Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface design.

TitleImproved modeling of side-chain--base interactions and plasticity in protein--DNA interface design.
Publication TypeJournal Article
Year of Publication2012
AuthorsThyme, S. B., Baker D., & Bradley P.
JournalJournal of molecular biology
Date Published2012 Jun 8
KeywordsAlgorithms, Amino Acids, Computer Simulation, DNA, DNA-Binding Proteins, Models, Molecular, Nucleic Acid Conformation, Primary Publication, Protein Binding, Protein Conformation, Protein Structure, Tertiary, Proteins

Combinatorial sequence optimization for protein design requires libraries of discrete side-chain conformations. The discreteness of these libraries is problematic, particularly for long, polar side chains, since favorable interactions can be missed. Previously, an approach to loop remodeling where protein backbone movement is directed by side-chain rotamers predicted to form interactions previously observed in native complexes (termed "motifs") was described. Here, we show how such motif libraries can be incorporated into combinatorial sequence optimization protocols and improve native complex recapitulation. Guided by the motif rotamer searches, we made improvements to the underlying energy function, increasing recapitulation of native interactions. To further test the methods, we carried out a comprehensive experimental scan of amino acid preferences in the I-AniI protein-DNA interface and found that many positions tolerated multiple amino acids. This sequence plasticity is not observed in the computational results because of the fixed-backbone approximation of the model. We improved modeling of this diversity by introducing DNA flexibility and reducing the convergence of the simulated annealing algorithm that drives the design process. In addition to serving as a benchmark, this extensive experimental data set provides insight into the types of interactions essential to maintain the function of this potential gene therapy reagent.


Alternate JournalJ. Mol. Biol.