Spatially Resolved Hydration Thermodynamics in Biomolecular Systems

Abstract

Water is essential for the structure, dynamics, energetics, and thus the function of biomolecules. It is a formidable challenge to elicit, in microscopic detail, the role of the solvation-related driving forces of biomolecular processes, such as the enthalpy and entropy contributions to the underlying free-energy landscape. In this Perspective, we discuss recent developments and applications of computational methods that provide a spatially resolved map of hydration thermodynamics in biomolecular systems and thus yield atomic-level insights to guide the interpretation of experimental observations. An emphasis is on the challenge of quantifying the hydration entropy, which requires characterization of both the motions of the biomolecules and of the water molecules in their surrounding.

Fortification of thermal and structural stability of hemoglobin using choline chloride-based deep eutectic solvents

“…As a solvent, which surrounds a protein, can potentially modify electrostatic and hydrophobic interactions, the nature of protein–solvent interactions (solvent-induced forces) is considered to be as crucial as that of protein–protein interactions (direct forces) in altering the thermal stability and maintaining the native structure of proteins. 7–12…”

“…As a solvent, which surrounds a protein, can potentially modify electrostatic and hydrophobic interactions, the nature of protein-solvent interactions (solvent-induced forces) is considered to be as crucial as that of protein-protein interactions (direct forces) in altering the thermal stability and maintaining the native structure of proteins. [7][8][9][10][11][12] Hemoglobin (Hb) is an important globular protein from a physiological point of view as it is the main protein in mammalian red blood cells, present in a concentration of about 30% by weight. 13 It consists of seven helical segments and seven non-helical segments in the alpha-chain, whereas, each betachain has eight helical segments and six non-helical ones.…”

Conformational Stability and Denaturation Processes of Proteins Investigated by Electrophoresis under Extreme Conditions

“…These are physical factors such as temperature [ 81 , 95 ], including processes leading to heat and cold denaturation [ 96 , 97 ], and pressure [ 98 , 99 , 100 ]. Studies of chemical factors are very extensive: effects of pH, role of hydrogen bonding, salt bridges, and hydration [ 101 , 102 , 103 , 104 ]; influence of various cosolvents and additives (osmolytes and crowding agents, including modeling of cytoplasm) [ 105 , 106 , 107 , 108 , 109 , 110 , 111 , 112 , 113 , 114 , 115 , 116 ]. The improvement of solubility [ 117 , 118 ] and the effect of point mutations on protein–protein interactions, and thus stability of quinary structures [ 119 ], are of biotechnological interest.…”

Protein 3D Hydration: A Case of Bovine Pancreatic Trypsin Inhibitor

“…As a result, one can determine a location only for some of the nearest waters with significant residence time close to some specific protein positions [ 9 ]. A way to overcome experimental difficulties and give a detailed description of biomolecule solvation is to use modern molecular dynamics (MD) simulations [ 10 , 11 , 12 , 13 ]. Another attractive option can be found in the three-dimensional reference interaction site model (3D-RISM)—an integral equation method of the statistical theory of liquids [ 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 ].…”