Modeling of peptides in implicit membrane-mimetic media

Molecular Simulation

Volumn 24, Issue 4-6, 2000, Pages 275-291

  Efremov, Roman G ^a   Nolde, Dmitry E ^a   Volynsky, Pavel E ^a   Arseniev, Alexander S ^a  

^a RUSSIAN ACADEMY OF SCIENCES   (Russian Federation)

Author keywords

Membrane peptides; Molecular modeling; Protein conformation; Solvation potential

Indexed keywords

EID: 0005131492     PISSN: 08927022     EISSN: None     Source Type: Journal    
DOI: 10.1080/08927020008022376     Document Type: Article

References (31)

1. Volynsky, P. E., Nolde, D. E., Arseniev, A. S. and Efremov, R. G. (1999) Internet J. Chem., 2, http://www.ijc.com/articles/1999v2/4/
2. Matsuzaki, K. (1998) Magainins as paradigm for the mode of action of pore forming polypeptides. Biochim. Biophys. Acta, 1376, 391-400.
3. White, S. H. and Wimley, W. C. (1998) Hydrophobic interactions of peptides with membrane interfaces. Biochim. Biophys. Acta, 1376, 339-352.
4. Ladokhin, A. S. and White, S. H. (1999) Folding of amphipathic α-helices on membranes: energetics of helix formation by melittin. J. Mol. Biol., 285, 1363-1369.
5. Dobson, C. M., Sali, A. and Karplus, M. (1998) Protein folding: a perspective from theory and experiment. Angew. Chem. Int. Ed., 37, 868-893.
6. Booth, P. J. and Curran, A. R. (1999) Membrane protein folding. Curr. Opin. Struct. Biol., 9, 115-121.
7. Stowell, M. H. B. and Rees, D. C. (1995) Structure and stability of membrane proteins. Adv. Prot. Chem., 46, 279-311.
8. Haltia, T. and Freire, E. (1995) Forces and factors that contribute to the structural stability of membrane proteins. Biochim. Biophys. Acta, 1228, 1-27.
9. Cramer, W. A., Engelman, D. M., von Heijne, G. and Rees, D. C. (1992) Forces involved in the assembly and stabilization of membrane proteins. FASEB J., 6, 3397-3402.
10. Sansom, M. S. P. (1998) Models and simulations of ion channels and related membrane proteins. Curr. Opin. Struct. Biol., 8, 237-244.
11. Tieleman, D. P., Marrink, S. J. and Berendsen, H. J. C. (1997) A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. Biochim. Biophys. Acta, 1331, 235-270.
12. Efremov, R. G., Nolde, D. E., Vergoten, G. and Arseniev, A. S. (1999a) A solvent model for simulations of peptides in bilayers. I. Testing on model systems. Biophys. J., 76, 2448-2459.
13. Efremov, R. G., Nolde, D. E., Vergoten, G. and Arseniev, A. S. (1999b) A solvent model for simulations of peptides in bilayers. II. Membrane-spanning alpha-helices. Biophys. J., 76, 2460-2471.
14. Nolde, D. E., Arseniev, A. S., Vergoten, G. and Efremov, R. G. (1997) Atomic solvation parameters for protein in a membrane environment. Application to transmembrane a-helices. J. Biomol. Struct. and Dyn., 14, 1-18.
15. Kabsch, W. and Sander, C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
16. Koradi, R., Billeter, M. and Wüthrich, K. (1996) MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graphics, 14, 51-55.
17. Metropolis, N., Rosenbluth, A. W., Teller, A. H. and Teller, E. (1953) Equation of state calculations for fast computing machines. J. Chem. Phys., 21, 1087-1092.
18. von Freyberg, B. and Braun, W. (1991) Efficient search for all low energy conformations of polypeptides by Monte Carlo methods. J. Comp. Chem., 12, 1065-1076.
19. Donnelly, D., Overington, J. P., Ruffle, S. V., Nugent, J. H. and Blundell, T. L. (1993) Modeling-helical transmembrane domains: the calculation and use of substitution tables for lipid-facing residues. Protein Sci., 2, 55-70.
20. Eisenberg, D., Weiss, R. M. and Terwilliger, T. C. (1984) The hydrophobic moment detects periodicity in protein hydrophobicity. Proc. Natl. Acad. Sci. U.S.A., 81, 140-144.
21. Killian, J. A. (1998) Hydrophobic mismatch between proteins and lipids in membranes. Biochim. Biophys. Acta, 1376, 401-416.
22. Munoz, V., Thompson, P. A., Hofrichter, J. and Eaton, W. A. (1997) Folding dynamics and mechanism of β-hairpin formation. Nature, 390, 196-199.
23. Bechinger, B., Gierasch, L. M., Montal, M., Zaloff, M. and Opella, S. J. (1996) Orientations of helical peptides in membrane bilayers by solid-state NMR spectroscopy. Solid State NMR Spec., 7, 185-192.
24. Chipot, C. and Pohorille, A. (1998) Folding and translocation of the undecamer of poly-L-Leucine across the water-hexane interface. A molecular dynamics study. J. Am. Chem. Soc., 120, 11912-11924.
25. Deber, C. M. and Li, S.-C. (1995) Peptides in membranes: helicity and hydrophobicity. Biopolymers, 37, 295-318.
26. Ducarme, P., Rahman, M. and Brasseur, R. (1998) IMPALA: A simple restraint field to simulate the biological membrane in molecular structure studies. Proteins, 30, 357-371.
27. Gazit, E., La Rocca, P., Sansom, M. S. P. and Shai, Y. (1998) The structure and organization within the membrane of the helices composing the pore-forming domain of Bacillus thuringiensis δ-endotoxin are consistent with an "umbrella-like" structure of the pore. Proc. Natl. Acad. Sci. U.S.A., 95, 12289-12294.
28. Milik, M. and Skolnick, J. (1993) Insertion of peptide chains into lipid membranes: an off-lattice Monte Carlo dynamics model. Proteins, 15, 10-25.
29. Brasseur, R., Pillot, T., Lins, L., Vandekerckhove, J. and Rosseneu, M. (1997) Peptides in membranes: tipping the balance of membrane stability. Trends Biochem. Sci., 22, 167-171.
30. Lemmon, M. A., Treutlein, H. R., Adams, P. D., Brünger, A. T. and Engelman, D. M. (1994) A dimerization motif for transmembrane α-helices. Nat. Struct. Biol., 1, 157-163.
31. Pervushin, K. V. and Arseniev, A. S. (1992) Three-dimensional structure of (1-36) bacterioopsin in methanol-chloroform mixture and SDS micelles determined by 2D 1H-NMR spectroscopy. FEBS Lett., 308, 190-196.