What Can Really Be Learned from Dielectric Spectroscopy of Protein Solutions? A Case Study of Ribonuclease A

Linear and Nonlinear Dielectric Response of Intrinsically Disordered Proteins

Linear and nonlinear dielectric responses of solutions of intrinsically disordered proteins (IDPs) were analyzed by combining molecular dynamics simulations with formal theories. A large increment of the linear dielectric function over that of the solvent is found and related to large dipole moments of IDPs. The nonlinear dielectric effect (NDE) of the IDP far exceeds that of the bulk electrolyte, offering a route to interrogate protein conformational and rotational statistics and dynamics. Conformational flexibility of the IDP makes the dipole moment statistics consistent with the gamma/log-normal distributions and contributes to the NDE through the dipole moment's non-Gaussian parameter. The intrinsic non-Gaussian parameter of the dipole moment combines with the protein osmotic compressibility in the nonlinear dielectric susceptibility when dipolar correlations are screened by the electrolyte. The NDE is dominated by dipolar correlations when electrolyte screening is reduced.

Nonlinear dielectric response of dilute protein solutions

A theory for the nonlinear dielectric response of dilute protein solutions is presented. The field-dependent dielectric function of the protein solution changes linearly with the electric field squared in the lowest order. The slope of this dependence is expressed in terms of the protein dipole moment M0, its volume fraction in solution η0, and the second osmotic virial coefficient. For practical conditions, the nonlinear dielectric response scales as η03M08. This strong dependence on the protein dipole moment and concentration establishes a sharp contrast between the nonlinear response of solvated proteins relative to the surrounding polar solvent. Nonlinear dielectric response can serve as a sensitive tool for monitoring protein conformations and physiological activity.

Terahertz spectroscopy as a method for investigation of hydration shells of biomolecules

The hydration of biomolecules is one of the fundamental processes underlying the construction of living matter. The formation of the native conformation of most biomolecules is possible only in an aqueous environment. At the same time, not only water affects the structure of biomolecules, but also biomolecules affect the structure of water, forming hydration shells. However, the study of the structure of biomolecules is given much more attention than their hydration shells. A real breakthrough in the study of hydration occurred with the development of the THz spectroscopy method, which showed that the hydration shell of biomolecules is not limited to 1-2 layers of strongly bound water, but also includes more distant areas of hydration with altered molecular dynamics. This review examines the fundamental features of the THz frequency range as a source of information about the structural and dynamic characteristics of water that change during hydration. The applied approaches to the study of hydration shells of biomolecules based on THz spectroscopy are described. The data on the hydration of biomolecules of all main types obtained from the beginning of the application of THz spectroscopy to the present are summarized. The emphasis is placed on the possible participation of extended hydration shells in the realization of the biological functions of biomolecules and at the same time on the insufficient knowledge of their structural and dynamic characteristics.

Quantifying the Effect of Guest Binding on Host Environment

The environment around a host-guest complex is defined by intermolecular interactions between the complex, solvent molecules, and counterions. These interactions govern both the solubility of these complexes and the rates of reactions occurring within the host molecules and can be critical to catalytic and separation applications of host-guest systems. However, these interactions are challenging to detect using standard analytical chemistry techniques. Here, we quantify the hydration and ion pairing of a FeII4L4 coordination cage with a set of guest molecules having widely varying physicochemical properties. The impact of guest properties on host ion pairing and hydration was determined through microwave microfluidic measurements paired with principal component analysis (PCA). This analysis showed that introducing guest molecules into solution displaced counterions that were bound to the cage, and that the solvent solubility of the guest has the greatest impact on the solvent and ion-pairing dynamics surrounding the host. Specifically, we found that when we performed PCA of the measured equivalent circuit parameters and the solubility and dipole moment, we observed a high (>90%) explained variance for the first two principal components for each circuit parameter. We also observed that cage-counterion pairing is well-described by a single ion-pairing type, with a one-step reaction model independent of the type of cargo, and that the ion-pairing association constant is reduced for cargo with higher water solubility. Quantifying hydration and cage-counterion interactions is a critical step to building the next generation of design criteria for host-guest chemistries.

Heterogeneous and Allosteric Role of Surface Hydration for Protein-Ligand Binding

Atomistic-level understanding of surface hydration mediating protein-protein interactions and ligand binding has been a challenge due to the dynamic nature of water molecules near the surface. We develop a computational method to evaluate the solvation free energy based on the density map of the first hydration shell constructed from all-atom molecular dynamics simulation and use it to examine the binding of two intrinsically disordered ligands to their target protein domain. One ligand is from the human protein, and the other is from the 1918 Spanish flu virus. We find that the viral ligand incurs a 6.9 kcal/mol lower desolvation penalty upon binding to the target, which is consistent with its stronger binding affinity. The difference arises from the spatially fragmented and nonuniform water density profiles of the first hydration shell. In particular, residues that are distal from the ligand-binding site contribute to a varying extent to the desolvation penalty, among which the "entropy hotspot" residues contribute significantly. Thus, ligand binding alters hydration on remote sites in addition to affecting the binding interface. The nonlocal effect disappears when the conformational motion of the protein is suppressed. The present results elucidate the interplay between protein conformational dynamics and surface hydration. Our approach of measuring the solvation free energy based on the water density of the first hydration shell is tolerant of the conformational fluctuation of protein, and we expect it to be applicable to investigating a broad range of biomolecular interfaces.

