On the role of the solvent in biosystems: atomistic insights from computer simulations

Abstract

This review describes recent progress of atomistic simulations to promote the understanding of the role of the solvent in biophysics and biochemistry. Fundamental aspects of aqueous solutions and their importance for the rationalization of biomolecular arrangements and metabolic transport are discussed. Many of these insights were obtained from molecular dynamics simulations performed during the last three decades. In combination with quantum mechanical descriptions this approach nowadays advanced to a reliable tool for the investigation of biochemical reactions. Apart from passive coordination of the reactants, the solvent studies may also address proton transfer over chains of hydrogen bonded molecules.

Molecular modeling of the interface of an egg yolk protein-based emulsion

“…[11][12][13][14] Molecular simulations can provide valuable insight into the relationship between molecular properties and structural organization that are relevant for a better understanding of the behavior of food emulsions, including the miscibility/immiscibility of liquids, the formation of surfactant micelles, the adsorption and displacement of emulsifiers at interfaces, the transport of nonpolar molecules through aqueous phases, the conformation and flexibility of biopolymers in solution, polymer interactions, and the formation of gels. [15][16][17][18][19][20][21][22][23][24] The first step in a molecular simulation is to define the characteristics of the molecules involved (e.g., size, shape, flexibility, and polarity) and the nature of the intermolecular pair potentials that act between them, making a number of simplifying assumptions as a compromise between the model reliability and a reasonable computational time. 25 A collection of these molecules is arbitrarily distributed within a box that represents a certain region of space, and the change in the conformation and/or organization of the molecules is then monitored as they are allowed to interact with each other.…”