Time Scale Of Motion Research Articles

Melting and Bubble Formation in a Double-Stranded DNA: Microscopic Aspects of Early Base-Pair Opening Events and the Role of Water.

Despite its rigid structure, DNA is a remarkably flexible molecule. Flexibility is essential for biological functions (such as transcription and gene repair), which require large-amplitude structural changes such as bubble formation. The bubbles thus formed are required to have a certain stability of their own and survive long on the time scale of molecular motions. A molecular understanding of fluctuations leading to quasi-stable structures is not available. Through extensive atomistic molecular dynamics simulations, we identify a sequence of microscopic events that culminate in local bubble formation, which is initiated by base-pair (BP) opening, resulting from the cleavage of native BP hydrogen bonds (HBs). This is followed by the formation of mismatched BPs with non-native contacts. These metastable structures can either revert to their original forms or undergo a flipping transition to form a local bubble that can span across 3-4 BPs. A substantial distortion of the DNA backbone and a disruption of BP stacking are observed because of the structural changes induced by these local perturbations. We also explored how water helps in the entire process. A small number of water molecules undergo rearrangement to stabilize the intermediate states by forming HBs with DNA bases. Water thus acts as a lubricant that counteracts the enthalpic penalty suffered from the loss of native BP contacts. Although the process of bubble formation is reversible, the sequence of steps involved poses an entropic barrier, preventing it from easily retracing the path to the native state.

Anisotropic dynamics of an interfacial enzyme active site observed using tethered substrate analogs and ultrafast 2D IR spectroscopy.

Enzymes accelerate the rates of biomolecular reactions by many orders of magnitude compared to bulk solution, and it is widely understood that this catalytic effect arises from a combination of polar pre-organization and electrostatic transition state stabilization. A number of recent reports have also implicated ultrafast (femtosecond-picosecond) timescale motions in enzymatic activity. However, complications arising from spatially-distributed disorder, the occurrence of multiple substrate binding modes, and the influence of hydration dynamics on solvent-exposed active sites still confound many experimental studies. Here we use ultrafast two-dimensional infrared (2D IR) spectroscopy and covalently-tethered substrate analogs to examine dynamical properties of the promiscuous Pyrococcus horikoshii ene-reductase (PhENR) active site in two binding configurations mimicking proposed "inactive" and "reactive" Michaelis complexes. Spectral diffusion measurements of aryl-nitrile substrate analogs reveal an end-to-end tradeoff between fast (sub-ps) and slow (>5ps) motions. Fermi resonant aryl-azide analogs that sense interactions of coupled oscillators are described. Lineshape and quantum beat analyses of these probes reveal characteristics that correlate with aryl-nitrile frequency fluctuation correlation functions parameters, demonstrating that this anisotropy is an intrinsic property of the water-exposed active site, where countervailing gradients of fast dynamics and disorder in the reactant ground state are maintained near the hydration interface. Our results suggest several plausible factors leading to state-selective rate enhancement and promiscuity in PhENR. This study also highlights a strategy to detect perturbations to vibrational modes outside the transparent window of the mid-IR spectrum, which may be extended to other macromolecular systems.

