An improved analytical model of protein dynamics at the sub-nanosecond timescale

Abstract

Thermal fluctuations of proteins at the ps-ns timescales are important for their functions and have extensively been studied using quasi-elastic neutron scattering (QENS). In general, QENS spectra of proteins are...

Phospholipid-induced secondary structural changes of lysozyme polymorphic amyloid fibrils studied using vacuum-ultraviolet circular dichroism

“…In general, interactions between molecules are strongly affected by molecular flexibility. 56 Therefore, in order to reveal the molecular mechanism of interactions between amyloid polymorphs and phospholipid membranes, not only their molecular structures but also their structural dynamics need to be characterized in detail, the latter of which is currently underway based on our recent analytical models of proteins 57 and phospholipid molecules 58–60 using neutron scattering. The present study thus lays a foundation to reveal the molecular mechanism of amyloid–phospholipid membrane interactions, which underlie the expression of cytotoxicity associated with the pathogenesis of various amyloidoses.…”

Investigation of the Dynamic Behaviour of H2 and D2 in a Kinetic Quantum Sieving System

“…After deducting the sample’s contribution from the raw data, the QENS spectra represented only adsorbed gas molecules. Lorentzian ,, peak was applied to represent the diffusion that happens during the adsorption process, and the Gaussian − equation, which represents the diffusion among the interstitial spaces of the lattices, was applied to model the movement of the molecules prevented from being adsorbed due to the quantum barrier. The data was then analyzed using DAVE to calculate the fitted half-width at half-maximum (HWHM) and elastic incoherent structure factor (EISF) , (eq ).…”

“…Additionally, the consistent HWHM of D 2 across the measured Q range further substantiates this interpretation. The fact that it can be accurately represented by a horizontal line serves as evidence for the highly localized or immobile phase of D 2 when confined within the pores. , …”

“…The fact that it can be accurately represented by a horizontal line serves as evidence for the highly localized or immobile phase of D 2 when confined within the pores. 50,61 An increase in temperature results in higher HWHM values since the atoms move faster with the kinetic energy of the molecules increase. For the localized H 2 (Lorentzian fitted, Figure 7a,b), the effect of temperature was pronounced compared to the jumping H 2 molecules (Gaussian fitted, Figure 7c,d) meaning the loss in kinetic energy affected the adsorbed molecules more compared to the atoms already undergoing quantum effect.…”