Atomistic level understanding of the stabilization of protein Trp cage in denaturing and mixed osmolyte solutions

Abstract

Using replica exchange molecular dynamics simulation technique we report urea-induced denaturation and its counteraction by TMAO (Trimethylamine-N-oxide) of protein Trp cage. We find that in binary solution urea molecules are very much prone to stay nearby the salt bridge. In presence of TMAO, salt bridge is protected from urea molecules. TMAO also prevents hydration of the hydrophobic core of the protein and thus provides counteraction. Emphasizing on the orientational preferences of different aromatic planes reveals that near parallel orientation of Trp6-Trp18 and near perpendicular orientations of Trp6-Trp17 and Trp6-Trp19 have significant contributions towards stabilization. Trp6-Tyr3 pair is more likely to maintain a tilt angle of 25°. These orientational preferences of the planes that are lost in binary urea solution regained significantly in mixed urea/TMAO solutions. We have also found a highly favorable interaction energy between protein and urea contributed from both electrostatic and van der Waals components. Addition of TMAO makes these interactions more unfavorable. Protein solvation behavior and hydrogen bond calculations show that TMAO molecules replace some urea molecules from the surface of the protein. As a result, a reduction in the protein-urea hydrogen bonds is observed when compared to that of binary urea system.