Solvation energetics of proteins and their aggregates analyzed by all-atom molecular dynamics simulations and the energy-representation theory of solvation

Abstract

Solvation is a controlling factor for the structures and functions of proteins. This article addresses the effects of solvation from the energetic perspective for the fluctuations and cosolvent-induced changes of...

Crystal Growth of Urea and Its Modulation by Additives as Analyzed by All-Atom MD Simulation and Solution Theory

“…A model of free energy needs to be adopted to conduct the separation, though, since the separated contributions from the crystal and water are not observable in general. In the energy-representation formalism employed in the present work, the solvation free energy (free-energy change for turning on the solute–solvent interaction; see Methods section and Appendix B) is given formally as a sum of the partial contributions Δμ i from species i , where i is either urea or water. , Accordingly, the adsorption free energy Δμ ads is written as where Δμ ads cry and Δμ ads wat are the contributions from the crystal and water to the (overall) free energy of adsorption Δμ ads , respectively, Δμ interface urea and Δμ interface water are the urea and water contributions to the solvation free energy at the interface (adsorption configuration), respectively, and Δμ bulk is the solvation free energy of the solute in bulk water. The separated roles of the crystal urea and liquid water can be analyzed on the basis of eq .…”

“…The solvent-reorganization term is the free-energy penalty corresponding to the change in the solvent distribution upon insertion of the solute and acts as a repulsive component. In the energy-representation formalism, the partial contribution Δμ i from species i ( i refers to either the crystal urea or liquid water) to the (total) solvation free energy is expressed as , where u elec, i and u vdW, i are the electrostatic and van der Waals components of the average sum of the interaction energy of the solute with solvent species i in the solution system, respectively, and F i denotes the solvent-reorganization term. It was observed in Figure that the (total) free energy of adsorption Δμ ads is well correlated to the crystal contribution Δμ ads cry .…”

“…In the energy-representation formalism, the partial contribution Δμ i from species i (i refers to either the crystal urea or liquid water) to the (total) solvation free energy is expressed as 34,62…”

“…The energy-representation method thus reduces the computational load, and among a variety of approximate free-energy methods, − it is unique in the accuracy and efficiency with applicability to interfaces and systems with nanoscale inhomogeneity. ,− The error due to the use of an approximate functional was reported not to be larger than the error from the force field, − and good agreements with numerically exact results were observed for the adsorption of a urea molecule on the urea–water interface over a wide variety of adsorption configurations . Another advantage of the energy-representation formalism is that it provides a framework for free-energy decomposition. ,,− The free energy of solvation in a mixed solvent can be decomposed into the contributions from the respective solvent species, and the roles of such interaction components as electrostatic, van der Waals, and excluded-volume can be analyzed. In this work, we decompose the adsorption free energy into the contributions from the crystal and liquid molecules and address the roles of the electrostatic and van der Waals interactions at adsorption.…”

Insights into aggregation dynamics of NACore peptides from coarse‐grained simulations

“…26 Effect of NACore aggregation degree on β-sheet quantity and solvation free energy was also studied. 21,27 For coarsegrained model, tube model was adopted for large-scale assembly of peptides, and a condensation-ordering aggregation mechanism was proposed. 28 The simplified models facilitate the exploration of a larger parameter spaces than that accessible in atomic simulations.…”