Membrane adsorption, folding, insertion and translocation of synthetic trans-membrane peptides

References

• de Groot BL, Grubmuller H. Water permeation across biological membranes: Mechanism and dynamics of aquaporin-1 and GlpF. Science 2001; 294: 2353–2357
   PubMed Web of Science ®Google Scholar
• Forrest LR, Sansom MSP. Membrane simulations: Bigger and better?. Curr Opin Structural Biol 2000; 10: 174–181
   PubMed Web of Science ®Google Scholar
• Biggin PC, Sansom MS. Interactions of alpha-helices with lipid bilayers: a review of simulation studies. Biophys Chem 1999; 76: 161–183
   PubMed Web of Science ®Google Scholar
• Domene C, Bond P, Sansom MSP. Membrane protein simulation: Ion channels and bacterial outer membrane proteins. Adv Prot Chem 2003; 66: 159–193
   PubMedGoogle Scholar
• Woolf TB, Zuckerman DM, Lu ND, Jang HB. Tools for channels: Moving towards molecular calculations of gating and permeation in ion channel biophysics. J Molec Graphics Modelling 2004; 22: 359–368
   PubMed Web of Science ®Google Scholar
• Efremov RG, Nolde DE, Konshina AG, Syrtcev NP, Arseniev AS. Peptides and proteins in membranes: What can we learn via computer simulations?. Curr Medicinal Chem 2004; 11: 2421–2442
   PubMed Web of Science ®Google Scholar
• Still WC, Tempczyk A, Hawley RC, Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc 1990; 112: 6127–6129
   Web of Science ®Google Scholar
• Tanizaki S, Feig M. A generalized Born formalism for heterogeneous dielectric environments: Application to the implicit modeling of biological membranes. J Chem Phys 2005; 122: 124706
   PubMed Web of Science ®Google Scholar
• Spassov VZ, Yan L, Szalma S. Introducing an implicit membrane in generalized Born/solvent accessibility continuum solvent models. J Phys Chem B 2002; 106: 8726–8738
   Web of Science ®Google Scholar
• Im W, Feig M, Brooks III CL. An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins. Biophys J 2003; 85: 2900–2918
   PubMed Web of Science ®Google Scholar
• Ulmschneider MB, Ulmschneider JP, Sansom MSP, Di Nola A. A generalized Born implicit membrane representation compared to experimental insertion free energies. Biophys J 2007; 92: 2338–2349
   PubMed Web of Science ®Google Scholar
• Chowdhury S, Zhang W, Wu C, Xiong GM, Duan Y. Breaking non-native hydrophobic clusters is the rate-limiting step in the folding of an alanine-based peptide. Biopolymers 2003; 68: 63–75
   PubMed Web of Science ®Google Scholar
• Jang S, Shin S, Pak Y. Molecular dynamics study of peptides in implicit water: Ab initio folding of beta-hairpin,beta-sheet, and beta beta alpha- motif. J Am Chem Soc 2002; 124: 4976–4977
   PubMed Web of Science ®Google Scholar
• Simmerling C, Strockbine B, Roitberg AE. All-atom structure prediction and folding simulations of a stable protein. J Am Chem Soc 2002; 124: 11258–11259
   PubMed Web of Science ®Google Scholar
• Snow CD, Nguyen N, Pande VS, Gruebele M. Absolute comparison of simulated and experimental protein-folding dynamics. Nature 2002; 420: 102–106
   PubMed Web of Science ®Google Scholar
• Ulmschneider JP, Ulmschneider MB. Folding simulations of the trans-membrane helix of virus protein U in an implicit membrane model. J Chem Theory Computation 2007; 3: 2335–2346
   PubMed Web of Science ®Google Scholar
• Ulmschneider JP, Ulmschneider MB, Di Nola A. Monte Carlo folding of trans-membrane helical peptides in an implicit generalized Born membrane. Proteins: Structure Function and Bioinformatics 2007; 69: 297–308
