Date of Award

Fall 2017

Document Type


Degree Name

Doctor of Philosophy in Applied Physics - (Ph.D.)



First Advisor

Cristiano L. Dias

Second Advisor

John Francis Federici

Third Advisor

Gordon A. Thomas

Fourth Advisor

Luis R. Cruz-Cruz

Fifth Advisor

Yong Ick Kim


The function of a protein is determined by its three-dimensional structure which emerges from the delicate balance of forces involving atoms of the protein and the solvent. This balance can be perturbed by changing temperature, pressure, pH and by adding organic molecules known as cosolvents to the solution. Despite the wide use of cosolvents to perturb protein structures in the lab and in living systems, their molecular mechanisms are still not well established. Understanding these mechanisms is a problem of substantial interest, with potential application to the design of new drugs to target proteins. In this dissertation, we probe the role of two major cosolvents, urea and trimethylamine N-oxide (TMAO) at atomic level.

Urea is widely used as a denaturant in the lab to destabilize native protein conformations. However, the atomic mechanism of this molecule remains a question of debate. To unravel its molecular mechanism, explicit all-atom molecular dynamics simulations of unrestrained and extended poly-alanine and poly-leucine dimers are performed. Consistent with experimental results, we find that the large non-polar side chain of leucine is affected by urea whereas backbone atoms and alanine’s side chain are not. Urea is found to occupy positions between leucine’s side chains that are not accessible to water. This accounts for extra Lennard-Jones bonds between urea and side chains that favors the unfolded state. These bonds compete with urea-solvent interactions that favor the folded state. The sum of these two energetic terms provides the enthalpic driving force for unfolding. It is shown here that this enthalpy correlates with the potential of mean force of poly-leucine dimers.

To provide insights into the stabilizing mechanisms TMAO on protein structures, microsecond all-atom molecular dynamics simulations of peptides and replica exchange molecular dynamics simulations (REMD) of the Trp-cage miniprotein are performed. Most previous studies have focused on the effect of this osmolyte on protein backbone. Our results are consistent with these studies as we show that TMAO induces the backbone to adopt compact conformations. However, it is shown that effects of TMAO on the backbone are not dominant. In particular, TMAO's effect on the backbone is overcompensated by its destabilizing effect on the hydrophobic core: non-polar peptides and residues forming the hydrophobic core of the Trp-cage protein adopt more extended conformations in solutions containing TMAO. It is found that a main interaction that can stabilize folded proteins are charge-charge interactions. In light of these results, we propose that competing effects of TMAO on hydrophobic and charge-charge interactions account for its net stabilizing role on proteins.

Included in

Other Physics Commons