Protein Hydration Shell Research Articles

The unfolding effects on the protein hydration shell and partial molar volume: a computational study.

In this paper we apply the computational analysis recently proposed by our group to characterize the solvation properties of a native protein in aqueous solution, and to four model aqueous solutions of globular proteins in their unfolded states thus characterizing the protein unfolded state hydration shell and quantitatively evaluating the protein unfolded state partial molar volumes. Moreover, by using both the native and unfolded protein partial molar volumes, we obtain the corresponding variations (unfolding partial molar volumes) to be compared with the available experimental estimates. We also reconstruct the temperature and pressure dependence of the unfolding partial molar volume of Myoglobin dissecting the structural and hydration effects involved in the process.

The statistical characteristics of protein hydration shells: A computer simulation

Water molecules and the hydrogen-bond network are essential structural components of many biological macromolecular systems, such as nucleic acids, as well as fibrillar and globular proteins. The water density in the protein hydration shell is known to differ from that of bulk water. In this paper, spatial density as function of the distance from the protein surface is discussed. The electric potential function is considered in the same way. The resulting profiles of the bound water density are characterized by the presence of several distinct maxima due to the existence of the regular structure of bound water at distances over 7 A. The minor discrepancies that are observed in both radial functions for different proteins are explained by topological variations that were revealed earlier by studying the valence and dihedral angle-distribution functions for water bound to the same proteins.

Hydration shell of the TS-Kappa protein: Higher density than bulk water

The density of the water molecules in the presence of hydrophobic and hydrophilic amino acids was studied. Molecular dynamic simulation were employed to analyze the behavior of hydrated TS Kappa protein in SPC/E and TIP4P-2005 water models. The simulations were performed in the NPT ensemble with the Nosé–Hoover thermostat and the Parrinello–Rahman barostat. The density profile of these systems were obtained for different temperatures at constant pressure. Two complementary phenomena were observed. The protein–water system exhibits a temperature of maximum density lower than the temperature observed in the pure water system. The densities of the water in vicinity of the hydrophobic and hydrophilic sites are higher than the density of the water in the bulk. Our results suggest that interactions between protein and water and the water–water Hydrogen bonds are essential to the understanding of these phenomena.

Gallic acid‐based alkyl esters synthesis in a water‐free system by celite‐bound lipase of Bacillus licheniformisSCD11501

Gallic acid (3, 4, 5- trihydroxybenzoic acid) is an important antioxidant, anti-inflammatory, and radical scavenging agent. In the present study, a purified thermo-tolerant extra-cellular lipase of Bacillus licheniformis SCD11501 was successfully immobilized by adsorption on Celite 545 gel matrix followed by treatment with a cross-linking agent, glutaraldehyde. The celite-bound lipase treated with glutaraldehyde showed 94.8% binding/retention of enzyme activity (36 U/g; specific activity 16.8 U/g matrix; relative increase in enzyme activity 64.7%) while untreated matrix resulted in 88.1% binding/retention (28.0 U/g matrix; specific activity 8.5 U/g matrix) of lipase. The celite-bound lipase was successfully used to synthesis methyl gallate (58.2%), ethyl gallate (66.9%), n-propyl gallate (72.1%), and n-butyl gallate (63.8%) at 55(o) C in 10 h under shaking (150 g) in a water-free system by sequentially optimizing various reaction parameters. The low conversion of more polar alcohols such as methanol and ethanol into their respective gallate esters might be due to the ability of these alcohols to severely remove water from the protein hydration shell, leading to enzyme inactivation. Molecular sieves added to the reaction mixture resulted in enhanced yield of the alkyl ester(s). The characterization of synthesised esters was done through fourier transform infrared (FTIR) spectroscopy and (1) H NMR spectrum analysis.

In silico characterization of protein partial molecular volumes and hydration shells.