Collective Spectroscopy of Solvation Phenomena: Conflicts, Challenges, and Opportunities

Different spectroscopy types reveal different aspects of molecular processes in soft matter. In particular, collective observables can provide insights into intermolecular correlations invisible to the more popular single-particle methods. In this perspective we feature the dielectric relaxation spectroscopy (DRS) with an emphasis on the proper interpretation of this complex observable aided by computational spectroscopy. While we focus on the history and recent advances of DRS in the fields of biomolecular hydration and nanoconfinement, the discussion transcends this particular field and provides a guide for how collective spectroscopy types supported by computational decomposition can be employed to further our understanding of soft matter phenomena.

Probing Adaptation of Hydration and Protein Dynamics to Temperature

Protein dynamics is strongly influenced by the surrounding environment and physiological conditions. Here we employ broadband megahertz-to-terahertz spectroscopy to explore the dynamics of water and myoglobin protein on an extended time scale from femto- to nanosecond. The dielectric spectra reveal several relaxations corresponding to the orientational polarization mechanism, including the dynamics of loosely bound, tightly bound, and bulk water, as well as collective vibrational modes of protein in an aqueous environment. The dynamics of loosely bound and bulk water follow non-Arrhenius behavior; however, the dynamics of water molecules in the tightly bound layer obeys the Arrhenius-type relation. Combining molecular simulations and effective-medium approximation, we have determined the number of water molecules in the tightly bound hydration layer and studied the dynamics of protein as a function of temperature. The results provide the important impact of water on the biochemical functions of proteins.

Stochastic Analysis of Molecular Dynamics Reveals the Rotation Dynamics Distribution of Water around Lysozyme

Water dynamics is essential to biochemical processes by mediating all such reactions, including biomolecular degeneration in solutions. To disentangle the molecular-scale distribution of water dynamics around a solute biomolecule, we investigated here the rotational dynamics of water around lysozyme by combining molecular dynamics (MD) simulations and broadband dielectric spectroscopy (BDS). A statistical analysis using the relaxation times and trajectories of every single water molecule was proposed, and the two-dimensional probability distribution of water at a distance from the lysozyme surface with a rotational relaxation time was given. For the observed lysozyme solutions of 34-284 mg/mL, we discovered that the dielectric relaxation time obtained from this distribution agrees well with the measured γ relaxation time, which suggests that rotational self-correlation of water molecules underlies the gigahertz domain of the dielectric spectra. Regardless of protein concentration, water rotational relaxation time versus the distance from the lysozyme surface revealed that the water rotation is severely retarded within 3 Å from the lysozyme surface and is nearly comparable to pure water when farther than 10 Å. The dimension of the first hydration layer was subsequently identified in terms of the relationship between the acceleration of water rotation and the distance from the protein surface.

Dipolar Interactions and Protein Hydration in Highly Concentrated Antibody Formulations

Molecular interaction mechanisms in high-concentrated protein systems are of fundamental importance for the rational development of biopharmaceuticals such as monoclonal antibody (mAb) formulations. In such high-concentrated protein systems, the intermolecular distances between mAb molecules are reduced to the size of the protein diameter (approx. 10 nm). Thus, protein-protein interactions are more pronounced at high concentrations; so a direct extrapolation of physicochemical properties obtained from measurements at a low protein concentration of the corresponding properties at a high protein concentration is highly questionable. Besides the charge-charge interaction, the effects of molecular crowding, dipolar interaction, changes in protein hydration, and self-assembling tendency become more relevant. Here, protein hydration, protein dipole moment, and protein-protein interactions were studied in protein concentrations up to 200 mg/mL (= 1.3 mM) in different formulations for selected mAbs using dielectric relaxation spectroscopy (DRS). These data are correlated with the second virial coefficient, A₂, the diffusion interaction parameter, k_D, the elastic shear modulus, G', and the dynamic viscosity, η. When large contributions of dipolar protein-protein interactions were observed, the tendency of self-assembling and an increase in solution viscosity were detected. These effects were examined using specific buffer conditions. Furthermore, different types of protein-water interactions were identified via DRS, whereby the effect of high protein concentration on protein hydration was investigated for different high-concentrated liquid formulations (HCLFs).

