Effects of protein dynamics on protein-DNA binding have not been analyzed thoroughly so far. Using GNM and ANM, we well predict conformational change between DNA-free/DNA-bound forms. However, we fail to find fluctuation-magnitude-based characteristics to predict DNA binding sites. GNM-based Domain-planes (D-planes) derived from the unbound proteins are used to determine significant DNA-binding orientations with the results that larger than 95% of the 110 DNA molecules being dissected through by these planes. In addition, we also report that enzyme active sites are close to the D-planes such that 90% of the studied 732 active sites are located within 50% rank from the D-planes. We compare and contrast the thermodynamic aspects of ligand-protein and DNA-protein binding. This study suggests potential applications for filtering out unlikely DNA-protein docking poses obtained from docking software.

Effects of protein dynamics on protein-DNA binding have not been analyzed thoroughly so far. Using GNM and ANM, we well predict conformational change between DNA-free/DNA-bound forms. However, we fail to find fluctuation-magnitude-based characteristics to predict DNA binding sites. GNM-based Domain-planes (D-planes) derived from the unbound proteins are used to determine significant DNA-binding orientations with the results that larger than 95% of the 110 DNA molecules being dissected through by these planes. In addition, we also report that enzyme active sites are close to the D-planes such that 90% of the studied 732 active sites are located within 50% rank from the D-planes. We compare and contrast the thermodynamic aspects of ligand-protein and DNA-protein binding. This study suggests potential applications for filtering out unlikely DNA-protein docking poses obtained from docking software.

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