Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Protein dynamical transition at 110 K.

ABSTRACT: Proteins are known to undergo a dynamical transition at around 200 K but the underlying mechanism, physical origin, and relationship to water are controversial. Here we report an observation of a protein dynamical transition as low as 110 K. This unexpected protein dynamical transition precisely correlated with the cryogenic phase transition of water from a high-density amorphous to a low-density amorphous state. The results suggest that the cryogenic protein dynamical transition might be directly related to the two liquid forms of water proposed at cryogenic temperatures.

SUBMITTER: Kim CU

PROVIDER: S-EPMC3248492 | biostudies-literature | 2011 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Protein dynamical transition at 110 K.

Kim Chae Un CU Tate Mark W MW Gruner Sol M SM

Proceedings of the National Academy of Sciences of the United States of America 20111213 52

Proteins are known to undergo a dynamical transition at around 200 K but the underlying mechanism, physical origin, and relationship to water are controversial. Here we report an observation of a protein dynamical transition as low as 110 K. This unexpected protein dynamical transition precisely correlated with the cryogenic phase transition of water from a high-density amorphous to a low-density amorphous state. The results suggest that the cryogenic protein dynamical transition might be direct ...[more]

PMID: 22167801

Similar Datasets

Dynamical transition and proteinquake in photoactive yellow protein.

Project description:Conformational dynamics in protein functioning covers a wide range of time scales from nanosecond fluctuations around a conformation to the large-amplitude conformational changes of milliseconds or longer. We illustrate a picture of cooperative coupling among such motions of different time scales in a model protein, photoactive yellow protein, by proposing a model that can consistently explain the experimental results on the photocycle of photoactive yellow protein. The model provides a scenario in which the global collective motion induced by the unfolding of the N-terminal domain promotes the loosening of the atomistic packing around the chromophore, which produces the favorable molecular environment for the photoexcited chromophore, thereby stabilizing the partially unfolded intermediate in the photocycle. The proteinquake, the large conformational change triggered by the local structural disturbance, plays a decisive role in controlling the kinetics of functioning.

| S-EPMC522019 | biostudies-literature

Dynamical Transition in Dehydrated Proteins.

Project description:Terahertz time-domain spectroscopy and differential scanning calorimetry were used to study the role of the dynamics of biomolecules decoupled from solvent effects. Lyophilized sucrose exhibited steadily increasing absorption with temperature as anharmonic excitations commenced as the system emerged from a deep minimum of the potential energy landscape where harmonic vibrations dominate. The polypeptide bacitracin and two globular proteins, lysozyme and human serum albumin, showed a more complex temperature dependence. Further analysis focused on the spectral signature below and above the boson peak. We found evidence of the onset of anharmonic motions that are characteristic for partial unfolding and molecular jamming in the dry biomolecules. The activation of modes of the protein molecules at temperatures comparable to the protein dynamical transition temperature was observed in the absence of hydration. No evidence of Fröhlich coherence, postulated to facilitate biological function, was found in our experiments.

| S-EPMC11000241 | biostudies-literature

Dynamical Quantum Phase Transition and Quasi Particle Excitation.

Project description:Dynamical phase transitions (DPTs) are signaled by the non-analytical time evolution of the dynamical free energy after quenching some global parameters in quantum systems. The dynamical free energy is calculated from the overlap between the initial and the time evolved states (Loschmidt amplitude). In a recent study it was suggested that DPTs are related to the equilibrium phase transitions (EPTs) (Heyl, M. et al. Phys. Rev. Lett. 110, 135704 (2013)). We here study an exactly solvable model, the extended XY model, the Loschmidt amplitude of which provides a counterexample. We show analytically that the connection between the DPTs and the EPTs does not hold generally. Analysing also the general compass model as a second example, assists us to propound the physical condition under which the DPT occurs without crossing the equilibrium critical point, and also no DPT by crossing the equilibrium critical point.

| S-EPMC6393518 | biostudies-literature

Threading-Induced Dynamical Transition in Tadpole-Shaped Polymers.

Project description:The relationship between polymer topology and bulk rheology remains a key question in soft matter physics. Architecture-specific constraints (or threadings) are thought to control the dynamics of ring polymers in ring-linear blends, which thus affects the viscosity to range between that of the pure rings and a value larger, but still comparable to, that of the pure linear melt. Here we consider qualitatively different systems of linear and ring polymers, fused together in "chimeric" architectures. The simplest example of this family is a "tadpole"-shaped polymer, a single ring fused to the end of a single linear chain. We show that polymers with this architecture display a threading-induced dynamical transition that substantially slows chain relaxation. Our findings shed light on how threadings control dynamics and may inform design principles for chimeric polymers with topologically tunable bulk rheological properties.

| S-EPMC8016395 | biostudies-literature

Dynamical phase transition in the open Dicke model.

Project description:The Dicke model with a weak dissipation channel is realized by coupling a Bose-Einstein condensate to an optical cavity with ultranarrow bandwidth. We explore the dynamical critical properties of the Hepp-Lieb-Dicke phase transition by performing quenches across the phase boundary. We observe hysteresis in the transition between a homogeneous phase and a self-organized collective phase with an enclosed loop area showing power-law scaling with respect to the quench time, which suggests an interpretation within a general framework introduced by Kibble and Zurek. The observed hysteretic dynamics is well reproduced by numerically solving the mean-field equation derived from a generalized Dicke Hamiltonian. Our work promotes the understanding of nonequilibrium physics in open many-body systems with infinite range interactions.

| S-EPMC4371957 | biostudies-literature

Water-Polymer Coupling Induces a Dynamical Transition in Microgels.

