Pressure Unfolding of Proteins: New Insights into the Role of Bound Water

High-Pressure Effects on Gelatin Sol-Gel Transition

We investigated the effects of high hydrostatic pressure on the sol-gel transition of gelatin dispersions. We used dynamic light scattering (DLS) and DLS-based passive microrheology to monitor the evolution of the viscoelasticity during isothermal gelation. It provided easy identification of the sol-gel transition and the isothermal critical gelation time (t c) and values of viscosities of sols and shear modulus of gels. At a given temperature, t c decreased with increasing pressure. Up to 100 MPa, the temperature dependence of t c followed the established empirical rule and the critical temperature T c increased with pressure by ∼0.04 K/MPa. The critical gelation time scaled with the quench depth T-T c or equivalently with the distance from the pressure-dependent collagen denaturation temperature (∼314 K, at 0.1 MPa), which also increases by ∼0.04 K/MPa in the first 100 MPa. The pressure dependence also reflected on the time evolution of the intrinsic viscosity, η i , or elastic modulus, G p, in the sol or gel state, respectively, are reported. Both η i or G P evolution speeds up with pressure. Finally, using a reverse quenching approach, we observed a slowing of the gel melting when the pressure increases. Our results confirmed that the rheological evolution reflects the helix formation process and that pressure stabilizes the helices.

Temperature-Dependent Trimethylamine N-Oxide Induced the Formation of Substance P Dimers

Interactions of the peptide substance P (SP) (RPKPQQFFGLM-NH2) with trimethylamine N-oxide (TMAO) were investigated by using cryo-ion mobility-mass spectrometry (cryo-IM-MS), variable-temperature (278-358 K) electrospray ionization (vT-ESI) MS, and molecular dynamics (MD) simulations. Cryo-IM-MS provides evidence that cold solutions containing SP and TMAO yield abundant hydrated SP dimer ions, but dimer formation is inhibited in solutions that also contain urea. In addition, we show that SP dimer formation at cold solution temperatures (<298 K) is favored when TMAO interacts with the hydrophobic C-terminus of SP and is subject to reduced entropic penalty when compared to warmer solution conditions (>298 K). MD simulations show that TMAO lowers the free energy barrier for dimerization and that monomers dimerize by forming hydrogen bonds (HBs). Moreover, differences in oligomer abundances for SP mutants (P4A, P2,4A, G9P, and P2,4A/G9P) provide evidence that oligomerization facilitated by TMAO is sensitive to the cis/trans orientation of residues at positions 2, 4, and 9.

Exploring the effect of high-pressure processing conditions on the deaggregation of natural major royal jelly proteins (MRJPs) fibrillar aggregates

High pressure processing is a safe and green novel non-thermal processing technique for modulating food protein aggregation behavior. However, the systematic relationship between high pressure processing conditions and protein deaggregation has not been sufficiently investigated. Major royal jelly proteins, which are naturally highly fibrillar aggregates, and it was found that the pressure level and exposure time could significantly promote protein deaggregation. The 100-200 MPa treatment favoured the deaggregation of proteins with a significant decrease in the sulfhydryl group content. Contrarily, at higher pressure levels (>400 MPa), the exposure time promoted the formation of disordered agglomerates. Notably, the inter-conversion of α-helix and β-strands in major royal jelly proteins after high pressure processing eliminates the solvent-free cavities inside the aggregates, which exerts a 'collapsing' effect on the fibrillar aggregates. Furthermore, the first machine learning model of the high pressure processing conditions and the protein deaggregation behaviour was developed, which provided digital guidance for protein aggregation regulation.

