On the interpretation of the temperature dependence of the mean square displacement (MSD) of protein, obtained from the incoherent neutron scattering

2018 ◽  
Vol 270 ◽  
pp. 218-226 ◽  
Author(s):  
Fumio Hirata
2010 ◽  
Vol 24 (3-4) ◽  
pp. 387-391 ◽  
Author(s):  
Salvatore Magazù ◽  
Federica Migliardo ◽  
Antonio Benedetto ◽  
Miguel Gonzalez ◽  
Claudia Mondelli

In the present contribution we present a new procedure for the Mean Square Displacement (MSD) determination from Elastic Incoherent Neutron Scattering (EINS) where the connection between the Self-Distribution Function (SDF) and the measured EINS intensity profile is highlighted. We show how the SDF procedure allows both the total and the partial MSD evaluation, through the total and the partial SDFs. The procedure is applied on EINS data collected, by the IN13 backscattering spectrometer (ILL, Grenoble), on aqueous mixtures of sucrose and trehalose.


2022 ◽  
Vol 8 ◽  
Author(s):  
Tatsuhito Matsuo ◽  
Alessio De Francesco ◽  
Judith Peters

Lysozyme amyloidosis is a hereditary disease, which is characterized by the deposition of lysozyme amyloid fibrils in various internal organs. It is known that lysozyme fibrils show polymorphism and that polymorphs formed at near-neutral pH have the ability to promote more monomer binding than those formed at acidic pH, indicating that only specific polymorphs become dominant species in a given environment. This is likely due to the polymorph-specific configurational diffusion. Understanding the possible differences in dynamical behavior between the polymorphs is thus crucial to deepen our knowledge of amyloid polymorphism and eventually elucidate the molecular mechanism of lysozyme amyloidosis. In this study, molecular dynamics at sub-nanosecond timescale of two kinds of polymorphic fibrils of hen egg white lysozyme, which has long been used as a model of human lysozyme, formed at pH 2.7 (LP27) and pH 6.0 (LP60) was investigated using elastic incoherent neutron scattering (EINS) and quasi-elastic neutron scattering (QENS). Analysis of the EINS data showed that whereas the mean square displacement of atomic motions is similar for both LP27 and LP60, LP60 contains a larger fraction of atoms moving with larger amplitudes than LP27, indicating that the dynamical difference between the two polymorphs lies not in the averaged amplitude, but in the distribution of the amplitudes. Furthermore, analysis of the QENS data showed that the jump diffusion coefficient of atoms is larger for LP60, suggesting that the atoms of LP60 undergo faster diffusive motions than those of LP27. This study thus characterizes the dynamics of the two lysozyme polymorphs and reveals that the molecular dynamics of LP60 is enhanced compared with that of LP27. The higher molecular flexibility of the polymorph would permit to adjust its conformation more quickly than its counterpart, facilitating monomer binding.


Fluids ◽  
2021 ◽  
Vol 6 (3) ◽  
pp. 111
Author(s):  
Leonid M. Ivanov ◽  
Collins A. Collins ◽  
Tetyana Margolina

Using discrete wavelets, a novel technique is developed to estimate turbulent diffusion coefficients and power exponents from single Lagrangian particle trajectories. The technique differs from the classical approach (Davis (1991)’s technique) because averaging over a statistical ensemble of the mean square displacement (<X2>) is replaced by averaging along a single Lagrangian trajectory X(t) = {X(t), Y(t)}. Metzler et al. (2014) have demonstrated that for an ergodic (for example, normal diffusion) flow, the mean square displacement is <X2> = limT→∞τX2(T,s), where τX2 (T, s) = 1/(T − s) ∫0T−s(X(t+Δt) − X(t))2 dt, T and s are observational and lag times but for weak non-ergodic (such as super-diffusion and sub-diffusion) flows <X2> = limT→∞≪τX2(T,s)≫, where ≪…≫ is some additional averaging. Numerical calculations for surface drifters in the Black Sea and isobaric RAFOS floats deployed at mid depths in the California Current system demonstrated that the reconstructed diffusion coefficients were smaller than those calculated by Davis (1991)’s technique. This difference is caused by the choice of the Lagrangian mean. The technique proposed here is applied to the analysis of Lagrangian motions in the Black Sea (horizontal diffusion coefficients varied from 105 to 106 cm2/s) and for the sub-diffusion of two RAFOS floats in the California Current system where power exponents varied from 0.65 to 0.72. RAFOS float motions were found to be strongly non-ergodic and non-Gaussian.


1972 ◽  
Vol 56 (7) ◽  
pp. 3217-3225 ◽  
Author(s):  
H. J. Prask ◽  
S. F. Trevino ◽  
J. D. Gault ◽  
K. W. Logan

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