Hydration of methemoglobin studied by in silico modeling and dielectric spectroscopy

The hemoglobin concentration of 35 g/dl of human red blood cells is close to the solubility threshold. Using microwave dielectric spectroscopy, we have assessed the amount of water associated with hydration shells of methemoglobin as a function of its concentration in the presence or absence of ions. We estimated water-hemoglobin interactions to interpret the obtained data. Within the concentration range of 5-10 g/dl of methemoglobin, ions play an important role in defining the free-to-bound water ratio competing with hemoglobin to recruit water molecules for the hydration shell. At higher concentrations, hemoglobin is a major contributor to the recruitment of water to its hydration shell. Furthermore, the amount of bound water does not change as the hemoglobin concentration is increased from 15 to 30 g/dl, remaining at the level of ∼20% of the total intracellular water pool. The theoretical evaluation of the ratio of free and bound water for the hemoglobin concentration in the absence of ions corresponds with the experimental results and shows that the methemoglobin molecule binds about 1400 water molecules. These observations suggest that within the concentration range close to the physiological one, hemoglobin molecules are so close to each other that their hydration shells interact. In this case, the orientation of the hemoglobin molecules is most likely not stochastic, but rather supports partial neutralization of positive and negative charges at the protein surface. Furthermore, deformation of the red blood cell shape results in the rearrangement of these structures.

Protein dielectrophoresis: Key dielectric parameters and evolving theory

Globular proteins exhibit dielectrophoresis (DEP) responses in experiments where the applied field gradient factor ∇E² appears far too small, according to standard DEP theory, to overcome dispersive forces associated with the thermal energy kT of disorder. To address this a DEP force equation is proposed that replaces a previous empirical relationship between the macroscopic and microscopic forms of the Clausius-Mossotti factor. This equation relates the DEP response of a protein directly to the dielectric increment δε⁺ and decrement δε^- that characterize its β-dispersion at radio frequencies, and also indirectly to its intrinsic dipole moment by way of providing a measure of the protein's effective volume. A parameter Γ_pw , taken as a measure of cross-correlated dipole interactions between the protein and its water molecules of hydration, is included in this equation. For 9 of the 12 proteins, for which an evaluation can presently be made, Γ_pw has a value of ≈4600 ± 120. These conclusions follow an analysis of the failure of macroscopic dielectric mixture (effective medium) theories to predict the dielectric properties of solvated proteins. The implication of a polarizability greatly exceeding the intrinsic value for a protein might reflect the formation of relaxor ferroelectric nanodomains in its hydration shell.

Highly precise characterization of the hydration state upon thermal denaturation of human serum albumin using a 65 GHz dielectric sensor

The biological functions of proteins depend on harmonization with hydration water surrounding them. Indeed, the dynamical transition of proteins, such as thermal denaturation, is dependent on the changes in the mobility of hydration water. However, the role of hydration water during dynamical transition is yet to be fully understood due to technical limitations in precisely characterizing the amount of hydration water. A state-of-the-art CMOS dielectric sensor consisting of 65 GHz LC resonators addressed this issue by utilizing the feature that oscillation frequency sensitively shifts in response to the complex dielectric constant at 65 GHz with extremely high precision. This study aimed to establish an analytical algorithm to derive the hydration number from the measured frequency shift and to demonstrate the transition of hydration number upon the thermal denaturation of human serum albumin. The determined hydration number in the native state drew a "global" hydration picture beyond the first solvation shell, with substantially reduced uncertainty of the hydration number (about ±1%). This allowed the detection of a rapid increase in the hydration number at about 55 °C during the heating process, which was in excellent phase with the irreversible rupture of the α-helical structure into solvent-exposed extended chains, whereas the hydration number did not trace the forward path in the subsequent cooling process. Our result indicates that the weakening of water hydrogen bonds trigger the unfolding of the protein structure first, followed by the changes in the number of hydration water as a consequence of thermal denaturation.

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.

Dielectric spectroscopy and time dependent Stokes shift: two faces of the same coin?

Different types of spectroscopy capture different aspects of dynamics and different ranges of intermolecular contributions.

