Dielectric Relaxations in Confined Hydrated Myoglobin

A Long Journey into the Investigation of the Structure–Dynamics–Function Paradigm in Proteins through the Activities of the Palermo Biophysics Group

An overview of the biophysics activity at the Department of Physics and Chemistry Emilio Segrè of the University of Palermo is given. For forty years, the focus of the research has been on the protein structure–dynamics–function paradigm, with the aim of understanding the molecular basis of the relevant mechanisms and the key role of solvent. At least three research lines are identified; the main results obtained in collaboration with other groups in Italy and abroad are presented. This review is dedicated to the memory of Professors Massimo Ugo Palma, Maria Beatrice Palma Vittorelli, and Lorenzo Cordone, which were the founders of the Palermo School of Biophysics. We all have been, directly or indirectly, their pupils; we miss their enthusiasm for scientific research, their deep physical insights, their suggestions, their strict but always constructive criticisms, and, most of all, their friendship. This paper is dedicated also to the memory of Prof. Hans Frauenfelder, whose pioneering works on nonexponential rebinding kinetics, protein substates, and energy landscape have inspired a large part of our work in the field of protein dynamics.

A protocol to measure slow protein dynamics of the cholera toxin B pentamers using broadband dielectric spectroscopy

The present protocol describes how to measure experimentally the slow protein dynamics that take place upon the thermal unfolding of the B subunit cholera toxin pentamers using broadband dielectric spectroscopy (BDS) in weakly hydrated and nanoconfined conditions. Transient unfolding intermediates, rarely identified otherwise, are revealed thanks to the B subunit's remarkable heat resistance up to 180°C and distinct molecular dynamics. The frequencies detected experimentally are consistent with the spatiotemporal scales of motions of molecular dynamics simulation.

For complete details on the use and execution of this protocol, please refer to Bourgeat et al. (2021, 2019).

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Measure protein dynamics experimentally using BDS in nanoconfined conditions

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Identify rare cholera toxin B subunit assembly and unfolding intermediates

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Detect cholera toxin B subunits in temperatures up to 180°C

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Match between protein molecular dynamics from experiments and simulations

Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Nanoconfined Fluids: Uniqueness of Water Compared to Other Liquids

Nanoconfinement can drastically change the behavior of liquids, puzzling us with counterintuitive properties. It is relevant in applications, including decontamination and crystallization control. However, it still lacks a systematic analysis for fluids with different bulk properties. Here we address this gap. We compare, by molecular dynamics simulations, three different liquids in a graphene slit pore: (1) A simple fluid, such as argon, described by a Lennard-Jones potential; (2) an anomalous fluid, such as a liquid metal, modeled with an isotropic core-softened potential; and (3) water, the prototypical anomalous liquid, with directional HBs. We study how the slit-pore width affects the structure, thermodynamics, and dynamics of the fluids. All the fluids show similar oscillating properties by changing the pore size. However, their free-energy minima are quite different in nature: (i) are energy-driven for the simple liquid; (ii) are entropy-driven for the isotropic core-softened potential; and (iii) have a changing nature for water. Indeed, for water, the monolayer minimum is entropy driven, at variance with the simple liquid, while the bilayer minimum is energy driven, at variance with the other anomalous liquid. Also, water has a large increase in diffusion for subnm slit pores, becoming faster than bulk. Instead, the other two fluids have diffusion oscillations much smaller than water, slowing down for decreasing slit-pore width. Our results, clarifying that water confined at the subnm scale behaves differently from other (simple or anomalous) fluids under similar confinement, are possibly relevant in nanopores applications, for example, in water purification from contaminants.

