Abstract
The topology of β-sheets is defined by the pattern of hydrogen-bonded strand pairing. Therefore, predicting hydrogen bonded strand partners is a fundamental step towards predicting β-sheet topology. In this work we report a new strand pairing algorithm. Our algorithm attempts to mimic elements of the folding process. Namely, in addition to ensuring that the predicted hydrogen bonded strand pairs satisfy basic global consistency constraints, it takes into account hypothetical folding pathways. Consistently with this view, introducing hydrogen bonds between a pair of strands changes the probabilities of forming other strand pairs. We demonstrate that this approach provides an improvement over previously proposed algorithms.
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References
Baldwin, R.L., Rose, G.D.: Is protein folding hierarchic? I. II. Folding intermediates and transition states. Trends in Biochemical Sciences 24(2), 77–83 (1999)
Baldwin, R.L., Rose, G.D.: Is protein folding hierarchic? I. Local structure and peptide folding. Trends in Biochemical Sciences 134(3), 26–33 (1999)
Berman, P., Jeong, J.: Consistent sets of secondary structures in proteins, http://www.cse.psu.edu/~jijeong
Bystroff, C., Baker, D.: Prediction of local structure in proteins using a library of sequence-structure motifs. Journal of Molecular Biology 281(3), 565–577 (1998)
Cheng, J., Baldi, P.: Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithms. Bioinformatics 21(suppl. 1), 75–84 (2005)
Crippen, G.M.: The tree structural organization of proteins. Journal of Molecular Biology 126, 315–332 (1978)
Hubbard, T.J., Park, J.: Fold recognition and ab initio structure predictions using hidden markov models and β-strand pair potentials. Proteins: Structure, Function, and Genetics 23(3), 398–402 (1995)
Huthinson, E.G., Sessions, R.B., Thornton, J.M., Woolfson, D.N.: Determinants of strand register in antiparallel β-sheets of proteins. Protein Science 7(11), 2287–2300 (1998)
Inbar, Y., Benyamini, H., Nussinov, R., Wolfson, H.J.: Protein structure prediction via combinatorial assembly of sub-structural units. Bioinformatics 19(suppl. 1), 158–168 (2003)
Kingford, C.L., Chazelle, B., Singh, M.: Solving and analyzing side-chain positioning problems using linear and integer programming. Bioinformatics 21(7), 1028–1036 (2004)
Klepeis, J.L., Floudas, C.A.: Astro-fold: A combinatorial and global optimization framework for ab initio prediction of three-dimensional structures of proteins from the amino acid sequence. Biophysical Journal 85, 2119–2146 (2003)
Kryshtafovych, A., Venclovas, C., Fidelis, K., Moult, J.: Protein folding: From the levinthal paradox to structure prediction. Journal of Molecular Biology 293(2), 283–293 (1999)
Lesk, A.M., Rose, G.D.: Folding Units in Globular Proteins. PNAS 78(7), 4304–4308 (1981)
Levinthal, C.: Are there pathways for protein folding? Journal de Chimie Physique et de Physico-Chimie Biologique 65, 44 (1968)
Menke, M., King, J., Berger, B., Cowen, L.: Wrap-and-pack: A new paradigm for beta structural motif recognition with application to recognizing beta trefoils. Journal of Computational Biology 12(6), 777–795 (2005)
Moult, J.: A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Current Opinion in Structural Biology 15(3), 285–289 (2005)
Przytycka, T.M., Srinivasan, R., Rose, G.D.: Recursive domains in proteins. Protein Science 11(2), 409–417 (2002)
Richardson, J.S.: beta-Sheet topology and the relatedness of proteins. Nature 268(5620), 495–500 (1977)
Rose, G.D.: Hierarchic organization of domains in globular proteins. Journal of Molecular Biology 134(3), 447–470 (1979)
Ruczinski, I., Kooperberg, C., Bonneau, R., Baker, D.: Distributions of beta sheets in proteins with application to structure prediction. Proteins: Structure, Function, and Genetics 48(1), 85–97 (2002)
Srinivasan, R., Rose, G.D.: LINUS: A hierarchic procedure to predict the fold of a protein. Proteins: Structure, Function, and Genetics 22(2), 81–99 (1995)
Steward, R.E., Thornton, J.M.: Prediction of strand pairing in antiparallel and parallel β-sheets using information theory. Proteins: Structure, Function, and Genetics 48(2), 178–191 (2002)
Woolfson, D.N., Evans, P.A., Hutchinson, E.G., Thornton, J.M.: On the conformation of proteins: The handedness of the connection between parallel β-strands. Journal of Molecular Biology 110, 269–283 (1977)
Xu, J., Li, M., Kim, D., Xu, Y.: Raptor: Optimal protein threading by linear programming. Journal of Bioinformatics and Computational Biology 1(1), 85–117 (2003)
Zhang, C., Kim, S.-H.: The anatomy of protein [beta]-sheet topology. Journal of Molecular Biology 299(4), 1075–1089 (2002)
Zhu, H., Braun, W.: Sequence specificity, statistical potentials, and three-dimensional structure prediction with self-correcting distance geometry calculations of beta-sheet formation in proteins. Protein Science 8(2), 326–342 (1999)
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Jeong, J.K., Berman, P., Przytycka, T.M. (2007). Bringing Folding Pathways into Strand Pairing Prediction. 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_5
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DOI: https://doi.org/10.1007/978-3-540-74126-8_5
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