Abstract
Protein-protein interfaces, which are regions of interaction between two protein molecules, contain information about patterns of interacting functional groups. Recognition of such patterns is useful both for prediction of binding partners and for the development of drugs that can interfere with the formation of the protein-protein complex. We present a novel method, Interface-to-Interface (I2I)-SiteEngine, for structural alignment between two protein-protein interfaces. The method simultaneously aligns two pairs of binding sites that constitute an interface. The method is based on recognition of similarity of physico-chemical properties and shapes. It assumes no similarity of sequences or folds of the proteins that comprise the interfaces. Similarities between interfaces recognized by I2I-SiteEngine provide an insight into the interactions that are essential for the formation of the complex and can be related to its function. Its high efficiency makes it suitable for large scale database searches and classifications.
Web server: http://bioinfo3d.cs.tau.ac.il/I2I-SiteEngine
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Valdar, W.S., Thornton, J.M.: Protein-protein interfaces: analysis of amino acid conservation in homodimers. Proteins 42, 108–124 (2001)
Lo Conte, L., Chothia, C., Janin, J.: The atomic structure of protein-protein recognition sites. J. Mol. Biol. 285, 2177–2198 (1999)
Falquet, L., Pagni, M., Bucher, P., Hulo, N., Sigrist, C., Hofmann, K., Bairoch, A.: The PROSITE database, its status in 2002. Nucleic Acids Res. 30, 235–238 (2002)
Wallace, A.C., Laskowski, R.A., Thornton, J.M.: Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases. Protein Sci. 5, 1001–1013 (1996)
Keskin, A., Tsai, C.H., Wolfson, H.J., Nussinov, R.: A new, structurally nonreduntant, diverse dataset of protein-protein interfaces and its implications. Protein Sci. (2004) (in press)
Schmitt, S., Kuhn, D., Klebe, G.: A new method to detect related function among proteins independent of sequence or fold homology. J. Mol. Biol. 323, 387–406 (2002)
Kinoshita, K., Nakamura, H.: Identification of protein biochemical functions by similarity search using the molecular surface database ef-site. Protein Sci. 12, 1589–1595 (2003)
Shulman-Peleg, A., Nussinov, R., Wolfson, H.J.: Recognition of functional sites in protein structures. J. Mol. Biol. 339(3), 607–633 (2004)
Connolly, M.: Analytical molecular surface calculation. J. Appl. Cryst. 16, 548–558 (1983)
Connolly, M.L.: Measurement of protein surfaces shape by solid angles. J. Mol. Graph. 4, 3–6 (1986)
Duhovny, D., Nussinov, R., Wolfson, H.J.: Efficient unbound docking of rigid molecules. In: Guigó, R., Gusfield, D. (eds.) WABI 2002. LNCS, vol. 2452, pp. 185–200. Springer, Heidelberg (2002)
Cormen, T.H., Leiserson, C.E., Rivest, R.L.: Introduction to Algorithms. MIT Press, Cambridge (1990)
Mehlhorn, K.: The LEDA platform of combinatorial and geometric computing. Cambridge University Press, Cambridge (1999)
Kabsch, W.: A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallogr. A 34, 827–828 (1978)
Paduch, M., Jelen, F., Otlewski, J.: Structure of small G proteins and their regulators. Acta Biochim Pol. 48, 829–850 (2001)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2004 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Shulman-Peleg, A., Mintz, S., Nussinov, R., Wolfson, H.J. (2004). Protein-Protein Interfaces: Recognition of Similar Spatial and Chemical Organizations. In: Jonassen, I., Kim, J. (eds) Algorithms in Bioinformatics. WABI 2004. Lecture Notes in Computer Science(), vol 3240. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30219-3_17
Download citation
DOI: https://doi.org/10.1007/978-3-540-30219-3_17
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-23018-2
Online ISBN: 978-3-540-30219-3
eBook Packages: Springer Book Archive