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Abstract

Nucleotide sequence dependent interactions between proteins and DNA are responsible for a wide range of gene regulatory functions. Accurate and generalizable methods to evaluate the strength of protein-DNA binding have been long sought after. While numerous computational approaches have been developed, most of them require fitting parameters to experimental data to a certain degree, e.g. machine learning algorithms or knowledge based statistical potentials. Molecular dynamics based free energy calculations offer a robust, system independent, first principles based method to calculate free energy differences upon nucleotide mutation. We present an automated procedure to setup alchemical MD based calculations to evaluate free energy changes occurring due to a nucleotide mutation in DNA. We further use these methods to perform a large scale mutation scan comprising 397 nucleotide mutation cases in 16 protein-DNA complexes. The obtained prediction accuracy reaches 5.6 kJ/mol average unsigned deviation from experiment. Subsequently, we utilize the MD based free energy calculations to construct protein-DNA binding profiles for a zinc finger protein Zif268. The calculation results compare remarkably well with the experimentally determined binding profiles. The software automating structure and topology setup for alchemical calculations is a part of pmx package; the utilities are also made available online: http://pmx.mpibpc.mpg.de/dna_webserver.html.