Experimental diagnostic of sequence-variant dynamic perturbations revealed by broadband dielectric spectroscopy

Genetic diversity leads to protein robustness, adaptability, and failure. Some sequence variants are structurally robust but functionally disturbed because mutations bring the protein onto unfolding/refolding routes resulting in misfolding diseases (e.g., Parkinson). We assume dynamic perturbations introduced by mutations foster the alternative unfolding routes and test this possibility by comparing the unfolding dynamics of the heat-labile enterotoxin B pentamers and the cholera toxin B pentamers, two pentamers structurally and functionally related and robust to 17 sequence variations. The B-subunit thermal unfolding dynamics are monitored by broadband dielectric spectroscopy in nanoconfined and weakly hydrated conditions. Distinct dielectric signals reveal the different B-subunits unfolding dynamics. Combined with network analyses, the experiments pinpoint the role of three mutations A1T, E7D, and E102A, in diverting LTB₅ to alternative unfolding routes that protect LTB₅ from dissociation. Altogether, the methodology diagnoses dynamics faults that may underlie functional disorder, drug resistance, or higher virulence of sequence variants.

Analytical Techniques for Structural Characterization of Proteins in Solid Pharmaceutical Forms: An Overview

Therapeutic proteins as biopharmaceuticals have emerged as a very important class of drugs for the treatment of many diseases. However, they are less stable compared to conventional pharmaceuticals. Their long-term stability in solid forms, which is critical for product performance, depends heavily on the retention of the native protein structure during the lyophilization (freeze-drying) process and, thereafter, in the solid state. Indeed, the biological function of proteins is directly related to the tertiary and secondary structure. Besides physical stability and biological activity, conformational stability (three-dimensional structure) is another important aspect when dealing with protein pharmaceuticals. Moreover, denaturation as loss of higher order structure is often a precursor to aggregation or chemical instability. Careful study of the physical and chemical properties of proteins in the dried state is therefore critical during biopharmaceutical drug development to deliver a final drug product with built-in quality that is safe, high-quality, efficient, and affordable for patients. This review provides an overview of common analytical techniques suitable for characterizing pharmaceutical protein powders, providing structural, and conformational information, as well as insights into dynamics. Such information can be very useful in formulation development, where selecting the best formulation for the drug can be quite a challenge.

Hemoglobin Dynamics in Solution vis-à-vis Under Confinement: An Electrochemical Perspective

Confining heme protein in silico often leads to beneficial functionalities such as an enhanced electrochemical response from the heme center. This can be harnessed to design effective biosensors for medical diagnostics. Proteins under confinement, surface confinement on the electrode to be precise, have more ordered and monodisperse structure compared to the protein in bulk solution. As the electrochemical response of a protein comes from those protein molecules that are confined within the electrical double layer across the electrode-electrolyte interface, it is expected that restriction of conformational fluctuations of the polymeric protein will help in enhancement of the electrochemical response. This is probably the prima facie reason for electrochemical response enhancement under confinement. We examine the dynamic features of hemoglobin under confinement vis-à-vis that in bulk solution. We use a variety of spectroscopic techniques across a wide time-space window to establish the following facts: (a) hardening of the protein polypeptide backbone, (b) slowing down of protein diffusion, (c) increase in relaxation times in NMR, and (d) slowing down of dielectric relaxation times under confinement. This indicates an overall quenching of protein dynamics when the protein is confined inside silica matrix. Thus, we hypothesize that along with retention of secondary structure, this quenching of dynamics contributes to the enhancement of electrochemical response observed.

Analysis of Nanoconfined Protein Dielectric Signals Using Charged Amino Acid Network Models

Protein slow motions involving collective molecular fluctuations on the timescale of microseconds to seconds are difficult to measure and not well understood despite being essential to sustain protein folding and protein function. Broadband dielectric spectroscopy (BDS) is one of the most powerful experimental techniques to monitor, over a broad frequency and temperature range, the molecular dynamics of soft matter through the orientational polarisation of permanent dipole moments that are generated by the chemical structure and morphological organisation of matter. Its typical frequency range goes from 107 Hz down to 10−3 Hz, being thus suitable for investigations on slow motions in proteins. Moreover, BDS has the advantage of providing direct experimental access to molecular fluctuations taking place on different length-scales, from local to cooperative dipolar motions. The unfolding of the cholera toxin B pentamer (CtxB5) after thermal treatment for 3h at 80°C is investigated by BDS under nanoconfined and dehydrated conditions. From the X-ray structure of the toxin pentamer, network-based models are used to infer the toxin dipoles present in the native state and to compute their stability and dielectric properties. Network analyses highlight three domains with distinct dielectric and stability properties that support a model where the toxin unfolds into three conformations after the treatment at 80°C. This novel integrative approach offers some perspective into the investigation of the relation between local perturbations (e.g. mutation, thermal treatment) and larger scale protein conformational changes. It might help ranking protein sequence variants according to their respective scale of dynamics perturbations.

