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Issue No.04 - October-December (2008 vol.5)
pp: 484-491
Jieun Jeong , Penn State University, University Park
Piotr Berman , Penn State University, University Park
Teresa M. Przytycka , NIH, Bethesda
ABSTRACT
The topology of $\beta$-sheets is defined by the pattern of hydrogen-bonded strand pairing. Therefore, predicting hydrogen bonded strand partners is a fundamental step towards predicting $\beta$-sheet topology. At the same time, finding the correct partners is very difficult due to long range interactions involved in strand pairing. Additionally, patterns of aminoacids involved, in $\beta$-sheet formations are very general and therefore difficult to use for computational recognition of specific contacts between strands. In this work, we report a new strand pairing algorithm. To address above mentioned difficulties, 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 hydrogen bonds between other pairs of strand. We demonstrate that this approach provides an improvement over previously proposed algorithms. We also compare the performance of this method to that of a global optimization algorithm that poses the problem as integer linear programming optimization problem and solves it using ILOG CPLEX\texttrademark\ package.
INDEX TERMS
Biology and genetics, Combinatorial algorithms
CITATION
Jieun Jeong, Piotr Berman, Teresa M. Przytycka, "Improving Strand Pairing Prediction through Exploring Folding Cooperativity", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.5, no. 4, pp. 484-491, October-December 2008, doi:10.1109/TCBB.2008.88
REFERENCES
[1] R.L. Baldwin and G.D. Rose, “Is Protein Folding Hierarchic? II. Folding Intermediates and Transition States,” Trends in Biochemical Sciences, vol. 24, no. 2, pp. 77-83, 1999.
[2] R.L. Baldwin and G.D. Rose, “Is Protein Folding Hierarchic? I. Local Structure and Peptide Folding,” Trends in Biochemical Sciences, vol. 134, no. 3, pp. 26-33, 1999.
[3] P. Berman and J. Jeong, “Consistent Sets of Secondary Structures in Proteins,” Algorithmica (Online First), 2007.
[4] C. Bystroff and D. Baker, “Prediction of Local Structure in Proteins Using a Library of Sequence-Structure Motifs,” J. Molecular Biology, vol. 281, no. 3, pp. 565-577, 1998.
[5] J. Cheng and P. Baldi, “Three-Stage Prediction of Protein Beta-Sheets by Neural Networks, Alignments and Graph Algorithms,” Bioinformatics, vol. 21, no. suppl 1, pp. i75-84, 2005.
[6] G.M. Crippen, “The Tree Structural Organization of Proteins,” J. Molecular Biology, vol. 126, pp. 315-332, 1978.
[7] K.A. Dill, K.M. Fiebig, and H.S. Chan, “Cooperativity in Protein-Folding Kinetics,” Proc. Nat'l Academy of Sciences, vol. 90, no. 5, pp. 1942-1946, 1993.
[8] A. Ginsburg and W.R. Carroll, “Some Specific Ion Effects on the Conformation and Thermal Stability of Ribonuclease,” Biochemistry, vol. 4, no. 10, pp. 2159-2174, 1965.
[9] T.J. Hubbard and J. Park, “Fold Recognition and Ab Initio Structure Predictions Using Hidden Markov Models and $\beta$ -Strand Pair Potentials,” Proteins: Structure, Function, and Genetics, vol. 23, no. 3, pp. 398-402, 1995.
[10] E.G. Huthinson, R.B. Sessions, J.M. Thornton, and D.N. Woolfson, “Determinants of Strand Register in Antiparallel $\beta$ -Sheets of Proteins,” Protein Science, vol. 7, no. 11, pp. 2287-2300, 1998.
[11] Y. Inbar, H. Benyamini, R. Nussinov, and H.J. Wolfson, “Protein Structure Prediction via Combinatorial Assembly of Sub-Structural Units,” Bioinformatics, vol. 19, no. suppl 1, pp. i158-168, 2003.
[12] W. Kabsch and C. Sander, “Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features,” Biopolymers, vol. 22, no. 12, pp. 2577-2637, 1983.
[13] A.P. Kamat and A.M. Lesk, “Contact Patterns between Helices and Strands of Sheet Define Protein Folding Patterns,” Proteins: Structure, Function, and Bioinformatics, vol. 66, no. 4, pp. 869-876, 2007.
[14] C.L. Kingford, B. Chazelle, and M. Singh, “Solving and Analyzing Side-Chain Positioning Problems Using Linear and Integer Programming,” Bioinformatics, vol. 21, no. 7, pp. 1028-1036, 2004.
[15] J.L. Klepeis and C.A. Floudas, “Astro-Fold: A Combinatorial and Global Optimization Framework for Ab Initio Prediction of Three-Dimensional Structures of Proteins from the Amino Acid Sequence,” Biophysical J., vol. 85, pp. 2119-2146, Oct. 2003.