Correlation between protein conformations and water structure and thermodynamics at high pressure: A molecular dynamics study of the Bovine Pancreatic Trypsin Inhibitor (BPTI) protein

Pressure-induced perturbation of a protein structure leading to its folding-unfolding mechanism is an important yet not fully understood phenomenon. The key point here is the role of water and its coupling with protein conformations as a function of pressure. In the current work, using extensive molecular dynamics simulation at 298 K, we systematically examine the coupling between protein conformations and water structures of pressures of 0.001, 5, 10, 15, 20 kbar, starting from (partially) unfolded structures of the protein Bovine Pancreatic Trypsin Inhibitor (BPTI). We also calculate localized thermodynamics at those pressures as a function of protein-water distance. Our findings show that both protein-specific and generic effects of pressure are operating. In particular, we found that (1) the amount of increase in water density near the protein depends on the protein structural heterogeneity; (2) the intra-protein hydrogen bond decreases with pressure, while the water-water hydrogen bond per water in the first solvation shell (FSS) increases; protein-water hydrogen bonds also found to increase with pressure, (3) with pressure hydrogen bonds of waters in the FSS getting twisted; and (4) water's tetrahedrality in the FSS decreases with pressure, but it is dependent on the local environment. Thermodynamically, at higher pressure, the structural perturbation of BPTI is due to the pressure-volume work, while the entropy decreases with the increase of pressure due to the higher translational and rotational rigidity of waters in the FSS. The local and subtle effects of pressure, found in this work, are likely to be typical of pressure-induced protein structure perturbation.

Hysteretic Pressure Dependence of Ca2+ Binding in LH1 Bacterial Membrane Chromoproteins

Much of the thermodynamic parameter values that support life are set by the properties of proteins. While the denaturing effects of pressure and temperature on proteins are well documented, their precise structural nature is rarely revealed. This work investigates the destabilization of multiple Ca²⁺ binding sites in the cyclic LH1 light-harvesting membrane chromoprotein complexes from two Ca-containing sulfur purple bacteria by hydrostatic high-pressure perturbation spectroscopy. The native (Ca-saturated) and denatured (Ca-depleted) phases of these complexes are well distinguishable by much-shifted bacteriochlorophyll a exciton absorption bands serving as innate optical probes in this study. The pressure-induced denaturation of the complexes related to the failure of the protein Ca-binding pockets and the concomitant breakage of hydrogen bonds between the pigment chromophores and protein environment were found cooperative, involving all or most of the Ca²⁺ binding sites, but irreversible. The strong hysteresis observed in the spectral and kinetic characteristics of phase transitions along the compression and decompression pathways implies asymmetry in the relevant free energy landscapes and activation free energy distributions. A phase transition pressure equal to about 1.9 kbar was evaluated for the complexes from Thiorhodovibrio strain 970 from the pressure dependence of biphasic kinetics observed in the minutes to 100 h time range.

Harnessing Pressure-Axis Experiments to Explore Volume Fluctuations, Conformational Substates, and Solvation of Biomolecular Systems

Intrinsic thermodynamic fluctuations within biomolecules are crucial for their function, and flexibility is one of the strategies that evolution has developed to adapt to extreme environments. In this regard, pressure perturbation is an important tool for mechanistically exploring the causes and effects of volume fluctuations in biomolecules and biomolecular assemblies, their role in biomolecular interactions and reactions, and how they are affected by the solvent properties. High hydrostatic pressure is also a key parameter in the context of deep-sea and subsurface biology and the study of the origin and physical limits of life. We discuss the role of pressure-axis experiments in revealing intrinsic structural fluctuations as well as high-energy conformational substates of proteins and other biomolecular systems that are important for their function and provide some illustrative examples. We show that the structural and dynamic information obtained from such pressure-axis studies improves our understanding of biomolecular function, disease, biological evolution, and adaptation.

