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Urea altered water structure and dynamics, thereby diminishing the hydrophobic effect and encouraging solvation of hydrophobic groups. In addition, through urea's weakening of water structure, water became free to compete with intraprotein interactions. Urea also interacted directly with polar residues and the peptide backbone, thereby stabilizing nonnative conformations. These simulations suggest that urea denatures proteins via both direct and indirect mechanisms.

http://www.pnas.org/content/100/9/5142.full

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"Chaotropic" agents, such as very high concentrations (e.g., 8M) of urea (H2N-CO-NH2) can form so many H-bonds that they compete with and disrupt interactions with water.

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A fellow named Christian Anfinsen did this experiment in the 1950's. He took a protein called ribonuclease, a protein that is a digestive enzyme, a protein that helps break down the macromolecule RNA. It must be in its native structure to do this job.
Actually he had to break disulfides here to get full denaturation. So he did: he added a reducing agent: mercaptoethanol (HO-CH3-CH2-SH). In the presence of this reagent, one gets exchange among the disulfides and the sulfhydryls:

Protein-CH2-S-S-CH2-Protein + 2 HO-CH2CH2-SH --->
Protein-CH2-SH + HS-CH2-Protein + HO-CH2CH2-S-S-CH2CH2-OH

The protein's disulfide gets reduced (and the S-S bond cleaved), while the mercaptoethanol gets oxidized.

After disruption of the disulfide bonds in ribonuclease, Anfinsen placed the polypeptide in a sack, and added urea, H2N-CO-NH2 to the solution outside the sack. Urea will break hydrogen bonds at high concentrations (e.g., 8M). {Q&A} The sack is made of a semi-permeable plastic material with pores big enough to allow small molecules like urea and water to pass through but not macromolecules like albumin or ribonuclease. This process of allowing the concentrations of changing small molecules to change while holding the concentrations of large molecules constant is a called dialysis. After allowing time for diffusion, the concentration of urea inside the sack should be the same as the concentration outside. {Q&A} He then checked that the protein had become denatured (e.g., by ultracentrifugation, see below)..

http://ccnmtl.columbia.edu/projects/biology/lecture5/index.htm

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Neutron diffraction studies on two important chaotropes (guanidinium and thiocyanate ions) show their very poor hydration, supporting the suggestion that they preferentially interact with the protein rather than the water.

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