Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Pressure effects on collective density fluctuations in water and protein solutions.

ABSTRACT: Neutron Brillouin scattering and molecular dynamics simulations have been used to investigate protein hydration water density fluctuations as a function of pressure. Our results show significant differences between the pressure and density dependence of collective dynamics in bulk water and in concentrated protein solutions. Pressure-induced changes in the tetrahedral order of the water HB network have direct consequences for the high-frequency sound velocity and damping coefficients, which we find to be a sensitive probe for changes in the HB network structure as well as the wetting of biomolecular surfaces.

SUBMITTER: Russo D

PROVIDER: S-EPMC5664497 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Pressure effects on collective density fluctuations in water and protein solutions.

Russo Daniela D Laloni Alessio A Filabozzi Alessandra A Heyden Matthias M

Proceedings of the National Academy of Sciences of the United States of America 20171009 43

Neutron Brillouin scattering and molecular dynamics simulations have been used to investigate protein hydration water density fluctuations as a function of pressure. Our results show significant differences between the pressure and density dependence of collective dynamics in bulk water and in concentrated protein solutions. Pressure-induced changes in the tetrahedral order of the water HB network have direct consequences for the high-frequency sound velocity and damping coefficients, which we f ...[more]

PMID: 29073065

Similar Datasets

Collective motion and density fluctuations in bacterial colonies.

Project description:Flocking birds, fish schools, and insect swarms are familiar examples of collective motion that plays a role in a range of problems, such as spreading of diseases. Models have provided a qualitative understanding of the collective motion, but progress has been hindered by the lack of detailed experimental data. Here we report simultaneous measurements of the positions, velocities, and orientations as a function of time for up to a thousand wild-type Bacillus subtilis bacteria in a colony. The bacteria spontaneously form closely packed dynamic clusters within which they move cooperatively. The number of bacteria in a cluster exhibits a power-law distribution truncated by an exponential tail. The probability of finding clusters with large numbers of bacteria grows markedly as the bacterial density increases. The number of bacteria per unit area exhibits fluctuations far larger than those for populations in thermal equilibrium. Such "giant number fluctuations" have been found in models and in experiments on inert systems but not observed previously in a biological system. Our results demonstrate that bacteria are an excellent system to study the general phenomenon of collective motion.

| S-EPMC2922251 | biostudies-literature

Density fluctuations, homeostasis, and reproduction effects in bacteria.

Project description:Single-cells grow by increasing their biomass and size. Here, we report that while mass and size accumulation rates of single Escherichia coli cells are exponential, their density and, thus, the levels of macromolecular crowding fluctuate during growth. As such, the average rates of mass and size accumulation of a single cell are generally not the same, but rather cells differentiate into increasing one rate with respect to the other. This differentiation yields a density homeostasis mechanism that we support mathematically. Further, we observe that density fluctuations can affect the reproduction rates of single cells, suggesting a link between the levels of macromolecular crowding with metabolism and overall population fitness. We detail our experimental approach and the "invisible" microfluidic arrays that enabled increased precision and throughput. Infections and natural communities start from a few cells, thus, emphasizing the significance of density-fluctuations when taking non-genetic variability into consideration.

| S-EPMC9050864 | biostudies-literature

Nuclear quantum effects and hydrogen bond fluctuations in water.

Project description:The hydrogen bond (HB) is central to our understanding of the properties of water. However, despite intense theoretical and experimental study, it continues to hold some surprises. Here, we show from an analysis of ab initio simulations that take proper account of nuclear quantum effects that the hydrogen-bonded protons in liquid water experience significant excursions in the direction of the acceptor oxygen atoms. This generates a small but nonnegligible fraction of transient autoprotolysis events that are not seen in simulations with classical nuclei. These events are associated with major rearrangements of the electronic density, as revealed by an analysis of the computed Wannier centers and (1)H chemical shifts. We also show that the quantum fluctuations exhibit significant correlations across neighboring HBs, consistent with an ephemeral shuttling of protons along water wires. We end by suggesting possible implications for our understanding of how perturbations (solvated ions, interfaces, and confinement) might affect the HB network in water.

| S-EPMC3785726 | biostudies-literature

On the role of water density fluctuations in the inhibition of a proton channel.

