The concept of effective correlation times for describing backbone motions in proteins. Part II. Tentative interpretation of the residue-specific correlation time in terms of overall rotation-diffusion

2005 ◽  
Vol 24A (1) ◽  
pp. 10-16 ◽  
Author(s):  
Sabine Bouguet-Bonnet ◽  
Pierre Mutzenhardt ◽  
Christian Roumestand ◽  
Daniel Canet
2017 ◽  
Vol 31 (28) ◽  
pp. 1750204 ◽  
Author(s):  
Yuangen Yao ◽  
Ming Yi ◽  
Dejia Hou

We study coherence resonance (CR) in the FitzHugh–Nagumo (FHN) neurons under cross-correlated sine-Wiener (CCSW) noises. It is numerically demonstrated that the reciprocal coefficient of variance of inter-spike intervals (R) increases with increasing amplitude or correlation time of CCSW noises, reaches the maximum at proper amplitude or correlation time, and then decreases, suggesting the appearance of CR phenomenon. In addition, the occurrence of CR is sensitive to a parameter range of amplitudes and correlation times of CCSW noises. Thus, CR can be controlled by regulating the amplitudes and correlation times of CCSW noises in the FHN excitable systems.


Polymers ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1764 ◽  
Author(s):  
Marek Sikora ◽  
Magdalena Krystyjan ◽  
Anna Dobosz ◽  
Piotr Tomasik ◽  
Katarzyna Walkowiak ◽  
...  

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.


2018 ◽  
Author(s):  
N. Kozer ◽  
A. H.A. Clayton

AbstractThe epidermal growth factor receptor (EGFR) is a membrane protein that regulates cell proliferation, differentiation and survival, and is a drug target for cancer therapy. Ligand-induced activation of the EGFR kinase is generally regarded to require ligand-bound-dimers, while phosphorylation and downstream signalling is modulated by higher-order oligomers. Recent work has unveiled changes in EGFR dynamics from ligand-induced dimerization in membranes extracted from cells, however less is known about the changes in EGFR dynamics that accompany the ligand-induced dimer to tetramer transition in a live cell environment. In the present report, we determine the dynamics of a c-terminal GFP tag attached to EGFR in the unliganded dimer and in the liganded tetramer by means of dynamic depolarization microscopy. We made use of a novel analysis method, the single-frequency polarized phasor ellipse approach, to extract two correlation times on the subnanosecond and super-nanosecond timescales, respectively. EGF binding to the EGFR-GFP dimer lengthened the sub-nanosecond correlation time (from 0.1ns to 1.3ns), and shortened the supernanosecond correlation time (from 210ns to 56ns) of the c-terminal GFP probe. The sub-nanosecond depolarization processes were assigned to electronic energy migration between proximal GFPs in the EGFR dimer or oligomer, while the super-nanosecond correlation times were assigned to nanosecond fluctuations of the GFP probe in the EGFR complex. Accordingly, these results show that ligand binding to the extracellular domain increased the average separation between the c-terminal tags and increased their rotational mobility. We propose that the dynamics are linked to an inhibitory function of the c-terminal tail in the un-liganded dimer and to the requirement of facile stochastic switching between kinase activation and cytoplasmic adaptor/effector binding in the active tetramer.


1977 ◽  
Vol 32 (12) ◽  
pp. 1571-1574 ◽  
Author(s):  
Hirofumi Okabayashi ◽  
Koji Ivihara ◽  
Masataka Okuyama

Abstract The rotational correlation times of two long-chain nitro­ xide spin probes (5-PASL and 1-LASL) were measured in the vicinity of the second critical micelle concentration of cetyltriniethylammonium bromide (CTAB) solutions. The radical part of 5-PASL is situated at the δ-carbon and that of 1-LASL in the polar head.In the 5-PASL-solubilized CTAB solutions a transition of the correlation time due to a sphere-rod transition seems to occur, while in the 1-LASL-solubilized CTAB solutions no such transition occurs. This reveals that the hydrophobic part around the δ-carbon of the probe becomes more rigid as a result of the micellar shape-variation while the hydrophilic part of 1-LASL is not so much restricted by the shape variation.


2017 ◽  
Vol 40 (1) ◽  
pp. 1-10
Author(s):  
Karol Monkos

Abstract One of the rarely used ways of determining the overall motion correlation time of proteins is method based on the Maxwell effect. This effect consists in the appearance of a stimulated birefringence in liquids or solutions and induced by the mechanical force like shear stress in a streamline flow. To determine the overall motion correlation time for protein in dilute solution is sufficient to know the molecular mass and the ratio of the principal axes of protein, and an intrinsic viscosity. The intrinsic viscosity has been measured using an Ubbelohde-type capillary microviscometer immersed in a water-bath controlled thermostatically in the range from 5°C to 45°C for six mammalian albumins. To check the influence of solution pH on the overall motion correlation time the intrinsic viscosity value of the human serum albumin in solutions at the isoelectric point and beyond of it was measured. The thus obtained correlation times were compared with the times determined on the basis of the Debye-Stokes-Einstein equation.


1989 ◽  
Vol 54 (11) ◽  
pp. 3011-3024 ◽  
Author(s):  
Vlastimil Fidler ◽  
Stefan Vajda ◽  
Zuzana Limpouchová ◽  
Jiří Dvořák ◽  
Karel Procházka ◽  
...  

The methodology of polarization time-resolved fluorometry and interpretation of its results are outlined at a general level, and the measurement on and use of facilities of the Edinburgh Instruments Model 299T apparatus are discussed in detail. The dynamics of conformational changes in chains of poly(methacrylic acid) containing covalently bonded dansyl labels are studied in aqueous solutions at various pH. It is shown that at pH > 6, the shorter effective rational correlation time τr < 2 ns corresponds to the rotation of the free dansyl label about bonds by which it is attached to the polymeric chain; at pH < 4 the longer effective rational correlation time τr = 20-26 ns corresponds to the rotation of the compact spherical formation constituted by a part of the collapsed polymeric chain in which the label is fixed and whose relative molecular mass is approx. 15 000-20 000.


2020 ◽  
Vol 44 (44) ◽  
pp. 19393-19403
Author(s):  
Krishna Kishor Dey ◽  
Manasi Ghosh

The correlation between the structure and dynamics of omeprazole is portrayed by extracting CSA parameters through the 13C 2DPASS CP-MAS SSNMR experiment, site specific spin–lattice relaxation time by Torchia CP experiment, and calculation of the molecular correlation time.


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