Electrostatic solvation and mobility in uniform and non-uniform electric fields: From simple ions to proteins

A number of observations related to interfacial electrostatics of polar liquids question the traditional assumption of dielectric theories that bulk dielectric properties can be continuously extended to the dividing surface separating the solute from the solvent. The deficiency of this approximation can be remedied by introducing local interface susceptibilities and the interface dielectric constant. Asymmetries of ionic hydration thermodynamics and of the mobility between cations and anions can be related to different propensities of the water molecules to orient their dipole toward and outward from solutes of opposite charges. This electrostatic asymmetry is reflected in different interface dielectric constants for cations and anions. The interface of water with neutral solutes is spontaneously polarized due to preferential water orientations in the interface. This phenomenon is responsible for a nonzero cavity potential directly related to a nonzero surface charge. This connection predicts that particles allowing a nonzero cavity potential must show mobility in an external electric field even if the net charge of the particle is zero. The theory predicts that a positive cavity potential and a positive surface charge translate to an effectively negative solute charge reported by mobility measurements. Passing of the cavity potential through a minimum found in simulations might be the origin of the maximum of mobility vs the ionic size observed experimentally. Finally, mobility of proteins in the field gradient (dielectrophoresis) is many orders of magnitude greater than predicted by the traditionally used Clausius-Mossotti equation. Two reasons contribute to this disagreement: (i) a failure of Maxwell's electrostatics to describe the cavity-field susceptibility and (ii) the neglect of the protein permanent dipole by the Clausius-Mossotti equation. An analytical relation between the dielectrophoretic susceptibility and dielectric spectroscopy of solutions provides direct access to this parameter, confirming the failure of the Clausius-Mossotti equation in application to protein dielectrophresis.

Dielectric relaxation studies of collagen - surfactant complexes in aqueous buffer solution

Dielectric relaxation studies of rat tail tendon collagen with anionic sodium dodecyl sulphate (SDS), cationic cetyltrimethyl ammonium bromide (CTAB) and nonionic Tween 80 in aqueous buffer solutions at four different temperatures have been carried out in the frequency range 1 GHz to 25 GHz using time domain dielectric spectroscopy. The frequency dependent normalized dielectric modulus function P of the collagen and surfactant solutions show up as peaks around 1-2 GHz which is due to the bound water around collagen macromolecule and surfactant micelles. For the collagen - surfactant complexes, the peak in normalized dielectric modulus function P is shifted towards high frequency side near 2-3 GHz upon addition of surfactants to collagen in buffer solution. The water structure around collagen is altered in the presence of micelle forming surfactant additives and this change may affect the degrees of freedom of their motion. Hence the significant changes are observed in the relaxation time of bound water around collagen macromolecule in the presence of surfactants. Further, it was observed that no considerable change in relaxation time of hydration water of the complexes with respect to change in temperature within the studied temperature range. The activation enthalpy and activation entropy for the dipolar orientation corresponding to the free water for the surfactants and their complexes with collagen have been calculated from the Arrhenius plot. Our thermodynamic results suggest that the two‑hydrogen-bonded model may be possible in SDS and Tween 80 environments, whereas the one‑hydrogen-bonded model is likely to be possible in buffer and CTAB environments.

Observation of high-temperature macromolecular confinement in lyophilised protein formulations using terahertz spectroscopy

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Structural dynamics in lyophilised protein formulations can be probed with terahertz spectroscopy and two glass transition processes, Tg,α and Tg,β, are observed.

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Vibrational confinement upon thermal activation is observed resulting in no detectable changes in secondary structure but strongly reduced the molecular mobility at temperatures above Tg,α.

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The confinement was found to be strongly dependent on the formulation.

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We hypothesise that confinement is linked to conformational states with potential effects on physical and chemical stability of the biomolecule during storage.

Characterising the structural dynamics of proteins and the effects of excipients are critical for optimising the design of formulations. In this work we investigated four lyophilised formulations containing bovine serum albumin (BSA) and three formulations containing a monoclonal antibody (mAb, here mAb1), and explored the role of the excipients polysorbate 80, sucrose, trehalose, and arginine on stabilising proteins. By performing temperature variable terahertz time-domain spectroscopy (THz-TDS) experiments it is possible to study the vibrational dynamics of these formulations. The THz-TDS measurements reveal two distinct glass transition processes in all tested formulations. The lower temperature transition, Tg,β, is associated with the onset of local motion due to the secondary relaxation whilst the higher temperature transition, Tg,α, marks the onset of the α-relaxation. For some of the formulations, containing globular BSA as well as mAb1, the absorption at terahertz frequencies does not increase further at temperatures above Tg,α. Such behaviour is in contrast to our previous observations for small organic molecules as well as linear polymers where absorption is always observed to steadily increase with temperature due to the stronger absorption of terahertz radiation by more mobile dipoles. The absence of such further increase in absorption with higher temperatures therefore suggests a localised confinement of the protein/excipient matrix at high temperatures that hinders any further increase in mobility. We found that subtle changes in excipient composition had an effect on the transition temperatures Tg,α and Tg,β as well as the vibrational confinement in the solid state. Further work is required to establish the potential significance of the vibrational confinement in the solid state on formulation stability and chemical degradation as well as what role the excipients play in achieving such confinement.

Dynamics of proteins in solution

The dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.

