Urea-induced unfolding of bovine beta-lactoglobulin by molecular dynamics

Abstract

Protein folding is a key process in all living organisms. In order to carry out their biochemical functions, proteins must be completely and correctly folded. In fact, some of the most investigated pathologies, for example some cancers or prion diseases, are due to the misfolding of specific proteins. Computational study of the folding process is however very difficult and only gives partial results. Many researchers thus prefer to focus their attention on the reverse process, i.e. protein unfolding, which can provide information on the structural features that keep the protein folded. In order to induce protein unfolding, the physical and/or the chemical environment can be modified by altering the temperature, pressure, pH or by adding chaotropic agents such as urea or guanidinium chloride. Short simulations of protein unfolding with the presence of urea and at relatively high temperatures have already been reported, but they show only a part of the whole process. With the aid of DEISA we wish to study the effect of chaotropic agents but without applying unreasonably high temperatures, which would accelerate the unfolding but would also add a further variable, the contribution of which is difficult to assess. Therefore we intend to use a standard molecular dynamics integrator (NAMD) to perform simulations on time scales well beyond those currently performed, but using realistic experimental conditions (room temperature, 1 bar pressure and neutral pH). We have decided to focus our attention on bovine beta-lactoglobulin (BLG) for which there is considerable experimental data that can validate our proposed simulations. Our aim is to perform a very long urea-driven unfolding simulation of BLG, together with a control simulation without urea, and by analysis of the resulting trajectories to achieve a better understanding of the protein (un)folding problem.