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

The functional structure of proteins results from marginally stable folded conformations. Reversible unfolding, irreversible denaturation, and deterioration can be caused by chemical and physical agents due to changes in the physicochemical conditions of pH, ionic strength, temperature, pressure, and electric field or due to the presence of a cosolvent that perturbs the delicate balance between stabilizing and destabilizing interactions and eventually induces chemical modifications. For most proteins, denaturation is a complex process involving transient intermediates in several reversible and eventually irreversible steps. Knowledge of protein stability and denaturation processes is mandatory for the development of enzymes as industrial catalysts, biopharmaceuticals, analytical and medical bioreagents, and safe industrial food. Electrophoresis techniques operating under extreme conditions are convenient tools for analyzing unfolding transitions, trapping transient intermediates, and gaining insight into the mechanisms of denaturation processes. Moreover, quantitative analysis of electrophoretic mobility transition curves allows the estimation of the conformational stability of proteins. These approaches include polyacrylamide gel electrophoresis and capillary zone electrophoresis under cold, heat, and hydrostatic pressure and in the presence of non-ionic denaturing agents or stabilizers such as polyols and heavy water. Lastly, after exposure to extremes of physical conditions, electrophoresis under standard conditions provides information on irreversible processes, slow conformational drifts, and slow renaturation processes. The impressive developments of enzyme technology with multiple applications in fine chemistry, biopharmaceutics, and nanomedicine prompted us to revisit the potentialities of these electrophoretic approaches. This feature review is illustrated with published and unpublished results obtained by the authors on cholinesterases and paraoxonase, two physiologically and toxicologically important enzymes.

Volumetric Properties of the Transition State Ensemble for Protein Folding

Understanding how high hydrostatic pressure affects biomacromolecular interaction is important for deciphering the molecular mechanisms by which organisms adapt to live at the bottom of the ocean. The relative effect of hydrostatic pressure on the rates of folding/unfolding reactions is defined by the volumetric properties of the transition state ensemble relative to the folded and unfolded states. All-atom structure-based molecular dynamics simulations combined with quantitative computational protocol to compute volumes from three-dimensional coordinates allow volumetric mapping of protein folding landscape. This, is turn, provides qualitative understanding of the effects of hydrostatic pressure on energy landscape of proteins. The computational results for six different proteins are directly benchmark against experimental data and show an excellent agreement. Both experiments and computation show that the transition-state ensemble volume appears to be in-between the folded and unfolded state volumes, and thus the hydrostatic pressure accelerates protein unfolding.

A New Transfer Free Energy Based Implicit Solvation Model for the Description of Disordered and Folded Proteins

Most biological events occur on time scales that are difficult to access using conventional all-atom molecular dynamics simulations in explicit solvent. Implicit solvent techniques offer a promising solution to this problem, alleviating the computational cost associated with the simulation of large systems and accelerating the sampling compared to explicit solvent models. The substitution of water molecules by a mean field, however, introduces simplifications that may penalize accuracy and impede the prediction of certain physical properties. We demonstrate that existing implicit solvent models developed using a transfer free energy approach, while satisfactory at reproducing the folding behavior of globular proteins, fare less well in characterizing the conformational properties of intrinsically disordered proteins. We develop a new implicit solvent model that maximizes the degree of accuracy for both disordered and folded proteins. We show, by comparing the simulation outputs to experimental data, that in combination with the a99SB-disp force field, the implicit solvent model can describe both disordered (aβ40, PaaA2, and drkN SH3) and folded ((AAQAA)₃, CLN025, Trp-cage, and GTT) peptides. Our implicit solvent model permits a computationally efficient investigation of proteins containing both ordered and disordered regions, as well as the study of the transition between ordered and disordered protein states.

A Transfer Free Energy Based Implicit Solvent Model for Protein Simulations in Solvent Mixtures: Urea-Induced Denaturation as a Case Study

We developed a method for implicit solvent molecular dynamics simulations of proteins in solvent mixtures (model with implicit solvation thermodynamics, MIST). The MIST method introduces experimental group transfer free energies to the generalized Born formulation for generating molecular trajectories without the need for developing rigorous explicit-solvent force fields for multicomponent solutions. As a test case, we studied the urea-induced denaturation of the Trp-cage miniprotein in water. We demonstrate that our method allows efficient exploration of the conformational space of the protein in only a few hundreds of nanoseconds of all-atom unbiased simulations. Furthermore, selective implementation of the transfer free energies of specific peptide groups, backbone, and side chains enables us to decouple their specific energetic contributions to the conformational changes of the protein. The approach herein developed can readily be extended to the investigation of complex matrices as well as to the characterization of protein aggregation. The MIST method is implemented in Plumed (ver. 2.8) as a separate module called SASA.