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Osmoprotectants effects on protein denaturation

Nature developed a variety of methods to allow many organisms to survive in extreme environmental conditions, such as high temperatures or pressures, or high salt concentrations. One of these methods is the use of osmoprotectants, small molecules present in the cellular fluid that are able to stabilize the native and functional structure of the proteins in the cell. Analogous, but opposite, is the effect of denaturants, also small molecules that, instead, destabilize the proteins structure making them not functional.

Osmoprotectants have a key role in very different industrial fields:

The aim of this project is to reproduce the action of osmoprotectants and denaturants via computational techniques with the ultimate goal of designing new osmoprotectants. The way chosen to measure the osmoprotectant/denaturant activity is to denature artificially a model protein and see how osmoprotectants and denaturants influence the process. This can be done via the determination of unfolding free energy profiles. Given the free energy difference for the unfolding of the protein in pure water, an increase in the free energy difference is expected in the presence of osmoprotectants as they stabilize the folded structure making the unfolding more difficult. A denaturant should instead decrease the stability of the folded state and thus decreasing the unfolding free energy difference.

In this preliminary work, the beta-hairpin fragment of G protein was used as model peptide to unfold in the presence of four cosolvents: glycine betaine and ectoine as osmoprotectants, urea and guanidinium chloride as denaturants. All four are standard compounds, widely used in both computational and experimental studies. The free energy difference was evaluated using Umbrella Sampling and WHAM, using as reaction coordinate the end-to-end distance of the peptide.

I worked on this project during my bachelor and master at the University of Milan in the group of prof. Maurizio Sironi. A BOINC project (SimOne@home, the first in Italy, not active anymore) was created to manage the computational work.