Probing free energy landscape around DNA base with amino acid side chain

Abstract

DNA-binding proteins recognize specific base sequences within DNA. To examine the origin of the specificity, we calculated the free energy maps of the base pair and amino acid side chain interactions, as well as the enthalpy change, entropy change and minimum energy maps. These maps are obtained from taking statistic average of the interaction energies. Total number of conformations to obtain these maps for each pair of Asn-AT, Asn-GC, Ser-AT and Ser-GC is 1,556,815,260. For each of the pairs, we found the region around the base pair where the amino acid side chain can form a profound interaction, and it coincides with the tendency found in PDB data. The minimum energy structures obtained from the maps were also in agreement with the interaction patterns found in PDB data.