COMPUTATIONAL STUDY OF THE STABILITY OF SECONDARY PEPTIDE STRUCTURE IN SOLVENTS MIXTURES

The structure of proteins and their folding mechanisms are dependent on the molecular environment and are sensitive to small variations in temperature, pressure, and the presence of some organic molecules, known as cosolvents. TMAO and urea are two cosolvents whose effects on the stability of protein structures are well known, but the underlying molecular mechanisms are still not completely understood. In this project, we intended to obtain a detailed molecular view of the effects of each cosolvent on the α-helix (AAQAA)3 peptide folding. We used the Hamiltonian Replica Exchange Molecular Dynamics to simulate the peptide in the presence of pure water and in different cosolvent concentrations: (1) water and urea (0.5 M, 1.0 M, and 1.5 M) and (2) water and TMAO (0.5 M, 1.0 M, and 1.5 M) during 500 ns, in a cubic box with side 70 Å at 300 K. Theoretical Circular Dichroism (CD) of the peptide in water was computed with SESCA software and compared with experimental data. We also analyzed the solvation structures around the peptide using the Minimum distance distribution functions (MDDFs) and the Kirkwood-Buff solutions theory by means of the ComplexMixture package. Our theoretical CD shows a qualitative agreement with experimental observation. The simulations confirmed qualitatively the denaturant character of urea and its accumulation in the peptide domain as the concentration increases, as expected from experimental data. Moreover, a two solvation layer structure was formed: the first one (and most intense) at a minimum distance around 2.8 Å and the other one around 5.0 Å. Yet, for all TMAO simulations, a well-known protein-stabilizer, the denaturation of the α-helix structure was observed. All systems showed similar average secondary structure contents despite the fact that TMAO was progressively excluded, with the increase of concentration, from the peptide domain as expected from experiments; forming two solvation layers with the same minimum-distances as the urea.