In this paper we present a computational approach, based on NVT molecular dynamics trajectories, that allows the direct evaluation of the protein partial molecular volume. The results obtained for five different globular proteins demonstrate the accuracy of this computational procedure in reproducing protein partial molecular volumes, providing quantitative characterization of the hydration shell in terms of the protein excluded volume, hydration shell ellipsoidal volume and related solvent density. Remarkably, our data indicate for the hydration shell a ≈10% solvent density increase with respect to the liquid water bulk density, in excellent agreement with the available experimental data.

Distribution of internal parameters of the hydration shell structure of proteins

The distribution functions of the valence and torsion angles of the hydration shells of proteins and bulk water are obtained by computer simulation. The obtained dependences are compared, and the differences between them are explained in terms of the topological regularities of the structures.

Enzyme activity in liquid lipase melts as a step towards solvent-free biology at 150 °C.

Water molecules play a number of critical roles in enzyme catalysis, including mass transfer of substrates and products, nucleophilicity and proton transfer at the active site, and solvent shell-mediated dynamics for accessing catalytically competent conformations. The pervasiveness of water in enzymolysis therefore raises the question concerning whether biocatalysis can be undertaken in the absence of a protein hydration shell. Lipase-mediated catalysis has been undertaken with reagent-based solvents and lyophilized powders, but there are no examples of molecularly dispersed enzymes that catalyse reactions at sub-solvation levels within solvent-free melts. Here we describe the synthesis, properties and enzyme activity of self-contained reactive biofluids based on solvent-free melts of lipase-polymer surfactant nanoconjugates. Desiccated substrates in liquid (p-nitrophenyl butyrate) or solid (p-nitrophenyl palmitate) form can be mixed or solubilized, respectively, into the enzyme biofluids, and hydrolysed in the solvent-free state. Significantly, the efficiency of product formation increases as the temperature is raised to 150 °C.

Dynamics of amorphous and partially crystallized proline solutions

Dynamics of water in the hydration shells of proteins in the no man's land temperature region is a currently debated topic. Previously [1], we proposed the use of lysine aqueous solutions as a model system to study the dynamics of water in a genuine biological solution at any temperature. We found that lysine can be completely dissolved in water without crystallization, making it possible to access the dynamics of amorphous water in a biological environment. By contrast, in this work we studied proline aqueous solutions, which partially crystallize upon cooling. We found similar results in the two systems: the presence of three water relaxations where the two slowest processes (processes 2 and 3) resemble the behavior of normal glasses. Moreover, we observed the change of a cooperative (α-like) water relaxation to a more local β-like water relaxation with decreasing temperature whereas a faster water relaxation process is also present. In addition, we studied amorphous samples in a restricted temperature interval, and also found three different dynamics (processes 3, 4 and 5). As in the case of the hydrated protein powders, the two faster dynamics (3 and 4) are coupled or slaved.

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.

Unusual structural properties of water within the hydration shell of hyperactive antifreeze protein.

Many hypotheses can be encountered explaining the mechanism of action of antifreeze proteins. One widespread theory postulates that the similarity of structural properties of solvation water of antifreeze proteins to ice is crucial to the antifreeze activity of these agents. In order to investigate this problem, the structural properties of solvation water of the hyperactive antifreeze protein from Choristoneura fumiferana were analyzed and compared with the properties of solvation water present at the surface of ice. The most striking observations concerned the temperature dependence of changes in water structure. In the case of solvation water of the ice-binding plane, the difference between the overall structural ordering of solvation water and bulk water diminished with increasing temperature; in the case of solvation water of the rest of the protein, the trend was opposite. In this respect, the solvation water of the ice-binding plane roughly resembled the hydration layer of ice. Simultaneously, the whole solvation shell of the protein displayed some features that are typical for solvation shells of many other proteins and are not encountered in the solvation water of ice. In the first place, this is an increase in density of water around the protein. The opposite is true for the solvation water of ice - it is less dense than bulk water. Therefore, even though the structure of solvation water of ice-binding plane and the structure of solvation water of ice seem to share some similarities, densitywise they differ.

