IMPALA: A simple restraint field to simulate the biological membrane in molecular structure studies

Proteins: Structure, Function and Genetics

Volumn 30, Issue 4, 1998, Pages 357-371

  Ducarme, Ph ^a   Rahman, M ^a   Brasseur, R ^a  

^a UNIVERSITY OF LIÈGE   (Belgium)

Author keywords

18A; Computer; Hydrophobicity; M2 ; Magainin; Melitt in; Membrane; PGLa; Prediction; Protein; Structure

Indexed keywords

MAGAININ 2; MELITTIN; MEMBRANE PROTEIN; SYNTHETIC PEPTIDE;

ARTICLE; HYDROPHOBICITY; LIPID BILAYER; MEMBRANE MODEL; MEMBRANE STRUCTURE; MOLECULAR INTERACTION; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN LIPID INTERACTION; PROTEIN STRUCTURE; SIMULATION; SYSTEM ANALYSIS;

ALGORITHMS; AMINO ACID SEQUENCE; COMPUTER SIMULATION; LIPID BILAYERS; MEMBRANE PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN CONFORMATION;

EID: 0032032107     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19980301)30:4<357::AID-PROT3>3.0.CO;2-G     Document Type: Article

References (27)

1. Jähnig, F. Structure predictions of membrane proteins are not that bad. TIBS 15:93-95, 1990.
2. De Loof, H., Harvey S.C., Segrest, J.P., Pastor, W. Mean field stochastic boundary molecular dynamics simulation of a phospholipid in membrane. Biochemistry 30:2099-2113, 1991.
3. Edholm, O., Jahnig, F. The structure of a membrane-spanning polypeptide studied by molecular dynamics. Biophys. Chem. 30:279-292, 1988.
4. Ram, P., Kim, E., Thomson, D.S., Howard, K.P., Prestegard, J.H. Computer modelling of glycolipids at membrane surfaces. Biophys. J. 63:1530-1535, 1992.
5. Sanders, C.R. 2d, Schwonek, J.P. An approximate model and empirical energy function for solute interactions with a water-phosphatidylcholine interface. Biophys. J. 65:1207-1218, 1993.
6. Milik, M., Skolnick, J. Insertion of peptide chains into lipid membranes: An off-lattice Monte Carlo dynamics model. Proteins 15:10-25, 1993.
7. Bechinger, B. Towards membrane protein design: pH-sensitive topology of histidine-containing polupeptides. J. Mol. Biol. 263:768-775, 1996.
8. Tamm, L.K. Physical studies of peptide-bilayer interactions. In: "Membrane Protein Structure: Experimental Approaches." White, S.H. (ed.). New York: Oxford University Press, 1994:283-313.
9. White, S.H. Hydropathy plots and the prediction of membrane protein topology. In: "Membrane Protein Structure: Experimental Approaches." White, S.H. (ed.). New York: Oxford University Press, 1994:97-124.
10. Popot, J.-L., De Vitry, C., Atteia, A. Folding and assembly of integral membrane proteins: An introduction. In: "Membrane Protein Structure: Experimental Approaches." White, S.H. (ed.). New York: Oxford University Press, 1994:41-96.
11. Eisenhaber, F., Argos, P. Improved strategy in analytic surface calculation for molecular systems: Handling singularities and computational efficiency J. Computat. Chem. 11:1272-1280, 1993.
12. Brasseur, R. Differentiation of lipid-associating helices by use of three-dimensional molecular hydrophobicity potential calculations. J. Biol. Chem. 24:16120-16127, 1991.
13. Lins, L., Brasseur, R. The Hydrophobic effect in protein folding. FASEBS J. 9:535-540, 1995.
14. Eisenberg, D., McLachlan, A.D. Solvatation energies in protein folding and binding. Nature 319:199-203, 1986.
15. Fauchère, J.L., Pliska, V. Hydrophobicity parameter π of amino acid side chains from the partitioning of N-acetyl-amino-acid-amides. Eur. J. Med. Chem. Chim. Ther. 18:369-375, 1983.
16. Rees, D.C., Chirino, A.J., Kim, K.-H., Komiya, H. Membrane protein structure and stability: Implications of the first crystallographic analyses. In: "Membrane Protein Structure: Experimental Approaches." White, S.H. (ed.). New York: Oxford University Press, 1994:3-26.
17. Rahman, M., Brasseur, R. WinMGM: A fast CPK molecular graphics program for analyzing molecular structure. J. Mol. Graphics 12:212-218, 1994.
18. Roseman, M.A. Hydrophilicity of polar amino acid side-chains is markedly reduced by flanking peptide bonds. J. Mol. Biol. 200:513-522, 1988.
19. Wimley, W.C., White, S.H. Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nature Struct. Biol. 3:842-848, 1996.
20. Lund-Katz, S., Anantharamaiah, G.M., Venkatachalapathi, Y.V., Segrest, J.P., Phillips, M.C. Nuclear magnetic resonance investigation of the interactions with phospholipid of an amphipathic α-helix-forming peptide of the apolipoprotein class. J. Biol. Chem. 21:12217-12223, 1990.
21. Bechinger, B., Kim, Y., Chirlian, L.E., Gessel, J., Neumann, J.-M., Montai, M., Tomich, J., Zasloff, M., Opella, S.J. Orientation of amphiphilic helical peptides in membrane bilayers determined by solid-state NMR spectroscopy. J. Biolmol. NMR 1:167-173, 1991.
22. Bechinger, B. Structure and functions of channel forming peptides: Magainins, cecropins, melittin and alamethicin. J. Mem. Biol. 156:197-211, 1997.
23. Kersh, G.J., Tomich, J.M., Montal, M. The M2δ transmembrane domain of the nicotiniccholinergic receptor forms ion channels in human erythrocyte membranes. Biochem. Biophys. Res. Commun. 162:352-356, 1989.
24. Dempsey, C.E. The action of melittin on membranes. Biochim. Biophys. Acta 1031:143-161, 1990.
25. Vogel, H., Jahnig, F. The structure of interface in membranes. Biophys. J. 50:573-582, 1986.
26. Eisenberg, D. Three-dimensional structure of membrane and surface proteins. Annu. Rev. Biochem. 53:595-623, 1984.
27. Bechinger, B., Gierasch, L.M., Montal, M., Zasloff, M., Opella, S.J. Orientations of helical peptides in membrane bilayers by solid-state NMR spectroscopy. Solid-State NMR Spec. 7:185-192, 1996.