Slow Internal Dynamics in Proteins:  Application of NMR Relaxation Dispersion Spectroscopy to Methyl Groups in a Cavity Mutant of T4 Lysozyme

2002 ◽  
Vol 124 (7) ◽  
pp. 1443-1451 ◽  
Author(s):  
Frans A. A. Mulder ◽  
Bin Hon ◽  
Anthony Mittermaier ◽  
Frederick W. Dahlquist ◽  
Lewis E. Kay
Keyword(s):  
Nmr Relaxation ◽  
Relaxation Dispersion ◽  
Methyl Groups ◽  
T4 Lysozyme ◽  
Internal Dynamics

scholarly journals Mapping transiently formed and sparsely populated conformations on a complex energy landscape

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Yong Wang ◽  
Elena Papaleo ◽  
Kresten Lindorff-Larsen
Keyword(s):  
Energy Landscape ◽  
Nmr Relaxation ◽  
Relaxation Dispersion ◽  
Conformational Exchange ◽  
Internal Cavity ◽  
T4 Lysozyme ◽  
Enhanced Sampling ◽  
Exchange Processes ◽  
Dynamics Simulations ◽  
A Minor

Determining the structures, kinetics, thermodynamics and mechanisms that underlie conformational exchange processes in proteins remains extremely difficult. Only in favourable cases is it possible to provide atomic-level descriptions of sparsely populated and transiently formed alternative conformations. Here we benchmark the ability of enhanced-sampling molecular dynamics simulations to determine the free energy landscape of the L99A cavity mutant of T4 lysozyme. We find that the simulations capture key properties previously measured by NMR relaxation dispersion methods including the structure of a minor conformation, the kinetics and thermodynamics of conformational exchange, and the effect of mutations. We discover a new tunnel that involves the transient exposure towards the solvent of an internal cavity, and show it to be relevant for ligand escape. Together, our results provide a comprehensive view of the structural landscape of a protein, and point forward to studies of conformational exchange in systems that are less characterized experimentally.

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

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

Dynamics of Alanine Methyl Groups in Alanine Oligopeptides and Spider Dragline Silks with Different Packing Structures As Studied by 13C Solid-State NMR Relaxation

2018 ◽  
Vol 51 (17) ◽  
pp. 6746-6756 ◽  
Author(s):  
Tetsuo Asakura ◽  
Yugo Tasei ◽  
Hironori Matsuda ◽  
Akira Naito
Keyword(s):  
Solid State ◽  
Solid State Nmr ◽  
Nmr Relaxation ◽  
Methyl Groups

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.

ChemInform Abstract: Characterization of Enzyme Motions by Solution NMR Relaxation Dispersion

ChemInform ◽  
2008 ◽  
Vol 39 (22) ◽  
Author(s):  
J. Patrick Loria ◽  
Rebecca B. Berlow ◽  
Eric D. Watt
Keyword(s):  
Nmr Relaxation ◽  
Relaxation Dispersion ◽  
Solution Nmr ◽  
Abstract Characterization

Investigation of Methyl Reorientations in 1,4-Dimethoxy- 2,6-dimethylbenzene by NMR and Inelastic Neutron Scattering

1979 ◽  
Vol 34 (5) ◽  
pp. 631-645 ◽  
Author(s):  
R. A. Wind ◽  
W. M. M. J. Bovée ◽  
J. C. F. Kupers ◽  
J. Smidt ◽  
Chr. Steenbergen
Keyword(s):  
Solid State ◽  
Neutron Scattering ◽  
Liquid State ◽  
Solid State Nmr ◽  
Inelastic Neutron Scattering ◽  
Nmr Relaxation ◽  
Inelastic Neutron ◽  
Methyl Groups ◽  
Methyl Group ◽  
Nmr Study

Abstract In this paper a solid state NMR relaxation study and inelastic neutron scattering (INS) experiments (the latter in the solid and liquid phase) are reported for a molecule containing methyl groups in different surroundings, namely 1,4-dimethoxy-2,6-dimethylbenzene. The results are compared with each other and with those of a liquid state NMR study reported earlier. It is found that in this way both the shapes and magnitudes of the various hindering potentials can be determined. The result is that the methyl groups 1, 2 and 4 possess a threefold cosine-shaped potential with heights given by 7.7, 9.0 and 15.0 kJ/mol according to the solid state NMR measurements (from the INS study the values 7.5, 7.5 and 16.0 kJ/mol were obtained). For methyl group 6 a mixture of a three-and six-fold symmetry had to be taken into account in order to explain the experiments. Except for methyl group 4 the liquid state NMR results deviate from those obtained with the other two techniques. A possible cause for this discrepancy is discussed. For the molecular structure it is concluded that the reorientations of the methyl groups 1 and 2 are influenced by mutual hindering and that the angle between the plane through the C4-O-C bond and the aromatic plane is small, whereas for the C1-O-C bond this angle is estimated to be about 70°.

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