Project description:Hv1 is a transmembrane four-helix bundle that transports protons in a voltage-controlled manner. Its crucial role in many pathological conditions, including cancer and ischemic brain damage, makes Hv1 a promising drug target. Starting from the recently solved crystal structure of Hv1, we used structural modeling and molecular dynamics simulations to characterize the channel's most relevant conformations along the activation cycle. We then performed computational docking of known Hv1 inhibitors, 2-guanidinobenzimidazole (2GBI) and analogs. Although salt-bridge patterns and electrostatic potential profiles are well-defined and distinctive features of activated versus nonactivated states, the water distribution along the channel lumen is dynamic and reflects a conformational heterogeneity inherent to each state. In fact, pore waters assemble into intermittent hydrogen-bonded clusters that are replaced by the inhibitor moieties upon ligand binding. The entropic gain resulting from releasing these conformationally restrained waters to the bulk solvent is likely a major contributor to the binding free energy. Accordingly, we mapped the water density fluctuations inside the pore of the channel and identified the regions of maximum fluctuation within putative binding sites. Two sites appear as outstanding: One is the already known binding pocket of 2GBI, which is accessible to ligands from the intracellular side; the other is a site located at the exit of the proton permeation pathway. Our analysis of the waters confined in the hydrophobic cavities of Hv1 suggests a general strategy for drug discovery that can be applied to any ion channel.

| S-EPMC5206518 | biostudies-literature

Daytime soybean transcriptome fluctuations during water deficit stress

Project description:By sequencing 36 cDNA libraries with Illumina technology, we identified genes differentially expressed in soybean plants in response to water deficit and genes that were either up- or down-regulated in different periods of the day. Of 54,175 predicted soybean genes (Glyma v1.1), 35.52% exhibited expression oscillations in a 24 h period. This number increased to 39.23% when plants were submitted to water deficit. Major differences in gene expression were observed in the control plants from late day (ZT16) until predawn (ZT20) periods, indicating that gene expression oscillates during the course of 24 h in normal development. Under water deficit, dissimilarity increased in all time-periods, indicating that the applied stress influenced gene expression. Results suggest that time of day, as well as light and temperature oscillations that occur considerably affect the regulation of water deficit stress response in soybean plants.

2015-07-07 | GSE69469 | GEO

Experimental evidence characterizing pressure fluctuations at the seafloor-water interface induced by an earthquake.

Project description:An unusual combination of a laboratory experiment and in situ measurement of pressure fluctuations during an earthquake allows us to resolve some uncertainties in bottom pressure recorders (BPRs). In situ BPRs are usually contaminated by seismic waves during earthquakes; thus uncertainty still remains in the data obtained from BPRs. We examine in situ BPR data together with pressure variations produced by a dead weight (a pressure standard) in a laboratory experiment during an earthquake. The features recorded by the in situ BPRs are analysed as part of the overall experiment. We demonstrated that a 10-kg dead weight on a piston-cylinder across an area of 10 mm2 is capable of reproducing pressure fluctuations at a depth of 1000 m in the water column. The experiment also indicates that the internal mechanics of BPRs are isolated from incident seismic waves, suggesting that BPRs measure true in situ pressures without instrumentally induced disturbances. This constitutes the first instance in which pressure fluctuations recorded by in situ BPRs during an earthquake were reproduced using a pressure standard in the laboratory.

| S-EPMC6219582 | biostudies-literature

Daytime soybean transcriptome fluctuations during water deficit stress

2015-07-07 | E-GEOD-69469 | biostudies-arrayexpress

Do collective atomic fluctuations account for cooperative effects? Molecular dynamics studies of the U1A-RNA complex.

