Abstract
The mitochondrial channel VDAC is presumed to fold as a β-barrel although the number and identity of transmembrane β-strands in the protein are controversial. Previously, a novel multiple alignment algorithm called the Gibbs sampler was used to detect a residue-frequency motif in sequences of bacterial outer-membrane proteins that corresponds to transmembrane β-strands in bacterial porins of known structure (Neuwaldet al., 1995,Protein Science,4, 1618. In the present study, this bacterial motif has been used to screen sets of mitochondrial membrane protein sequences, with matches occurring in only two classes of proteins: VDACs and the outer-membrane protein import pore (ISP42, MOM38). These results suggest a structural (and perhaps evolutionary) relatedness between the bacterial and mitochondrial pore proteins, with the mitochondrial subsequences that match the bacterial motif corresponding to transmembrane β-strands as in the porins.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Baker, K. P., and Schatz, G. (1991)Nature 349, 205–208.
Blachly-Dyson, E., Peng, S. Z., Colombini, M., and Forte, M. (1990).Science 247, 1233–1236.
Colombini, M. (1979).Nature 279, 643–645.
Colombini, M. (1989).J. Membr. Biol. 111, 103–111.
Cowan, S. W., Schirmer, T., Rummel, G., Steiert, M., Ghosh, R., Pauptit, R. A., Jansonius, J. N., and Rosenbusch, J. P. (1992).Nature 358, 727–733.
De Pinto, V. Prezioso, G., Thinnes, F., Link, T. A., and Palmieri, F. (1991).Biochemistry 30, 10191–10200.
Fischbarg, J., Cheung, M., Czegledy, F., Li, J., Iserovich, P., Kuang, K., Hubbard, J., Garner, M., Rosen, O. M., Golde, D. W., and Vera, J. C. (1993).Proc. Natl. Acad. Sci. USA 90, 11658–11662.
Forte, M., Guy, H. R., and Mannella, C. A. (1987).J. Bioenerg. Biomembr. 19, 341–350.
Guo, X. W., Smith, P. R., Cognon, B., D'Arcangelis, D., Dolginova, E., and Mannella, C. A. (1995).J. Struct. Biol. 114, 41–59.
Heins, L., Mentzel, H., Schmid, A., Benz, R., and Schmitz, U. K. (1994).J. Biol. Chem. 269, 26402–26410.
Lawrence, C. E., Altschul, S. F., Boguski, M. S., Liu, J. S., Neuwald, A. F., and Wootton, J. C. (1993).Science 262, 208–214.
Liu, J. S., Neuwald, A. F., and Lawrence, C. E. (1995).J. Am. Stat. Assoc.,90, 1156–1170.
Mannella, C. (1994). InMolecular Biology of Mitochondrial Transport Systems (Forte, M. and Colombini, C., eds.), Springer-Verlag, Berlin Heidelberg, pp. 249–263.
Mannella, C. A., Guo, X. W., and Cognon, B. (1989).FEBS Lett. 253, 231–234.
Mannella, C. A., Forte, M., and Colombini, M. (1992).J. Bioenerg. Biomembr. 24, 7–19.
Neuwald, A. F., Liu, J. S., and Lawrence, C. E. (1995).Protein Sci.,4, 1618–1632.
Peng, S., Blachly-Dyson, E., Forte, M., and Colombini, M. (1992).Biophys. J. 62, 123–135.
Rauch, G., and Moran, O. (1994).Biochem. Biophys. Res. Commun. 200, 908–915.
Schirmer, T., Keller, T. A., Wang, Y.-F., and Rosenbusch, J. P. (1995).Science 267, 512–514.
Shao, L. (1994).Biophysical characterization of the structural and functional states of the mitochondrial voltage-dependent anion-selective channel. Ph.D. Thesis, University at Albany, SUNY.
Shao, L., Van Roey, P., Kinnally, K., and Mannella, C. A. (1994).Biophys. J. 66, A21.
Stanley, S., Dias, J. A., D'Arcangelis, D., and Mannella, C. A. (1995).J. Biol. Chem. 270, 16694–16700.
Troll, H., Malchow, D., Muller-Taubenberger, A., Humbel, B., Lottspeich, F., Ecke, M., Gerisch, G., Scmid, A., and Benz, R. (1992).J. Biol. Chem. 267, 21072–21079.
Weiss, M. S., and Schulz, G. E. (1992).J. Mol. Biol. 227, 493–509.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Mannella, C.A., Neuwald, A.F. & Lawrence, C.E. Detection of likely transmembrane β-strand regions in sequences of mitochondrial pore proteins using the Gibbs sampler. J Bioenerg Biomembr 28, 163–169 (1996). https://doi.org/10.1007/BF02110647
Received:
Revised:
Issue Date:
DOI: https://doi.org/10.1007/BF02110647