Hydration, cavities and volume in protein folding, aggregation and amyloid assembly

Water Leakage Pathway Leads to Internal Hydration of the p53 Core Domain

The gene encoding the p53 tumor suppressor protein is the most frequently mutated oncogene in cancer patients; yet, generalized strategies for rescuing the function of different p53 mutants remain elusive. This work investigates factors that may contribute to the low inherent stability of the wild-type p53 core domain (p53C) and structurally compromised Y220C mutant. Pressure-induced unfolding of p53C was compared to p63C, the p53 family member with the highest stability, the engineered superstable p53C hexamutant (p53C HM), and lower stability p53C Y220C cancer-associated mutant. The following pressure unfolding values (P50% bar) were obtained: p53C 3346, p53C Y220C 2217, p53C HM 3943, and p63C 4326. Molecular dynamics (MD) simulations revealed that p53C Y220C was most prone to water infiltration, followed by p53C, whereas the interiors of p53C HM and p63C remained comparably dry. A strong correlation (r² = 0.92) between P50% and extent of interior hydration was observed. The pathways of individual water molecule entry and exit were mapped and analyzed, revealing a common route preserved across the p53 family involving a previously reported pocket, along with a novel surface cleft, both of which appear to be targetable by small molecules. Potential determinants of propensity to water incursion were assessed, including backbone hydrogen bond protection and combined sequence and structure similarity. Collectively, our results indicate that p53C has an intrinsic susceptibility to water leakage, which is exacerbated in a structural class mutant, suggesting that there may be a common avenue for rescuing p53 function.

Behavior of Proteins under Pressure from Experimental Pressure-Dependent Structures

Structure-based models are coarse-grained representations of the interactions responsible for the protein folding process. In their simplest form, they use only the native contact map of a given protein to predict the main features of its folding process by computer simulation. Given their limitations, these models are frequently complemented with sequence-dependent contributions or additional information. Specifically, to analyze the effect of pressure on the folding/unfolding transition, special forms of these interaction potentials are employed, which may a priori determine the outcome of the simulations. In this work, we have tried to keep the original simplicity of structure-based models. Therefore, we have used folded structures that have been experimentally determined at different pressures to define native contact maps and thus interactions dependent on pressure. Despite the apparently tiny structural differences induced by pressure, our simulation results provide different thermodynamic and kinetic behaviors, which roughly correspond to experimental observations (when there is a possible comparison) of two proteins used as benchmarks, hen egg-white lysozyme and dihydrofolate reductase. Therefore, this work shows the feasibility of using experimental native structures at different pressures to analyze the global effects of this physical property on the protein folding process.

The Roles of Water in the Protein Matrix: A Largely Untapped Resource for Drug Discovery

The value of thoroughly understanding the thermodynamics specific to a drug discovery/design study is well known. Over the past decade, the crucial roles of water molecules in protein structure, function, and dynamics have also become increasingly appreciated. This Perspective explores water in the biological environment by adopting its point of view in such phenomena. The prevailing thermodynamic models of the past, where water was seen largely in terms of an entropic gain after its displacement by a ligand, are now known to be much too simplistic. We adopt a set of terminology that describes water molecules as being "hot" and "cold", which we have defined as being easy and difficult to displace, respectively. The basis of these designations, which involve both enthalpic and entropic water contributions, are explored in several classes of biomolecules and structural motifs. The hallmarks for characterizing water molecules are examined, and computational tools for evaluating water-centric thermodynamics are reviewed. This Perspective's summary features guidelines for exploiting water molecules in drug discovery.

Effect of high pressure processing on dispersive and aggregative properties of almond milk

BACKGROUND

A study was conducted to investigate the impact of high pressure (450 and 600 MPa at 30 °C) and thermal (72, 85 and 99 °C at 0.1 MPa) treatments on dispersive and aggregative characteristics of almond milk. Experiments were conducted using a kinetic pressure testing unit and water bath. Particle size distribution, microstructure, UV absorption spectra, pH and color changes of processed and unprocessed samples were analyzed.