Inertial effects in sedimenting suspensions of solid spheres in a liquid

Particle-resolved Direct Numerical Simulations have been performed on the gravitational settling of mono-disperse solid spheres in a viscous fluid and triply periodic domain. In a comprehensive study, the bulk solid volume concentration was varied from ϕ=0.5 to 30%. To study the effect of inertia, three different Galileo numbers were considered in the inertial regime, Ga=144, 178 and 210, for which a single settling sphere exhibits distinctly different wake and path characteristics. The particle/fluid mass density ratio was fixed at 1.5. We find that for ϕ=2−30% the suspension microstructure and dynamics depend predominantly on the bulk concentration. In qualitative agreement with previous studies in literature, three different sedimentation regimes can be distinguished: (1) the dilute concentration regime for ϕ≲2% with preferential settling of particles in vertical trains, (2) the moderate concentration regime for 2%≲ϕ≲10% with preferential settling of particles in horizontal pairs with an interparticle distance of ∼ 1.5 particle diameters, and (3) the dense concentration regime for ϕ≳10% with a nearly random (“hard-sphere”) distribution of the particles in space. The clustering of particles is dictated by, respectively, trapping of particles in the wake of other particles, a drafting–kissing–tumbling (DKT) instability by which two vertically aligned particles quickly reorient themselves into a horizontally aligned particle pair, and short-range multiparticle interactions through viscous lubrication and to a lesser extent collisions between particles. In all cases, hindered settling at a reduced speed is observed as compared to a single settling sphere. The well-known Richardson–Zaki relation for the mean sedimentation velocity appears valid only for the dense concentration regime. We provide ample evidence that in the dense regime the characteristic velocity and time scales of particle motion are proportional to gDp and Dp/g, respectively, with g the gravitational acceleration and Dp the particle diameter. We also observe an ω−3 scaling of the particle velocity spectra for ωDp/g≳0.4 and we propose a model to explain this scaling behavior, based on the inertial response of the particles to small-scale flow perturbations. Kinematic waves, i.e., vertically propagating plane waves in the local concentration field, are observed in all cases, though unrelated particle motions are responsible for significant loss of the spatio-temporal coherence of the waves. The wave speed was determined from repeated space–time autocorrelations of the local concentration field and appears in reasonable agreement with Kynch sedimentation theory using the Richardson–Zaki relation. The passage of kinematic waves causes perturbations in the particle velocity at a frequency that matches well with peak frequencies in the particle velocity spectra for concentrations up to ϕ≈10%. The time-lagged cross-correlation of the vertical and horizontal particle velocity suggests that kinematic waves may trigger DKT instabilities, while conversely DKT instabilities may be responsible for the onset of kinematic waves. Finally, we suggest that obstruction and perturbation of the particle wake by neighboring particles could offer an explanation for the small influence of the Galileo number on the suspension behavior for ϕ=2−30%.

Dynamic allostery in thrombin-a review.

Thrombin is a serine protease that catalyzes a large number of different reactions including proteolytic cleave of fibrinogen to make the fibrin clot (procoagulant activity), of the protease activated receptors (for cell signaling) and of protein C generating activated protein C (anticoagulant activity). Thrombin has an effector binding site called the anion binding exosite 1 that is allosterically coupled to the active site. In this review, we survey results from thermodynamic characterization of the allosteric coupling as well as hydrogen-deuterium exchange mass spectrometry to reveal which parts of the thrombin structure are changed upon effector binding and/or mutagenesis, and finally NMR spectroscopy to characterize the different timescales of motions elicited by the effectors. We also relate the experimental work to computational network analysis of the thrombin-thrombomodulin complex.

Stabilization of pre-existing neurotensin receptor conformational states by β-arrestin-1 and the biased allosteric modulator ML314

The neurotensin receptor 1 (NTS1) is a G protein-coupled receptor (GPCR) with promise as a drug target for the treatment of pain, schizophrenia, obesity, addiction, and various cancers. A detailed picture of the NTS1 structural landscape has been established by X-ray crystallography and cryo-EM and yet, the molecular determinants for why a receptor couples to G protein versus arrestin transducers remain poorly defined. We used 13CεH3-methionine NMR spectroscopy to show that binding of phosphatidylinositol-4,5-bisphosphate (PIP2) to the receptor’s intracellular surface allosterically tunes the timescale of motions at the orthosteric pocket and conserved activation motifs – without dramatically altering the structural ensemble. β-arrestin-1 further remodels the receptor ensemble by reducing conformational exchange kinetics for a subset of resonances, whereas G protein coupling has little to no effect on exchange rates. A β-arrestin biased allosteric modulator transforms the NTS1:G protein complex into a concatenation of substates, without triggering transducer dissociation, suggesting that it may function by stabilizing signaling incompetent G protein conformations such as the non-canonical state. Together, our work demonstrates the importance of kinetic information to a complete picture of the GPCR activation landscape.

Revealing Excited-State Trajectories on Potential Energy Surfaces with Atomic Resolution in Real Time.

