Multiple-Site Exchange in Proteins Studied with a Suite of Six NMR Relaxation Dispersion Experiments:  An Application to the Folding of a Fyn SH3 Domain Mutant

2005 ◽  
Vol 127 (44) ◽  
pp. 15602-15611 ◽  
Author(s):  
Dmitry M. Korzhnev ◽  
Philipp Neudecker ◽  
Anthony Mittermaier ◽  
Vladislav Yu. Orekhov ◽  
Lewis E. Kay
Keyword(s):  
Nmr Relaxation ◽  
Sh3 Domain ◽  
Relaxation Dispersion ◽  
Multiple Site ◽  
Site Exchange

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

scholarly journals Analysis of Artifacts Caused by Pulse Imperfections in CPMG Pulse Trains in NMR Relaxation Dispersion Experiments

2018 ◽  
Vol 4 (3) ◽  
pp. 33 ◽  
Author(s):  
Tsuyoshi Konuma ◽  
Aritaka Nagadoi ◽  
Jun-ichi Kurita ◽  
Takahisa Ikegami
Keyword(s):  
Dipolar Coupling ◽  
Residual Dipolar Coupling ◽  
Nmr Relaxation ◽  
Relaxation Dispersion ◽  
Conformational Exchange ◽  
Resonance Effects ◽  
Pulse Trains ◽  
At Resonance ◽  
Selective Inversion ◽  
Resonance Relaxation

Nuclear magnetic resonance relaxation dispersion (rd) experiments provide kinetics and thermodynamics information of molecules undergoing conformational exchange. Rd experiments often use a Carr-Purcell-Meiboom-Gill (CPMG) pulse train equally separated by a spin-state selective inversion element (U-element). Even with measurement parameters carefully set, however, parts of 1H–15N correlations sometimes exhibit large artifacts that may hamper the subsequent analyses. We analyzed such artifacts with a combination of NMR measurements and simulation. We found that particularly the lowest CPMG frequency (νcpmg) can also introduce large artifacts into amide 1H–15N and aromatic 1H–13C correlations whose 15N/13C resonances are very close to the carrier frequencies. The simulation showed that the off-resonance effects and miscalibration of the CPMG π pulses generate artifact maxima at resonance offsets of even and odd multiples of νcpmg, respectively. We demonstrate that a method once introduced into the rd experiments for molecules having residual dipolar coupling significantly reduces artifacts. In the method the 15N/13C π pulse phase in the U-element is chosen between x and y. We show that the correctly adjusted sequence is tolerant to miscalibration of the CPMG π pulse power as large as ±10% for most amide 15N and aromatic 13C resonances of proteins.

scholarly journals Accelerating 2D NMR relaxation dispersion experiments using iterated maps

2019 ◽  
Vol 73 (10-11) ◽  
pp. 561-576 ◽  
Author(s):  
Jared Rovny ◽  
Robert L. Blum ◽  
J. Patrick Loria ◽  
Sean E. Barrett
Keyword(s):  
Nmr Relaxation ◽  
2D Nmr ◽  
Relaxation Dispersion ◽  
Iterated Maps

scholarly journals Dynamic ensemble of HIV-1 RRE stem IIB reveals non-native conformations that disrupt the Rev-binding site

2019 ◽  
Vol 47 (13) ◽  
pp. 7105-7117 ◽  
Author(s):  
Chia-Chieh Chu ◽  
Raphael Plangger ◽  
Christoph Kreutz ◽  
Hashim M Al-Hashimi
Keyword(s):  
Binding Site ◽  
Nuclear Export ◽  
Dynamic Equilibrium ◽  
Nmr Relaxation ◽  
Conformational Flexibility ◽  
Relaxation Dispersion ◽  
Conformational States ◽  
Rev Response Element ◽  
Local Secondary Structure ◽  
Hiv 1

AbstractThe HIV-1 Rev response element (RRE) RNA element mediates the nuclear export of intron containing viral RNAs by forming an oligomeric complex with the viral protein Rev. Stem IIB and nearby stem II three-way junction nucleate oligomerization through cooperative binding of two Rev molecules. Conformational flexibility at this RRE region has been shown to be important for Rev binding. However, the nature of the flexibility has remained elusive. Here, using NMR relaxation dispersion, including a new strategy for directly observing transient conformational states in large RNAs, we find that stem IIB alone or when part of the larger RREII three-way junction robustly exists in dynamic equilibrium with non-native excited state (ES) conformations that have a combined population of ∼20%. The ESs disrupt the Rev-binding site by changing local secondary structure, and their stabilization via point substitution mutations decreases the binding affinity to the Rev arginine-rich motif (ARM) by 15- to 80-fold. The ensemble clarifies the conformational flexibility observed in stem IIB, reveals long-range conformational coupling between stem IIB and the three-way junction that may play roles in cooperative Rev binding, and also identifies non-native RRE conformational states as new targets for the development of anti-HIV therapeutics.

High-field liquid state NMR hyperpolarization: a combined DNP/NMRD approach

2014 ◽  
Vol 16 (35) ◽  
pp. 18781-18787 ◽  
Author(s):  
Petr Neugebauer ◽  
Jan G. Krummenacker ◽  
Vasyl P. Denysenkov ◽  
Christina Helmling ◽  
Claudio Luchinat ◽  
...  
Keyword(s):  
Magnetic Field ◽  
High Magnetic Field ◽  
Dynamic Nuclear Polarization ◽  
Liquid State ◽  
High Field ◽  
Nuclear Polarization ◽  
Nmr Relaxation ◽  
Relaxation Dispersion ◽  
Liquid Solutions ◽  
High Fields

Dynamic nuclear polarization and NMR relaxation dispersion measurements have been performed on liquid solutions of TEMPOL radicals in solvents with different viscosities at a high magnetic field of 9.2 T. The results indicate that fast dynamics significantly contribute to DNP enhancements at high fields.

scholarly journals Nonnative Interactions in the FF Domain Folding Pathway from an Atomic Resolution Structure of a Sparsely Populated Intermediate: An NMR Relaxation Dispersion Study

2011 ◽  
Vol 133 (28) ◽  
pp. 10974-10982 ◽  
Author(s):  
Dmitry M. Korzhnev ◽  
Robert M. Vernon ◽  
Tomasz L. Religa ◽  
Alexandar L. Hansen ◽  
David Baker ◽  
...  
Keyword(s):  
Nmr Relaxation ◽  
Relaxation Dispersion ◽  
Atomic Resolution ◽  
Folding Pathway ◽  
Resolution Structure
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