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Annual International Conference on Research in Computational Molecular Biology

RECOMB 2005: Research in Computational Molecular Biology pp 440–455Cite as

Recognition of Binding Patterns Common to a Set of Protein Structures

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 3500))

Abstract

We present a novel computational method, MultiBind, for recognition of binding patterns common to a set of protein structures. It is the first method which performs a multiple alignment between protein binding sites in the absence of overall sequence, fold or binding partner similarity. MultiBind recognizes common spatial arrangements of physico-chemical properties in the binding sites. These should be important for recognition of function, prediction of binding and drug design. We discuss the theoretical aspects of the computational problem of multiple structure alignment. This problem involves solving a 3D k-partite matching problem, which we show to be NP-Hard. The MultiBind method, applies an efficient Geometric Hashing technique to detect a potential set of multiple alignments of the given binding sites. To overcome the exponential number of possible multiple combinations it applies a very efficient filtering procedure which is heavily based on the selected scoring function. Our method guarantees detection of an approximate solution in terms of pattern proximity as well as cardinality of multiple alignment. We show applications of MultiBind to several biological targets. The method recognizes patterns which are responsible for binding small molecules such as estradiol, ATP/ANP and transition state analogues. The presented computational results agree with the available biological ones.

Availability: http://bioinfo3d.cs.tau.ac.il/MultiBind/.

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References

  1. Falquet, L., Pagni, M., Bucher, P., Hulo, N., Sigrist, C.J., Hofmann, K., Bairoch, A.: The PROSITE database, its status in 2002. Nucleic Acids Res. 30, 235–238 (2002)

    Article  Google Scholar 

  2. 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 Science 5, 1001–1013 (1996)

    Article  Google Scholar 

  3. Russell, R.: Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution. J. Mol. Biol. 279(5), 1211–1227 (1998)

    Article  Google Scholar 

  4. Artymiuk, P.J., Poirrette, A.R., Grindley, H.M., Rice, D.W., Willett, P.: A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures. J. Mol. Biol. 243, 327–344 (1994)

    Article  Google Scholar 

  5. Moodie, S.L., Mitchell, J.B.O., Thornton, J.M.: Protein recognition of adenylate: An example of a fuzzy recognition template. J. Mol. Biol. 263, 486–500 (1996)

    Article  Google Scholar 

  6. Denessiouk, K.A., Rantanen, V., Johnson, M.: Adenine Recognition: A motif present in ATP-,CoA-,NAD-,NADP-, and FAD-dependent proteins. PROTEINS: Structure, Function and Genetics 44, 282–291 (2001)

    Article  Google Scholar 

  7. Shulman-Peleg, A., Nussinov, R., Wolfson, H.J.: Recognition of functional sites in protein structures. J. Mol. Biol. 339(3), 607–633 (2004), http://bioinfo3d.cs.tau.ac.il/SiteEngine/

    Article  Google Scholar 

  8. Russell, R., Barton, G.: Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. PROTEINS: Structure, Function and Genetics 14, 309–323 (1992)

    Article  Google Scholar 

  9. Taylor, W.R., Flores, T., Orengo, C.: Multiple protein structure alignment. Protein Science 3, 1858–1870 (1994)

    Article  Google Scholar 

  10. Leibowitz, N., Nussinov, R., Wolfson, H.: MUSTA-a general, efficient, automated method for multiple structure alignment and detection of common motifs: application to proteins. J. Comput. Biol. 8, 93–121 (2001)

    Article  Google Scholar 

  11. Shatsky, M., Nussinov, R., Wolfson, H.: A method for simultaneous alignment of multiple protein structures. Proteins: Structure, Function, and Genetics 56(1), 143–156 (2004), http://bioinfo3d.cs.tau.ac.il/MultiProt/

    Article  Google Scholar 

  12. Dror, O., Benyamini, H., Nussinov, R., Wolfson, H.J.: MASS: multiple structural alignment by secondary structures. Bioinformatics 19(suppl. 1), 95–104 (2003), http://bioinfo3d.cs.tau.ac.il/MASS

    Article  Google Scholar 

  13. Lemmen, C., Lengauer, T.: Computational methods for the structural alignment of molecules. J. of Computer-Aided Mol. Design 14, 215–232 (2000)

    Article  Google Scholar 

  14. Dror, O., Shulman-Peleg, A., Nussinov, R., Wolfson, H.J.: Predicting molecular interactions in silico: I. A guide to pharmacophore identification and its applications for drug design. Curr. Med. Chem. 11, 71–90 (2004)

    Article  Google Scholar 

  15. Kuttner, Y.Y., Sobolev, V., Raskind, A., Edelman, M.: A consensus-binding structure for adenine at the atomic level permits searching for the ligand site in a wide spectrum of adenine-containing complexes. PROTEINS: Structure, Function and Genetics 52, 400–411 (2003)

    Article  Google Scholar 

  16. Kinoshita, K., Nakamura, H.: Identification of protein biochemical functions by similarity search using the molecular surface database ef-site. Protein Science 12, 1589–1595 (2003)

    Article  Google Scholar 

  17. 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)

    Article  Google Scholar 

  18. Akutsu, T., Halldorson, M.M.: On the approximation of largest common subtrees and largest common point sets. Theoretical Computer Science 233, 33–50 (2000)