Photoexcited molecular trajectories on potential energy surfaces (PESs) prior to thermalization are intimately connected to the photochemical reaction outcome. The excited-state trajectories of a diplatinum complex featuring photo-activated metal-metal σ-bond formation and associated Pt-Pt stretching motions were detected in real time using femtosecond wide-angle X-ray solution scattering. The observed motions correspond well with coherent vibrational wavepacket motions detected by femtosecond optical transient absorption. Two key coordinates for intersystem crossing have been identified, the Pt-Pt bond length and the orientation of the ligands coordinated with the platinum centers, along which the excited-state trajectories can be projected onto the calculated PESs of the excited states. This investigation has gleaned novel insight into electronic transitions occurring on the time scales of vibrational motions measured in real time, revealing ultrafast nonadiabatic or non-equilibrium processes along excited-state trajectories involving multiple excited-state PESs.

Revealing Excited‐State Trajectories on Potential Energy Surfaces with Atomic Resolution in Real Time

AbstractPhotoexcited molecular trajectories on potential energy surfaces (PESs) prior to thermalization are intimately connected to the photochemical reaction outcome. The excited‐state trajectories of a diplatinum complex featuring photo‐activated metal–metal σ‐bond formation and associated Pt−Pt stretching motions were detected in real time using femtosecond wide‐angle X‐ray solution scattering. The observed motions correspond well with coherent vibrational wavepacket motions detected by femtosecond optical transient absorption. Two key coordinates for intersystem crossing have been identified, the Pt−Pt bond length and the orientation of the ligands coordinated with the platinum centers, along which the excited‐state trajectories can be projected onto the calculated PESs of the excited states. This investigation has gleaned novel insight into electronic transitions occurring on the time scales of vibrational motions measured in real time, revealing ultrafast nonadiabatic or non‐equilibrium processes along excited‐state trajectories involving multiple excited‐state PESs.

Light ion dynamics in the topside ionosphere and plasmasphere during geomagnetic storms

Storm-time topside ionosphere plasma composition, especially the light ion fraction, is an important parameter which controls magnetosphere–ionosphere coupling, plays a part in the growth of local instabilities, and provides information about the ring current, ion upflow, movement of ionization and other important physical processes and parameters. Ion composition is difficult to estimate on fine scales as empirical models tend to be parametrized by fixed inputs, ignoring the role of memory in plasma, and to preferentially capture large scales, while ground radars have limited coverage. In particular, ionospheric composition measurements at mid-latitude are lacking. Here we show, using the new Swarm SLIDEM effective ion mass measurement, a superposed epoch analysis of storm-time dayside and nightside effective ion mass changes, demonstrating the extent and timescales of motion of the [O+]/[H+] transition height with the main phase of geomagnetic storms, as well as directly observing evidence for the latitude dependence of these dynamics.Graphical

Modeling of three-dimensional betatron oscillation and radiation reaction in plasma accelerators

Betatron oscillation is a commonly known phenomenon in laser or beam driven plasma wakefield accelerators. In the conventional model, the plasma wake provides a linear focusing force to a relativistic electron, and the electron oscillates in one transverse direction with the betatron frequency proportional to $1/\sqrt{\gamma}$, where $\gamma$ is the Lorentz factor of the electron. In this work, we extend this model to three-dimensional by considering the oscillation in two transverse and one longitudinal directions. The long-term equations, with motion in the betatron time scale averaged out, are obtained and compared with the original equations by numerical methods. In addition to the longitudinal and transverse damping due to radiation reaction which has been found before, we show phenomena including the longitudinal phase drift, betatron phase shift and betatron polarization change based on our long-term equations. This work can be highly valuable for future plasma based high-energy accelerators and colliders.

Long-time behavior of swimming Euglena gracilis in a heterogenous light environment.

