scholarly journals Searching for Correlated Conformational Dynamics: Analysis of the NMR Relaxation Dispersions with Akaike's Information Theory and Hierarchical Clustering

2017 ◽  
Author(s):  
Evgenii L. Kovrigin
Keyword(s):  
Conformational Dynamics ◽  
Nmr Relaxation ◽  
Hierarchical Cluster ◽  
Information Criteria ◽  
Relaxation Dispersion ◽  
Spin Groups ◽  
Dispersion Data ◽  
Poorly Soluble ◽  
The Difference ◽  
Best Fit

ABSTRACT:In this manuscript, I am proposing an approach for identification of correlated exchange in proteins via analysis of the NMR relaxation dispersion data. For a set of spins experiencing exchange, every relaxation dispersion datasets is fit individually and then—globally while paired with every other dataset. The corrected Akaike’ s Information Criteria (AICc) for individual and global fits are used to evaluate the likelihood of two spins to report on the same dynamic event. Application of hierarchical cluster analysis reveals correlated spin groups using the difference in AICcs as a measure of similarity within the pairs. This approach to detection of correlated dynamics is independent of accuracy of best-fit parameters rendering it less sensitive to experimental noise. High throughput and the absence of the operator bias might make it applicable to a relatively lower quality NMR relaxation dispersion data from large and poorly soluble systems.

Microsecond Time-Scale Conformational Exchange in Proteins: Using Long Molecular Dynamics Trajectory To Simulate NMR Relaxation Dispersion Data

2012 ◽  
Vol 134 (5) ◽  
pp. 2555-2562 ◽  
Author(s):  
Yi Xue ◽  
Joshua M. Ward ◽  
Tairan Yuwen ◽  
Ivan S. Podkorytov ◽  
Nikolai R. Skrynnikov
Keyword(s):  
Molecular Dynamics ◽  
Time Scale ◽  
Nmr Relaxation ◽  
Relaxation Dispersion ◽  
Conformational Exchange ◽  
Dispersion Data ◽  
Molecular Dynamics Trajectory

scholarly journals relax: the analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data

2014 ◽  
Vol 30 (15) ◽  
pp. 2219-2220 ◽  
Author(s):  
Sébastien Morin ◽  
Troels E Linnet ◽  
Mathilde Lescanne ◽  
Paul Schanda ◽  
Gary S Thompson ◽  
...  
Keyword(s):  
Nmr Relaxation ◽  
Relaxation Dispersion ◽  
Kinetics And Thermodynamics ◽  
Dispersion Data

Investigation of Molecular Motion in Smectic Phases of the Liquid Crystal TBBA by NMR Relaxation Dispersion

1980 ◽  
Vol 35 (9) ◽  
pp. 924-929 ◽  
Author(s):  
Th. Mugele ◽  
V. Graf ◽  
W. Wülfel
Keyword(s):  
Nmr Relaxation ◽  
Larmor Frequency ◽  
Proton Spin ◽  
Relaxation Dispersion ◽  
Self Diffusion ◽  
Smectic Phases ◽  
Field Cycling ◽  
The Difference ◽  
Nmr Methods ◽  
Fast Field

Abstract The proton spin T1 relaxation dispersion in the smectic A and C phase of TBBA, and for comparison also in the nematic phase, have been studied using time dependent fast field-cycling techniques in the Larmor frequency range from νp = 100 Hz to 44 MHz. Our measurements considerably extend recent ones by Blinc et al., performed with other NMR methods for frequencies ≧ 140 kHz. The new experimental data are consistent with the reported ones for Sm C but not for Sm A, the difference being that the essential T1 dispersion observed with our technique occurs at much lower frequencies, namely below about 100 kHz. As a consequence, the relaxation dispersion for both smectic phases looks very similar. It can be described quantitatively in terms of relaxation by "nematic-like" order fluctuations, self-diffusion, and by a third molecular mechanism with (for simplicity) Debve-like power spectrum, which is possibly a second type of order fluctuation or a molecular rotation about the short axis. The analysis reveals surprisingly far going parallels between the spin relaxation of simple smectics and that of high-temperature nematics like PAA.

scholarly journals Conformational dynamics of yeast calmodulin in the Ca2+-bound state probed using NMR relaxation dispersion

