Molecular Dynamics Simulations of the E1/E2 Transmembrane Domain of the Semliki Forest Virus

Biophysical Journal

Volumn 85, Issue 6, 2003, Pages 3646-3658

  Caballero Herrera, Ana ^a   Nilsson, Lennart ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; GLYCINE; GLYCOPROTEIN E; GLYCOPROTEIN E1; GLYCOPROTEIN E2; LEUCINE; MEMBRANE PROTEIN; SERINE; UNCLASSIFIED DRUG;

ALPHA VIRUS; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; BUDDING; COMPLEX FORMATION; HYDROGEN BOND; MOLECULAR DYNAMICS; NONHUMAN; SEMLIKI FOREST ALPHAVIRUS;

ALPHAVIRUS; RNA VIRUSES; SEMLIKI FOREST VIRUS;

EID: 0344551106     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)74782-1     Document Type: Article

References (51)

1. Adams, P. D., D. M. Engelman, and A. T. Brunger. 1996. Improved prediction for the structure of the dimeric transmembrane of glycophorin A obtained through global searching. Proteins. 26:257-261.
2. Bright, J. N., and M. S. P. Sansom. 2003. The flexing/twirling helix: exploring the flexibility about molecular hinges formed by proline and glycine motifs in transmembrane helices. J. Phys. Chem. B. 107:627-636.
3. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4:187-217.
4. Crick, F. H. 1953a. The Fourier transform of a coiled-coil. Acta Crystallogr. 6:685-689.
5. Crick, F. H. 1953b. The packing of alpha-helices: simple coiled-coils. Acta Crystallogr. 6:689-697.
6. Duneau, J. P., S. Crouzy, N. Gamier, Y. Chapron, and M. Genest. 1999. Molecular dynamics simulations of the ErbB-2 transmembrane domain within an explicit membrane environment: comparison with vacuum simulations. Biophys. Chem. 76:35-53.
7. Duneau, J. P., D. Genest, and M. Genest. 1996. Detailed description of an alpha helix→pi bulge transition detected by molecular dynamics simulations of the p185c-erbB2 V659G transmembrane domain. J. Biomol. Struct. Dyn. 13:753-769.
8. Eilers, M., S. C. Shekar, T. Shieh, S. O. Smith, and P. J. Fleming. 2000. Internal packing of helical membrane proteins. Proc. Natl. Acad. Sci. USA. 97:5796-5801.
9. Feig, M., A. D. MacKerell, and C. L. Brooks. 2003. Force field influence on the observation of pi-helical protein structures in molecular dynamics simulations. J. Phys. Chem. B. 107:2831-2836.
10. Fleming, K. G., and D. M. Engelman. 2001. Specificity in transmembrane helix-helix interactions can define a hierarchy of stability for sequence variants. Proc. Natl. Acad. Sci. USA. 98:14340-14344.
11. Forrest, L. R., A. Kukol, I. T. Arkin, D. P. Tieleman, and M. S. Sansom. 2000. Exploring models of the influenza A M2 channel: MD simulations in a phospholipid bilayer. Biophys. J. 78:55-69.
12. Fraser, R. D. B., and T. P. MacRae. 1973. Conformation in Fibrous Proteins and Related Synthetic Polypeptides. Academic Press: New York and London.
13. Garoff, H., and R. H. Cheng. 2001. The missing link between envelope formation and fusion in alphaviruses. Trends Microbiol. 9:408-410.
14. Haag, L., H. Garoff, L. Xing, L. Hammar, S. T. Kan, and R. H. Cheng. 2002. Acid-induced movements in the glycoprotein shell of an alphavirus turn the spikes into membrane fusion mode. EMBO J. 21:4402-4410.
15. Hahn, C. S., S. Lustig, E. G. Strauss, and J. H. Strauss. 1988. Western equine encephalitis virus is a recombinant virus. Proc. Natl. Acad. Sci. USA. 85:5997-6001.
16. Henderson, R. 1975. The structure of the purple membrane from Halobacterium hallobium: analysis of the X-ray diffraction pattern. J. Mol. Biol. 93:123-138.
17. Henderson, R. 1977. The purple membrane from Halobacterium halobium. Annu. Rev. Biophys. Bioeng. 6:87-109.
18. Javadpour, M. M., M. Eilers, M. Groesbeek, and S. O. Smith. 1999. Helix packing in polytopic membrane proteins: role of glycine in transmembrane helix association. Biophys. J. 77:1609-1618.
19. Keefe, L. J., J. Sondek, D. Shortle, and E. E. Lattman. 1993. The alpha aneurism: a structural motif revealed in an insertion mutant of staphylococcal nuclease. Proc. Natl. Acad. Sci. USA. 90:3275-3279.
20. Krogh, A., B. Larsson, G. von Heijne, and E. L. Sonnhammer. 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305:567-580.
21. Laage, R., J. Rohde, B. Brosig, and D. Langosch. 2000. A conserved membrane-spanning amino acid motif drives homomeric and supports heteromeric assembly of presynaptic SNARE proteins. J. Biol. Chem. 275:17481-17487.
22. Law, R. J., L. R. Forrest, K. M. Ranatunga, P. La Rocca, D. P. Tieleman, and M. S. Sansom. 2000. Structure and dynamics of the pore-lining helix of the nicotinic receptor: MD simulations in water, lipid bilayers, and transbilayer bundles. Proteins. 39:47-55.