The cell motion of Euglena gracilis in homogeneous and heterogeneous light environments was analyzed. Homogeneous and heterogeneous environments were prepared, with only a red color or with a red circle surrounded by brighter white regions, respectively. In a heterogeneous environment, the cells move into the red circle. Swimming orbits at 1/25s intervals for 120s were analyzed. The speed distribution of the 1 s-averaged cell orbits in a homogeneous environment was different from that in a heterogeneous environment, where the faster swimming fraction was enhanced. The relationship between speed and curvature radius was analyzed using a joint histogram. Histograms for short timescale motion, constructed by 1 s-averaged orbits, suggest that the cell swimming curves are not biased, while those for long timescale motion, constructed by 10 s-averaged orbits, suggest that the cell swimming curves are biased in the clockwise direction. Furthermore, the curvature radius determines the speed, which does not seem to depend on the light environment. The mean squared displacement in a heterogeneous environment is larger than that in a homogeneous environment on a 1s timescale. These results will be the basis for constructing a model for the long-time behavior of photomovement for light differences.

Bottom-Up Informed and Iteratively Optimized Coarse-Grained Non-Markovian Water Models with Accurate Dynamics.

Molecular dynamics (MD) simulations based on coarse-grained (CG) particle models of molecular liquids generally predict accelerated dynamics and misrepresent the time scales for molecular vibrations and diffusive motions. The parametrization of Generalized Langevin Equation (GLE) thermostats based on the microscopic dynamics of the fine-grained model provides a promising route to address this issue, in conjunction with the conservative interactions of the CG model obtained with standard coarse graining methods, such as iterative Boltzmann inversion, force matching, or relative entropy minimization. We report the application of a recently introduced bottom-up dynamic coarse graining method, based on the Mori-Zwanzig formalism, which provides accurate estimates of isotropic GLE memory kernels for several CG models of liquid water. We demonstrate that, with an additional iterative optimization of the memory kernels (IOMK) for the CG water models based on a practical iterative optimization technique, the velocity autocorrelation function of liquid water can be represented very accurately within a few iterations. By considering the distinct Van Hove function, we demonstrate that, with the presented methods, an accurate representation of structural relaxation can be achieved. We consider several distinct CG potentials to study how the choice of the CG potential affects the performance of bottom-up informed and iteratively optimized models.

Femtosecond-resolved imaging of a single-particle phase transition in energy-filtered ultrafast electron microscopy

Using an energy filter in transmission electron microscopy has enabled elemental mapping at the atomic scale and improved the precision of structural determination by gating inelastic and elastic imaging electrons, respectively. Here, we use an energy filter in ultrafast electron microscopy to enhance the temporal resolution toward the domain of atomic motion. Visualizing transient structures with femtosecond temporal precision was achieved by selecting imaging electrons in a narrow energy distribution from dense chirped photoelectron packets with broad longitudinal momentum distributions and thus typically exhibiting picosecond durations. In this study, the heterogeneous ultrafast phase transitions of vanadium dioxide (VO2) nanoparticles, a representative strongly correlated system, were filmed and attributed to the emergence of a transient, low-symmetry metallic phase caused by different local strains. Our approach enables electron microscopy to access the time scale of elementary nuclear motion to visualize the onset of the structural dynamics of matter at the nanoscale.

Slow methyl axes motions in perdeuterated villin headpiece subdomain probed by cross-correlated NMR relaxation measurements.

Protein methyl groups can participate in multiple motional modes on different time scales. Sub-nanosecond to nano-second time scale motions of methyl axes are particularly challenging to detect for small proteins in solutions. In this work we employ NMR relaxation interference between the methyl H-H/H-C dipole-dipole interactions [Sun&Tugarinov, J. Magn. Reason. 2012] to characterize methyl axes motions as a function of temperature in a small model protein villin headpiece subdomain (HP36), in which all non-exchangeable protons are deuterated with the exception of methyl groups of leucine and valine residues. The data points to the existence of slow motional modes of methyl axes on sub-nanosecond to nanosecond time scales. Further, at high temperatures for which the overall tumbling of the protein is on the order of 2 ns, we observe a coupling between the slow internal motion and the overall molecular tumbling, based on the anomalous order parameters and their temperature-dependent trends. The addition of 28%(w/w) glycerol-d8 increases the viscosity of the solvent and separates the timescales of internal and overall tumbling, thus permitting for another view of the necessity of the coupling assumption for these sites at high temperatures.

