Investigation of the probable homo-dimer model of the <i>Xeroderma pigmentosum</i> complementation group A (XPA) protein to represent the DNA-binding core

<p>The <i>Xeroderma pigmentosum</i> complementation group A (XPA) protein functions as a primary damage verifier and as a scaffold protein in nucleotide excision repair (NER) in all higher organisms. New evidence of XPA’s existence as a dimer and the redefinition of its DNA-binding domain (DBD) raises new questions regarding the stability and functional position of XPA in NER. Here, we have investigated XPA’s dimeric status with respect to its previously defined DBD (XPA<sub>98-219</sub>) as well as with its redefined DBD (XPA<sub>98-239</sub>). We studied the stability of XPA<sub>98-210</sub> and XPA<sub>98-239</sub> homo-dimer systems using all-atom molecular dynamics simulation, and we have also characterized the protein–protein interactions (PPI) of these two homo-dimeric forms of XPA. After conducting the root mean square deviation (RMSD) analyses, it was observed that the XPA<sub>98-239</sub> homo-dimer has better stability than XPA<sub>98-210</sub>. It was also found that XPA<sub>98-239</sub> has a larger number of hydrogen bonds, salt bridges, and hydrophobic interactions than the XPA<sub>98-210</sub> homo-dimer. We further found that Lys, Glu, Gln, Asn, and Arg residues shared the major contribution toward the intermolecular interactions in XPA homo-dimers. The binding free energy (BFE) analysis, which used the molecular mechanics Poisson–Boltzmann method (MM-PBSA) and the generalized Born and surface area continuum solvation model (GBSA) for both XPA homo-dimers, also substantiated the positive result in favor of the stability of the XPA<sub>98-239</sub> homo-dimer.</p> <p>Communicated by Ramaswamy H. Sarma</p>