Title: Conformational Determinants for the Recruitment of ERCC1 by XPA in the Nucleotide Excision Repair (NER) Pathway: Structure and Dynamics of the XPA Binding Motif
Abstract: Xeroderma Pigmentosum complementation group A (XPA) is an essential protein in the Nucleotide Excision Repair (NER) pathway. In one of the critical steps of the NER pathway, XPA recruits the ERCC1-XPF excision repair protein complex to the DNA damage site for the repair to proceed. The XPA/ERCC1-XPF interaction takes place between the N-terminus tail of XPA and ERCC1. The only structural insight available on the XPA-ERCC1 interaction is from the complex between the ERCC1 central fragment and a 14-residue peptide corresponding to the highly conserved binding motif of the XPA N-terminus, namely XPA67-80 (Tsodikov, et al., Structural basis for the recruitment of ERCC1-XPF to nucleotide excision repair complexes by XPA. Embo Journal, 2007. 26: p. 4768-4776). Based on these structural data, in this work I present the results of an extensive Molecular Dynamics (MD) simulation study of the XPA67-80 peptide, both when free and bound to the ERCC1 central fragment. These results highlight previously unidentified and critical structural and dynamic features of the ERCC1-XPA67-80 complex. More specifically, this study shows that, when in complex the XPA67-80 peptide forms specific interactions with residues in the ERCC1 binding pocket, which are essential for binding. Based on the identification of these interactions, I assessed the critical role of two highly conserved residues in the XPA67-80 binding motif and of their interaction with ERCC1 by studying the XPA67-80 F75A and D70A mutants in complex with ERCC1. Additionally, the results of an extensive 10 microseconds MD simulation of the free peptide in solution show its conformational propensity for a hairpin structure, similar to the bound conformation.