Heterogeneity of water structure and dynamics at the protein-water interface

In this molecular dynamics simulation study, we analyze the local structural and dynamic properties of water hydrating the protein ubiquitin on a spatial grid with 1 Å resolution. This allows for insights into the spatial distribution of water number densities, molecular orientations, translations, and rotations as a function of distance from the protein surface. Water molecule orientations follow a heterogeneous distribution with preferred local orientations of water dipoles and O-H bond vectors up to 10-15 Å distances from the protein, while local variations of the water number density converge to homogeneous bulk-like values within less than 8 Å. Interestingly, we find that the long-ranged orientational structure of water does not impact either the translational or rotational dynamics of water. Instead, heterogeneous distributions of local dynamical parameters and averaged dynamical retardation factors are only found close to the protein surface and follow a distance dependence comparable to heterogeneities in the local water number density. This study shows that the formation of nanodomains of preferred water orientations far from the protein does not significantly impact dynamical processes probed as a non-local average in most experiments.

Towards capturing cellular complexity: combining encapsulation and macromolecular crowding in a reverse micelle

This paper studies the orientational structure and dynamics of multi-protein systems under confinement and discusses the implications on biological cells.

Fundamental limitations of the time-dependent Stokes shift for investigating protein hydration dynamics

In the TDSS measured in protein systems, large protein contributions fully obscure hydration dynamics.

High-Precision Megahertz-to-Terahertz Dielectric Spectroscopy of Protein Collective Motions and Hydration Dynamics

The low-frequency collective vibrational modes in proteins as well as the protein-water interface have been suggested as dominant factors controlling the efficiency of biochemical reactions and biological energy transport. It is thus crucial to uncover the mystery of the hydration structure and dynamics as well as their coupling to collective motions of proteins in aqueous solutions. Here, we report dielectric properties of aqueous bovine serum albumin protein solutions as a model system using an extremely sensitive dielectric spectrometer with frequencies spanning from megahertz to terahertz. The dielectric relaxation spectra reveal several polarization mechanisms at the molecular level with different time constants and dielectric strengths, reflecting the complexity of protein-water interactions. Combining the effective-medium approximation and molecular dynamics simulations, we have determined collective vibrational modes at terahertz frequencies and the number of water molecules in the tightly bound and loosely bound hydration layers. High-precision measurements of the number of hydration water molecules indicate that the dynamical influence of proteins extends beyond the first solvation layer, to around 7 Å distance from the protein surface, with the largest slowdown arising from water molecules directly hydrogen-bonded to the protein. Our results reveal critical information of protein dynamics and protein-water interfaces, which determine biochemical functions and reactivity of proteins.

Effect of Temperature and Hydration Level on Purple Membrane Dynamics Studied Using Broadband Dielectric Spectroscopy from Sub-GHz to THz Regions

To investigate the effects of temperature and hydration on the dynamics of purple membrane (PM), we measured the broadband complex dielectric spectra from 0.5 GHz to 2.3 THz using a vector network analyzer and terahertz time-domain spectroscopy from 233 to 293 K. In the lower temperature region down to 83 K, the complex dielectric spectra in the THz region were also obtained. The complex dielectric spectra were analyzed through curve fitting using several model functions. We found that the hydrated states of one relaxational mode, which was assigned as the coupled motion of water molecules with the PM surface, began to overlap with the THz region at approximately 230 K. On the other hand, the relaxational mode was not observed for the dehydrated state. On the basis of this result, we conclude that the protein-dynamical-transition-like behavior in the THz region is due to the onset of the overlap of the relaxational mode with the THz region. Temperature hysteresis was observed in the dielectric spectrum at 263 K when the hydration level was high. It is suggested that the hydration water behaves similarly to supercooled liquid at that temperature. The third hydration layer may be partly formed to observe such a phenomenon. We also found that the relaxation time is slower than that of a globular protein, lysozyme, and the microscopic environment in the vicinity of the PM surface is suggested to be more heterogeneous than lysozyme. It is proposed that the spectral overlap of the relaxational mode and the low-frequency vibrational mode is necessary for the large conformational change of protein.

Macromolecular crowding and the importance of proper hydration for the structure and dynamics of protein solutions

Extensive computational studies of ubiquitin crowding with a special focus on protein hydration directly visible in dielectric spectra.

Complex Dynamics of Water in Protein Confinement

This paper studies single-molecule and collective dynamics of water confined in protein powders by means of molecular dynamics simulations. The single-particle dynamics show a modest retardation compared to the bulk but become highly stretched in the powder, with the stretching exponent of ≃0.2. The collective dynamics of the total water dipole are affected by intermolecular correlations inside water and by cross-correlations between the water and the protein. The dielectric spectrum of water in the powder has two nearly equal-amplitude peaks: a Debye peak with ≃16 ps relaxation time and a highly stretched peak with the relaxation time of ≃13 ns and a stretching exponent of ≃0.12. The slower relaxation component is not seen in the single-molecule correlation functions and can be assigned to elastic protein motions displacing water in the powder. The loss spectrum of the intermediate scattering function reported by neutron-scattering experiments is also highly stretched, with the high-frequency wing scaling according to a power law. Translational dynamics can become much slower in the powder than in the bulk but are overshadowed by the rotational loss in the overall loss spectrum of neutron scattering.

