Further evidence that interfacial water is the main "driving force" of protein dynamics: a neutron scattering study on perdeuterated C-phycocyanin

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.

Vibrational Analysis of Hydration-Layer Water around Ubiquitin, Unpeeled Layer by Layer: Molecular-Dynamics Perceptions

Classical molecular-dynamics simulations have been performed to examine the interplay between ubiquitin and its hydration-water sub-layers, chiefly from a vibrational-mode and IR viewpoint-where we analyse individual sub-layers characteristics. The vibrational Density of States (VDOS) revealed that the first solvation sub-shell indicates a confined character therein. For layers of increasing distance from the surface, the adoption of greater bulk-like spectral behaviour was evident, suggesting that vibrational harmonisation to bulk occurs within 6-7 Å of the surface.

The thermodynamic theory of action potential propagation: a sound basis for unification of the physics of nerve impulses

The thermodynamic theory of action potential propagation challenges the conventional understanding of the nerve signal as an exclusively electrical phenomenon. Often misunderstood as to its basic tenets and predictions, the thermodynamic theory is virtually ignored in mainstream neuroscience. Addressing a broad audience of neuroscientists, we here attempt to stimulate interest in the theory. We do this by providing a concise overview of its background, discussion of its intimate connection to Albert Einstein's treatment of the thermodynamics of interfaces and outlining its potential contribution to the building of a physical brain theory firmly grounded in first principles and the biophysical reality of individual nerve cells. As such, the paper does not attempt to advocate the superiority of the thermodynamic theory over any other approach to model the nerve impulse, but is meant as an open invitation to the neuroscience community to experimentally test the assumptions and predictions of the theory on their validity.

Interfacial Water Many-Body Effects Drive Structural Dynamics and Allosteric Interactions in SARS-CoV-2 Main Protease Dimerization Interface

Following our previous work ( Chem. Sci. 2021, 12, 4889-4907), we study the structural dynamics of the SARS-CoV-2 Main Protease dimerization interface (apo dimer) by means of microsecond adaptive sampling molecular dynamics simulations (50 μs) using the AMOEBA polarizable force field (PFF). This interface is structured by a complex H-bond network that is stable only at physiological pH. Structural correlations analysis between its residues and the catalytic site confirms the presence of a buried allosteric site. However, noticeable differences in allosteric connectivity are observed between PFFs and non-PFFs. Interfacial polarizable water molecules are shown to appear at the heart of this discrepancy because they are connected to the global interface H-bond network and able to adapt their dipole moment (and dynamics) to their diverse local physicochemical microenvironments. The water-interface many-body interactions appear to drive the interface volume fluctuations and to therefore mediate the allosteric interactions with the catalytic cavity.

Protein-Water and Water-Water Long-Time Relaxations in Protein Hydration Water upon Cooling-A Close Look through Density Correlation Functions

We report results on the translational dynamics of the hydration water of the lysozyme protein upon cooling obtained by means of molecular dynamics simulations. The self van Hove functions and the mean square displacements of hydration water show two different temperature activated relaxation mechanisms, determining two dynamic regimes where transient trapping of the molecules is followed by hopping phenomena to allow to the structural relaxations. The two caging and hopping regimes are different in their nature. The low-temperature hopping regime has a time scale of tenths of nanoseconds and a length scale on the order of 2–3 water shells. This is connected to the nearest-neighbours cage effect and restricted to the supercooling, it is absent at high temperature and it is the mechanism to escape from the cage also present in bulk water. The second hopping regime is active at high temperatures, on the nanoseconds time scale and over distances of nanometers. This regime is connected to water displacements driven by the protein motion and it is observed very clearly at high temperatures and for temperatures higher than the protein dynamical transition. Below this temperature, the suppression of protein fluctuations largely increases the time-scale of the protein-related hopping phenomena at least over 100 ns. These protein-related hopping phenomena permit the detection of translational motions of hydration water molecules longly persistent in the hydration shell of the protein.