RESULTS

Raw almond milk represented the mono model particle size distribution with average particle diameters of 2 to 3 µm. Thermal or pressure treatment of almond milk shifted the particle size distribution towards right and increased particle size by five- to six-fold. Micrographs confirmed that both the treatments increased particle size due to aggregation of macromolecules. Pressure treatment produced relatively more and larger aggregates than those produced by heat treated samples. The apparent aggregation rate constant for 450 MPa and 600 MPa processed samples were k450MPa,30°C  = 0.0058 s(-1) and k600MPa,30°C  = 0.0095 s(-1) respectively.

CONCLUSIONS

This study showed that dispersive and aggregative properties of high pressure and heat-treated almond milk were different due to differences in protein denaturation, particles coagulation and aggregates morphological characteristics. Knowledge gained from the study will help food processors to formulate novel plant-based beverages treated with high pressure. © 2015 Society of Chemical Industry.

High Pressure Small-Angle X-Ray Scattering

Small-angle scattering, solution scattering from proteins in solution, reflects the shape of the scatter as a spread of electron density, which is common to protein crystallography. Although the obtained resolution of small-angle scattering is inferior to that of crystallography, it shows the global image of protein structure in solution without constraints of neighboring molecules in crystal lattice. At ambient pressure, data collection technology and analyses of small-angle scattering method developed so greatly in recent 10 years that it is recognized as one of the powerful method of structural biology. In parallel, many efforts have been made to apply this technique under high pressure. The instrumentation and interpretation of small-angle scattering under pressure, however, requires special considerations. The present chapter reviews the technological aspect of scattering from protein solution especially optimized for synchrotron X-ray sources.

Pressure-Inactivated Virus: A Promising Alternative for Vaccine Production

In recent years, many applications in diverse scientific fields with various purposes have examined pressure as a thermodynamic parameter. Pressure studies on viruses have direct biotechnological applications. Currently, most studies that involve viral inactivation by HHP are found in the area of food engineering and focus on the inactivation of foodborne viruses. Nevertheless, studies of viral inactivation for other purposes have also been conducted. HHP has been shown to be efficient in the inactivation of many viruses of clinical importance and the use of HHP approach has been proposed for the development of animal and human vaccines. Several studies have demonstrated that pressure can result in virus inactivation while preserving immunogenic properties. Viruses contain several components that can be susceptible to the effects of pressure. HHP has been a valuable tool for assessing viral structure function relationships because the viral structure is highly dependent on protein-protein interactions. In the case of small icosahedral viruses, incremental increases in pressure produce a progressive decrease in the folding structure when moving from assembled capsids to ribonucleoprotein intermediates (in RNA viruses), free dissociated units (dimers and/or monomers) and denatured monomers. High pressure inactivates enveloped viruses by trapping their particles in a fusion-like intermediate state. The fusogenic state, which is characterized by a smaller viral volume, is the final conformation promoted by HHP, in contrast with the metastable native state, which is characterized by a larger volume. The combined effects of high pressure with other factors, such as low or subzero temperature, pH and agents in sub-denaturing conditions (urea), have been a formidable tool in the assessment of the component's structure, as well as pathogen inactivation. HHP is a technology for the production of inactivated vaccines that are free of chemicals, safe and capable of inducing strong humoral and cellular immune responses. Here we present a current overview about the pressure-induced viral inactivation and the production of inactivated viral vaccines.

Truncation of a β-barrel scaffold dissociates intrinsic stability from its propensity to aggregation

Δ98Δ is a functional all-β sheet variant of intestinal fatty acid binding protein (IFABP) that was generated by controlled proteolysis. This framework is useful to study the molecular determinants related to aggregation of β-barrel proteins. Albeit displaying increased conformational plasticity, Δ98Δ exhibits a nativelike β-barrel topology and is able to support a cooperative folding behavior. Here we present a comparative study of IFABP and Δ98Δ regarding their conformational perturbation and aggregation propensity triggered by trifluoroethanol. Both proteins share a common nucleation-elongation mechanism, whereby the rate-limiting step is the formation of stable dimeric nuclei followed by the association of monomers to the growing aggregates. Despite leading to a less stable structure, the extensive truncation of IFABP yields a form exhibiting a somewhat lower tendency to aggregate. This finding appears at odds with the established notion that a perturbation of the native compact fold should necessarily favor the population of aggregation-prone species. In addition to the aggregation propensity dictated by a given amino-acid sequence, our contention holds that long-range interactions might also play a major role in determining the overall aggregation propensity.