The dynamics of peptide-water interactions in dialanine: An ultrafast amide I 2D IR and computational spectroscopy study

We present a joint experimental and computational study of the dynamic interactions of dialanine (Ala-Ala) with water, comparing the results of ultrafast 2D IR and infrared transient absorption spectroscopy of its amide I vibration with spectra modeled from molecular dynamics (MD) simulations. The experimental data are analyzed to describe vibrational frequency fluctuations, vibrational energy relaxation, and chemical exchange processes. The origin of these processes in the same underlying fluctuating forces allows a common description in terms of the fluctuations and conformational dynamics of the peptide and associated solvent. By comparing computational spectroscopy from MD simulations with multiple force fields and water models, we describe how the dynamics of water hydrogen bond fluctuations and switching processes act as a source of friction that governs the dephasing and vibrational relaxation, and provide a description of coupled water and peptide motions that give rise to spectroscopic exchange processes.

Water Dynamics in the Hydration Shells of Biomolecules

The structure and function of biomolecules are strongly influenced by their hydration shells. Structural fluctuations and molecular excitations of hydrating water molecules cover a broad range in space and time, from individual water molecules to larger pools and from femtosecond to microsecond time scales. Recent progress in theory and molecular dynamics simulations as well as in ultrafast vibrational spectroscopy has led to new and detailed insight into fluctuations of water structure, elementary water motions, electric fields at hydrated biointerfaces, and processes of vibrational relaxation and energy dissipation. Here, we review recent advances in both theory and experiment, focusing on hydrated DNA, proteins, and phospholipids, and compare dynamics in the hydration shells to bulk water.

Towards a complete characterization of the δ-dispersion in dielectric spectroscopy of protein–water systems

The δ-process in dielectric spectroscopy of protein–water systems is computationally analyzed in great detail, in relation to other experiments.

Fabrication of a Horizontal and a Vertical Large Surface Area Nanogap Electrochemical Sensor

Nanogap sensors have a wide range of applications as they can provide accurate direct detection of biomolecules through impedimetric or amperometric signals. Signal response from nanogap sensors is dependent on both the electrode spacing and surface area. However, creating large surface area nanogap sensors presents several challenges during fabrication. We show two different approaches to achieve both horizontal and vertical coplanar nanogap geometries. In the first method we use electron-beam lithography (EBL) to pattern an 11 mm long serpentine nanogap (215 nm) between two electrodes. For the second method we use inductively-coupled plasma (ICP) reactive ion etching (RIE) to create a channel in a silicon substrate, optically pattern a buried 1.0 mm × 1.5 mm electrode before anodically bonding a second identical electrode, patterned on glass, directly above. The devices have a wide range of applicability in different sensing techniques with the large area nanogaps presenting advantages over other devices of the same family. As a case study we explore the detection of peptide nucleic acid (PNA)−DNA binding events using dielectric spectroscopy with the horizontal coplanar device.

Rotational dynamics of water molecules near biological surfaces with implications for nuclear quadrupole relaxation

Based on Molecular Dynamics simulations of two different systems, the protein ubiquitin dissolved in water and an AOT reverse micelle, we present a broad analysis of the single particle rotational dynamics of water. A comprehensive connection to NQR, which is a prominent experimental method in this field, is developed, based on a reformulation of its theoretical framework. Interpretation of experimental NQR results requires a model which usually assumes that the NQR experiences retardation only in the first hydration shell. Indeed, the present study shows that this first-shell model is correct. Moreover, previous experimental retardation factors are quantitatively reproduced. All of this is seemingly contradicted by results of other methods, e.g., dielectric spectroscopy, responsible for a long-standing debate in this field. Our detailed analysis shows that NQR omits important information contained in overall water dynamics, most notably, the retardation of the water dipole axis in the electric field exerted by a biological surface.

Hydration of proteins and nucleic acids: Advances in experiment and theory. A review

BACKGROUND

Most biological processes involve water, and the interactions of biomolecules with water affect their structure, function and dynamics.

SCOPE OF REVIEW

This review summarizes the current knowledge of protein and nucleic acid interactions with water, with a special focus on the biomolecular hydration layer. Recent developments in both experimental and computational methods that can be applied to the study of hydration structure and dynamics are reviewed, including software tools for the prediction and characterization of hydration layer properties.

MAJOR CONCLUSIONS

In the last decade, important advances have been made in our understanding of the factors that determine how biomolecules and their aqueous environment influence each other. Both experimental and computational methods contributed to the gradually emerging consensus picture of biomolecular hydration.

