Abstract
A protein-protein interface (PPI) is defined by a pair of regions of two interacting protein molecules that are linked by non-covalent bonds. Recognition of conserved 3D patterns of physico-chemical interactions may suggest their importance for the function as well as for the stability and formation of the protein-protein complex. It may assist in discovery of new drug leads that target these interactions. We present a novel method, MAPPIS, for multiple structural alignment of PPIs which allows recognition of a set of common physico-chemical properties and their interactions without the need to assume similarity of sequential patterns or backbone patterns. We show its application to several biological examples, such as alignment of interfaces of G proteins with their effectors and regulators, as well as previously created clusters of interfaces.
Availability: The program and supplementary information, including colored figures, can be found at: http://bioinfo3d.cs.tau.ac.il/mappis/
This is a preview of subscription content, log in via an institution to check access.
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
Lo Conte, L., Chothia, C., Janin, J.: The atomic structure of protein-protein recognition sites. J. Mol. Biol. 285, 2177–2198 (1999)
Mintseris, J., Weng, Z.: Atomic contact vectors in protein-protein recognition. Proteins 53, 629–639 (2003)
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 non-reduntant, diverse dataset of protein-protein interfaces and its implications. Prot. Sci. 13(4), 1043–1055 (2004)
Spriggs, R.V., Artymiuk, P.J., Willett, P.: Searching for patterns of amino acids in 3d protein structures. J. Chem. Inf. Comput. Sci. 43, 412–421 (2003)
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)
Russell, R.: Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution. J. Mol. Biol. 279(5), 1211–1227 (1998)
Shulman-Peleg, A., Mintz, S., Nussinov, R., Wolfson, H.: Protein-protein interfaces: Recognition of similar spatial and chemical organizations. In: Jonassen, I., Kim, J. (eds.) WABI 2004. LNCS (LNBI), vol. 3240, pp. 194–205. Springer, Heidelberg (2004)
Mintz, S., Shulman-Peleg, A., Wolfson, H.J., Nussinov, R.: Generation and analysis of a protein-protein interface dataset with similar chemical and spatial patterns of interactions. Proteins (2005) (in press), http://bioinfo3d.cs.tau.ac.il/Interfaces/
Ambuhl, C., Chakraborty, S., Gartner, B.: Computing largest common point sets under approximate congruence. In: Proceedings of the 8th Annual European Symposium on Algorithms, pp. 52–63. Springer, Heidelberg (2000)
Heffernan, P.J., Schirra, S.: Approximate decision algorithms for point set congruence. Comput. Geom. Theory Appl. 4, 137–156 (1994)
Akutsu, T., Halldorson, M.M.: On the approximation of largest common subtrees and largest common point sets. Theoretical Computer Science 233, 33–50 (2000)
Shatsky, M., Shulman-Peleg, A., Nussinov, R., Wolfson, H.: Recognition of binding patterns common to a set of protein structures. In: Miyano, S., Mesirov, J., Kasif, S., Istrail, S., Pevzner, P.A., Waterman, M. (eds.) RECOMB 2005. LNCS (LNBI), vol. 3500, pp. 440–455. Springer, Heidelberg (2005)
McDonald, I.K., Thornton, J.M.: Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238, 777–793 (1994)
Paduch, M., Jelen, F., Otlewski, J.: Structure of small G proteins and their regulators. Acta Biochim. Pol. 48, 829–850 (2001)
Dvorsky, R., Ahmadian, M.R.: Always look on the bright site of Rho: structural implications for a conserved intermolecular interface. EMBO Rep. 5, 1130–1136 (2004)
Shatsky, M., Nussinov, R., Wolfson, H.: MultiProt - A multiple protein structural alignment algorithm. In: Guigó, R., Gusfield, D. (eds.) WABI 2002. LNCS, vol. 2452, pp. 235–250. Springer, Heidelberg (2002)
Dror, O., Benyamini, H., Nussinov, R., Wolfson, H.: MASS: multiple structural alignment by secondary structures. Bioinformatics 19 (suppl. 1), i95–i104 (2003)
Rodier, F., Bahadur, R., Chakrabarti, P., Janin, J.: Hydration of protein-protein interfaces. Proteins 60, 36–45 (2005)
Connolly, M.L.: Measurement of protein surfaces shape by solid angles. J. Mol. Graph 4, 3–6 (1986)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Shulman-Peleg, A., Shatsky, M., Nussinov, R., Wolfson, H.J. (2005). MAPPIS: Multiple 3D Alignment of Protein-Protein Interfaces. In: R. Berthold, M., Glen, R.C., Diederichs, K., Kohlbacher, O., Fischer, I. (eds) Computational Life Sciences. CompLife 2005. Lecture Notes in Computer Science(), vol 3695. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11560500_9
Download citation
DOI: https://doi.org/10.1007/11560500_9
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-29104-6
Online ISBN: 978-3-540-31726-5
eBook Packages: Computer ScienceComputer Science (R0)