Experimental Protein Molecular Dynamics: Broadband Dielectric Spectroscopy coupled with nanoconfinement

Protein dynamics covers multiple spatiotemporal scale processes, among which slow motions, not much understood even though they are underlying protein folding and protein functions. Protein slow motions are associated with structural heterogeneity, short-lived and poorly populated conformations, hard to detect individually. In addition, they involve collective motions of many atoms, not easily tracked by simulation and experimental devices. Here we propose a biophysical approach, coupling geometrical nanoconfinement and broadband dielectric spectroscopy (BDS), which distinguishes protein conformations by their respective molecular dynamics. In particular, protein-unfolding intermediates, usually poorly populated in macroscopic solutions are detected. The protein dynamics is observed under unusual conditions (sample nanoconfinement and dehydration) highlighting the robustness of protein structure and protein dynamics to a variety of conditions consistent with protein sustainability. The protein dielectric signals evolve with the temperature of thermal treatments indicating sensitivity to atomic and molecular interaction changes triggered by the protein thermal unfolding. As dipole fluctuations depend on both collective large-scale motions and local motions, the approach offers a prospect to track in-depth unfolding events.

Control of Solvent Dynamics around the B12-Dependent Ethanolamine Ammonia-Lyase Enzyme in Frozen Aqueous Solution by Using Dimethyl Sulfoxide Modulation of Mesodomain Volume

The temperature-dependent structure and dynamics of two concentric solvent phases, the protein-associated domain (PAD) and the mesodomain, that surround the ethanolamine ammonia-lyase (EAL) protein from Salmonella typhimurium in frozen polycrystalline aqueous solution are addressed by using electron paramagnetic resonance spectroscopy of the paramagnetic nitroxide spin probe, TEMPOL, over the temperature ( T) range 190-265 K. Dimethyl sulfoxide (DMSO), added at 0.5, 2.0, and 4.0% v/v and present at the maximum freeze concentration at T ≤ 245 K, varies the volume of the interstitial aqueous DMSO mesodomain ( V_meso) relative to a fixed PAD volume ( V_PAD). The increase in V_meso/ V_PAD from 0.8 to 6.0 is quantified by the partitioning of TEMPOL between the two phases. As V_meso/ V_PAD is increased, the Arrhenius parameters for activated TEMPOL rotational motion in the mesodomain remain uniform, whereas the parameters for TEMPOL in the PAD show a progressive transformation toward the mesodomain values (higher mobility). An order-disorder transition (ODT) in the PAD is detected by the exclusion of TEMPOL from the PAD into the mesodomain. The ODT T value is systematically lowered by increased V_meso/ V_PAD (from 215 to 200 K), and PAD ordering kinks the mesodomain Arrhenius dependence. Thus there is reciprocity in PAD-mesodomain solvent coupling. The results are interpreted as a dominant influence of ice-boundary confinement on the PAD solvent structure and dynamics, which is transmitted through the mesodomain and which decreases with mesodomain volume at increased added DMSO. The systematic tuning of PAD and mesodomain solvent dynamics by the variation of added DMSO is an incisive approach for the resolution of contributions of protein-solvent dynamical coupling to EAL catalysis.

