Predicting the Effects of Basepair Mutations in DNA-Protein Complexes by Thermodynamic Integration
Beierlein F, Kneale GG, Clark T (2011)
Publication Type: Journal article
Publication year: 2011
Journal
Publisher: Elsevier (Cell Press) / Biophysical Society
Book Volume: 101
Pages Range: 1130--1138
Volume: 101
DOI: 10.1016/j.bpj.2011.07.003
Abstract
Thermodynamically rigorous free energy methods in principle allow the exact computation of binding free energies in biological systems. Here, we use thermodynamic integration together with molecular dynamics simulations of a DNA-protein complex to compute relative binding free energies of a series of mutants of a protein-binding DNA operator sequence. A guanine-cytosine basepair that interacts strongly with the DNA-binding protein is mutated into adenine-thymine, cytosine-guanine, and thymine-adenine. It is shown that basepair mutations can be performed using a conservative protocol that gives error estimates of 10\% of the change in free energy of binding. Despite the high CPU-time requirements, this work opens the exciting opportunity of being able to perform basepair scans to investigate protein-DNA binding specificity in great detail computationally.
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APA:
Beierlein, F., Kneale, G.G., & Clark, T. (2011). Predicting the Effects of Basepair Mutations in DNA-Protein Complexes by Thermodynamic Integration. Biophysical Journal, 101, 1130--1138. https://doi.org/10.1016/j.bpj.2011.07.003
MLA:
Beierlein, Frank, G. Geoff Kneale, and Timothy Clark. "Predicting the Effects of Basepair Mutations in DNA-Protein Complexes by Thermodynamic Integration." Biophysical Journal 101 (2011): 1130--1138.
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