Abstract
Molecular dynamics simulations and energy analysis have been carried out to study the structural mobility and stability of the four α-helix bundle motifs. The simulation results as well as the X-ray data show that the atomic RMS fluctuation is larger at the loop region for four representative proteins investigated: methemerythrin, cytochrome b-562, cytochrome c′, and bovine somatotropin. The loop-loop, helix-helix, and loop-helix interactions are computed for the unfolded and folded proteins. In the folded and solvated protein structures the loop-helix interaction is stronger than the helix-helix interaction, especially in the electrostatic component. But the stabilization energies of both the loop-helix and the helix-helix interactions relative to the those of an unfolded structure are of the same order of magnitude. The stabilization due to protein-solvent interaction is greater in the helix region than in the loop region. The percentage of hydrophilic solvent accessible area for the four proteins studied was calculated with the method of Eisenberg and McLachlan. The percentage of the hydrophilic area is greater in the loops than in the helices. A Poisson-Boltzmann calculation shows that the potential from the loops acting on a helix is generally more negative than that from other helices.
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Argos, P., Rossman, M. G., and Johnson, J. E. (1977).Biochem. Biophys. Res. Commun. 75, 83–86.
Banner, D. W., Kokkinidis, M., and Tsernoglu, D. (1987).J. Mol. Biol. 196, 657–675.
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F. J., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., and Tasumi, M. (1977).J. Mol. Biol. 112, 535–542.
Bloomer, A. C., Champness, J. N., Bricogne, G., Staden, R., and Klug, A. (1978).Nature 276, 362–368.
Brandhuber, B. J., Boone, T., Kenney, W. C., and McKay, D. B. (1987).Science 238, 1707–1709.
Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., and Karplus, M. (1983).J. Computational Chem. 4, 187–217.
Carlacci, L., and Chou, K. C. (1990a).Protein Eng. 4, 225–227.
Carlacci, L., and Chou, K. C. (1990b).Protein Eng. 3, 509–514.
Carlacci, L., Chou, K. C., and Maggiora, G. M. (1991).Biochemistry 30, 4389–4398.
Chou, K. C., and Zheng, C. (1992).Biophys. J. 63, 682–688.
Chou, K. C., Maggiora, G. M., and Scheraga, H. A. (1992).Proc. Natl. Acad. Sci. USA 89, 7315–7319.
Clegg, G. A., Stansfield, R. F. D., Bourne, P. E., and Harrison, P. M. (1980).Nature 288, 298–300.
Davis, M. E., and McCammon, J. A. (1989).J. Computational Chem. 10, 386–391.
Davis, M. E., and McCammon, J. A. (1990).J. Computational Chem. 11, 401–409.
Demchuk, E., Mueller, T., Oschkinat, H., Sebald, W., and Wade, R. C. (1994).Protein Sci. 3, 920–935.
Eisenberg, D., and McLachlan, A. D. (1986).Nature 319, 199–203.
Fairman, R., Anthony-Cahill, S. J., and DeGrado, W. F. (1992).J. Am. Chem. Soc. 114, 5458–5459.
Finzel, B. C., Weber, P. C., Hardman, K. D., and Salemme, F. R. (1985).J. Mol. Biol. 186, 627–643.
Gilson, M. K., and Honig, B. (1989).Proc. Natl. Acad. Sci. USA 86, 1524–1528.
Hendrickson, W. A., Klippenstein, G. L., and Ward, K. B. (1975).Proc. Natl. Acad. Sci. USA 72, 2160–2164.
Kyte, J., and Doolittle, R. F. (1982).J. Mol. Biol. 157, 105–132.
Lee, B., and Richards, F. M. (1971).J. Mol. Biol. 55, 379–400.
Leszczyński, J. F., and Rose, G. D. (1986).Science 234, 849–855.
Lovejoy, B., Choe, S., Cascio, D., McRorie, D. K., DeGrado, W. F., and Eisenberg, D. (1993).Science 259, 1288–1293.
Matthews, F. S., Bethge, P. H., and Czerwinski, E. W. (1979).J. Biol. Chem. 254, 1699–1706.
Momany, F. A., McGuire, R. F., Burgess, A. W., and Scheraga, H. A. (1975).J. Phys. Chem. 79, 2361–2381.
Mornon, J. P., Fridlansky, F., Bally, R., and Milgrom, E. (1980).J. Mol. Biol. 137, 415–429.
Mutter, M., and Vuillermier, S. (1989).Angew. Chem. Int. Ed. Engl. 28, 535–554.
Némethy, G., Pottle, M. S., and Scheraga, H. A. (1983).J. Phys. Chem. 87, 1883–1887.
Osterhout, J. J. J., Handel, T., Na, G., Toumadje, A., Long, R. C., Connolly, P. J., Hoch, J. C., Johnson, W. C. J., Live, D., and DeGrado, W. F. (1992).J. Am. Chem. Soc. 114, 331–337.
Richardson, J. S. (1981).Adv. Protein Chem. 34, 167–339.
Stenkamp, R. E., Sieker, L. C., Jensen, L. H., and McQueen, J. E., Jr. (1978).Biochemistry 17, 2499–2504.
Van Gunsteren, W. F., Berendsen, H. J. C., Hermans, J., Hol, W. G. J., and Postma, J. P. M. (1983).Proc. Natl. Acad. Sci. USA 80, 4315–4319.
Weaver, D. L. (1992).Biopolymers 32, 477–490.
Weber, P. C., Bartsch, R. G., Cusanovich, M. A., Hamlin, R. C., Howard, A., Jordan, S. R., Kamen, M. D., Meyer, T. E., Weatherford, D. W., Xuong, N. H., and Salemme, F. R. (1980).Nature 286, 302–304.
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Thompson, T.B., Chou, KC. & Zheng, C. Analysis of the loop-helix interaction in bundle motif protein structures. J Protein Chem 14, 559–566 (1995). https://doi.org/10.1007/BF01886882
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DOI: https://doi.org/10.1007/BF01886882