The molecular dynamics of bacterial spore and the role of calcium dipicolinate in core properties at the sub-nanosecond time-scale

Bacterial spores are among the most resistant forms of life on Earth. Their exceptional resistance properties rely on various strategies, among them the core singular structure, organization and hydration. By using elastic incoherent neutron scattering, we probed the dynamics of Bacillus subtilis spores to determine whether core macromolecular motions at the sub-nanosecond timescale could also contribute to their resistance to physical stresses. In addition, in order to better specify the role of the various spore components, we used different mutants lacking essential structure such as the coat (PS4150 mutant), or the calcium dipicolinic acid complex (CaDPA) located in the core (FB122 mutant). PS4150 allows to better probe the core’s dynamics, as proteins of the coat represent an important part of spore proteins, and FB122 gives information about the role of the large CaDPA depot for the mobility of core’s components. We show that core’s macromolecular mobility is not particularly constrained at the sub-nanosecond timescale in spite of its low water content as some dynamical characteristics as force constants are very close to those of vegetative bacteria such as Escherichia coli or to those of fully hydrated proteins. Although the force constants of the coatless mutant are similar to the wild-type’s ones, it has lower mean square displacements (MSDs) at high Q showing that core macromolecules are somewhat more constrained than the rest of spore components. However, no behavior reflecting the glassy state regularly evoked in the literature could be drawn from our data. As hydration and macromolecules’ mobility are highly correlated, the previous assumption, that core low water content might explain spores’ exceptional resistance properties seems unlikely. Thus, we confirm recent theories, suggesting that core water is mostly as free as bulk water and proteins/macromolecules are fully hydrated. The germination of spores leads to a much less stable system with a force constant of 0.1 N/m and MSDs ~2.5 times higher at low Q than in the dormant state. DPA has also an influence on core mobility with a slightly lower force constant for the DPA-less mutant than for the wild-type, and MSDs that are ~ 1.8 times higher on average than for the wild-type at low Q. At high Q, germinated and DPA-less spores were very similar to the wild-type ones, showing that DPA and core compact structure might influence large amplitude motions rather than local dynamics of macromolecules.

An introduction to neutrons for biology

The overlap of biology and neutron scattering remains a relatively narrow domain of research. This is partly due to the a priori maladjustment between real space problems and methods based on spatial and temporal correlations. In addition, some major assets of neutron scattering, such as isotopic substitution, can be tricky with biological molecules. More generally, a mutual lack of knowledge of the two concerned communities precluded potential rich interactions in early times. However, the situation changed to the point that, today, biology represents a substantial part of the research activity at neutron facilities. The purpose of this introduction is not to present one more overview of the subject of “neutron scattering” (excellent comprehensive articles are easily accessible to the interested readers [1–4]), but rather to facilitate the reading of the present book by introducing a few neutron scattering notions that may be useful for the community of biologists eventually less familiar with this technique.

Dynamics Properties of Photosynthetic Microorganisms Probed by Incoherent Neutron Scattering

Studies on the dynamical properties of photosynthetic membranes of land plants and purple bacteria have been previously performed by neutron spectroscopy, revealing a tight coupling between specific photochemical reactions and macromolecular dynamics. Here, we probed the intrinsic dynamics of biotechnologically useful mutants of the green alga Chlamydomonas reinhardtii by incoherent neutron scattering coupled with prompt chlorophyll fluorescence experiments. We brought to light that single amino acid replacements in the plastoquinone (PQ)-binding niche of the photosystem II D1 protein impair electron transport (ET) efficiency between quinones and confer increased flexibility to the host membranes, expanding to the entire cells. Hence, a more flexible environment in the PQ-binding niche has been associated to a less efficient ET. A similar function/dynamics relationship was also demonstrated in Rhodobacter sphaeroides reaction centers having inhibited ET, indicating that flexibility at the quinones region plays a crucial role in evolutionarily distant organisms. Instead, a different functional/dynamical correlation was observed in algal mutants hosting a single amino acid replacement residing in a D1 domain far from the PQ-binding niche. Noteworthy, this mutant displayed the highest degree of flexibility, and besides having a nativelike ET efficiency in physiological conditions, it acquired novel, to our knowledge, phenotypic traits enabling it to preserve a high maximal quantum yield of photosystem II photochemistry in extreme habitats. Overall, in the nanosecond timescale, the degree of the observed flexibility is related to the mutation site; in the picosecond timescale, we highlighted the presence of a more pronounced dynamic heterogeneity in all mutants compared to the native cells, which could be related to a marked chemically heterogeneous environment.

