Molecular Dynamics of Protein Denaturation by Urea

The project will be focused on the denaturation of proteins by urea. It will be conducted using computer simulations, where four selected proteins, including 4bir, 3bov, 2vim, and 2yxf, were set into a 130 x 130 x 130 A3 water box filled with 8M of urea and run under 500K for 200 ns with a control of the same water box size and without urea, only using thermal denaturation. By analyzing these simulations, the way of denaturing a protein done by urea will be better understood