Conformational Changes in Calcium‐Sensor Proteins under Molecular Crowding Conditions

Fundamental components of signaling pathways are switch modes in key proteins that control start, duration, and ending of diverse signal transduction events. A large group of switch proteins are Ca(2+) sensors, which undergo conformational changes in response to oscillating intracellular Ca(2+) concentrations. Here we use dynamic light scattering and a recently developed approach based on surface plasmon resonance to compare the protein dynamics of a diverse set of prototypical Ca(2+)-binding proteins including calmodulin, troponin C, recoverin, and guanylate cyclase-activating protein. Surface plasmon resonance biosensor technology allows monitoring conformational changes under molecular crowding conditions, yielding for each Ca(2+)-sensor protein a fingerprint profile that reflects different hydrodynamic properties under changing Ca(2+) conditions and is extremely sensitive to even fine alterations induced by point mutations. We see, for example, a correlation between surface plasmon resonance, dynamic light scattering, and size-exclusion chromatography data. Thus, changes in protein conformation correlate not only with the hydrodynamic size, but also with a rearrangement of the protein hydration shell and a change of the dielectric constant of water or of the protein-water interface. Our study provides insight into how rather small signaling proteins that have very similar three-dimensional folding patterns differ in their Ca(2+)-occupied functional state under crowding conditions.

THz time scale structural rearrangements and binding modes in lysozyme-ligand interactions

Predicting the conformational changes in proteins that are relevant for substrate binding is an ongoing challenge in the aim of elucidating the functional states of proteins. The motions that are induced by protein-ligand interactions are governed by the protein global modes. Our measurements indicate that the detected changes in the global backbone motion of the enzyme upon binding reflect a shift from the large-scale collective dominant mode in the unbound state towards a functional twisting deformation that assists in closing the binding cleft. Correlated motion in lysozyme has been implicated in enzyme function in previous studies, but detailed characterization of the internal fluctuations that enable the protein to explore the ensemble of conformations that ultimately foster large-scale conformational change is yet unknown. For this reason, we use THz spectroscopy to investigate the picosecond time scale binding modes and collective structural rearrangements that take place in hen egg white lysozyme (HEWL) when bound by the inhibitor (NAG)3. These protein thermal motions correspond to fluctuations that have a role in both selecting and sampling from the available protein intrinsic conformations that communicate function. Hence, investigation of these fast, collective modes may provide knowledge about the mechanism leading to the preferred binding process in HEWL-(NAG)3. Specifically, in this work we find that the picosecond time scale hydrogen-bonding rearrangements taking place in the protein hydration shell with binding modify the packing density within the hydrophobic core on a local level. These localized, intramolecular contact variations within the protein core appear to facilitate the large cooperative movements within the interfacial region separating the α- and β- domain that mediate binding. The THz time-scale fluctuations identified in the protein-ligand system may also reveal a molecular mechanism for substrate recognition.

Water dynamics in protein hydration shells: the molecular origins of the dynamical perturbation.

Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra.

Biopolymers and Biomacromolecules Solvent Dynamics

SummaryBiomacromolecules in solution modify the structure and the dynamics of the bulk water at the solute‐solvent interface. The ordering effects of biomolecules, in particular proteins, are extended for several angstroms. The role of the hydration shells around a protein has yet to be completely understood. Hydrated proteins maintain more dynamic flexibility with respect to the dried system, which is an important property in protein‐protein and/or protein‐ligand recognition processes. In this paper we propose a method for analyzing the dynamical properties of the water molecules present in the hydration shells of proteins. The approach is based on analysis of the effects of protein‐solvent interactions on water protons NMR relaxation parameters. The water proton spin‐lattice relaxation rate in protein solution is analyzed considering all possible dipolar contributions from coupled protons environments. The analysis of both selective and non‐selective water spin‐lattice relaxation rates allowed the calculation of the average effective correlation time for the water molecules at the protein interface and the evaluation of the long range ordering effect of the protein surface.

