Pressure-assisted dissociation and degradation of "proteinase K-resistant" fibrils prepared by seeding with scrapie-infected hamster prion protein

Proteins in Wonderland: The Magical World of Pressure

Admitting the "Native", "Unfolded" and "Fibril" states as the three basic generic states of proteins in nature, each of which is characterized with its partial molar volume, here we predict that the interconversion among these generic states N, U, F may be performed simply by making a temporal excursion into the so called "the high-pressure regime", created artificially by putting the system under sufficiently high hydrostatic pressure, where we convert N to U and F to U, and then back to "the low-pressure regime" (the "Anfinsen regime"), where we convert U back to N (U→N). Provided that the solution conditions (temperature, pH, etc.) remain largely the same, the idea provides a general method for choosing N, U, or F of a protein, to a great extent at will, assisted by the proper use of the external perturbation pressure. A successful experiment is demonstrated for the case of hen lysozyme, for which the amyloid fibril state F prepared at 1 bar is turned almost fully back into its original native state N at 1 bar by going through the "the high-pressure regime". The outstanding simplicity and effectiveness of pressure in controlling the conformational state of a protein are expected to have a wide variety of applications both in basic and applied bioscience in the future.

Real-time nuclear magnetic resonance spectroscopy in the study of biomolecular kinetics and dynamics

The review describes the application of nuclear magnetic resonance (NMR) spectroscopy to study kinetics of folding, refolding and aggregation of proteins, RNA and DNA. Time-resolved NMR experiments can be conducted in a reversible or an irreversible manner. In particular, irreversible folding experiments pose large requirements for (i) signal-to-noise due to the time limitations and (ii) synchronising of the refolding steps. Thus, this contribution discusses the application of methods for signal-to-noise increases, including dynamic nuclear polarisation, hyperpolarisation and photo-CIDNP for the study of time-resolved NMR studies. Further, methods are reviewed ranging from pressure and temperature jump, light induction to rapid mixing to induce rapidly non-equilibrium conditions required to initiate folding.

High Pressure NMR Spectroscopy

The combination of high-resolution NMR spectroscopy with pressure perturbation, known as variable-pressure NMR spectroscopy or simply high pressure NMR spectroscopy, is a relatively recent accomplishment, but is a technique expanding rapidly with high promise in future. The importance of the method is that it allows, for the first time in history, a systematic means of detecting and analyzing the structures and thermodynamic stability of high-energy sub-states in proteins. High-energy sub-states have been only vaguely known so far, as normally their populations are too low to be detected by conventional spectroscopic techniques including NMR spectroscopy. By now, however, high pressure NMR spectroscopy has established unequivocally that high-energy conformers are universally present in proteins in equilibrium with their stable folded counterparts. This chapter describes briefly the techniques of high pressure NMR spectroscopy and its unique and novel aspects as a method to explore protein structure in its high-energy paradigm with illustrative examples. It is now well established that high pressure NMR spectroscopy is a method to study intrinsic fluctuations of proteins, rather than those forced by pressure, by detecting structural changes amplified by pressure. Extension of the method to other bio-macromolecular systems is considered fairly straightforward.

Basic Equations in Statics and Kinetics of Protein Polymerization and the Mechanism of the Formation and Dissociation of Amyloid Fibrils Revealed by Pressure Perturbation

Studies of the pressure-dissociation of several amyloid or amyloid-like fibrils have shown that the fibril state is considerably voluminous. Quantitative characterization of the protein fibrillation reaction with respect to volumetric parameters is necessary to elucidate mechanisms of amyloid fibrillation in molecular terms such as protein cavity and hydration. Here we discuss, firstly, basic equations in statics and kinetics of protein polymerization as employed to obtain thermodynamic, volumetric, and kinetic parameters. Equilibrium treatment of the reactions with the scheme such as one-step polymerization, linear-association polymerization, or nucleation-dependent polymerization, and kinetic treatment of seeded linear-polymerization or spontaneous nucleation-elongation polymerization are described. In particular we will detail kinetics of the dissociation of fibrils which have been produced under the linear-association mechanism and therefore the length-distribution of which conforms to a geometric sequence in the degree of polymerization with a common ratio r, which is less than, and usually very close to, unity. In this case, an observed macroscopic rate of dissociation is shown to be a product of the microscopic elementary dissociation rate constant and a factor (1-r), extremely reduced compared with the intrinsic elementary rate. Secondly, we discuss protein conformational states in fibrillogenesis with molecular and volumetric observations reported, such as the unfolded state responsible for the association with seeds and the extension of amyloid fibrils, the transition state in which protein cavity formation and dehydration occur to intermediate levels, and the fibril state in which they occur to final respective levels which, in some cases, depend on the maturity of the fibril.