Simulation studies on bacteriorhodopsin α-helices

European Biophysics Journal

Volumn 28, Issue 8, 2000, Pages 674-682

  Son, Hyeon S ^a,b   Sansom, Mark S P ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b Pohang University of Science and Technology (POSTECH)   (South Korea)

Author keywords

Bacteriorhodopsin; Bilayer potential; Molecular dynamics simulation; Simulated annealing

Indexed keywords

BACTERIORHODOPSIN;

ARTICLE; CONTROLLED STUDY; ELECTRICITY; GEOMETRY; LIPID BILAYER; MEMBRANE POTENTIAL; MOLECULAR DYNAMICS; PROTEIN FOLDING; PROTEIN STRUCTURE; SIMULATION; STRUCTURE ANALYSIS;

EID: 0033951896     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002490050007     Document Type: Article

References (38)

1. 1H-NMR study of bacterioopsin-(34-65)-polypeptide conformation. FEBS Lett 231: 81-88
2. Barlow DJ, Thornton JM (1988) Helix geometry in proteins. J Mol Biol 201: 601-619
3. Barsukov L, Nolde DE, Lomiz AL, Arseniev AS (1992) Three-dimensional structure of proteolytic fragment 163-231 of bacterioopsin determined from nuclear magnetic resonance data in solution. Eur J Biochem 206: 665-672
4. Berendsen HJC, Postma JPM, Gunsteren WF van, Di Nola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81: 3684-3690
5. Blaurock AE, Stoeckenius W (1971) Structure of the purple membrane. Nature 233: 152-155
6. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) CHARMM: a program for macromolecular energy minimisation, and dynamics calculations. J Comput Chem 4: 187-217
7. Brünger AT (1992) X-PLOR version 3.0:system for X-ray crystallography and NMR. Yale University Press, New Haven
8. Brünger AT, Krukowski A, Erickson JW (1990) Slow-cooling protocols for crystallographic refinement by simulated annealing. Acta Crystallogr A46: 585-593
9. Chothia C, Levitt M, Richardson D (1981) Helix to helix packing in proteins. J Mol Biol 145: 215-250
10. Edholm O, Jähnig F (1988) The structure of a membrane-spanning polypeptide studied by molecular dynamics. Biophys Chem 30: 279-292
11. Engelman DM, Steitz TA, Goldman TA (1986) Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu Rev Biophys Chem 15: 321-353
12. Grigorieff N, Ceska TA, Downing KH, Baldwin JM, Henderson R (1996) Electron-crystallographic refinement of the structure of bacteriorhodopsin. J Mol Biol 259: 393-421
13. Henderson R, Unwin PNT (1975) Three-dimensional model of purple membrane obtained by electron microscopy. Nature 257: 28-32
14. Henderson R, Baldwin JM, Ceska TA, Zemlin F, Beckmann E, Downing KH (1990) Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J Mol Biol 213: 899-929
15. Herzyk P, Hubbard RE (1995) Automated method for modeling seven-helix transmembrane receptors from experimental data. Biophys J 69: 2419-2442
16. Herzyk P, Hubbard RE (1998) Using the experimental information to produce a model of the transmembrane domain of the ion channel phospholamban. Biophys J 74: 1203-1214
17. Hubbell WL, Altenbach C (1994) Investigation of structure and dynamics in membrane proteins using side-directed spin labelling. Curr Opin Struct Biol 4: 566-573
18. Jähnig F, Edholm O (1992) Modelling of the structure of bacteriorhodopsin: a molecular dynamics study. J Mol Biol 226: 837-850
19. Kahn TW, Engelman DM (1992) Bacteriorhodopsin can be refolded from two independently stable transmembrane helices and the complementary five-helix fragment. Biochemistry 31: 6144-6151
20. Karplus M, Pesko GA (1990) Molecular dynamics simulations biology. Nature 347: 631-639
21. Kerr ID, Sankararamakrishnan R, Smart OS, Sansom MSP (1994) Parallel helix bundles and ion channels: molecular modeling via simulated annealing and restrained molecular dynamics. Biophys J 67: 1501-1515
22. Kirkpatrick S, Gelatt CD Jr, Vecchi MP (1983) Optimization by simulated annealing. Science 220: 671-680
23. Lakshmanan KL, Saraswathi V (1996) The stability of transmembrane helices: a molecular dynamics study on the isolated helices of bacteriorhodopsin. Biopolymers 38: 401-421
24. Milik M, Skolnick J (1993) Insertion of peptide chains into lipid membranes: an off-lattice Monte Carlo dynamics model. Proteins 15: 10-25
25. Milik M, Skolnick J (1995) A Monte Carlo model of fd and Pfl coat proteins in lipid membranes. Biophys J 69: 1382-1386
26. Mouritsen OG, Bloom M (1993) Models of lipid-protein interactions in membranes. Annu Rev Biophys Biomol Struct 22: 145-147
27. Nilges M, Brünger AT (1991) Automated modelling of coiled coils: application to the GCN4 dimerization region. Protein Eng 4: 649-659
28. Oesterhelt D, Stoecknius W (1973) Functions of a new photoreceptor membrane. Proc Natl Acad Sci USA 70: 2853-2857
29. 15N NMR spectroscopy. Eur J Biochem 219: 887-896
30. 1H-NMR spectroscopy. FEBS Lett 308: 190-196
31. Popot J-L, Engelman DM (1990) Membrane protein folding and oligomerization: the two-stage model. Biochemistry 29: 4031-4037
32. Sankararamakrishnan R, Vishveshwara S (1992) Geometry of proline-containing alpha-helices in proteins. Int J Pept Res 39: 356-363
33. Sansom MSP (1995) Twist to open. Curr Biol 5: 373-375
34. Sansom MSP, Kerr ID (1995) Principles of membrane protein structure. Biomembranes 1: 29-78
35. Son HS, Sansom MSP (1999) Simulation of the packing of transmembrane α-helix bundles. Eur Biophys J 28: 489-498
36. Stoekenius W, Rawen R (1967) A morphological study of Halobacterium halobium and its lysis in media of low salt concentration. J Cell Biol 34: 365-393
37. Woolf TB (1997) Molecular dynamics of individual α-helices of bacteriorhodopsin in dimyristolphosphatidylocholine. I. Structure and dynamics. Biophys J 73: 2376-2392
38. Woolf TB (1998) Molecular dynamics simulations of individuals α- helices of bacteriorhodopsin in dimyristoylphosphatidylocholine. II. Interaction energy analysis. Biophys J 74: 115-131