Project description:The long debated protein dynamical transition was recently found also in nonbiological macromolecules, such as poly- N-isopropylacrylamide (PNIPAM) microgels. Here, by using atomistic molecular dynamics simulations, we report a description of the molecular origin of the dynamical transition in these systems. We show that PNIPAM and water dynamics below the dynamical transition temperature T d are dominated by methyl group rotations and hydrogen bonding, respectively. By comparing with bulk water, we unambiguously identify PNIPAM-water hydrogen bonding as mainly responsible for the occurrence of the transition. The observed phenomenology thus crucially depends on the water-macromolecule coupling, being relevant to a wide class of hydrated systems, independently from the biological function.

| S-EPMC6416711 | biostudies-literature

Effect of water activity on the mechanical glass transition and dynamical transition of bacteria.

Project description:The purpose of this study was to clarify the glass-transition behavior of bacteria (Cronobacter sakazakii) as a function of water activity (aw). From the water sorption isotherm (298 K) for C. sakazakii, monolayer water content and monolayer aw were determined to be 0.0724 g/g-dry matter and 0.252, respectively. Mechanical relaxation was investigated at 298 K. In a higher aw range of over 0.529, the degree of mechanical relaxation increased with an increase in aw. From the effect of aw on the degree of mechanical relaxation, the mechanical awc (aw at which mechanical glass transition occurs at 298 K) was determined to be 0.667. Mean-square displacement of atoms in the bacteria was investigated by incoherent elastic neutron scattering. The mean-square displacement increased gradually with an increase in temperature depending on the aw of samples. From the linear fitting, two or three dynamical transition temperatures (low, middle, and high Tds) were determined at each aw. The low-Td values (142-158 K) were almost independent from aw. There was a minor effect of aw on the middle Td (214-234 K) except for the anhydrous sample (261 K). The high Td (252-322 K) largely increased with the decrease in aw. From the aw dependence of the high Td, the dynamical awc was determined to be 0.675, which was almost equivalent to the mechanical awc. The high Td was assumed to be the glass-transition temperature (Tg), and anhydrous Tg was estimated to be 409 K. In addition, molecular relaxation time (τ) of the bacteria was calculated as a function of aw. From the result, it is suggested that the progress of metabolism in the bacterial system requires a lower τ than approximately 6 × 10-5 s.

| S-EPMC9674979 | biostudies-literature

Dynamical transition of heat transport in a physical gel near the sol-gel transition.

Project description:We experimentally study heat transport in a gelatin solution near a reversible sol-gel transition point where viscosity strongly depends on temperature. We visualize the temperature field and velocity field using thermochromic liquid crystals and polystyrene latex particles, respectively. During the initial stages of heating, we find that heat transport undergoes a dynamical transition from conductive to convective. Subsequently, during later stages, we observe that the transport dynamics are much more complex than conventional thermal convections. At the sample's surface we observe the formation of stagnant domains, which lack fluid flow. Their formation is not due to the effects of local cooling. We determine that it is the dynamics of these stagnant domains that induce convective-conductive-convective transitions.

| S-EPMC4687040 | biostudies-literature

Theoretical Insights into 1D Transition-Metal Nanoalloys Grown on the NiAl(110) Surface.

Project description:Metallic nanoalloys are essential because of the synergistic effects rather than the merely additive effects of the metal components. Nanoscience is currently able to produce one-atom-thick linear atomic chains (LACs), and the NiAl(110) surface is a well-tested template used to build them. We report the first study based on ab initio density functional theory methods of one-dimensional transition-metal (TM) nanoalloys (i.e., LACs) grown on the NiAl(110) surface. This is a comprehensive and detailed computational study of the effect of alloying groups 10 and 11 metals (Pd, Pt, Cu, Ag, and Au) in LACs supported on the NiAl(110) surfaces to elucidate the structural, energetic, and electronic properties. From the TM series studied here, Pt appears to be an energy-stabilization species; meanwhile, Ag has a contrasting behavior. The work function changes because the alloying in LACs was satisfactorily explained from the explicit surface dipole moment calculations using an ab initio calculation-based approach, which captured the electron density redistribution upon building the LAC.

| S-EPMC6644807 | biostudies-literature

Transition from Reconstruction toward Thin Film on the (110) Surface of Strontium Titanate.

Project description:The surfaces of metal oxides often are reconstructed with a geometry and composition that is considerably different from a simple termination of the bulk. Such structures can also be viewed as ultrathin films, epitaxed on a substrate. Here, the reconstructions of the SrTiO3 (110) surface are studied combining scanning tunneling microscopy (STM), transmission electron diffraction, and X-ray absorption spectroscopy (XAS), and analyzed with density functional theory calculations. Whereas SrTiO3 (110) invariably terminates with an overlayer of titania, with increasing density its structure switches from n × 1 to 2 × n. At the same time the coordination of the Ti atoms changes from a network of corner-sharing tetrahedra to a double layer of edge-shared octahedra with bridging units of octahedrally coordinated strontium. This transition from the n × 1 to 2 × n reconstructions is a transition from a pseudomorphically stabilized tetrahedral network toward an octahedral titania thin film with stress-relief from octahedral strontia units at the surface.

| S-EPMC4834633 | 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