Intrinsic compressibility and volume compression in solvated proteins by molecular dynamics simulation at high pressure

High pressure NMR study of a small protein, gurmarin

The effect of pressure on the structure of gurmarin, a globular, 35-residue protein from Gymnema sylvestre, was studied in aqueous environment (95% 1H2O/5% 2H2O, pH 2.0) with an on-line variable pressure NMR system operating at 750 MHz. Two-dimensional TOCSY and NOESY spectra were measured as functions of pressure between 1 and 2000 bar at 40 degrees C. Practically all the proton signals of gurmarin underwent some shifts with pressure, showing that the entire protein structure responds to, and is altered by, pressure. Most amide protons showed different degrees of low field shifts with pressure, namely 0-0.2 ppm with an average of 0.051 ppm at 2000 bar, showing that they are involved in hydrogen bonding and that these hydrogen bonds are shortened by pressure by different degrees. The tendency was also confirmed that the chemical shifts of the amide protons exposed to the solvent (water) are more sensitive to pressure than those internally hydrogen bonded with carbonyls. The pressure-induced shifts of the H alpha signals of the residues in the beta-sheet showed a negative correlation with the 'folding' shifts (difference between the shift at 1 bar and that of a random coil), suggesting that the main-chain torsion angles of the beta-sheet are slightly altered by pressure. Significant pressure-induced shifts were also observed for the side-chain protons (but no larger than 10% of the 'folding' shifts), demonstrating that the tertiary structure of gurmarin is also affected by pressure. Finally, the linearity of the pressure-induced shifts suggest that the compressibility of gurmarin is invariant in the pressure range between 1 and 2000 bar.

Thermodynamic analysis of biomolecules: a volumetric approach

Fundamental thermodynamic relationships reveal that volumetric studies on molecules of interest can yield useful new information. In particular, appropriately designed volumetric studies can characterize the properties of molecules as a function of solution conditions, including the role of solvation. Until recently, such studies on biologically interesting molecules have been limited because of the lack of readily available instrumentation with the requisite sensitivity; however, during the past decade, advances in the development of highly sensitive, small-volume densimetric, acoustic and high-pressure spectroscopic instrumentation have enabled biological molecules to be subjected to a wide range of volumetric studies. In fact, the volumetric methods used in these studies have already provided unique insights into the molecular origins of the intramolecular and intermolecular recognition events that modulate biomolecular processes. Of particular note are recent volumetric studies on globular proteins and nucleic acid duplexes. These studies have provided unique insights into the role of hydration in modulating the stabilities of these biopolymers, as well as their conformational transitions and ligand-binding properties.