[16] M.M.G. Krishna and S.W. Englander, “A Unified Mechanism for Protein Folding: Predetermined Pathways with Optional Errors,” Protein Science, vol. 16, no. 3, pp. 449-464, 2007.
[17] A. Kryshtafovych, C. Venclovas, K. Fidelis, and J. Moult, “Protein Folding: From the Levinthal Paradox to Structure Prediction,” J.Molecular Biology, vol. 293, no. 2, pp. 283-293, 1999.
[18] A.M. Lesk and G.D. Rose, “Folding Units in Globular Proteins,” Proc. Nat'l Academy of Sciences, vol. 78, no. 7, pp. 4304-4308, 1981.
[19] C. Levinthal, “Are There Pathways for Protein Folding,” J. de Chimie Physique et de Physico-Chimie Biologique, vol. 65, p. 44, 1968.
[20] H. Maity, M. Maity, M.M.G. Krishna, L. Mayne, and S.W. Englander, “Protein Folding: The Stepwise Assembly of Foldon Units,” Proc. Nat'l Academy of Sciences, vol. 102, no. 13, pp.4741-4746, 2005.
[21] M. Menke, J. King, B. Berger, and L. Cowen, “Wrap-and-Pack: A New Paradigm for Beta Structural Motif Recognition with Application to Recognizing Beta Trefoils,” J. Computational Biology, vol. 12, no. 6, pp. 777-795, 2005.
[22] J. Moult, “A Decade of CASP: Progress, Bottlenecks and Prognosis in Protein Structure Prediction,” Current Opinion in Structural Biology, vol. 15, no. 3, pp. 285-289, 2005.
[23] S.B. Ozkan, G.A. Wu, J.D. Chodera, and K.A. Dill, “Protein Folding by Zipping and Assembly,” Proc. Nat'l Academy of Sciences, vol. 104, no. 29, pp. 11987-11992, 2007.
[24] T.M. Przytycka, R. Srinivasan, and G.D. Rose, “Recursive Domains in Proteins,” Protein Science, vol. 11, no. 2, pp. 409-417, 2002.
[25] J.S. Richardson, “Beta-Sheet Topology and the Relatedness of Proteins,” Nature, vol. 268, no. 5620, pp. 495-500, 1977.
[26] G.D. Rose, “Hierarchic Organization of Domains in Globular Proteins,” J. Molecular Biology, vol. 134, no. 3, pp. 447-470, 1979.
[27] G.D. Rose, P.J. Fleming, J.R. Banavar, and A. Maritan, “A Backbone-Based Theory of Protein Folding,” Proc. Nat'l Academy of Sciences, vol. 103, no. 45, pp. 16623-16633, 2006.
[28] I. Ruczinski, C. Kooperberg, R. Bonneau, and D. Baker, “Distributions of Beta Sheets in Proteins with Application to Structure Prediction,” Proteins: Structure, Function, and Genetics, vol. 48, no. 1, pp. 85-97, 2002.
[29] R. Srinivasan and G.D. Rose, “LINUS: A Hierarchic Procedure to Predict the Fold of a Protein,” Proteins: Structure, Function, and Genetics, vol. 22, no. 2, pp. 81-99, 1995.
[30] R. Srinivasan and D.G. Rose, “Ab Initio Prediction of Protein Structure Using LINUS,” Proteins: Structure, Function, and Genetics, vol. 47, no. 4, pp. 489-495, 2002.
[31] R.E. Steward and J.M. Thornton, “Prediction of Strand Pairing in Antiparallel and Parallel $\beta$ -Sheets Using Information Theory,” Proteins: Structure, Function, and Genetics, vol. 48, no. 2, pp. 178-191, 2002.
[32] D.N. Woolfson, P.A. Evans, E.G. Hutchinson, and J.M. Thornton, “On the Conformation of Proteins: The Handedness of the Connection between Parallel $\beta$ -Strands,” J. Molecular Biology, vol. 110, pp. 269-283, 1977.
[33] J. Xu, M. Li, D. Kim, and Y. Xu, “Raptor: Optimal Protein Threading by Linear Programming,” J. Bioinformatics and Computational Biology, vol. 1, no. 1, pp. 85-117, 2003.
[34] C. Zhang and S.-H. Kim, “The Anatomy of Protein $\beta$ -Sheet Topology,” J. Molecular Biology, vol. 299, no. 4, pp. 1075-1089, 2002.
[35] H. Zhu and W. Braun, “Sequence Specificity, Statistical Potentials, and Three-Dimensional Structure Prediction with Self-Correcting Distance Geometry Calculations of Beta-Sheet Formation in Proteins,” Protein Science, vol. 8, no. 2, pp. 326-342, 1999.
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