Analyzing Molecular Interactions

互联网2013-12-31

891

Abstract
Table of Contents
Figures
Literature Cited

Abstract

Molecular interactions are key processes that drive the functions of molecules. Large data sets of protein interaction data are being assembled that will help analyze structural and functional aspects of interactions. This chapter introduces techniques for analyzing both the structural aspects of molecular interactions and methods to use this information to understand and define biological pathways. Curr. Protoc. Bioinform. 36:8.1.1?8.1.4. © 2011 by John Wiley & Sons, Inc.

Keywords: protein?protein interactions; protein?ligand interactions; protein?water interactions; complexes; structural dynamics

GO TO THE FULL PROTOCOL:

PDF or HTML at Wiley Online Library

Introduction
Literature Cited
Figures

GO TO THE FULL PROTOCOL:

PDF or HTML at Wiley Online Library

Materials

GO TO THE FULL PROTOCOL:

PDF or HTML at Wiley Online Library

Figures

Figure 8.1.1 The crystal structure of the bacterial serine protease subtilisin with the bound water molecules observed crystallographically indicated as blue spheres. Figure courtesy of Dagmar Ringe, Brandeis University.

View Image

Videos

Literature Cited

Literature Cited
	Al‐Lazikani, B., Sheinerman, F.B., and Honig, B. 2001. Combining multiple structure and sequence alignments to improve sequence detection and alignment: Application to the SH2 domains of Janus kinases. Proc. Natl. Acad. Sci. U.S.A. 98:14796‐14801.
	Bartel, P.L., Roecklein, J.A., SenGupta, D., and Fields, S. 1996. A protein linkage map of Escherichia coli bacteriophage T7. Nat. Genet 12:72‐77.
	Fields, S. and Song, O. 1989. A novel genetic system to detect protein‐protein interactions. Nature 340:245‐246.
	Gavin, A.C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J.M., Michon, A.M., Cruciat, C.M., Remor, M., Höfert, C., Schelder, M., Brajenovic, M., Ruffner, H., Merino, A., Klein, K., Hudak, M., Dickson, D., Rudi, T., Gnau, V., Bauch, A., Bastuck, S., Huhse, B., Leutwein, C., Heurtier, M.A., Copley, R.R., Edelmann, A., Querfurth, E., Rybin, V., Drewes, G., Raida, M., Bouwmeester, T., Bork, P., Seraphin, B., Kuster, B., Neubauer, G., and Superti‐Furga, G. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415:141‐147.
	Hazbun, T.R., Malmstrom, L., Anderson, S., Graczyk, B.J., Fox, B., Riffle, M., Sundin, B.A., Aranda, J.D., McDonald, W.H., Chiu, C.H., Snydsman, B.E., Bradley, P., Muller, E.G., Fields, S., Baker, D., Yates, J.R. 3rd, and Davis, T.N. 2003. Assigning function to yeast proteins by integration of technologies. Mol. Cell 12:1353‐1365.
	Ho, Y., Gruhler, A., Heilbut, A., Bader, G.D., Moore, L., Adams, S.L., Millar, A., Taylor, P., Bennett, K., Boutilier, K., Yang, L., Wolting, C., Donaldson, I., Schandorff, S., Shewnarane, J., Vo, M., Taggart, J., Goudreault, M., Muskat, B., Alfarano, C., Dewar, D., Lin, Z., Michalickova, K., Willems, A.R., Sassi, H., Nielsen, P.A., Rasmussen, K.J., Andersen, J.R., Johansen, L.E., Hansen, L.H., Jespersen, H., Podtelejnikov, A., Nielsen, E., Crawford, J., Poulsen, V., Sørensen, B.D., Matthiesen, J., Hendrickson, R.C., Gleeson, F., Pawson, T., Moran, M.F., Durocher, D., Mann, M., Hogue, C.W., Figeys, D., and Tyers, M. 2002. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415:180‐183.
	Mattos, C. 2002. Protein‐water interactions in a dynamic world. Trends Biochem. Sci. 27:203‐208.
	Rual, J.F., Venkatesan, K., Hao, T., Hirozane‐Kishikawa, T., Dricot, A., Li, N., Berriz, G.F., Gibbons, F.D., Dreze, M., Ayivi‐Guedehoussou, N., Klitgord, N., Simon, C., Boxem, M., Milstein, S., Rosenberg, J., Goldberg, D.S., Zhang, L.V., Wong, S.L., Franklin, G., Li, S., Albala, J.S., Lim, J., Fraughton, C., Llamosas, E., Cevik, S., Bex, C., Lamesch, P., Sikorski, R.S., Vandenhaute, J., Zoghbi, H.Y., Smolyar, A., Bosak, S., Sequerra, R., Doucette‐Stamm, L., Cusick, M.E., Hill, D.E., Roth, F.P., and Vidal, M. 2005. Towards a proteome‐scale map of the human protein‐protein interaction network. Nature 437:1173‐1178.
	Schwikowski, B., Uetz, P., and Fields, S. 2000. A network of protein‐protein interactions in yeast. Nat. Biotechnol. 18:1257‐1261.
	Uetz, P., Giot, L., Cagney, G., Mansfield, T.A., Judson, R.S., Knight, J.R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., Qureshi‐Emili, A., Li, Y., Godwin, B., Conover, D., Kalbfleisch, T., Vijayadamodar, G., Yang, M., Johnston, M., Fields, S., and Rothberg, J.M. 2000. A comprehensive analysis of protein‐protein interactions in Saccharomyces cerevisiae. Nature 403:623‐627.