Abstract
Protein structural alignment is an indispensable tool used for many different studies in bioinformatics. Most structural alignment algorithms assume that the structural units of two similar proteins will align sequentially. This assumption may not be true for all similar proteins and as a result, proteins with similar structure but with permuted sequence arrangement are often missed. We present a solution to the problem based on an approximation algorithm that finds a sequence-order independent structural alignment that is close to optimal. We first exhaustively fragment two proteins and calculate a novel similarity score between all possible aligned fragment pairs. We treat each aligned fragment pair as a vertex on a graph. Vertices are connected by an edge if there are intra residue sequence conflicts. We regard the realignment of the fragment pairs as a special case of the maximum-weight independent set problem and solve this computationally intensive problem approximately by iteratively solving relaxations of an appropriate integer programming formulation. The resulting structural alignment is sequence order independent. Our method is insensitive to gaps, insertions/deletions, and circular permutations.
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References
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997)
Arora, S., Lund, C., Motwani, R., Sudan, M., Szegedy, M.: Proof verification and hardness of approximation problems. Journal of the ACM 45(3), 501–555 (1998)
Bar-Yehuda, R., Halldorsson, M.M., Naor, J., Shacknai, H., Shapira, I.: Scheduling split intervals. In: 14th ACM-SIAM SODA, pp. 732–741. ACM Press, New York (2002)
Binkowski, T.A., Adamian, L., Liang, J.: Inferring functional relationship of proteins from local sequence and spatial surface patterns. J. Mol. Biol. 332, 505–526 (2003)
Binkowski, T.A., DasGupta, B., Liang, J.: Order independent structural alignment of circularly permutated proteins. In: EMBS 2004, pp. 2781–2784 (2004)
Chen, L., Wu, L., Wang, Y., Zhang, S., Zhang, X.: Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison. BMC Struct. Biol. 6, 18 (2006)
Hermoso, J.A., Monterroso, B., Albert, A., Galan, B., Ahrazem, O., Garcia, P., Martinez-Ripoll, M., Garcia, J.L., Menendez, M.: Structural Basis for Selective Recognition of Penumococcal Cell Wall by Modular Endolysin from Phage Cp-1. Structure v11, 1239 (2003)
Hobohm, U., Sander, C.: Enlarged representative set of protein structures. Protein Science 3, 522 (1994)
Holm, L., Park, J.: DaliLite workbench for protein structure comparison. Bioinformatics 16, 566–567 (2000)
Jung, J., Lee, B.: Protein structure alignment using enviromental profiles. Prot. Eng. 13(8), 535–543 (2000)
Kabsch, W., Sander, C.: Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577–2637 (1983)
Lindqvist, Y., Schneider, G.: Circular permutations of natural protein sequences: structural evidence. Curr. Opinions Struct. Biol. 7, 422–427 (1997)
Liu, L., Iwata, K., Yohada, M., Miki, K.: Structural insight into gene duplication, gene fusion and domain swapping in the evolution of PLP-independent amino acid racemases. FEBS LETT v528, 114–118 (2002)
Meszaros, C.S.: Fast Cholesky factorization for interior point methods of linear programming. Comp. Math. Appl. 31, 49–51 (1996)
Mizuguchi, K., Deane, C.M., Blundell, T.L, Overington, J.P.: HOMSTRAD: a database of protein structur alignments for homologous families. Protein Sci. 7, 2469–2471 (1998)
Murzin, A.G., Brenner, S.E., Hubbard, T., Chothia, C.: SCOP: a structural classification of proteins database for the investigation of sequences and structure. J. Mol. Biol. 247, 536–540 (1995)
Peisajovich, S.G., Rockah, L., Tawfik, D.S.: Evolution of new protein topologies through multistep gene rearrangements. Nature Genetics 38, 168–173 (2006)
Ponting, R.B., Russell, R.B.: Swaposins: circular permutations within genes encoding saposin homologues. Trends Biochem Sci. 20, 179–180 (1995)
Suzuki, M., Takamura, Y., Maeno, M., Tochinai, S., Iyaguchi, D., Tanaka, I., Nishihira, J., Ishibashi, T.: Xenopus laevis Macrophage Migration Inhibitory Factor is Essential for Axis Formation and Neural Development. J. Biol. Chem. 279, 21406–21414 (2004)
Szustakowski, J.D., Weng, Z.: Protein structure alignment using a genetic algorithm. Proteins: Structure, Function, and Genetics 38, 428–440 (2000)
Tabtiang, R.K., Cezairliyan, B.O., Grand, R.A., Cochrane, J.C., Sauer, R.T.: Consolidating critical binding determinants by noncyclic rearrangement of protein secondary structure. PNAS 7, 2305–2309 (2004)
Van Duyne, G.D., Ghosh, G., Maas, W.K., Sigler, P.B.: Structure of the oligomerization and L-arginine binding domain of the arginine repressor of Escherichia coli. J. Mol. Biol. 256, 377–391 (1996)
Zhu, J., Weng, Z.: FAST: A Novel Protein Structure Alignment Algorithm. PROTEINS: Structure, Function, and Bioinformatics 58, 618–627 (2005)
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Dundas, J., Binkowski, T.A., DasGupta, B., Liang, J. (2007). Topology Independent Protein Structural Alignment . In: Giancarlo, R., Hannenhalli, S. (eds) Algorithms in Bioinformatics. WABI 2007. Lecture Notes in Computer Science(), vol 4645. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-74126-8_16
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DOI: https://doi.org/10.1007/978-3-540-74126-8_16
Publisher Name: Springer, Berlin, Heidelberg
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