Increased slow dynamics defines ligandability of BTB domains

Efficient determination of protein ligandability, or the propensity to bind small-molecules, would greatly facilitate drug development for novel targets. Ligandability is currently assessed using computational methods that typically consider the static structural properties of putative binding sites or by experimental fragment screening. Here, we evaluate ligandability of conserved BTB domains from the cancer-relevant proteins LRF, KAISO, and MIZ1. Using fragment screening, we discover that MIZ1 binds multiple ligands. However, no ligands are uncovered for the structurally related KAISO or LRF. To understand the principles governing ligand-binding by BTB domains, we perform comprehensive NMR-based dynamics studies and find that only the MIZ1 BTB domain exhibits backbone µs-ms time scale motions. Interestingly, residues with elevated dynamics correspond to the binding site of fragment hits and recently defined HUWE1 interaction site. Our data argue that examining protein dynamics using NMR can contribute to identification of cryptic binding sites, and may support prediction of the ligandability of novel challenging targets.

Nanosecond pulsed discharge dynamics during passage of a transient laminar flame

This work presents an experimental study of a nanosecond repetitively pulsed dielectric barrier discharge interacting with a transient laminar flame propagating in a channel of height near the quenching distance of the flame. The discharge and the flame are of comparable size, and the discharge is favoured at a location where it is coupled with the reaction zone and burnt gas. The primary goal is to determine how the discharge evolves on the time scale of the flame passage, with the evolution driven by the changing gas state produced by the moving flame front. This work complements the large body of work investigating the effect of plasma to modify flame dynamics, by considering the other side of the interaction (how the discharge is modified by the flame). The hot gas produced by the combustion had a strong effect on the discharge, with the discharge preferentially forming in the region of hot combustion products. The per-pulse energy deposited by the discharge was measured and found to increase with the size of the discharge region and applied voltage. The pulse repetition frequency did not have a direct impact on the per-pulse energy, but did have an effect on the morphology and size of the discharge region. Two distinct discharge regimes were observed: uniform and filamentary (microdischarges). Higher pulse repetition frequencies and faster-cooling combustion products were more likely to transition to the filamentary regime, while lower frequencies and slower-cooling combustion products maintained a uniform regime for the entirety of the time the discharge was active. This regime transition was influenced by the ratio of the time scale of fluid motion to the pulse repetition rate (with no noticeable impact caused by the reduced electric field), with the filamentary regime preferentially observed in situations where this ratio was small. This work demonstrates the importance of considering how the discharge properties will change due to combustion processes in applications utilizing plasma assistance for transient combustion systems.

Thermal effects in short laser pulses: Suppression of wave collapse

An envelope model for short laser pulses is proposed. These pulses are short compared to fluid motion timescales and long compared to electron thermalization timescales. Numerical simulation of the thermal blooming of laser pulses at powers near the boundary of the self-focusing regime is presented in this model. The model includes terms representing the contributions of thermal blooming and the Kerr effect. In the context of the model, thermal blooming and the Kerr effect compete; Kerr driving and thermal blooming suppressing wave collapse. The dynamics of pulses whose energies are near the collapse threshold are numerically simulated.

Disorder in the Human Skp1 Structure is the Key to its Adaptability to Bind Many Different Proteins in the SCF Complex Assembly

Skp1(S-phase kinase-associated protein 1 - Homo sapiens) is an adapter protein of the SCF(Skp1-Cullin1-Fbox) complex, which links the constant components (Cul1-RBX) and the variable receptor (F-box proteins) in Ubiquitin E3 ligase. It is intriguing how Skp1 can recognise and bind to a variety of structurally different F-box proteins. For practical reasons, previous efforts have used truncated Skp1, and thus it has not been possible to track the crucial aspects of the substrate recognition process. In this background, we report the solution structure of the full-length Skp1 protein determined by NMR spectroscopy for the first time and investigate the sequence-dependent dynamics in the protein. The solution structure reveals that Skp1 has an architecture: β1-β2-H1-H2-L1–H3-L2-H4-H5-H6-H7(partially formed) and a long tail-like disordered C-terminus. Structural analysis using DALI (Distance Matrix Alignment) reveals conserved domain structure across species for Skp1. Backbone dynamics investigated using NMR relaxation suggest substantial variation in the motional timescales along the length of the protein. The loops and the C-terminal residues are highly flexible, and the (R2/R1) data suggests μs-ms timescale motions in the helices as well. Further, the dependence of amide proton chemical shift on temperature and curved profiles of their residuals indicate that the residues undergo transitions between native state and excited state. The curved profiles for several residues across the length of the protein suggest that there are native-like low-lying excited states, particularly for several C-terminal residues. Our results provide a rationale for how the protein can adapt itself, bind, and get functionally associated with other proteins in the SCF complex by utilising its flexibility and conformational sub-states.

