Hypergraph Model of Multi-Residue Interactions in Proteins: Sequentially-Constrained Partitioning Algorithms for Optimization of Site-Directed Protein Recombination

Xiaoduan Ye, Alan M. Friedman, Chris Bailey-Kellogg
2007 Journal of Computational Biology  
Relationships among amino acids determine stability and function and are also constrained by evolutionary history. We develop a probabilistic hypergraph model of residue relationships that generalizes traditional pairwise contact potentials to account for the statistics of multi-residue interactions. Using this model, we detected non-random associations in protein families and in the protein database. We also use this model in optimizing site-directed recombination experiments to preserve
more » ... icant interactions and thereby increase the frequency of generating useful recombinants. We formulate the optimization as a sequentially-constrained hypergraph partitioning problem; the quality of recombinant libraries wrt a set of breakpoints is characterized by the total perturbation to edge weights. We prove this problem to be NP-hard in general, but develop exact and heuristic polynomial-time algorithms for a number of important cases. Application to the beta-lactamase family demonstrates the utility of our algorithms in planning site-directed recombination.
doi:10.1089/cmb.2007.r016 pmid:17691894 fatcat:ctbglk6g7ndyxoxoy4z6b7twm4