GENERAL SIGNIFICANCE

An improved knowledge of the structural and thermodynamic properties of the hydration layer will enable a detailed understanding of the various biological processes in which it is involved, with implications for a wide range of applications, including protein-structure prediction and structure-based drug design.

Broadband Dielectric Spectroscopy on Lysozyme in the Sub-Gigahertz to Terahertz Frequency Regions: Effects of Hydration and Thermal Excitation

We have performed dielectric spectral measurements of lysozyme in a solid state to understand the effects of hydration and thermal excitation on the low-frequency dynamics of protein. Dielectric measurements were performed under changing hydration conditions at room temperature in the frequency region of 0.5 GHz to 1.8 THz. We also studied the temperature dependence (83 to 293 K) of the complex dielectric spectra in the THz frequency region (0.3 THz to 1.8 THz). Spectral analyses were performed using model functions for the complex dielectric constant. To reproduce the spectra, we found that two relaxational modes and two underdamped modes are necessary together with an ionic conductivity term in the model function. At room temperature, the two relaxational modes have relaxation times of ∼20 ps and ∼100 ps. The faster component has a major spectral intensity and is suggested to be due to coupled water-protein motion. The two underdamped modes are necessary to reproduce the temperature dependence of the spectra in the THz region satisfactorily. The protein dynamical transition is a well-known behavior in the neutron-scattering experiment for proteins, where the atomic mean-square displacement shows a sudden change in the temperature dependence at approximately 200 K, when the samples are hydrated. A similar behavior has also been observed in the temperature dependence of the absorption spectra of protein in the THz frequency region. From our broadband dielectric spectroscopic measurements, we conclude that the increase in the spectral intensities in the THz region at approximately 200 K is due to a spectral blue-shift of the fast relaxational mode.

Water Determines the Structure and Dynamics of Proteins

Water is an essential participant in the stability, structure, dynamics, and function of proteins and other biomolecules. Thermodynamically, changes in the aqueous environment affect the stability of biomolecules. Structurally, water participates chemically in the catalytic function of proteins and nucleic acids and physically in the collapse of the protein chain during folding through hydrophobic collapse and mediates binding through the hydrogen bond in complex formation. Water is a partner that slaves the dynamics of proteins, and water interaction with proteins affect their dynamics. Here we provide a review of the experimental and computational advances over the past decade in understanding the role of water in the dynamics, structure, and function of proteins. We focus on the combination of X-ray and neutron crystallography, NMR, terahertz spectroscopy, mass spectroscopy, thermodynamics, and computer simulations to reveal how water assist proteins in their function. The recent advances in computer simulations and the enhanced sensitivity of experimental tools promise major advances in the understanding of protein dynamics, and water surely will be a protagonist.

Atomistic details of protein dynamics and the role of hydration water

BACKGROUND

The importance of protein dynamics for their biological activity is now well recognized. Different experimental and computational techniques have been employed to study protein dynamics, hierarchy of different processes and the coupling between protein and hydration water dynamics. Yet, understanding the atomistic details of protein dynamics and the role of hydration water remains rather limited.

SCOOP OF REVIEW

Based on overview of neutron scattering, molecular dynamic simulations, NMR and dielectric spectroscopy results we present a general picture of protein dynamics covering time scales from faster than ps to microseconds and the influence of hydration water on different relaxation processes.

MAJOR CONCLUSIONS

Internal protein dynamics spread over a wide time range from faster than picosecond to longer than microseconds. We suggest that the structural relaxation in hydrated proteins appears on the microsecond time scale, while faster processes present mostly motion of side groups and some domains. Hydration water plays a crucial role in protein dynamics on all time scales. It controls the coupled protein-hydration water relaxation on 10-100ps time scale. This process defines the friction for slower protein dynamics. Analysis suggests that changes in amount of hydration water affect not only general friction, but also influence significantly the protein's energy landscape.

GENERAL SIGNIFICANCE

The proposed atomistic picture of protein dynamics provides deeper understanding of various relaxation processes and their hierarchy, similarity and differences between various biological macromolecules, including proteins, DNA and RNA. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo".

