O. Pizio, A. Patrykiejew, S. Sokołowski , J.M. Ilnytskyi 1 Instituto de Química, Universidad Nacional Autonoma de México, Circuito Exterior, Ciudad Universitaria, 04360 México, D.F., México 2 Department for the Modelling of Physico-Chemical Processes, Maria Curie-Skłodowska University, 20031 Lublin, Poland 3 Institute for Condensed Matter Physics of the National Academy of Sciences of Ukraine, ...

Accurate description of the solvent environment is critical in computer simulations of protein structure and dynamics. An implicit treatment of solvent aims to capture the mean influence of water molecules on the solute via direct estimation of the solvation free energy. It has emerged as a powerful alternative to explicit solvent, and provides a favorable compromise between computational cost ...

The highly anisotropic environment of the lipid bilayer membrane imposes significant constraints on the structures and functions of membrane proteins. However, NMR structure calculations typically use a simple repulsive potential that neglects the effects of solvation and electrostatics, because explicit atomic representation of the solvent and lipid molecules is computationally expensive and i...

We study microtubular supramolecular architectures of tubulin dimers self-assembling into linear protofilaments, in turn forming a closed tube, which is an important component of the cytoskeleton. We identify the protofilament arrangements with the lowest free energy using molecular dynamics to optimize tubulin conformations. We then use the three-dimensional molecular theory of solvation to ob...