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Urea and Guanidinium Chloride Denature Protein L in Different Ways in Molecular Dynamics Simulations

C. Camilloni ^*, A. Guerini Rocco , I. Eberini , E. Gianazza , R. A. Broglia ^*  and G. Tiana ^*

^* Department of Physics, University of Milano and INFN, I-20133 Milan, Italy; Gruppo di Studio per la Proteomica e la Struttura delle Proteine, Dipartimento di Scienze Farmacologiche, Università degli Studi di Milano, I-20133 Milan, Italy; and The Niels Bohr Institute, University of Copenhagen, DK-2100 Copenhagen, Denmark

Correspondence: Address reprint requests to G. Tiana, Dept. of Physics, University of Milano and INFN, via Celoria 16, I-20133 Milan, Italy. E-mail: tiana{at}mi.infn.it.

In performing protein-denaturation experiments, it is common to employ different kinds of denaturants interchangeably. We make use of molecular dynamics simulations of Protein L in water, in urea, and in guanidinium chloride (GdmCl) to ascertain if there are any structural differences in the associated unfolding processes. The simulation of proteins in solutions of GdmCl is complicated by the large number of charges involved, making it difficult to set up a realistic force field. Furthermore, at high concentrations of this denaturant, the motion of the solvent slows considerably. The simulations show that the unfolding mechanism depends on the denaturing agent: in urea the β-sheet is destabilized first, whereas in GdmCl, it is the -helix. Moreover, whereas urea interacts with the protein accumulating in the first solvation shell, GdmCl displays a longer-range electrostatic effect that does not perturb the structure of the solvent close to the protein.

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