   PubMed Web of Science ®Google Scholar
• Im W, Brooks CL., III. De novo folding of membrane proteins: An exploration of the structure and NMR properties of the fd coat protein. J Molec Biol 2004; 337: 513–519
   PubMed Web of Science ®Google Scholar
• Ulmschneider JP, Jorgensen WL. Monte Carlo backbone sampling for polypeptides with variable bond angles and dihedral angles using concerted rotations and a Gaussian bias. J Chem Phys 2003; 118: 4261–4271
   Web of Science ®Google Scholar
• Ulmschneider JP, Jorgensen WL. Polypeptide folding using Monte Carlo sampling, concerted rotation, and continuum solvation. J Am Chem Soc 2004; 126: 1849–1857
   PubMed Web of Science ®Google Scholar
• Ulmschneider JP, Ulmschneider MB, Di Nola A. Monte Carlo vs. Molecular Dynamics for all-atom polypeptide folding simulations. J Phys Chem B 2006; 110: 16733–16742
   PubMed Web of Science ®Google Scholar
• Killian JA. Synthetic peptides as models for intrinsic membrane proteins. FEBS Lett 2003; 555: 134–138
   PubMed Web of Science ®Google Scholar
• de Planque MRR, Killian JA. Protein-lipid interactions studied with designed transmembrane peptides: Role of hydrophobic matching and interfacial anchoring (Review). Molec Membrane Biol 2003; 20: 271–284
   PubMed Web of Science ®Google Scholar
• Nymeyer H, Woolf TB, Garcia AE. Folding is not required for bilayer insertion: Replica exchange simulations of an alpha-helical peptide with an explicit lipid bilayer. Proteins-Structure Function and Bioinformatics 2005; 59: 783–790
   PubMed Web of Science ®Google Scholar
• Im W, Brooks CL. Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations. Proc Nat Acad Sci USA 2005; 102: 6771–6776
   PubMed Web of Science ®Google Scholar
• Petrache HI, Zuckerman DM, Sachs JN, Killian JA, Koeppe RE, Woolf TB. Hydrophobic matching mechanism investigated by molecular dynamics simulations. Langmuir 2002; 18: 1340–1351
   Web of Science ®Google Scholar
• Qiu D, Shenkin PS, Hollinger FP, Still WC. The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii. J Phys Chem A 1997; 101: 3005–3014
   Web of Science ®Google Scholar
• Jorgensen WL, Ulmschneider JP, Tirado-Rives J. Free energies of hydration from a generalized Born model and an ALL-atom force field. J Phys Chem B 2004; 108: 16264–16270
   Web of Science ®Google Scholar
• Parsegian A. Energy of an ion crossing a low dielectric membrane: Solutions to four relevant electrostatic problems. Nature 1969; 221: 844–846
   PubMed Web of Science ®Google Scholar
• Radzicka A, Wolfenden R. Comparing the polarities of the amino-acids – side-chain distribution coefficients between the vapor-phase, cyclohexane, 1-octanol, and neutral aqueous-solution. Biochemistry 1988; 27: 1664–1670
   Web of Science ®Google Scholar
• Jorgensen WL, Maxwell DS, Tirado-Rives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 1996; 118: 11225–11236
   Web of Science ®Google Scholar
• Ulmschneider JP, Jorgensen WL. Monte Carlo backbone sampling for nucleic acids using concerted rotations including variable bond angles. J Phys Chem B 2004; 108: 16883–16892
   Web of Science ®Google Scholar
• Earl DJ, Deem MW. Parallel tempering: Theory, applications, and new perspectives. Phys Chem Chem Phys 2005; 7: 3910–3916
   PubMed Web of Science ®Google Scholar
• Engelman DM, Chen Y, Chin CN, Curran AR, Dixon AM, Dupuy AD, Lee AS, Lehnert U, Matthews EE, Reshetnyak YK and others. 2003. Membrane protein folding: Beyond the two stage model. FEBS Letters 555:122–125.
