Simulation of protein diffusion: a sensitive probe of protein–solvent interactions

• Main Authors: Ferrario, Valerio, Pleiss, Jürgen
• Format: Text
• Language: unknown
• Published: Taylor & Francis 2018
• Subjects: Biophysics; Biochemistry; 29999 Physical Sciences not elsewhere classified; FOS Physical sciences; Biotechnology; 39999 Chemical Sciences not elsewhere classified; FOS Chemical sciences; Ecology; FOS Biological sciences; Immunology; FOS Clinical medicine; 69999 Biological Sciences not elsewhere classified; Cancer; Inorganic Chemistry; Plant Biology; Antarc*; Antarctica
• Online Access: https://dx.doi.org/10.6084/m9.figshare.6154604.v2; https://tandf.figshare.com/articles/Simulation_of_protein_diffusion_a_sensitive_probe_of_protein-solvent_interactions/6154604/2

Aqueous solutions of Candida antarctica lipase B (CALB) were simulated considering three different water models (SPC/E, TIP3P, TIP4P) by a series of molecular dynamics (MD) simulations of three different box sizes ( L = 9, 14, and 19 nm) to determine the diffusion coefficient, the water viscosity and the protein density. The protein–water systems were equilibrated for 500 ns, followed by 100 ns production runs which were analysed. The diffusional properties of CALB were characterized by the Stokes radius ( R S ), which was derived from the diffusion coefficient and the viscosity. R S was compared to the geometric radius ( R G ) of CALB, which was derived from the protein density. R S and R G differed by 0.27 nm for SPC/E and by 0.40 and 0.39 nm for TIP3P and TIP4P, respectively, which characterizes the thickness of the diffusive hydration layer on the protein surface. The simulated hydration layer of CALB resulted in agreement with those experimentally determined for other seven different proteins of comparable size. By avoiding the most common pitfalls, protein diffusion can be reliably simulated: simulating different box sizes to account for the finite size effect, equilibrating the protein–water system sufficiently, and using the complete production run for the determination of the diffusion coefficient.