FEBS Letters ◽  
2012 ◽  
Vol 586 (16) ◽  
pp. 2548-2554 ◽  
Author(s):  
Kenji Ogura ◽  
Hideyasu Okamura ◽  
Masato Katahira ◽  
Etsuko Katoh ◽  
Fuyuhiko Inagaki
Keyword(s):  
Conformational Dynamics ◽  
Nmr Relaxation ◽  
Bound State ◽  
Relaxation Dispersion

scholarly journals relax: the analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data

2019 ◽  
Vol 35 (20) ◽  
pp. 4205-4205
Author(s):  
Sébastien Morin ◽  
Troels E Linnet ◽  
Mathilde Lescanne ◽  
Paul Schanda ◽  
Gary S Thompson ◽  
...  
Keyword(s):  
Nmr Relaxation ◽  
Relaxation Dispersion ◽  
Kinetics And Thermodynamics ◽  
Dispersion Data

scholarly journals Automated NMR relaxation dispersion data analysis using NESSY

2011 ◽  
Vol 12 (1) ◽  
Author(s):  
Michael Bieri ◽  
Paul R Gooley
Keyword(s):  
Data Analysis ◽  
Nmr Relaxation ◽  
Relaxation Dispersion ◽  
Dispersion Data

Theoretical classification of exchange geometries from the perspectives of NMR relaxation dispersion

2021 ◽  
pp. 107003
Author(s):  
Fa-An Chao ◽  
Yue Zhang ◽  
R. Andrew Byrd
Keyword(s):  
Nmr Relaxation ◽  
Relaxation Dispersion

Conformational dynamics and thermodynamics of protein–ligand binding studied by NMR relaxation

2012 ◽  
Vol 40 (2) ◽  
pp. 419-423 ◽  
Author(s):  
Mikael Akke
Keyword(s):  
Ligand Binding ◽  
Bound States ◽  
Conformational Dynamics ◽  
Nmr Relaxation ◽  
Titration Calorimetry ◽  
Conformational Entropy ◽  
Chain Order ◽  
Ligand Interactions ◽  
Galectin 3 ◽  
Relaxation Experiments

Protein conformational dynamics can be critical for ligand binding in two ways that relate to kinetics and thermodynamics respectively. First, conformational transitions between different substates can control access to the binding site (kinetics). Secondly, differences between free and ligand-bound states in their conformational fluctuations contribute to the entropy of ligand binding (thermodynamics). In the present paper, I focus on the second topic, summarizing our recent results on the role of conformational entropy in ligand binding to Gal3C (the carbohydrate-recognition domain of galectin-3). NMR relaxation experiments provide a unique probe of conformational entropy by characterizing bond-vector fluctuations at atomic resolution. By monitoring differences between the free and ligand-bound states in their backbone and side chain order parameters, we have estimated the contributions from conformational entropy to the free energy of binding. Overall, the conformational entropy of Gal3C increases upon ligand binding, thereby contributing favourably to the binding affinity. Comparisons with the results from isothermal titration calorimetry indicate that the conformational entropy is comparable in magnitude to the enthalpy of binding. Furthermore, there are significant differences in the dynamic response to binding of different ligands, despite the fact that the protein structure is virtually identical in the different protein–ligand complexes. Thus both affinity and specificity of ligand binding to Gal3C appear to depend in part on subtle differences in the conformational fluctuations that reflect the complex interplay between structure, dynamics and ligand interactions.

Identification of a Collapsed Intermediate with Non-native Long-range Interactions on the Folding Pathway of a Pair of Fyn SH3 Domain Mutants by NMR Relaxation Dispersion Spectroscopy

2006 ◽  
Vol 363 (5) ◽  
pp. 958-976 ◽  
Author(s):  
Philipp Neudecker ◽  
Arash Zarrine-Afsar ◽  
Wing-Yiu Choy ◽  
D. Ranjith Muhandiram ◽  
Alan R. Davidson ◽  
...  
Keyword(s):  
Long Range ◽  
Nmr Relaxation ◽  
Sh3 Domain ◽  
Relaxation Dispersion ◽  
Folding Pathway ◽  
Long Range Interactions
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