   PubMed Web of Science ®Google Scholar
• Popot JL, Engelman DM. Membrane-protein folding and oligomerization – the 2-stage model. Biochemistry 1990; 29: 4031–4037
   PubMed Web of Science ®Google Scholar
• Jacobs RE, White SH. The nature of the hydrophobic binding of small peptides at the bilayer interface: Implications for the insertion of transbilayer helices. Biochemistry 1989; 28: 3421–3437
   PubMed Web of Science ®Google Scholar
• White SH, Wimley WC. Membrane protein folding and stability: Physical principles. Ann Rev Biophysics Biomolec Structure 1999; 28: 319–365
   PubMedGoogle Scholar
• BenTal N, Sitkoff D, Topol IA, Yang AS, Burt SK, Honig B. Free energy of amide hydrogen bond formation in vacuum, in water, and in liquid alkane solution. J Phys Chem B 1997; 101: 450–457
   Web of Science ®Google Scholar
• Roseman MA. Hydrophobicity of the peptide C = O … H-N hydrogen-bonded group. J Mol Biol 1988; 201: 621–623
   PubMed Web of Science ®Google Scholar
• Wimley WC, Creamer TP, White SH. Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides. Biochemistry 1996; 35: 5109–5124
   PubMed Web of Science ®Google Scholar
• MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S and others. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586–3616.
   PubMed Web of Science ®Google Scholar
• Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. Charmm – a program for macromolecular energy, minimization, and dynamics calculations. J Computational Chem 1983; 4: 187–217
   Web of Science ®Google Scholar
• Bond PJ, Holyoake J, Ivetac A, Khalid S, Sansom MSP. Coarse-grained molecular dynamics simulations of membrane proteins and peptides. J Structural Biol 2007; 157: 593–605
   PubMed Web of Science ®Google Scholar
• de Planque MRR, Goormaghtigh E, Greathouse DV, Koeppe RE, Kruijtzer JAW, Liskamp RMJ, de Kruijff B, Killian JA. 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 2001; 40: 5000–5010
   PubMed Web of Science ®Google Scholar
• van der Wel PCA, Strandberg E, Killian JA, Koeppe RE. Geometry and intrinsic tilt of a tryptophan-anchored transmembrane alpha-helix determined by H-2 NMR. Biophysical J 2002; 83: 1479–1488
   PubMed Web of Science ®Google Scholar
• Weiss TM, van der Wel PCA, Killian JA, Koeppe RE, Huang HW. Hydrophobic mismatch between helices and lipid bilayers. Biophysical J 2003; 84: 379–385
   PubMed Web of Science ®Google Scholar
• de Planque MRR, Greathouse DV, Koeppe RE, Schafer H, Marsh D, Killian JA. 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 1998; 37: 9333–9345
   PubMed Web of Science ®Google Scholar
• Sengupta D, Meinhold L, Langosch D, Ullmann GM, Smith JC. Understanding the energetics of helical peptide orientation in membranes. Proteins-Structure Funct Genetics 2005; 58: 913–922
   PubMed Web of Science ®Google Scholar
• de Planque MR, Bonev BB, Demmers JA, Greathouse DV, Koeppe RE, 2nd, Separovic F, Watts A, Killian JA. Interfacial anchor properties of tryptophan residues in transmembrane peptides can dominate over hydrophobic matching effects in peptide-lipid interactions. Biochemistry 2003; 42: 5341–5348
   PubMed Web of Science ®Google Scholar
• Im W, Chen J, Brooks CL, 3rd. Peptide and protein folding and conformational equilibria: theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models. Adv Protein Chem 2005; 72: 173–198
   PubMedGoogle Scholar
• Hessa T, Kim H, Bihlmaier K, Lundin C, Boekel J, Andersson H, Nilsson I, White SH, von Heijne G. Recognition of transmembrane helices by the endoplasmic reticulum translocon. Nature 2005; 433: 377–381
   PubMed Web of Science ®Google Scholar