Rotating Frame Relaxation in Magic Angle Spinning Solid State NMR, a Promising Tool for Characterizing Biopolymer Motion.

Magic angle spinning NMR rotating frame relaxation measurements provide a unique experimental window into biomolecules dynamics, as is illustrated by numerous recent applications. We discuss experimental strategies for this class of experiments, with a particular focus on systems where motion-driven modulation of the chemical shift interaction is the main mechanism for relaxation. We also explore and describe common strategies for interpreting the data sets to extract motion time scale, activation energy, and angle or order parameters from rotating frame relaxation data. Using model free analysis and numerical simulations, including time domain treatment, we explore conditions under which it is possible to obtain accurate and precise information about the time scales of motions. Overall, with rapid technical advances in solid state NMR, there is a bright future for this class of studies.

Enhanced diffusion in soft-walled channels with a periodically varying curvature.

The motion of particles along channels of finite width is known to be hindered by either the presence of energy barriers along the channel direction or by variations in the width of the channel in the transverse direction (rugged channel). Remarkably, when both features are present, they can interact to produce a counterintuitive result: adding energy barriers to a rugged channel can enhance the rate of diffusion along it. This is the result of competing energetic and entropic effects. Under the approximation of particles instantaneously in equilibrium in the transverse direction, one can tailor the energy barriers to the ruggedness to recover free diffusion. However, such fine-tuning and potentially restrictive approximations are not necessary to observe an enhanced rate of diffusion as we demonstrate by adding a range of (non-fine-tuned) energy barriers to a channel of sinusoidally varying curvature. Furthermore, this was observed to hold for systems with a finite characteristic timescale for motion in the transverse direction, thus, suggesting that the phenomenon lends itself to be exploited for practical applications.

Applying Crystallography and 19F NMR to investigate dynamics and partner protein interactions in a long chain Flavodoxin

Flavodoxin (Fld) is a small FMN containing protein that is involved in single electron transfer. The long‐chain flavodoxin in Rhodopseudomonas palustris bacteria replaces ferredoxin as a low‐potential electron carrier when iron is scarce. Thus it is proposed to interact with the bifurcating electron transfer flavoprotein (ETF) that yields low‐potential electrons. A surface loop on Fld interacts with another of Fld's partner proteins, so we hypothesize that it also mediates Fld's interaction with ETF. To monitor interactions with ETF directly and investigate dynamics in this loop, we are using 19F NMR in solution. 19F is hyperresponsive to changes in its chemical environment with a chemical shift range of >300 ppm. To provide a static reference point and assess structural heterogeneity, we are also exploiting X‐ray crystallography.In this study we selectively fluorinated the five tyrosine residues in Fld. We obtained resonance assignments from 19F spectra of Fld variants in which individual tyrosine residues have been replaced. We obtain well resolved signals for each residue, but the resonances' linewidths indicate dynamics that affects some resonances more than others. Y90 residue displays two resonances demonstrating two different conformations that interconvert slowly on an NMR time scale. Meanwhile the crystal structure solved at 2.1Å resolution reveals two molecules per asymmetric unit providing two perspectives on the details of the structure. The crystal symmetry is monoclinic in contrast to most of the other Flds, which are orthorhombic. Interestingly, the long loop bearing Y121 and Y123 is not well resolved in chain B of the crystal structure, and the NMR line of Y123 is exceptionally broad, both indicating that the loop is dynamic and capable of altering its conformation to accomodate binding to a partner protein.Future directions include monitoring the changes in the 19F NMR of the Fld when titrated with the partner protein, temperature dependence of the NMR spectrum and relaxation studies to evaluate time scales of motions.