Abstract
Misfolding of membrane proteins plays an important role in many human diseases such as retinitis pigmentosa, hereditary deafness, and diabetes insipidus. Little is known about membrane proteins as there are only a very few high-resolution structures. Single molecule force spectroscopy is a novel technique, which measures the force necessary to pull a protein out of a membrane. Such force curves contain valuable information on the protein’s structure, conformation, and inter- and intra-molecular forces. High-throughput force spectroscopy experiments generate hundreds of force curves including spurious ones and good curves, which correspond to different unfolding pathways. As it is not known what is the origin of the interactions that estabilish unfolding barriers, in the present work we analyse the unfolding patterns coming from experiments of unfolding of bacteriorhodopsin and four mutants (P50A, P91A, P186A and M56). We correlate the postition, magnitude and probability of occurrence of force peaks with the results of a bioinformatics analysis of residue conservations, structural alignments and residue-residue contact area in the wild type and in the mutants, in order to gain insights about the interaction pattern stabilizing bacteriorhodopsin structure. From residue-residue contact area calculations we show that the analysed point mutations do not affect the stability of the protein in a significant way. We conclude that, even if the arrangement of intra-moleular interactions locally change in the mutated structures, the overall structural stability is not affected.
Keywords
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Bowie, J.U.: Solving the membrane protein folding problem. Nature 438(7068), 581–589 (2005)
Eddy, S.R.: What is dynamic programming? Nature Biotechnology 22(7), 909–910 (2004)
Faham, S., Yang, D., Bare, E., Yohannan, S., Whitelegge, J.P., Bowie, J.U.: Side-chain contributions to membrane protein structure and stability. J. Mol. Biol. 335(1), 297–305 (2004)
Filipek, S., Teller, D.C., Palczewski, K., Stenkamp, R.: The crystallographic model of rhodopsin and its use in studies of other g protein-coupled receptors. Annu. Rev. Biophys. Biomol. Struct. 32, 375–397 (2003)
Holm, L., Park, J.: Dalilite workbench for protein structure comparison. Bioinformatics 16(6), 566–567 (2000)
Janovjak, H., Struckmeier, J., Hubain, M., Kedrov, A., Kessler, M., Muller, D.J.: Probing the energy landscape of the membrane protein br. Structure 12(5), 871–879 (2004)
Janshoff, A., Neitzert, M., Oberdorfer, Y., Fuchs, H.: Force spectroscopy of molecular systems-single molecule spectroscopy of polymers and biomolecules. Angew Chem. Int. Ed Engl. 39(18), 3212–3237 (2000)
Kessler, M., Gottschalk, K.E., Janovjak, H., Muller, D.J., Gaub, H.E.: Bacteriorhodopsin folds into the membrane against an external force. J. Mol. Biol. 357(2), 644–654 (2006)
Kuhn, M., Janovjak, H., Hubain, M., Muller, D.J.: Automated alignment and pattern recognition of single-molecule force spectroscopy data. J. Microsc. 218(Pt 2), 125–132 (2005)
Marsico, A., Sapra, K.T., Muller, D., Labudde, D., Schroeder, M.: A novel pattern recognition algorithm to classify membrane protein unfolding pathways with high-throughput single molecule force spectroscopy. J. Bioinformatics (accepted)
Mirzadegan, T., Benko, G., Filipek, S., Palczewski, K.: Sequence analyses of g-protein coupled receptors: similarities to rhodopsin. Biochemistry 42(10), 2759–2767 (2003)
Mogi, T., Stern, L.J., Chao, B.H., Khorana, H.G.: Structure-function studies on bacteriorhodopsin. viii. substitutions of the membrane-embedded prolines 50, 91, and 186: the effects are determined by the substituting amino acids. J. Biol. Chem. 264(24), 14192–14196 (1989)
Muller, D., Sass, H., Muller, S., Buldt, G., Engel, A.: Surface structures of native bacteriorhodopsin depend on the molecular packing arrangement in the membrane. J. Mol. Biol. 33(285), 1903–1909 (1999)
Muller, D.J., Kessler, M., Oesterhelt, F., Moller, C., Oesterhelt, D., Gaub, H.: Stability of bacteriorhodopsin alpha-helices and loops analyzed by single-molecule force spectroscopy. Biophys. J. 83(6), 3578–3588 (2002)
Oesterhelt, D., Stoeckenius, W.: Isolation of the cell membrane of halobacterium halobium and its fraction into red and purple membrane. Methods Enzymol. 31, 667–678 (1974)
Oesterhelt, F., Oesterhelt, D., Pfeiffer, M., Engel, A., Gaub, H., Muller, D.J.: Unfolding pathways of individual bacteriorhodopsins. Science 288(5463), 143–146 (2000)
Onuchic, J.N., Wolynes, P.G.: Theory of protein folding. Current Opinion in Structural Biology (14), 70–75 (2004)
Rief, M., Gautel, M., Oesterhelt, F., Fernandez, J.M., Gaub, H.E.: Reversible unfolding of individual titin immunoglobulin domains by afm. Science 276(5315), 1109–1112 (1997)
Sander, C., Schneider, R.: Database of homlogy-derived protein structures and structural meaning of sequence alignment. Proteins 101(9), 56–68 (1991)
Sapra, K.T., Besir, H., Oesterhelt, D., Muller, D.J.: Characterizing molecular interactions in different bacteriorhodopsin assemblies by single-molecule force spectroscopy. J. Mol. Biol. 355(4), 640–650 (2006)
Sobolev, V., Eyal, E., Gerzon, S., Potapov, V., Babor, M., Prilusky, J., Edelman, M.: Space: a suite of tools for protein structure prediction and analysis based on complementarity and environment. Nucleic Acids Research 33(4), 39–43 (2005)
Sobolev, V., Sorokine, A., Prilusky, E., Edelman, M.: Automated analysis of interatomic contacts in proteins. Bioinformatics 15(4), 321–332 (1999)
Yohannan, S., Faham, S., Yang, D., Whitelegge, P., Bowie, J.: The evolution of transmembrane helix kinks and the structural diverstity of g protein-coupled receptors. PNAs 101(4), 959–963 (2003)
Zhuang, X., Rief, M.: Single-molecule folding. Curr. Opin. Struct. Biol. 13(1), 88–97 (2003)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Marsico, A., Sapra, K.T., Muller, D.J., Schroeder, M., Labudde, D. (2006). A Structure-Based Analysis of Single Molecule Force Spectroscopy (SMFS) Data for Bacteriorhodopsin and Four Mutants. In: R. Berthold, M., Glen, R.C., Fischer, I. (eds) Computational Life Sciences II. CompLife 2006. Lecture Notes in Computer Science(), vol 4216. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11875741_16
Download citation
DOI: https://doi.org/10.1007/11875741_16
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-45767-1
Online ISBN: 978-3-540-45768-8
eBook Packages: Computer ScienceComputer Science (R0)