Colloids versus solution state adsorption of proteins: Interaction of Myoglobin with supported lipid bilayers

This study examines adsorption of Myoglobin (Mb) in solution and as colloid on supported lipid bilayers of neutral phospholipids and a mixture of neutral+cationic lipids formed on gold coated quartz in a Quartz crystal microbalance (QCM). Results indicate that thin adsorbed films of Mb in solution and as colloids, show atleast 3 steps in the interaction with the bilayers: i) An initial strain of a viscoelastic film ii) Entrained water that moves in and out of the adsorbed film and iii) The coupled load from the bulk liquid which increases the strain of the film. These three components constitute an effective viscoelastic film which is rigidly coupled to the QCM. Grazing incidence XRD (GIXD) shows that the bilayer head group remains nearly undisturbed for Mb solution with pure (neutral) and (neutral+cationic) mixtures, whereas for the colloids there is an increase in head group thickness with neutral and decrease in the case of mixture. Unsaturation in the alkyl tails in the neutral lipid resulting in flexible disordered bilayers and more entrained water in the cationic system results in these changes. The sensitivity of QCM-D, makes it useful to study real-time monitoring of bilayer structural robustness cytotoxicity, drug delivery and lipid self-assembly.

Properties of Hydrogen-Bonded Liquids at Interfaces

Effects of interfaces on hydrogen-bonded liquids play major roles in nature and technology. Despite their importance, a fundamental understanding of these effects is still lacking. In large parts, this shortcoming is due to the high complexity of these systems, leading to an interference of various interactions and effects. Therefore, it is advisable to take gradual approaches, which start from well designed and defined model systems and systematically increase the level of intricacy towards more complex mimetics. Moreover, it is necessary to combine insights from a multitude of methods, in particular, to link novel preparation strategies and comprehensive experimental characterization with inventive computational and theoretical modeling. Such concerted approach was taken by a group of preparative, experimentally, and theoretically working scientists in the framework of Research Unit FOR 1583 funded by the Deutsche Forschungsgemeinschaft (German Research Foundation). This special issue summarizes the outcome of this collaborative research. In this introductory article, we give an overview of the covered topics and the main results of the whole consortium. The following contributions are review articles or original works of individual research projects.

Evidence of Coupling between the Motions of Water and Peptides

Studies of protein dynamics at low temperatures are generally performed on hydrated powders and not in biologically realistic solutions of water because of water crystallization. However, here we avoid the problem of crystallization by reducing the size of the biomolecules. We have studied oligomers of the amino acid l-lysine, fully dissolved in water, and our dielectric relaxation data show that the glass transition-related dynamics of the oligomers is determined by the water dynamics, in a way similar to that previously observed for solvated proteins. This implies that the crucial role of water for protein dynamics can be extended to other types of macromolecular systems, where water is also able to determine their conformational fluctuations. Using the energy landscape picture of macromolecules, the thermodynamic criterion for such solvent-slaved macromolecular motions may be that the macromolecules need the entropy contribution from the solvent to overcome the enthalpy barriers between different conformational substates.

Communication: Protein dynamical transition vs. liquid-liquid phase transition in protein hydration water

In this work, we compare experimental data on myoglobin hydrated powders from elastic neutron scattering, broadband dielectric spectroscopy, and differential scanning calorimetry. Our aim is to obtain new insights on the connection between the protein dynamical transition, a fundamental phenomenon observed in proteins whose physical origin is highly debated, and the liquid-liquid phase transition (LLPT) possibly occurring in protein hydration water and related to the existence of a low temperature critical point in supercooled water. Our results provide a consistent thermodynamic/dynamic description which gives experimental support to the LLPT hypothesis and further reveals how fundamental properties of water and proteins are tightly related.