Terahertz Spectral Domain Computational Analysis of Hydration Shell of Proteins with Increasingly Complex Tertiary Structure

Solvation dynamics of biomolecules and water in a hydration shell have been studied by different methods; however, a clear picture of this process is not yet established. Terahertz (THz) studies of molecular behavior in binary solutions present unique information on the picosecond motions of molecules. A complete mechanical interpretation of THz absorption spectra associated with solvated biomolecules remains a challenging task. The Gromacs molecular dynamics (MD) simulation package is used here to examine the spectral characteristics of water molecules in close proximity to biomolecules using vibrational density of states (VDOS). Systematic simulation of solvation dynamics of proteins of different size and tertiary structure are presented. The following have been selected for analysis. They range from less to more complex tertiary structure (corresponding to an increased number of secondary structure elements): TRP-cage13-20 peptide, TRP-cage, BPTI, and lysozyme. The initial study predicts that the depth of the hydration shell, determined by VDOS of water, extends to approximately 10 Å and does not depend on protein size. Furthermore the integral perturbation coefficient of the whole solvation layer is found to be increased for larger proteins due to a higher retardation rate of water molecules in their shells. Differences in solvation dynamics among the proteins considered originate primarily from the water molecules buried in the interior of the protein and not from the on-surface molecules.

Analysis of Bulk and Hydration Water During Thermal Lysozyme Denaturation Using Raman Scattering

We describe a method for analyzing protein hydration by Raman spectroscopy on the model protein lysozyme. The analysis of the protein hydration shell is made possible by dissolving the protein in D2O, providing via isotopic exchange the uncoupled O – H stretching spectrum of water molecules early bound to the protein, which are thereafter spread into the solvent. The spectrum of the hydration water can be obtained by subtracting the spectrum of the contribution of D2O from that of the aqueous lysozyme solution in the intramolecular O – D stretching vibrations region (2,200–2,800 cm−1). Raman investigations were simultaneously carried out in the amide I region (1,500–1,800 cm−1) and in the O – D/H stretching spectrum (3,200–3,800 cm−1) during thermal denaturation of lysozyme, to analyze structural changes of the protein in relation to the physical properties of hydration water. It was found that the H-bond network of hydration water is slightly distorted compared to the bulk water at room temperature, with a loss of the tetrahedral local order. The difference between hydration and bulk water is significantly enhanced at T = 90 °C in the denaturated state of the protein. The quantification of water molecules in direct interaction with the protein provides the temperature dependence of the solvent-accessible surface area during the denaturation process. Both kinds of information on hydration water and protein structure lead to a detailed description and overall understanding of the mechanism of protein denaturation.

Librational fluctuations in protein glasses

Librational motions in the region of the protein “glass” (or dynamic) transition are analysed for spin-labelled haemoglobin, serum albumin and β-lactoglobulin by EPR spectroscopy. A discontinuity in the temperature dependence of the mean-square librational amplitude, <α2>, occurs in the region of 200K as found for the mean-square atomic displacement, <r2>, at the protein dynamic transition by Mössbauer spectroscopy and neutron scattering. The discontinuity in <α2> vs. T can be described by the Vogel–Tammann–Fulcher equation, implying a finite glass transition temperature. Above the dynamic transition, <α2> vs. 1/T can be approximated by the Arrhenius law with activation energies similar to those usually found for <r2>, and relaxation processes in glass-forming media and the hydration shells of proteins. Similar results are found for librational fluctuations of membranous Na,K-ATPase spin-labelled either on superficial SH groups or on those essential to activity.

