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Article: Urea and Guanidinium Chloride Denature Protein L in Different Ways in Molecular Dynamics Simulations
- Article from:
- Biophysical Journal
- Article date:
- June 15, 2008
- Author:
CopyrightCopyright Biophysical Society Jun 15, 2008. Provided by ProQuest LLC. (Hide copyright information)
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ABSTRACT
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 ...