Predicting 13C chemical shifts for cysteines residues

MARTIN O.A.; VILLEGAS M.E.; VILA J.A.

Quilmes, Buenos Aires. Argentina

Workshop; Workshop de Biología Computacional; 2009

Cysteine residues and disulfide bonds are important for protein structure and function. Cysteines in their reduced form participate in the active site of different enzymes and together with histidine are the two most common residues involved in the coordination of Zinc ion at the Zn finger motifs, which are the most commonly observed structural motifs in transcription factors. Moreover, in the last few years it had been recognized the importance, and impact, that the disulfide bonds play in the catalytic cycle of enzymes like thioredoxin, switching between reduced and oxidized forms.Recently, we have been able to show that the computed 13C(alpha) chemical shifts, at DFT level of theory, can be used to validate protein conformations as well as to determine and refine protein structures (provided that distant constraint are available). However, our method was developed to compute 13C(alpha) chemical shifts of single residues, hence, cysteine involved in disulfide bonds were excluded from the analysis. In this work we present a method to solve this problem, i.e., to compute, fast and accurate, the 13C(alpha) chemical shifts for cysteine involved in disulfide bonds. Because of a coarse grained parallelization of the calculations the computational time for oxidized cysteines is comparable to that of single residue, namely 6 hrs per disulfide bond per processor. This new method has been applied to protein models, rich in disulfide bonds, obtained by both NMR spectroscopy and X-ray diffraction. No significant differences on the quality of the NMR- and X-ray-derived protein models, in terms of the agreement between computed and observed 13C(alpha) chemical shifts for the cysteines, were found. In addition, we also carry out a brief analysis of the 13C(beta) chemical shifts dependence with the redox state of the cysteines. We find two basins in good agreement with previously statistical reported values of chemical shifts of reduced and oxidized cysteines.