles. Proc Natl Acad Sci USA 105: 7177 – 7181. | en_US |
dc.identifier.citedreference | Mitchell DC ( 2012 ) Progress in understanding the role of lipids in membrane protein folding. Biochim Biophys Acta 1818: 951 – 956. | en_US |
dc.identifier.citedreference | Andersen OS, Koeppe RE ( 2007 ) Bilayer thickness and membrane protein function: an energetic perspective. Annu Rev Biophys Biomol Struct 36: 107 – 130. | en_US |
dc.identifier.citedreference | Marsh D ( 2008 ) Protein modulation of lipids, and vice‐versa, in membranes. Biochim Biophys Acta 1778: 1545 – 1575. | en_US |
dc.identifier.citedreference | Phillips R, Ursell T, Wiggins P, Sens P ( 2009 ) Emerging roles for lipids in shaping membrane‐protein function. Nature 459: 379 – 385. | en_US |
dc.identifier.citedreference | Yano Y, Yamamoto A, Ogura M, Matsuzaki K ( 2011 ) Thermodynamics of insertion and self‐association of a transmembrane helix: a lipophobic interaction by phosphatidylethanolamine. Biochemistry 50: 6806 – 6814. | en_US |
dc.identifier.citedreference | Ben‐Tal N, Ben‐Shaul A, Nicholls A, Honig B ( 1996 ) Free‐energy determinants of alpha‐helix insertion into lipid bilayers. Biophys J 70: 1803 – 1812. | en_US |
dc.identifier.citedreference | Israelachvili JN ( 1992 ) Intermolecular and surface forces. London: Academic Press. | en_US |
dc.identifier.citedreference | Faham S, Yang D, Bare E, Yohannan S, Whitelegge JP, Bowie JU ( 2004 ) Side‐chain contributions to membrane protein structure and stability. J Mol Biol 335: 297 – 305. | en_US |
dc.identifier.citedreference | Lomize AL, Reibarkh MY, Pogozheva ID ( 2002 ) Interatomic potentials and solvation parameters from protein engineering data for buried residues. Protein Sci 11: 1984 – 2000. | en_US |
dc.identifier.citedreference | Shakhnovich EI, Finkelstein AV ( 1989 ) Theory of cooperative transitions in protein molecules. I. Why denaturation of globular protein is a first‐order phase transition. Biopolymers 28: 1667 – 1680. | en_US |
dc.identifier.citedreference | Grigoryan G, DeGrado WF ( 2011 ) Probing designability via a generalized model of helical bundle geometry. J Mol Biol 405: 1079 – 1100. | en_US |
dc.identifier.citedreference | Eilers M, Patel AB, Liu W, Smith SO ( 2002 ) Comparison of helix interactions in membrane and soluble alpha‐bundle proteins. Biophys J 82: 2720 – 2736. | en_US |
dc.identifier.citedreference | Zhang Y, Kulp DW, Lear JD, DeGrado WF ( 2009 ) Experimental and computational evaluation of forces directing the association of transmembrane helices. J Am Chem Soc 131: 11341 – 11343. | en_US |
dc.identifier.citedreference | Zhou FX, Cocco MJ, Russ WP, Brunger AT, Engelman DM ( 2000 ) Interhelical hydrogen bonding drives strong interactions in membrane proteins. Nat Struct Biol 7: 154 – 160. | en_US |
dc.identifier.citedreference | Zhou FX, Merianos HJ, Brunger AT, Engelman DM ( 2001 ) Polar residues drive association of polyleucine transmembrane helices. Proc Natl Acad Sci USA 98: 2250 – 2255. | en_US |
dc.identifier.citedreference | Choma C, Gratkowski H, Lear JD, DeGrado WF ( 2000 ) Asparagine‐mediated self‐association of a model transmembrane helix. Nat Struct Biol 7: 161 – 166. | en_US |
dc.identifier.citedreference | Call ME, Pyrdol J, Wiedmann M, Wucherpfennig KW ( 2002 ) The organizing principle in the formation of the T cell receptor‐CD3 complex. Cell 111: 967 – 979. | en_US |
dc.identifier.citedreference | Marsh D ( 2008 ) Energetics of hydrophobic matching in lipid–protein interactions. Biophys J 94: 3996 – 4013. | en_US |
dc.identifier.citedreference | Holt A, Killian JA ( 2010 ) Orientation and dynamics of transmembrane peptides: the power of simple models. Eur Biophys J 39: 609 – 621. | en_US |
dc.identifier.citedreference | Ursell T, Huang KC, Peterson E, Phillips R ( 2007 ) Cooperative gating and spatial organization of membrane proteins through elastic interactions. PLoS Comput Biol 3: e81. | en_US |
dc.identifier.citedreference | de Planque MR, Killian JA ( 2003 ) Protein–lipid interactions studied with designed transmembrane peptides: role of hydrophobic matching and interfacial anchoring. Mol Membr Biol 20: 271 – 284. | en_US |
dc.identifier.citedreference | Benjamini A, Smit B ( 2012 ) Robust driving forces for transmembrane helix packing. Biophys J 103: 1227 – 1235. | en_US |
dc.identifier.citedreference | Sparr E, Ash WL, Nazarov PV, Rijkers DT, Hemminga MA, Tieleman DP, Killian JA ( 2005 ) Self‐association of transmembrane alpha‐helices in model membranes: importance of helix orientation and role of hydrophobic mismatch. J Biol Chem 280: 39324 – 39331. | en_US |
dc.identifier.citedreference | Thomas D, Bron P, Weimann T, Dautant A, Giraud MF, Paumard P, Salin B, Cavalier A, Velours J, Brethes D ( 2008 ) Supramolecular organization of the yeast F1Fo‐ATP synthase. Biol Cell 100: 591 – 601. | en_US |
dc.identifier.citedreference | Lee AG ( 2011 ) Lipid–protein interactions. Biochem Soc Trans 39: 761 – 766. | en_US |
dc.owningcollname | Interdisciplinary and Peer-Reviewed |
Files in this item
Remediation of Harmful Language
The University of Michigan Library aims to describe library materials in a way that respects the people and communities who create, use, and are represented in our collections. Report harmful or offensive language in catalog records, finding aids, or elsewhere in our collections anonymously through our metadata feedback form. More information at Remediation of Harmful Language.
Accessibility
If you are unable to use this file in its current format, please select the Contact Us link and we can modify it to make it more accessible to you.