scholarly journals Minute Additions of DMSO Affect Protein Dynamics Measurements by NMR Relaxation Experiments through Significant Changes in Solvent Viscosity

ChemPhysChem ◽  
2018 ◽  
Vol 20 (2) ◽  
pp. 326-332 ◽  
Author(s):  
Johan Wallerstein ◽  
Mikael Akke
Keyword(s):  
Protein Dynamics ◽  
Nmr Relaxation ◽  
Solvent Viscosity ◽  
Relaxation Experiments

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.

Backbone dynamics of the CDK inhibitor p19INK4d studied by 15N NMR relaxation experiments at two field strengths

1998 ◽  
Vol 283 (1) ◽  
pp. 221-229 ◽  
Author(s):  
Christian Renner ◽  
Roland Baumgartner ◽  
Angelika A Noegel ◽  
Tad A Holak
Keyword(s):  
Nmr Relaxation ◽  
Backbone Dynamics ◽  
15N Nmr ◽  
Cdk Inhibitor ◽  
15N Nmr Relaxation ◽  
Relaxation Experiments ◽  
Field Strengths

scholarly journals Characterization of Internal Protein Dynamics and Conformational Entropy by NMR Relaxation

2019 ◽  
pp. 237-284 ◽  
Author(s):  
Matthew A. Stetz ◽  
José A. Caro ◽  
Sravya Kotaru ◽  
Xuejun Yao ◽  
Bryan S. Marques ◽  
...  
Keyword(s):  
Protein Dynamics ◽  
Nmr Relaxation ◽  
Conformational Entropy ◽  
Internal Protein

Sampling of Protein Dynamics in Nanosecond Time Scale by15N NMR Relaxation and Self-Diffusion Measurements

1999 ◽  
Vol 17 (1) ◽  
pp. 157-174 ◽  
Author(s):  
Vladislav Yu. Orekhov ◽  
Dmitry M. Korzhnev ◽  
Konstantine V. Pervushin ◽  
Eberhard Hoffmann ◽  
Alexander S. Arseniev
Keyword(s):  
Protein Dynamics ◽  
Time Scale ◽  
Nmr Relaxation ◽  
Self Diffusion ◽  
Nanosecond Time Scale

Quantifying Lipari–Szabo modelfree parameters from 13CO NMR relaxation experiments

2006 ◽  
Vol 36 (2) ◽  
pp. 79-102 ◽  
Author(s):  
Tianzhi Wang ◽  
Daniel S. Weaver ◽  
Sheng Cai ◽  
Erik R. P. Zuiderweg
Keyword(s):  
Nmr Relaxation ◽  
Relaxation Experiments

Protein dynamics and NMR relaxation: comparison of simulations with experiment

Nature ◽  
1982 ◽  
Vol 300 (5888) ◽  
pp. 197-198 ◽  
Author(s):  
Giovanni Lipari ◽  
Attila Szabo ◽  
Ronald M. Levy
Keyword(s):  
Protein Dynamics ◽  
Nmr Relaxation

A Digital rf Pulse Burst Generator for NMR Relaxation Experiments

1970 ◽  
Vol 41 (12) ◽  
pp. 1766-1770 ◽  
Author(s):  
V. Radeka ◽  
R. L. Chase ◽  
M. Petrinovic ◽  
J. A. Glasel
Keyword(s):  
Nmr Relaxation ◽  
Pulse Burst ◽  
Digital Rf ◽  
Relaxation Experiments ◽  
Rf Pulse
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