Potency under pressure: the impact of hydrostatic pressure on antigenic properties of influenza virus hemagglutinin

Background

Influenza vaccines are effective in protecting against illness and death caused by this seasonal pathogen. The potency of influenza vaccines is measured by single radial immunodiffusion (SRID) assay that quantifies antigenic forms of hemagglutinin (HA). Hydrostatic pressure results in loss of binding of influenza virus to red blood cells, but it is not known whether this infers loss of potency.

Objectives

Our goal was to determine the impact of pressure on HA antigenic structure.

Methods

Viruses included in the 2010–2011 trivalent influenza vaccine were subjected to increasing number of cycles at 35 000 psi in a barocycler, and the impact of this treatment measured by determining hemagglutination units (HAU) and potency. Potency was assessed by SRID and immunogenicity in mice.

Results

After 25 cycles of pressure, the potency measured by SRID assay was below the limit of quantification for the H1N1 and B viruses used in our study, while the H3N2 component retained some potency that was lost after 50 pressure cycles. Pressure treatment also resulted in loss of HAU, but this did not strictly correlate with the potency value. Curiously, loss of potency was abrogated when influenza A, but not B, antigens were exposed to pressure in chicken egg allantoic fluid. Protection against pressure appeared to be mediated by specific interactions because addition of bovine serum albumin did not have the same effect.

Conclusions

Our results show that pressure‐induced loss of potency is strain dependent and suggests that pressure treatment may be useful for identifying vaccine formulations that improve HA stability.

Role of hydration in collagen recognition by bacterial adhesins

Protein-protein recognition regulates the vast majority of physiological or pathological processes. We investigated the role of hydration in collagen recognition by bacterial adhesin CNA by means of first principle molecular-dynamics samplings. Our characterization of the hydration properties of the isolated partners highlights dewetting-prone areas on the surface of CNA that closely match the key regions involved in hydrophobic intermolecular interactions upon complex formation, suggesting that the hydration state of the ligand-free CNA predisposes the protein to the collagen recognition. Moreover, hydration maps of the CNA-collagen complex reveal the presence of a number of structured water molecules that mediate intermolecular interactions at the interface between the two proteins. These hydration sites feature long residence times, significant binding free energies, and a geometrical distribution that closely resembles the hydration pattern of the isolated collagen triple helix. These findings are striking evidence that CNA recognizes the collagen triple helix as a hydrated molecule. For this structural motif, the exposure of several unsatisfied backbone carbonyl groups results in a strong interplay with the solvent, which is shown to also play a role in collagen recognition.

Development of high hydrostatic pressure in biosciences: pressure effect on biological structures and potential applications in biotechnologies

Compared to temperature, the development of pressure as a tool in the research field has emerged only recently (at the end of the XIXth century). Following several developments in Physics and Chemistry during the first half of the XXth century (in particular the synthesis of diamond in 1953-1954), high pressures were applied in Food Science, especially in Japan. The main objective was then to achieve the decontamination of foods while preserving their organoleptic properties. Now, a new step is engaged: the biological applications of high pressures, from food to pharmaceuticals and biomedical applications. This paper will focus on three main points: (i) a brief presentation of the pressure parameter and its characteristics, (ii) a description of the pressure effects on biological constituents from simple to more complex structures and (iii) a review of the different domains for which the application of high pressures is able to initiate potential developments in Biotechnologies.

