Improved Modeling of Side-Chain–Base Interactions and Plasticity in Protein–DNA Interface Design
By Summer B. Thyme, David Baker, Philip Bradley. 2012
23 citations recorded by the source corpus.
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.
Subfields: Molecular Biology, Radiology, Nuclear Medicine and Imaging
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In Molecular Biology
- David Baker
- Philip Bradley
- Summer B. Thyme
- Yifan Song
- Lara Kusak
- Justin Ashworth
- S. Quadri
- Tanja Kortemme
In Radiology, Nuclear Medicine and Imaging
Citations in the corpus
- Massively parallel determination and modeling of endonuclease substrate specificity (2014, methodology): “Base pairs are placed based on the given target sequence using DNA substitution methods described earlier (3,41).”
- Reprogramming homing endonuclease specificity through computational design and directed evolution (2013, methodology): “We showed previously that inclusion of the rotamers making motif interactions improved results for computational benchmarks (33), but the methods were not evaluated with experimental testing.”