10.5452/MA-ASQIV
Fernandes, Carlos Alexandre Henrique; Matioli, Fabio Filippi; Fontes, Marcos Roberto de Mattos; Pavani, Raphael de Souza; Elias, Maria Carolina
In silico structural model of OB-fold domain from Replication Protein A2 from Trypanosoma cruzi
modelarchive.org
2016
3D macromolecular model
2016-01-20
en
Replication Protein A (RPA) is the major single-stranded binding protein from eukaryotes. RPA is a conserved heterotrimeric complex composed by subunits RPA-1, RPA-2 and RPA-3 (or RPA70, RPA32 and RPA14 respectively). One of the major structural features of RPA is the presence of the oligonucleotide/oligosaccharide binding (OB) domains within the subunits. Here, we created the in silico model of OB-fold domain of RPA2 from Trypanosoma cruzi in order to evaluate the DNA binding mode. Here we show that TcRPA-2 has a insertion containig glycines and alanines in a loop close to DNA binding channel. In fact, this region during molecular dynamics (MD) simulations presented a high root mean square fluctuation (r.m.s.f.) of the main chain, adopting multiple positions during of 50 ns of MD simulation, often even occluding DNA binding channel. This data suggest that DNA binding site on TcRPA-2 is more structurally unstable than upper eukaryotes, which can promote changes on the DNA binding affinity of TcRPA-2.