Bioinformatyka strukturalna białek transbłonowych

• Authors: Sławomir Filipek

Title variants

EN

Structural bioinformatics of membrane proteins

• Languages of publication: PL EN

Abstracts

EN

Our genome is composed of 20-30 % of membrane proteins but number of structures of these proteins known and deposited in public databases is still small. However, new achievements in experimental techniques, especially microfocusing of X-ray beam enabling diffracting of microcrystals, as well as mutagenesis leading to obtaining of thermostable mutants are real hope for quick emerging of new structures. Theoretical methods for determination of structure of membrane proteins are still in infant phases. Usage of homology modeling is limited by small number of membrane proteins which are necessary to serve as templates whereas ab-initio methods are confined to predicting of small membrane proteins or parts of larger ones only. The area which the bioinformatics is foremost in is prediction of dynamical behavior of proteins in lipid bilayer which is still mostly inaccessible to experimental methods. Full-atom as well as coarse-grain molecular dynamics methods are used to describe investigated systems in different time scales and with different accuracy.

• Journal: Kosmos
• Year: 2009
• Volume: 58
• Issue: 1-2
• Pages: 57-66

Dates

published

2009

Contributors

author

Sławomir Filipek

• Międzynarodowy Instytut Biologii Molekularnej i Komórkowej, Ks. Trojdena 4, 02-109 Warszawa, Polska

References

• Arkin I. T., Xu H. F., Jensen M. O., Arbely E., Bennett E. R., Bowers K. J., Chow E., Dror R. O., Eastwood M. P., Flitman-Tene R., Gregersen B. A., Klepeis J. L., Kolossvary I., Shan Y. B., Shaw D. E., 2007. Mechanism of Na+/H+ antiporting. Science 317, 799-803.
• Bernsel A., Viklund H., Falk J., Lindahl E., von Heijne G., Elofsson A., 2008. Prediction of membrane-protein topology from first principles. Proc. Natl. Acad. Sci. USA 105, 7177-7181.
• Cieplak M., Filipek S., Janovjak H., Krzysko K. A., 2006. Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment. Biochim. Biophys. Acta-Biomembr. 1758, 537-544.
• Dror R. O., Arlow D. H., Borhani D. W., Jensen M. O., Piana S., Shaw D. E., 2009. Identification of two distinct inactive conformations of the beta(2)-adrenergic receptor reconciles structural and biochemical observations. Proc. Natl. Acad. Sci. USA 106, 4689-4694.
• Fleishman S. J., Ben-Tal N., 2006. Progress in structure prediction of alpha-helical membrane proteins. Curr. Opin. Struct. Biol. 16, 496-504.
• Fleishman S. J., Unger V. M., Ben-Tal N., 2006. Transmembrane protein structures without X-rays. Trends Biochem. Sci. 31, 106-113.
• Gimpelev M., Forrest L. R., Murray D., Honig B., 2004. Helical packing patterns in membrane and soluble proteins. Biophys. J. 87, 4075-4086.
• Jensen M. O., Dror R. O., Xu H. F., Borhani D. W., Arkin I. T., Eastwood M. P., Shaw D. E., 2008. Dynamic control of slow water transport by aquaporin 0: Implications for hydration and junction stability in the eye lens. Proc. Natl. Acad. Sci. USA 105, 14430-14435.
• Kobilka B. K., Deupi X., 2007. Conformational complexity of G-protein-coupled receptors. Trends Pharmacol. Sci. 28, 397-406.
• Langosch D., Heringa J., 1998. Interaction of transmembrane helices by a knobs-into-holes packing characteristic of soluble coiled coils. Proteins 31, 150-159.
• Monticelli L., Kandasamy S. K., Periole X., Larson R. G., Tieleman D. P., Marrink S. J., 2008. The MARTINI coarse-grained force field: Extension to proteins. J. Chem. Theory Comput. 4, 819-834.
• Neri M., Baaden M., Carnevale V., Anselmi C., Maritan A., Carloni P., 2008. Microseconds dynamics simulations of the outer-membrane protease T. Biophys. J. 94, 71-78.
• Palczewski K., Kumasaka T., Hori T., Behnke C. A., Motoshima H., Fox B. A., Le Trong I., Teller D. C., Okada T., Stenkamp R. E., Yamamoto M., Miyano M., 2000. Crystal structure of rhodopsin: A G protein-coupled receptor. Science 289, 739-745.
• Park P. S. H., Sapra K. T., Kolinski M., Filipek S., Palczewski K., Muller D. J., 2007. Stabilizing effect of Zn2+ in native bovine rhodopsin. J. Biol. Chem. 282, 11377-11385.
• Risselada H. J., Marrink S. J., 2008. The molecular face of lipid rafts in model membranes. Proc. Natl. Acad. Sci. USA 105, 17367-17372.
• Sapra K. T., Park P. S. H., Filipek S., Engel A., Muller D. J., Palczewski K., 2006. Detecting molecular interactions that stabilize native bovine rhodopsin. J. Mol. Biol. 358, 255-269.
• Schneider D., Finger C., Prodohl A., 2007. From interactions of single transmembrane helices to folding of alpha-helical membrane proteins: Analyzing transmembrane helix- helix interactions in bacteria. Curr. Protein Pept. Sci. 8, 45-61.
• Seeber M., Fanelli F., Paci E., Caflisch A., 2006. Sequential unfolding of individual helices of bacterioopsin observed in molecular dynamics simulations of extraction from the purple membrane. Biophys. J. 91, 3276-3284.
• Serrano-Vega M. J., Magnani F., Shibata Y., Tate C. G., 2008. Conformational thermostabilization of the beta 1-adrenergic receptor in a detergent-resistant form. Proc. Natl. Acad. Sci. USA 105, 877-882.
• Walters R. F. S., DeGrado W. F., 2006. Helix-packing motifs in membrane proteins. Proc. Natl. Acad. Sci. USA 103, 13658-13663.
• Wong-Ekkabut J., Baoukina S., Triampo W., Tang I. M., Tieleman D. P., Monticelli L., 2008. Computer simulation study of fullerene translocation through lipid membranes. Nat. Nanotechnol. 3, 363-368.