Dielectric spectroscopy study of myoglobin in glycerol-water mixtures

Due to the interest in protein dynamics, there are numerous dielectric relaxation studies of proteins in water and in glass-forming aqueous solvents such as glycerol-water mixtures. In the regime of low frequencies, the inevitable dc-conductivity of such systems limits the resolution of dynamics that are slow compared with the solvent relaxation. Solutions of myoglobin in glycerol/water mixtures of various compositions are measured by dielectric spectroscopy in the frequency range from 10mHz to 10MHz. The resolution of low frequency modes is improved by two approaches: electrical 'cleaning' and the analysis of the derivative of the real component of permittivity, which shows no direct signature of dc-conductivity. Effects of internal interfacial polarization are also addressed by measuring the same solvents in confinement as well as mixed with glass beads. We find two processes, the structural relaxation of the solvent and the slower rotational mode of the protein, with no indication at even lower frequencies of a dielectric signature of fluctuations associated with protein dynamics.

Hydration dependence of myoglobin dynamics studied with elastic neutron scattering, differential scanning calorimetry and broadband dielectric spectroscopy

In this work we present a thorough investigation of the hydration dependence of myoglobin dynamics. The study is performed on D2O-hydrated protein powders in the hydration range 0<h<0.5 (h≡gr[D2O]/gr[protein]) and in the temperature range 20-300K. The protein equilibrium fluctuations are investigated with Elastic Neutron Scattering using the spectrometer IN13 at ILL (Grenoble), while the relaxations of the protein+hydration water system are investigated with Broadband Dielectric Spectroscopy; finally, Differential Scanning Calorimetry is used to obtain a thermodynamic description of the system. The effect of increasing hydration is to speed up the relaxations of the myoglobin+hydration water system and, thermodynamically, to decrease the glass transition temperature; these effects tend to saturate at h values greater than ~0.3. Moreover, the calorimetric scans put in evidence the occurrence of an endothermic peak whose onset temperature is located at ~230K independent of hydration. From the point of view of the protein equilibrium fluctuations, while the amplitude of anharmonic mean square displacements is found to increase with hydration, their onset temperature (i.e. the onset temperature of the well known "protein dynamical transition") is hydration independent. On the basis of the above results, the relevance of protein+hydration water relaxations and of the thermodynamic state of hydration water to the onset of the protein dynamical transition is discussed.

Fabrication of novel hierarchical structured Fe₃O₄ @LnPO₄ (Ln=Eu, Tb, Er) multifunctional microspheres for capturing and labeling phosphopeptides

Novel core-shell structured Fe3O4@LnPO4 (Ln=Eu, Tb, Er) multifunctional microspheres with a magnetic Fe3O4 core and a LnPO4 shell covered with spikes are synthesized for the first time through the combination of a homogeneous precipitation approach and an ion-exchange process. Their potential for selective capture, rapid separation, and easy mass spectrometry (MS) labeling of the phosphopeptides from complex proteolytic digests are evaluated. These affinity microspheres can improve the specificity for capture of the phosphopeptides, realize fast magnetic separation, enhance the MS detection signals, and directly identify phosphopeptides through 80 Da mass loss in the mass spectra. The synthesis strategy could become a general and effective technique for similar core-shell hierarchical structures.

Localized hydration in lyophilized myoglobin by hydrogen-deuterium exchange mass spectrometry. 1. Exchange mapping

The local effects of hydration on myoglobin (Mb) in solid matrices containing mannitol or sucrose (1:1 w/w, protein:additive) were mapped using hydrogen-deuterium exchange with mass spectrometric analysis (HDX-MS) at 5 °C and compared to solution controls. Solid powders were exposed to D₂O(g) at controlled activity (a(w)) followed by reconstitution and analysis of the intact protein and peptides produced by pepsin digestion. HDX varied with matrix type, a(w), and position along the protein backbone. HDX was less in sucrose matrices than in mannitol matrices at all a(w) while the difference in solution was negligible. Differences in HDX in the two matrices were detectable despite similarities in their bulk water content. The extent of exchange in solids is proposed as a measure of the hydration of exchangeable amide groups, as well as protein conformation and dynamics; pepsin digestion allows these effects to be mapped with peptide-level resolution.