    Article  MATH  MathSciNet  Google Scholar 

  19. Akutsu, T.: Protein structure alignment using dynamic programming and iterative improvement. IEICE Trans. Information and Systems E79-D, 1629–1636 (1996)

    Google Scholar 

  20. Efrat, A., Itai, A., Katz, M.J.: Geometry helps in bottleneck matching and related problems. Algorithmica 31, 1–28 (2001)

    Article  MATH  MathSciNet  Google Scholar 

  21. Ambuhl, C., Chakraborty, S., Gartner, B.: Computing largest common point sets under approximate congruence. In: Proc. of the 8th Ann. European Symp. on Alg., pp. 52–63. Springer, Heidelberg (2000)

    Google Scholar 

  22. Huttenlocher, D., Ullman, S.: Recognizing solid objects by alignment with an image. International Journal of Computer Vision 5(2), 195–212 (1990)

    Article  Google Scholar 

  23. Goodrich, M.T., Mitchell, J.S.B., Orletsky, M.W.: Practical methods for approximate geometric pattern matching under rigid motions (preliminary version). In: Proc. of the 10th Ann. Symp. on Comp. Geom., pp. 103–112. ACM Press, New York (1994)

    Chapter  Google Scholar 

  24. Chakraborty, S., Biswas, S.: Approximation algorithms for 3-d commom substructure identification in drug and protein molecules. In: Proc. 6th Int. Workshop on Algorithms and Data Structures, Vancouver, Can., pp. 253–264. Springer, Heidelberg (1999)

    Google Scholar 

  25. Garey, M.R., Johnson, D.S.: Computers and Intractability. W. H. Freeman, San Francisco (1979)

    MATH  Google Scholar 

  26. Hazan, E., Safra, S., Schwartz, O.: On the Complexity of Approximating k-Dimensional Matching. In: Arora, S., Jansen, K., Rolim, J.D.P., Sahai, A. (eds.) RANDOM 2003 and APPROX 2003. LNCS, vol. 2764, pp. 83–97. Springer, Heidelberg (2003)

    Google Scholar 

  27. Wolfson, H.J.: Model-Based Object Recognition by Geometric Hashing. In: Proc. of the 1st European Conf. on Comp. Vision (ECCV). LNCS, pp. 526–536. Springer, Heidelberg (1990)

    Google Scholar 

  28. Connolly, M.L.: Analytical molecular surface calculation. J. Appl. Cryst. 16, 548–558 (1983)

    Article  Google Scholar 

  29. Hurkens, C.A.J., Schrijver, A.: On the size of systems of sets every t of which have an sdr, with an application to the worst-case ratio of heuristics for packing problems. SIAM J. Discret. Math. 2, 68–72 (1989)

    Article  MATH  MathSciNet  Google Scholar 

  30. Heffernan, P.J., Schirra, S.: Approximate decision algorithms for point set congruence. Comput. Geom. Theory Appl. 4, 137–156 (1994)

    MATH  MathSciNet  Google Scholar 

  31. Gavrilov, M., Indyk, P., Motwani, R., Venkatasubramanian, S.: Combinatorial and experimental methods for approximate point pattern matching. Algorithmica 38, 59–90 (2004)

    Article  MATH  MathSciNet  Google Scholar 

  32. 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 (2004) (submitted)

    Google Scholar 

  33. Connolly, M.L.: Measurement of protein surfaces shape by solid angles. J. Mol. Graph. 4, 3–6 (1986)

    Article  Google Scholar 

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Author information

Authors and Affiliations

  1. School of Computer Science, Raymond and Beverly Sackler, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel

    Maxim Shatsky, Alexandra Shulman-Peleg & Haim J. Wolfson

  2. Sackler Inst. of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel

    Ruth Nussinov

  3. Basic Research Program, SAIC-Frederick, Inc, Lab. of Experimental and Computational Biology, Bldg. 469, Rm. 151, Frederick, MD, 21702, USA

    Ruth Nussinov

Authors
  1. Maxim Shatsky
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  2. Alexandra Shulman-Peleg
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  3. Ruth Nussinov
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  4. Haim J. Wolfson
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Editor information

Editors and Affiliations

  1. Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, 108-8639, Minato-ku, Tokyo, Japan

    Satoru Miyano

  2. Broad Institute of MIT and Harvard, 320 Charles Street, 02141-2023, Cambridge, MA, USA

    Jill Mesirov

  3. Computational Genomics Laboratory, Department of Bioengineering, Boston University, 44 Cummington St., 02215, Boston, MA, USA

    Simon Kasif

  4. Center for Molecular Biology and Computer Sciecne Department, Brown University, 115 Waterman St., 02912, Providence, RI, USA

    Sorin Istrail

  5. University of California, San Diego, USA

    Pavel A. Pevzner

  6. Department of Molecular and Computational Biology, University of Southern California, 1050 Childs Way, 90089-2910, Los Angeles, CA, USA

    Michael Waterman

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© 2005 Springer-Verlag Berlin Heidelberg

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Shatsky, M., Shulman-Peleg, A., Nussinov, R., Wolfson, H.J. (2005). 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) Research in Computational Molecular Biology. RECOMB 2005. Lecture Notes in Computer Science(), vol 3500. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11415770_33

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  • DOI: https://doi.org/10.1007/11415770_33

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-25866-7

  • Online ISBN: 978-3-540-31950-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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