Project description:A complete understanding of gene expression relies on a comprehensive understanding of the protein-RNA recognition process. However, the study of protein-RNA recognition is complicated by many factors that contribute to both binding affinity and specificity, including structure, energetics, dynamical motions, and cooperative interactions. Several recent studies have suggested that energetic coupling between residues contributes to formation of the complex between the U1A protein and stem loop 2 of U1 snRNA as a consequence of a cooperative network of interactions. We have performed molecular dynamics simulations on the U1A-RNA complex, including explicit water and counterions, and analyzed the results based on the calculated positional cross-correlations of atomic fluctuations. The results indicate that cross-correlations calculated on a per residue basis agree well with the observed inter-residue cooperativity and predict that the networks identified to date may also be coupled into an extensive hyper-network that reflects the intrinsic rigidity of the RNA recognition motif. In addition, we report a comparison of the MD calculated correlations with the results of a positional covariance analysis based on the sequences of 330 RNA recognition motifs, including U1A. The calculated inter-residue cross-correlations agree very well with the results of the sites exhibiting positional covariance. Collectively, these results strongly support the hypothesis that collective fluctuations contribute to cooperativity and the corresponding observed thermodynamic coupling. Predictions of additional sites in U1A that may be involved in cooperative networks are advanced.

| S-EPMC2603296 | biostudies-literature

Ion-specificity and surface water dynamics in protein solutions.

Project description:Ion-specific effects at the protein surface are investigated here in light of the changes they infer to surface water dynamics, as observed by 1H NMR relaxation (at 20 MHz). Two well-known proteins, hen egg-white lysozyme (LZM) and bovine serum albumin (BSA), show qualitatively opposite trends in the transverse relaxation rate, R2(1H), along a series of different monovalent salt anions in the solution. Presence of salt ions increases R2(1H) in the case of lysozyme and diminishes it in the case of BSA. The effect magnifies for larger and more polarizable ions. The same contrasting effect between the two proteins is observed for protein-solvent proton exchange. This hints at subtle effects ion-binding might have on the accessibility of water surface sites on the protein. We suggest that the combination of the density of surface charge residues and surface roughness, at the atomic scale, dictates the response to the presence of salt ions and is proper to each protein. Further, a dramatic increase in R2(1H) is found to correlate closely with the formation of protein aggregates. The same ordering of salts in their ability to aggregate lysozyme, as seen previously by cloud point measurements, is reproduced here by R2(1H). 1H NMR relaxation data is supplemented by 35Cl and 14N NMR relaxation for selected salt ions to probe the ion-binding itself.

| S-EPMC6318450 | biostudies-literature

Gaussian and Non-Gaussian Solvent Density Fluctuations within Solute Cavities in a Water-like Solvent.

Project description:We report a Monte Carlo simulation study of length-scale-dependent density fluctuations in cavities in the coarse-grained mW representation of water at ambient conditions. Specifically, we use a combination of test particle insertion and umbrella sampling techniques to examine the full range of water occupation states in spherical cavities up to 6.3 Å radius in water. As has previously been observed, water density fluctuations are found to be effectively Gaussian in nature for atomic-scale cavities, but as the cavities get larger, they exhibit a non-Gaussian "fat-tail" distribution for lower occupancy states. We introduce a new statistical thermodynamic approach to analyze non-Gaussian fluctuations based on the radial distribution of waters about cavities with varying numbers of waters within its boundaries. It is shown that the onset of these non-Gaussian fluctuations is a result of the formation of a bubble within the cavity as it is emptied, which is accompanied by the adsorption of waters onto its interior surface. We revisit a theoretical framework we previously introduced to describe Gaussian fluctuations within cavities to incorporate bubble formation by including surface tension contributions. This modified theory accurately describes density fluctuations within both atomic and meso-scale cavities. Moreover, the theory predicts the transition from Gaussian to non-Gaussian fluctuations at a specific cavity occupancy, in excellent agreement with simulation observations.

| S-EPMC10902835 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data