Electrostatics of the protein-water interface and the dynamical transition in proteins

Atomic displacements of hydrated proteins are dominated by phonon vibrations at low temperatures and by dissipative large-amplitude motions at high temperatures. A crossover between the two regimes is known as a dynamical transition. Recent experiments indicate a connection between the dynamical transition and the dielectric response of the hydrated protein. We analyze two mechanisms of the coupling between the protein atomic motions and the protein-water interface. The first mechanism considers viscoelastic changes in the global shape of the protein plasticized by its coupling to the hydration shell. The second mechanism involves modulations of the local motions of partial charges inside the protein by electrostatic fluctuations. The model is used to analyze mean-square displacements of iron of metmyoglobin reported by Mössbauer spectroscopy. We show that high displacement of heme iron at physiological temperatures is dominated by electrostatic fluctuations. Two onsets, one arising from the viscoelastic response and the second from electrostatic fluctuations, are seen in the temperature dependence of the mean-square displacements when the corresponding relaxation times enter the instrumental resolution window.

Coupling of protein and environment fluctuations

We review the concepts of protein dynamics developed over the last 35years and extend applications of the unified model of protein dynamics to heat flow and spatial fluctuations in hydrated myoglobin (Mb) powders. Differential scanning calorimetry (DSC) and incoherent neutron scattering (INS) data on hydration Mb powders are explained by the temperature-dependence of the hydration-shell β(h) process measured by dielectric relaxation spectroscopy (DRS). The unified model explains the temperature dependence of DSC and INS data as a kinetic effect due to a fixed experimental time window and a broad distribution of hydration-shell β(h) fluctuation rates. We review the slaving of large scale protein motions to the bulk solvent α process, and the metastability of Mb molecules in glass forming bulk solvent at low temperatures. This article is part of a Special Issue entitled: "Protein Dynamics: Experimental and Computational Approaches".

Role of solvent for the dynamics and the glass transition of proteins

For the first time, a systematic investigation of the glass transition and its related dynamics of myoglobin in water-glycerol solvent mixtures of different water contents is presented. By a combination of broadband dielectric spectroscopy and differential scanning calorimetry (DSC), we have studied the relation between the protein and solvent dynamics with the aim to better understand the calorimetric glass transition, T(g), of proteins and the role of solvent for protein dynamics. The results show that both the viscosity related α-relaxation in the solvent as well as several different protein relaxations are involved in the calorimetric glass transition, and that the broadness (ΔT(g)) of the transition depends strongly on the total amount of solvent. The main reason for this seems to be that the protein relaxation processes become more separated in time with decreasing solvent level. The results are compared to that of hydrated myoglobin where the hydration water does not give any direct contribution to the calorimetric T(g). However, the large-scale α-like relaxation in the hydration water is still responsible for the protein dynamics that freeze-in at T(g). Finally, the dielectric data show clearly that the protein relaxation processes exhibit similar temperature dependences as the α-relaxation in the solvent, as suggested for solvent-slaved protein motions.

Probing the effect of water-water interactions on enzyme activity with salt gradients: a case-study using ribonuclease t1

Water molecules interact with one another via hydrogen bonds. Experimental and theoretical evidence indicates that these hydrogen bonds occur in two modalities--high- and low-angle hydrogen bonding--and that the addition of various solutes to water affects only the number of water molecules participating in a specific type of hydrogen bond interactions, not the nature of the water-water interactions. In this work, we have investigated the effect of each of these hydrogen bonding types upon the activity of the enzyme ribonuclease t1. This was done through perturbation of the water hydrogen bonding distribution by using various salts. Our results indicate that various salts differ in their ability to reduce the enzymatic activity of ribonuclease t1, and this ability is well correlated with the ability of each salt to promote high-angle hydrogen bonding in water. By applying the two-phase model of liquid water (i.e., liquid water being modeled as an equilibrium existing between two phases, LD and HD water), we demonstrate that our results are compatible with the assumption that increasing the population of high-angle hydrogen bonds among water molecules stabilizes the more compact, less active conformations of the enzyme. This indicates that the structures that proteins adopt in water solution depend upon the nature of interactions between water molecules.