388736 Understanding the Behavior of Human Serum Albumin in Ionic Liquids Using Molecular Dynamics and Metadynamics
We performed molecular dynamics simulations to analyze the effects of two ionic liquids (ILs) on the structure and dynamics of serum albumin (HSA), a ubiquitous blood plasma protein. ILs are a class of solvents comprised of liquid organic salts. ILs have been shown to stabilize certain conformations of various proteins, and the activity, enatioselectivity, and products of enzymes can be modified by dissolving them in ILs. Because of the potential benefits of combining proteins with ILs, we are interested in understanding their interactions at the molecular scale. We compare the results of our molecular dynamics simulations to published experimental data in order to gain new insight into the mechanisms by which HSA is affected by the presence of ILs and in order to test the validity of using molecular dynamics to interrogate the interactions of proteins and ILs.
We first analyze the effects of ILs on the structure and dynamics of HSA by root mean square displacement and fluctuation. Notable differences arise that depend on the species of ionic liquid and its concentration in binary mixtures with water. Next, we find differences in the slow modes of motion by using principal component analysis and compare it experimental observations of the coupling of the motions of the three domains of HSA. We find that ILs prefer interaction sites on the protein where charged residues are exposed to the solvent and that this preferential interaction leads to the observed structural and dynamic changes. Published frequency-domain fluorescence spectroscopy data shows that loop 1 of domain I is significantly denatured by the presence of high concentrations of the ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]). We focus on this region of the protein and use metadynamics to uncover the underlying free energy of the unfolding of this region. In summary, not only do we add molecular level understanding to the specific interactions of ILs with HSA, but our simulations and analyses also demonstrate that key structural and dynamic changes of proteins in ILs can be reproduced by molecular simulation using existing force fields.
See more of this Group/Topical: Engineering Sciences and Fundamentals