A method to construct the dynamic landscape of a bio-membrane with experiment and simulation

Biomolecular function is based on a complex hierarchy of molecular motions. While biophysical methods can reveal details of specific motions, a concept for the comprehensive description of molecular dynamics over a wide range of correlation times has been unattainable. Here, we report an approach to construct the dynamic landscape of biomolecules, which describes the aggregate influence of multiple motions acting on various timescales and on multiple positions in the molecule. To this end, we use 13C NMR relaxation and molecular dynamics simulation data for the characterization of fully hydrated palmitoyl-oleoyl-phosphatidylcholine bilayers. We combine dynamics detector methodology with a new frame analysis of motion that yields site-specific amplitudes of motion, separated both by type and timescale of motion. In this study, we show that this separation allows the detailed description of the dynamic landscape, which yields vast differences in motional amplitudes and correlation times depending on molecular position.

Rotating-Frame Overhauser Transfer via Long-Lived Coherences

Solution-state distance restraints for protein structure determination with Ångström-level resolution rely on through-space transfer of magnetization between nuclear spins. Such magnetization transfers, named Overhauser effects, occur via dipolar magnetic couplings. We demonstrate improvements in magnetization transfer using long-lived coherences (LLCs)—singlet-triplet superpositions that are antisymmetric with respect to spin-permutation within pairs of coupled magnetic nuclei—as the magnetization source. Magnetization transfers in the presence of radio-frequency irradiation, known as ‘rotating-frame’ Overhauser effects (ROEs), are predicted by theory to improve by the use of LLCs; calculations are matched by preliminary experiments herein. The LLC-ROE transfers were compared to the transmission of magnetization via classical transverse routes. Long-lived coherences accumulate magnetization on an external third proton, K, with transfer rates that depended on the tumbling regime. I,S →K transfers in the LLC configuration for (I,S) are anticipated to match, and then overcome, the same transfer rates in the classical configuration as the molecular rotational correlation times increase. Experimentally, we measured the LLC-ROE transfer in dipeptide AlaGly between aliphatic protons in different residues K = Ala − Hα and (I,S) = Gly − Hα1,2 over a distance dK,I,S = 2.3 Å. Based on spin dynamics calculations, we anticipate that, for such distances, a superior transfer of magnetization occurs using LLC-ROE compared to classical ROE at correlation times above τC=10 ns. The LLC-ROE effect shows potential for improving structural studies of large proteins and offering constraints of increased precision for high-affinity protein-ligand complexes in slow tumbling in the liquid state.

Impact of Time Delay and Cross-Correlated Gaussian Colored Noises on Dynamical Characteristics and Stochastic Resonance for a Metapopulation System

In this paper, the regime shift behaviors between the prosperous state and the extinction state and stochastic resonance (SR) phenomenon for a metapopulation system subjected to time delay and correlated Gaussian colored noises are investigated. Through the numerical calculation of the modified potential function and the stationary probability density function (SPDF), one can make clearly the following results: Both multiplicative noise and noise correlation times can improve effectively the ecological stability and prolong the survival time of the system; while additive noise, time delay and noise correlation strength can weaken significantly the biological stability and speed up the extinction of the population. As for the signal-to-noise ratio (SNR), it is found that time delay, multiplicative noise and noise correlation strength can all impair the SR effect. Conversely, the two noise correlation times and additive noise are in favor of the improvement of the peak values of SNR. It is particularly worth mentioning that in the case of [Formula: see text], time delay [Formula: see text] and self-correlation time [Formula: see text] of the additive noise display exactly the opposite effect on the stimulation of the resonant peak in the SNR–[Formula: see text] plots.

On the settling of small grains in dusty discs: analysis and formulae

ABSTRACT Instruments achieve sharper and finer observations of micrometre-in-size dust grains in the top layers of young stellar discs. To provide accurate models, we revisit the theory of dust settling for small grains, when gas stratification, dust inertia, and finite correlation times for the turbulence should be handled simultaneously. We start from a balance of forces and derive distributions at steady state. Asymptotic expansions require caution since limits do not commute. In particular, non-physical bumpy distributions appear when turbulence is purely diffusive. This excludes very short correlation times for real discs, as predicted by numerical simulations.

Molecular Analysis of Retrogradation of Corn Starches

Changes of the molecular dynamics of water in 5% corn starch pastes and 5% systems composed of starch and non-starchy hydrocolloid were studied during short and long term retrogradation. Low Field NMR was used to record mean correlation times (τc) of water molecules. This molecular parameter reflects the rotation of water molecules within the network of paste. Starches of different amylose and amylopectin content were selected for this study. Comparison of the changes of τc shows how particular polymers bind water molecules. During 90 days of storage, over 50% increase in mean correlation time was recorded in pastes of starches with high amylose content. This suggests that the formation of polymeric network is controlled by amylose to which water is binding. Amylopectin was found to influence the mobility of water in the pastes to a lesser extent with changes in mean correlation times of approximately 10–15% over 90 days. On retrogradation, amylopectin, Arabic and xanthan gums hindered the formation of solid phase structures. Guar gum evoked an increase in mean correlation times of approximately 40–50% during the prolonged process of changes of the molecular dynamics of water. This indicates continued expansion of the polymeric network. Mean correlation time available from spin–lattice and spin–spin relaxation times can be useful in the analysis of the rotational vibrations of the water molecules in biopolymeric structures.

Simultaneous determination of deuteron quadrupole coupling constants and rotational correlation times: the model case of hydrogen bonded ionic liquids

We show that deuteron quadrupole coupling constants, and reorientational correlation times of molecular bonds N–D that are involved in hydrogen bonding, can be determined from NMR T1 relaxation time experiments simultaneously by assuming anisotropic motion.