Studying the Dielectric Properties of a Protein Solution by Computer Simulation

Abstract

We report the static and frequency-dependent dielectric properties of a 9 mmol/L ubiquitin solution based on the analysis of a 5 ns molecular dynamics (MD) simulation. In accord with available experimental results, we obtain a significant dielectric increment for the dielectric constant (DC) at low frequencies (including the static DC (ω = 0)), but a decrement at higher frequencies. The overall dielectric properties were decomposed into the protein−protein and the water−water self-terms, as well as the protein−water cross-term. The most significant contributions arise from the two self-terms, approximately 65% from water and 21% from the protein. These two components, corresponding to what experimentalists often refer to as β- and γ-processes, also determine the bimodal shape of the dielectric loss function (χ‘ ‘(ω)). The quantitatively smallest protein−water cross-term (14%) corresponds to the experimentally observed δ-relaxation; it accentuates the bimodal shape of χ‘ ‘(ω) even further. A finer partitioning of the solvent into two solvation shells and bulk reveals the special role and properties of the first hydration layer surrounding the protein. Our findings point to protein−water interactions and, in particular, bound biological water as the microscopic origin of the δ-relaxation.