Analysis of elastic incoherent neutron scattering data beyond the Gaussian approximation

This work addresses the use of the Gaussian approximation as a common tool to extract atomic motions in proteins from elastic incoherent neutron scattering and whether improvements in data analysis and additional information can be obtained when going beyond that. We measured alpha-lactalbumin with different levels of hydration on three neutron backscattering spectrometers, to be able to resolve a wide temporal and spatial range for dynamics. We demonstrate that the Gaussian approximation gives qualitatively similar results to models that include heterogeneity, if one respects a certain procedure to treat the intercept of the elastic intensities with the momentum transfer axis. However, the inclusion of motional heterogeneity provides better fits to the data. Our analysis suggests an approach of limited heterogeneity, where including only two kinds of motions appears sufficient to obtain more quantitative results for the mean square displacement. Finally, we note that traditional backscattering spectrometers pose a limit on the lowest accessible momentum transfer. We therefore suggest that complementary information about the spatial evolution of the elastic intensity close to zero momentum transfer can be obtained using other neutron methods, in particular, neutron spin-echo together with polarization analysis.

Evidence of a low-temperature dynamical transition in concentrated microgels

A low-temperature dynamical transition has been reported in several proteins. We provide the first observation of a "protein-like" dynamical transition in nonbiological aqueous environments. To this aim, we exploit the popular colloidal system of poly-N-isopropylacrylamide (PNIPAM) microgels, extending their investigation to unprecedentedly high concentrations. Owing to the heterogeneous architecture of the microgels, water crystallization is avoided in concentrated samples, allowing us to monitor atomic dynamics at low temperatures. By elastic incoherent neutron scattering and molecular dynamics simulations, we find that a dynamical transition occurs at a temperature T _d ~ 250 K, independently from PNIPAM mass fraction. However, the transition is smeared out on approaching dry conditions. The quantitative agreement between experiments and simulations provides evidence that the transition occurs simultaneously for PNIPAM and water dynamics. The similarity of these results with hydrated protein powders suggests that the dynamical transition is a generic feature in complex macromolecular systems, independently from their biological function.

Description of Hydration Water in Protein (Green Fluorescent Protein) Solution

The structurally and dynamically perturbed hydration shells that surround proteins and biomolecules have a substantial influence upon their function and stability. This makes the extent and degree of water perturbation of practical interest for general biological study and industrial formulation. We present an experimental description of the dynamical perturbation of hydration water around green fluorescent protein in solution. Less than two shells (∼5.5 Å) were perturbed, with dynamics a factor of 2-10 times slower than bulk water, depending on their distance from the protein surface and the probe length of the measurement. This dependence on probe length demonstrates that hydration water undergoes subdiffusive motions (τ ∝ q^-2.5 for the first hydration shell, τ ∝ q^-2.3 for perturbed water in the second shell), an important difference with neat water, which demonstrates diffusive behavior (τ ∝ q^-2). These results help clarify the seemingly conflicting range of values reported for hydration water retardation as a logical consequence of the different length scales probed by the analytical techniques used.

Comparative thermal unfolding study of psychrophilic and mesophilic subtilisin-like serine proteases by molecular dynamics simulations

Molecular dynamics (MD) simulations of a subtilisin-like serine protease VPR from the psychrophilic marine bacterium Vibrio sp. PA-44 and its mesophilic homologue, proteinase K (PRK), have been performed for 20 ns at four different temperatures (300, 373, 473, and 573 K). The comparative analyses of MD trajectories reveal that at almost all temperatures, VPR exhibits greater structural fluctuations/deviations, more unstable regular secondary structural elements, and higher global flexibility than PRK. Although these two proteases follow similar unfolding pathways at high temperatures, VPR initiates unfolding at a lower temperature and unfolds faster at the same high temperatures than PRK. These observations collectively indicate that VPR is less stable and more heat-labile than PRK. Analyses of the structural/geometrical properties reveal that, when compared to PRK, VPR has larger radius of gyration (Rg), less intramolecular contacts and hydrogen bonds (HBs), more protein-solvent HBs, and smaller burial of nonpolar area and larger exposure of polar area. These suggest that the increased flexibility of VPR would be most likely caused by its reduced intramolecular interactions and more favourable protein-solvent interactions arising from the larger exposure of the polar area, whereas the enhanced stability of PRK could be ascribed to its increased intramolecular interactions arising from the better optimized hydrophobicity. The factors responsible for the significant differences in local flexibility between these two proteases were also analyzed and ascertained. This study provides insights into molecular basis of thermostability of homologous serine proteases adapted to different temperatures.

