Many proteins are considered to perform their functions by dynamic excursion to “other” conformations that deviate from the basic structure found in crystal. These “other” conformations have seldom become targets of detailed structural study. The on-line cell high pressure NMR technique developed at Kobe is the only available technique capable of producing “other” conformations of proteins and simultaneously reporting their structures at residue-specific resolution using multi-dimensional NMR spectroscopy. The principle is based on the recognition that the partial molar volume of a protein strongly depends on its conformational state. Examples are given from two proteins, basic pancreatic trypsin inhibitor and the Ras-binding domain of RalGEF.
This paper aims to review recent trends and developments in high-pressure FTIR studies on proteins. Methodological principles of research in this field, the assignment of the diagnostically-useful IR bands, as well as several examples illustrating the application of IR spectroscopy in high pressure studies on proteins are all within the scope of this article. This work is also an attempt to show that IR spectroscopy can find application not only for studies of the pressure-induced unfolding of protein structure, but also for the examination of minor unfolding events or local conformational changes induced by high pressure. A more elaborate discussion of the high-pressure study on bovine α-lactalbumin is also presented.
Protein dynamics is a basis for understanding the principles of constructing three-dimensional structures and the structure-function relationship of proteins. A novel measure of the flexibility of protein in water is compressibility because it is directly linked to the volume fluctuation. It is known that the adiabatic compressibility sensitively reflects the structural characteristics of proteins although it is a thermodynamic quantity. This article is a review of recent studies on the compressibility-structure relationship of native globular proteins.
From the many studies in enzyme reactions under high pressure, the activation volume for the catalytic process and the reaction volume for the dissociation process of the Michaelis complex evaluated from the pressure dependence of the enzyme reaction are found to be powerful tools for studying the reaction mechanisms in these processes. The above volume changes not only clarify the enzyme reaction mechanism, but also may explain the relationship between the high catalytic efficiency/specificity and the reactaonmechanism. As an example of an enzyme reaction, the reaction mechanism of α-chymotrypsin (α-CHT) catalysis is discussed in terms of the volume change.
To investigate the possibility that pressure can control the products for the enzyme reactions, pressure effects on the time course of the products' composition accompanying the hydrolysis of maltooligosaccharides [maltotetraose (G4), maltopentaose (G5), and maltohexaose (G6) ] and amylose catalyzed by porcine pancreatic α-amylase (PPA) were measured up to 300 MPa at 30°C. The composition of products for the hydrolysis of G5 substrates changed slightly by compression. But for G4, G6 and amylose substrate, pressure induced some changes in the composition of the products. These results tell us that pressure is one of the efficacious tools to control the products of enzyme reaction of α-amylase. The mechanism of an interesting pressure-induced reaction catalyzed by PPA is discussed in terms of the volume differences among enzyme-substrate (ES) complexes.
H2O is an important volatile material in the Earth, and it affects the physical properties (e. g. density, elastic velocity, viscosity, rheobgical property, diffusion, electrical conductivity and melting temperature) of the Earth's materials. Recently, it has been darified that significant amounts of H2O can be accommodated in β and γ phases of olivine, which means that the mantle transition zone has the potential of being a water reservoir in the Earth. In this paper, I review the H2O contents, lattice parameters and elastic properties of hydrous β and γ phases, the effect of H2O on the phase transformation of olivine, and the possibilities of water transportation into the mantle transition zone are discussed on the basis of these experimental data.
The constant-pressure first-principles molecular dynamics (CP-FPMD) method shows its great power in the investigation of high-pressure phenomena which are difficult to observe in experiments. In this article, I present a survey of this CP-FPMD method as well as a new technique we developed for the determination of transition states. I also illustrate their ability with our investigations of high-pressure synthesis of BCN heterodiamonds and pressure induced metallization of organic monomolecular crystals.