23. Lee, K. H., D. R. Benson, and K. Kuczera. 2000. Transitions from alpha to pi helix observed in molecular dynamics simulations of synthetic peptides. Biochemistry. 39:13737-13747.
24. Lemmon, M. A., H. R. Treutlein, P. D. Adams, A. T. Brunger, and D. M. Engelman. 1994. A dimerization motif for transmembrane alpha-helices. Nat. Struct. Biol. 1:157-163.
25. Liu, L. P., and C. M. Deber. 1998. Uncoupling hydrophobicity and helicity in transmembrane segments. Alpha-helical propensities of the amino acids in non-polar environments. J. Biol. Chem. 273:23645-23648.
26. Lupas, A. 1996. Coiled coils: new structures and new functions. Trends Biochem. Sci. 21:375-382.
27. MacKenzie, K. R., J. H. Prestegard, and D. M. Engelman. 1997. A transmembrane helix dimer: structure and implications. Science. 276:131-133.
28. MacKerell, A. D., D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:3586-3616.
29. Mancini, E. J., M. Clarke, B. E. Gowen, T. Rutten, and S. D. Fuller. 2000. Cryo-electron microscopy reveals the functional organization of an enveloped virus, Semliki Forest virus. Mol. Cell. 5:255-266.
30. Morgan, D. M., D. G. Lynn, H. Miller-Auer; and S. C. Meredith. 2001. A designed Zn2+-binding amphiphilic polypeptide: energetic consequences of pi-helicity. Biochemistry. 40:14020-14029.
31. Norberg, J., and L. Nilsson. 2000. On the truncation of long-range electrostatic interactions in DNA. Biophys. J. 79:1537-1553.
32. Pappu, R. V., G. R. Marshall, and J. W. Ponder. 1999. A potential smoothing algorithm accurately predicts transmembrane helix packing. Nat. Struct. Biol. 6:50-55.
33. Petrache, H. I., A. Grossfield, K. R. MacKenzie, D. M. Engelman, and T. B. Woolf. 2000. Modulation of glycophorin A transmembrane helix interactions by lipid bilayers: molecular dynamics calculations. J. Mol. Biol. 302:727-746.
34. Popot, J. L. and D. M. Engelman. 1990. Membrane protein folding and oligomerization: the two-stage model. Biochemistry. 29:4031-4037.
35. Popot, J. L., and D. M. Engelman. 2000. Helical membrane protein folding, stability, and evolution. Annu. Rev. Biochem. 69:881-922.
36. Rajashankar, K. R., and S. Ramakumar. 1996. Pi-turns in proteins and peptides: classification, conformation, occurrence, hydration and sequence. Protein Sci. 5:932-946.
37. Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comp. Phys. 23:327-341.
38. Scheiner, S., T. Kar, and Y. Gu. 2001. Strength of the Calpha H.O hydrogen bond of amino acid residues. J. Biol. Chem. 276:9832-9837.
39. Senes, A., I. Ubarretxena-Belandia, and D. M. Engelman. 2001. The Calpha-H.O hydrogen bond: a determinant of stability and specificity in transmembrane helix interactions. Proc. Natl. Acad. Sci. USA. 98:9056-9061.
40. Singer, S. J. 1990. The structure and insertion of integral proteins in membranes. Annu. Rev. Cell Biol. 6:247-296.
41. Singer, S. J., and M. P. Yaffe. 1990. Embedded or not? Hydrophobic sequences and membranes. Trends Biochem. Sci. 15:369-373.
42. Sjöberg M., and H. Garoff. 2003. Interactions between the transmembrane segments of the alphavirus El and E2 proteins play a role in virus budding and fusion. J. Virol. 77:3441-3450.
43. Stemberg, M. J., and W. J. Gullick. 1989. Neu receptor dimerization. Nature. 339:587.
44. Stemberg, M. J., and W. J. Gullick. 1990. A sequence motif in the transmembrane region of growth factor receptors with tyrosine kinase activity mediates dimerization. Protein Eng. 3:245-248.
45. Treutlein, H. R., M. A. Lemmon, D. M. Engelman, and A. T. Brunger. 1992. The glycophorin A transmembrane domain dimer: sequence-specific for a fight-handed supercoil of helices. Biochemistry. 31:12726-12732.
46. Vogel, H., L. Nilsson, R. Rigler, K. P. Voges, and G. Jung. 1988. Structural fluctuations of a helical polypeptide traversing a lipid bilayer. Proc. Natl. Acad. Sci. USA. 85:5067-5071.
47. Walther, D., F. Eisenhaber, and P. Argos. 1996. Principles of helix-helix packing in proteins: the helical lattice superposition model. J. Mol. Biol. 255:536-553.
48. Weaver, T. M. 2000. The pi-helix translates structure into function. Protein Sci. 9:201-206.
49. Whitley, P., L. Nilsson, and G. von Heijne. 1993. Three-dimensional model for the membrane domain of Escherichia coli leader peptidase based on disulfide mapping. Biochemistry. 32:8534-8539.
50. Woolf, T. B. 1997. Molecular dynamics of individual alpha-helices of bacteriorhodopsin in dimyristol phosphatidylocholine. I. Structure and dynamics. Biophys. J. 73:2376-2392.
51. Woolf, T. B. 1998. Molecular dynamics simulations of individual alpha-helices of bacteriorhodopsin in dimyristoylphosphatidylcholine. II. Interaction energy analysis. Biophys. J. 74:115-131.