Variability of the Cyclin-Dependent Kinase 2 Flexibility Without Significant Change in the Initial Conformation of the Protein or Its Environment; a Computational Study

BACKGROUND

Protein flexibility, which has been referred as a dynamic behavior has various roles in proteins' functions. Furthermore, for some developed tools in bioinformatics, such as protein-protein docking software, considering the protein flexibility, causes a higher degree of accuracy. Through undertaking the present work, we have accomplished the quantification plus analysis of the variations in the human Cyclin Dependent Kinase 2 (hCDK2) protein flexibility without affecting a significant change in its initial environment or the protein per se.

OBJECTIVES

The main goal of the present research was to calculate variations in the flexibility for each residue of the hCDK2, analysis of their flexibility variations through clustering, and to investigate the functional aspects of the residues with high flexibility variations.

MATERIALS AND METHODS

Using Gromacs package (version 4.5.4), three independent molecular dynamics (MD) simulations of the hCDK2 protein (PDB ID: 1HCL) was accomplished with no significant changes in their initial environments, structures, or conformations, followed by Root Mean Square Fluctuations (RMSF) calculation of these MD trajectories. The amount of variations in these three curves of RMSF was calculated using two formulas.

RESULTS

More than 50% of the variation in the flexibility (the distance between the maximum and the minimum amount of the RMSF) was found at the region of Val-154. As well, there are other major flexibility fluctuations in other residues. These residues were mostly positioned in the vicinity of the functional residues. The subsequent works were done, as followed by clustering all hCDK2 residues into four groups considering the amount of their variability with respect to flexibility and their position in the RMSF curves.

CONCLUSIONS

This work has introduced a new class of flexibility aspect of the proteins' residues. It could also help designing and engineering proteins, with introducing a new dynamic aspect of hCDK2, and accordingly, for the other similar globular proteins. In addition, it could provide a better computational calculation of the protein flexibility, which is, especially important in the comparative studies of the proteins' flexibility.

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.

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.

Dynamics of human acetylcholinesterase bound to non-covalent and covalent inhibitors shedding light on changes to the water network structure

We investigated the effects of non-covalent reversible and covalent irreversible inhibitors on human acetylcholinesterase and human butyrylcholinesterase. Remarkably a non-covalent inhibitor, Huperzine A, has almost no effect on the molecular dynamics of the protein, whereas the covalently binding nerve agent soman renders the molecular structure stiffer in its aged form. The modified movements were studied by incoherent neutron scattering on different time scales and they indicate a stabilization and stiffening of aged human acetylcholinesterase. It is not straightforward to understand the forces leading to this strong effect. In addition to the specific interactions of the adduct within the protein, some indications point towards an extensive water structure change for the aged conjugate as water Bragg peaks appeared at cryogenic temperature despite an identical initial hydration state for all samples. Such a change associated to an apparent increase in free water volume upon aging suggests higher ordering of the hydration shell that leads to the stiffening of protein. Thus, several additive contributions seem responsible for the improved flexibility or stiffening effect of the inhibitors rather than a single interaction.

Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures

Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. The results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon-donor hydrogen bonds, OH-π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.

Water-Peptide Dynamics during Conformational Transitions

Transitions between metastable conformations of a dipeptide are investigated using classical molecular dynamics simulation with explicit water molecules. The distribution of the surrounding water at different moments before the transitions and the dynamical correlations of water with the peptide's configurational motions indicate that the water molecules represent an integral part of the molecular system during the conformational changes, in contrast with the metastable periods when water and peptide dynamics are essentially decoupled.

Importance of protein conformational motions and electrostatic anchoring sites on the dynamics and hydrogen bond properties of hydration water

The microscopic dynamic properties of water molecules present in the vicinity of a protein are expected to be sensitive to its local conformational motions and the presence of polar and charged groups at the surface capable of anchoring water molecules through hydrogen bonds. In this work, we attempt to understand such sensitivity by performing detailed molecular dynamics simulations of the globular protein barstar solvated in aqueous medium. Our calculations demonstrate that enhanced confinement at the protein surface on freezing its local motions leads to increasingly restricted water mobility with long residence times around the secondary structures. It is found that the inability of the surface water molecules to bind with the protein residues by hydrogen bonds in the absence of protein-water (PW) electrostatic interactions is compensated by enhanced water-water hydrogen bonds around the protein with uniform bulklike behaviors. Importantly, it is further noticed that in contrast to the PW hydrogen bond relaxation time scale, the kinetics of the breaking and formation of such bonds are not affected on freezing the protein's conformational motions.