Impact of secondary structure and hydration water on the dielectric spectrum of poly-alanine and possible relation to the debate on slaved versus slaving water

Using extensive molecular dynamics simulations of a single eight-residue alanine polypeptide in explicit water, we investigate the influence of α-helix formation on the dielectric spectrum. For this, we project long equilibrium trajectories into folded and unfolded states and thereby obtain dielectric spectra representative for disordered as well α-helical conformations without the need to change any other system parameter such as pH or temperature. The absorption spectrum in the α-helical state exhibits a feature in the sub-GHz range that is significantly stronger than in the unfolded state. As we show by an additional decomposition into peptide and water contributions, this slow dielectric mode, the relaxation time of which matches the independently determined peptide rotational relaxation time, is mostly caused by peptide polarization correlations, but also contains considerable contributions from peptide-water correlations. In contrast, the peptide spectral contribution shows no features in the GHz range where bulk water absorbs, not even in the peptide-water correlation part, we conclude that hydration water around Ala8 is more influenced by peptide polarization relaxation effects than the other way around. A further decomposition into water-self and water-collective polarization correlations shows that the dielectric response of hydration water is, in contrast to electrolyte solutions, retarded and that this retardation is mostly due to collective effects, the self relaxation of hydration water molecules is only slightly slowed down compared to bulk water. We find the dynamic peptide-water polarization cross correlations to be rather long-ranged and to extend more than one nanometer away from the peptide-water interface into the water hydration shell, in qualitative agreement with previous simulation studies and recent THz absorption experiments.

Salt effects on the picosecond dynamics of lysozyme hydration water investigated by terahertz time-domain spectroscopy and an insight into the Hofmeister series for protein stability and solubility

The addition of salts into protein aqueous solutions causes changes in protein solubility and stability, the ability of which is known to be ordered in the Hofmeister series.

A 9 MHz-2.4 GHz Fully Integrated Transceiver IC for a Microfluidic-CMOS Platform Dedicated to Miniaturized Dielectric Spectroscopy

This paper presents a fully integrated transceiver IC as part of a self-sustained, microfluidic-CMOS platform for miniaturized dielectric spectroscopy (DS) from MHz to GHz. Fabricated in AMS 0.35 μm 2P/4M RF CMOS, the transmitter (TX) part of the IC generates a single-tone sinusoidal signal with frequency tunability in the range of ~ 9 MHz-2.4 GHz to excite a three-dimensional (3D), parallel-plate, capacitive sensor with a floating electrode and 9 μL microfluidic channel for sample delivery. With a material-under-test (MUT) loaded into the sensor, the receiver (RX) part of the IC employs broadband frequency response analysis (bFRA) methodology to measure the amplitude and phase of the RF excitation signal after transmission through the sensor. A one-time, 6-point sensor calibration algorithm then extracts both the real and imaginary parts of the MUT complex permittivity, ϵr, from IC measurements of the sensor transmission characteristics in the voltage domain. The "sensor + IC" is fully capable of differentiating among de-ionized (DI) water, phosphate-buffered saline (PBS), and alcoholic beverages in tests conducted at four excitation frequencies of ∼ 50 MHz , 500 MHz, 1.5 GHz, and 2.4 GHz generated by the TX. Moreover, permittivity readings of PBS by the sensor interfaced with the IC at six excitation frequencies in the range of ~ 50 MHz-2.4 GHz are in excellent agreement (rms error of 1.7% (real) and 7.2% (imaginary)) with those from bulk-solution reference measurements by commercial benchtop equipment. The total power consumption of the IC is with 1.5 V (analog) and 3.3 V (digital) supplies.

Dynamics of protein hydration water

We present the frequency- and temperature-dependent dielectric properties of lysozyme solutions in a broad concentration regime, measured at subzero temperatures, and compare the results with measurements above the freezing point of water and on hydrated lysozyme powder. Our experiments allow examining the dynamics of unfreezable hydration water in a broad temperature range. The obtained results prove the bimodality of the hydration shell dynamics. In addition, we find indications of a fragile-to-strong transition of hydration water.

Hydration shells of proteins probed by depolarized light scattering and dielectric spectroscopy: orientational structure is significant, positional structure is not

Water interfacing hydrated proteins carry properties distinct from those of the bulk and is often described as a separate entity, a "biological water." We address here the question of which dynamical and structural properties of hydration water deserve this distinction. The study focuses on different aspects of the density and orientational fluctuations of hydration water and the ability to separate them experimentally by combining depolarized light scattering with dielectric spectroscopy. We show that the dynamics of the density fluctuations of the hydration shells reflect the coupled dynamics of the solute and solvent and do not require a special distinction as "biological water." The orientations of shell water molecules carry dramatically different physics and do require a separation into a sub-ensemble. Depending on the property considered, the perturbation of water's orientational structure induced by the protein propagates 3-5 hydration shells into the bulk at normal temperature.

Protein dynamics: from rattling in a cage to structural relaxation

We present an overview of protein dynamics based mostly on results of neutron scattering, dielectric relaxation spectroscopy and molecular dynamics simulations. We identify several major classes of protein motions on the time scale from faster than picoseconds to several microseconds, and discuss the coupling of these processes to solvent dynamics. Our analysis suggests that the microsecond backbone relaxation process might be the main structural relaxation of the protein that defines its glass transition temperature, while faster processes present some localized secondary relaxations. Based on the overview, we formulate a general picture of protein dynamics and discuss the challenges in this field.