Introduction to high-pressure bioscience and biotechnology

The manipulation of biological materials using elevated pressure is providing an ever-growing number of opportunities in both the applied and basic sciences. Manipulation of pressure is a useful parameter for enhancing food quality and shelf life; inactivating microbes, viruses, prions, and deleterious enzymes; affecting recombinant protein production; controlling DNA hybridization; and improving vaccine preparation. In biophysics and biochemistry, pressure is used as a tool to study intermediates in protein folding, enzyme kinetics, macromolecular interactions, amyloid fibrous protein aggregation, lipid structural changes, and to discern the role of solvation and void volumes in these processes. Biologists, including many microbiologists, examine the utility and basis of pressure inactivation of cells and cellular processes, and conversely seek to discover how deep-sea life has evolved a preference for high-pressure environments. This introduction and the papers that follow provide information on the nature and promise of the highly interdisciplinary field of high-pressure bioscience and biotechnology (HPBB).

Molecular modeling of two distinct triangular oligomers in amyloid beta-protein

Amyloid-beta (Abeta) peptides exhibit many distinct structural morphology at the early aggregate stage, some of which are biological relevant to the pathogenesis of Alzheimer's disease (AD). Atomic-resolution structures of the early Abeta aggregates and their conformational changes in amyloid aggregation remain elusive. Here, we perform all-atom molecular modeling and dynamics simulations to obtain two stable triangular-like Abeta structures with the lowest packing energy, one corresponding to the Tycko's model (Paravastu, A.; Leapman, R.; Yau, W.; Tycko, R. Proc. Nat. Acad. Soc. U.S.A. 2008, 105, 18349-18354) (referred to C-WT model) and the other corresponding to computational model (N-WT model). Both models have the same 3-fold symmetry but distinct beta-sheet organizations in which three Abeta hexamers pack together via either C-terminal beta-strand residues or N-terminal beta-strand residues forming distinct hydrophobic cross section. Structural and energetic comparisons of two 3-fold Abeta oligomers, coupled with structural changes upon the mutations occurring at the interacting interfaces, reveal that although hydrophobic interactions are still dominant forces, electrostatic interactions are more favorable in the N-WT model due to the formation of more and stable intersheet salt bridges, while solvation energy is more favorable in the C-WT model due to more exposed hydrophilic residues to solvent. Both models display many common features similar to other amyloid oligomers and therefore are likely to be biologically relevant.

Thermodynamics and kinetics of the pressure unfolding of phosphoglycerate kinase

Due to the relationship between compressibility and volume fluctuations, high-pressure studies provide vital insight into protein dynamics and function. Most high-pressure experiments were performed on small and fast folding proteins or model peptides. Here we show that a detailed kinetic study is necessary to extract reliable information from the high-pressure-induced structural conversion of large, slowly folding proteins. The pressure-jump unfolding kinetics of yeast phosphoglycerate kinase was recorded at pressures between 50 and 150 MPa. The time dependence of the conformational state of the protein was followed by tryptophan fluorescence measurements from 30 s to 2 h. The observed changes were described by a three-state model, and the volume change and the activation volume as well as the midpoint pressure of the transitions between the folded, intermediate, and unfolded states were determined. An interesting feature of the pressure unfolding of phosphoglycerate kinase was that the unfolding process speeds up with increasing pressure, which is the consequence of negative activation volumes for the folded --> intermediate, intermediate --> unfolded, and unfolded --> intermediate transitions.

Elastic incoherent neutron scattering as a probe of high pressure induced changes in protein flexibility

We report here the results of elastic incoherent neutron scattering experiments on three globular proteins (trypsin, lysozyme and beta-lactoglobulin) in different pressure intervals ranging from 1 bar to 5.5 kbar. A decrease of the mean square hydrogen fluctuations, u(2), has been observed upon increasing pressure. Trypsin and beta-lactoglobulin behave similarly while lysozyme shows much larger changes in u(2). This can be related to different steps in the denaturing processes and to the high propensity of lysozyme to form amyloids. Elastic incoherent neutron scattering has proven to be an effective microscopic technique for the investigation of pressure induced changes in protein flexibility.