Identifying relationships between structure and function of the bacterial metabolic pathway TR?TRX?TPX

DIEGO SEBASTIAN VAZQUEZ; JAVIER ISERTE; AGUDELO, WILLIAM A.; FERRER-SUETA, GERARDO; BRUNO MANTA; MARIANO CAMILO GONZÁLEZ LEBRERO; JAVIER SANTOS

San Carlos de Bariloche

Congreso; 5th Argentinian Conference on Bioinformatics and Computational Biology; 2014

Asociación Argentina de Bioinformatica y Biología Computacional

Background: Throughout all the kingdoms, the cellular antioxidant and redox homeostasis are regulated by the thioredoxin and glutathione systems [1,2] which comprise several TRX-like fold proteins such as glutaredoxins, thiol-dependent peroxidases (PRXs), thioredoxin, among others. Our interest inthis system, from a biophysical viewpoint, is mainly based on (i) the elasticity in the thioredoxin (TRX) substrate recognition process. TRX has different targets and is only reduced by the FAD-dependent thioredoxin reductase in vivo [1]; (ii) the existence of large conformational changes in PRX family (helix-coil transitions) that take place coupled to catalysis [3] and may impact over the catalytic rate; (iii) electron canalization in TR [4]. These aspects among others prompted us to hypothesize the existence of an evolutionary preserved interaction network involved in protein-protein contact and substrate recognition as well as in internal dynamic and thermodynamic stability. For this, we performed an exhaustivebioinformatic and structural analysis of three well-characterized proteins: thioredoxin reductase (TR), thioredoxin 1 (TRX) and the thiol-dependent peroxidase (TPX, an atypical 2-Cys-peroxiredoxin).Methodology: Mutual co-evolutionary relationships between positions in a multiple sequence alignment containing 3430 sequences of TR, TRX and TPX proteins from the bacterial domain, were performed using the MISTIC on line server (http://mistic.leloir.org.ar [5]). The most promised inter- and intra- protein pair-of-residues obtained by mutual information (MI)were subjected to in silico mutations and molecular dynamic (MD) simulations and principal components analysis (PCA) in order to study the role in the dynamic/thermodynamic of the protein. MDs were performed in the AMBER14 ? GPU package [6]. PCA were analyzed and post-processed with the ccptraj module of AmberTools13.Results: Preliminary results from mutual information analysis suggest the existence of qualitatively different pair of residues: (i) located near of the active site suggesting a role in catalysis, (ii) residues with high accessible surface area suggesting a role in protein-protein interaction and (iii) a group located principally in the core of the proteins.