13Ca and 13Cb chemical shift-driven refinement of protein structures

RAMÍREZ P.G.; MARTÍN OSVALDO A.; VILA, JORGE A.

Bariloche

Congreso; V Congreso Argentino de Bioinformática; 2014

 X-ray crystallography (XRC) and nuclear magnetic resonance (NMR) spectroscopy are the most powerful and predominant techniques used to experimentally determine the three-dimensional structures of biological macromolecules at near atomic resolution. On one hand, XRC has no size limitations and provides the most precise atomic detail, whereas information about the dynamics of the molecule may be limited. On the other hand, NMR-spectroscopy tops XRC in those cases where no protein crystals are available and, besides, it provides solution state dynamics. However, the main drawback of NMR-spectroscopy is the fact that it delivers lower resolution structures. Because of this, validation, the process of evaluating the reliability for 3-dimensional atomic models, becomes critically important to protein structure determination via NMR-spectroscopy.Our group has developed a protein structure validation method called CheShift-2, which allows us to calculate the "differences" between observed and calculated chemical shifts for the nuclei of interest (13Ca and 13Cb) this validation method indicates where, in the protein structure, the biggest "differences" are found. Thus, allowing us to modify the desired torsional angles, but keeping compatibility with all the existent experimental information, in such a way that the observed and computed chemical shift values at a local and global level are optimized.We use a refinement algorithm that identifies the residues that contain flaws and then modifies the protein structure´s torsional angles in a way that tend to diminish these flaws. The information to identify these residues is obtained by CheShift-2, and to perturb the protein structure we use the software package for prediction and design of protein structures, ROSETTA.We evaluate our methodology by comparing the group of refined structures root mean square deviation (RMSD) and global distance test high accuracy score (GDT-HA) against the same protein experimentally determined at high-quality level. Moreover, the physicochemical quality of the results were assessed with validation methods like PROCHECK and MolProbity.