Water-Protein Interactions: The Secret of Protein Dynamics

Water-protein interactions help to maintain flexible conformation conditions which are required for multifunctional protein recognition processes. The intimate relationship between the protein surface and hydration water can be analyzed by studying experimental water properties measured in protein systems in solution. In particular, proteins in solution modify the structure and the dynamics of the bulk water at the solute-solvent interface. The ordering effects of proteins on hydration water are extended for several angstroms. In this paper we propose a method for analyzing the dynamical properties of the water molecules present in the hydration shells of proteins. The approach is based on the analysis of the effects of protein-solvent interactions on water protons NMR relaxation parameters. NMR relaxation parameters, especially the nonselective (R 1 NS ) and selective (R 1 SE ) spin-lattice relaxation rates of water protons, are useful for investigating the solvent dynamics at the macromolecule-solvent interfaces as well as the perturbation effects caused by the water-macromolecule interactions on the solvent dynamical properties. In this paper we demonstrate that Nuclear Magnetic Resonance Spectroscopy can be used to determine the dynamical contributions of proteins to the water molecules belonging to their hydration shells.

Water mobility, denaturation and the glass transition in proteins

A quantitative mechanism is presented that links protein denaturation and the protein–water glass transition through an energy criterion for the onset of mobility of strong protein–water bonds. Differences in the zero point vibrational energy in the ordered and disordered bonded states allow direct prediction of the two transition temperatures. While the onset of water mobility induces the same change in heat capacity for both transitions, the order–disorder transition of denaturation also predicts the observed excess enthalpy gain. The kinetics of the water and protein components through the glass transition are predicted and compared with dielectric spectroscopy observations. The energetic approach provides a consistent mechanism for processes such as refolding and aggregation of proteins involved in protein maintenance and adaptability, as the conformational constraints of strong water–amide bonds are lost with increased molecular mobility. Moreover, we suggest that the ordered state of peptide–water bonds is induced at the point of protein synthesis and could play a key role in the function of proteins through the enhancement of electronic activity by ferroelectric domains in the protein hydration shell, which is lost upon denaturation.

Hydration dynamics of protein molecules in aqueous solution: Unity among diversity#

Dielectric dispersion and NMRD experiments have revealed that a significant fraction of water molecules in the hydration shell of various proteins do not exhibit any slowing down of dynamics. This is usually attributed to the presence of the hydrophobic residues (HBR) on the surface, although HBRs alone cannot account for the large amplitude of the fast component. Solvation dynamics experiments and also computer simulation studies, on the other hand, repeatedly observed the presence of a non-negligible slow component. Here we show, by considering three well-known proteins (lysozyme, myoglobin and adelynate kinase), that the fast component arises partly from the response of those water molecules that are hydrogen bonded with the backbone oxygen (BBO) atoms. These are structurally and energetically less stable than those with the side chain oxygen (SCO) atoms. In addition, the electrostatic interaction energy distribution (EIED) of individual water molecules (hydrogen bonded to SCO) with side chain oxygen atoms shows a surprising two peak character with the lower energy peak almost coincident with the energy distribution of water hydrogen bonded to backbone oxygen atoms (BBO). This two peak contribution appears to be quite general as we find it for lysozyme, myoglobin and adenylate kinase (ADK). The sharp peak of EIED at small energy (at less than 2 k B T) for the BBO atoms, together with the first peak of EIED of SCO and the HBRs on the protein surface, explain why a large fraction (~ 80%) of water in the protein hydration layer remains almost as mobile as bulk water. Significant slowness arises only from the hydrogen bonds that populate the second peak of EIED at larger energy (at about 4 kBT). Thus, if we consider hydrogen bond interaction alone, only 15–20% of water molecules in the protein hydration layer can exhibit slow dynamics, resulting in an average relaxation time of about 5–10 ps. The latter estimate assumes a time constant of 20–100 ps for the slow component. Interestingly, relaxation of water molecules hydrogen bonded to back bone oxygen exhibit an initial component faster than the bulk, suggesting that hydrogen bonding of these water molecules remains frustrated. This explanation of the heterogeneous and non-exponential dynamics of water in the hydration layer is quantitatively consistent with all the available experimental results, and provides unification among diverse features. This study reveals a bimodal electrostatic energy distribution of protein–water hydrogen bonds involving side chain oxygen and faster than bulk water hydrogen bond breaking dynamics of protein–water hydrogen bond involving backbone oxygen.