Comparison of Aqueous Molecular Dynamics with NMR Relaxation and Residual Dipolar Couplings Favors Internal Motion in a Mannose Oligosaccharide

2001 ◽  
Vol 123 (20) ◽  
pp. 4792-4802 ◽  
Author(s):  
Andrew Almond ◽  
Jakob Bunkenborg ◽  
Thomas Franch ◽  
Charlotte H. Gotfredsen ◽  
Jens Ø. Duus
Keyword(s):  
Molecular Dynamics ◽  
Residual Dipolar Couplings ◽  
Nmr Relaxation ◽  
Internal Motion ◽  
Dipolar Couplings

scholarly journals Developing NMR methods for macromolecular machines: Measurement of residual dipolar couplings to probe dynamic regions of the ribosome

2018 ◽  
Author(s):  
Xiaolin Wang ◽  
John P. Kirkpatrick ◽  
Hélène M. M. Launay ◽  
Alfonso de Simone ◽  
Daniel Häussinger ◽  
...  
Keyword(s):  
Residual Dipolar Couplings ◽  
3D Structure ◽  
Nmr Relaxation ◽  
Dipolar Couplings ◽  
Functional Regions ◽  
Chain Complexes ◽  
Relaxation Measurements ◽  
Nascent Chain ◽  
Dynamic Regions ◽  
Nmr Methods

ABSTRACTWe describe an NMR approach based on the measurement of residual dipolar couplings (RDCs) to probe the structural and motional properties of the dynamic regions of the ribosome. Alignment of intact 70S ribosomes in filamentous bacteriophage enabled measurement of RDCs in the stalk protein bL12, and this information was used to refine a 3D structure of its C-terminal domain (CTD). Orientational constraints on the CTD alignment arising from the semiflexible linker sequence were further probed by a paramagnetic alignment strategy, and provided direct experimental validation of a structural ensemble previously derived from SAXS and NMR relaxation measurements. Our results demonstrate the prospect of better characterising dynamical and functional regions of more challenging macromolecular machines and systems, for example ribosome–nascent chain complexes.

Direct prediction of residual dipolar couplings of small molecules in a stretched gel by stochastic molecular dynamics simulations

2015 ◽  
Vol 53 (3) ◽  
pp. 213-217 ◽  
Author(s):  
Andreas O. Frank ◽  
J. Christoph Freudenberger ◽  
Alexey K. Shaytan ◽  
Horst Kessler ◽  
Burkhard Luy
Keyword(s):  
Molecular Dynamics ◽  
Small Molecules ◽  
Molecular Dynamics Simulations ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings ◽  
Dynamics Simulations

scholarly journals Residual dipolar couplings as a tool to study molecular recognition of ubiquitin

2008 ◽  
Vol 36 (6) ◽  
pp. 1433-1437 ◽  
Author(s):  
Nils-Alexander Lakomek ◽  
Oliver F. Lange ◽  
Korvin F.A. Walter ◽  
Christophe Farès ◽  
Dalia Egger ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Residual Dipolar Couplings ◽  
Time Window ◽  
Protein Complexes ◽  
Nmr Relaxation ◽  
Dipolar Couplings ◽  
Relaxation Methods ◽  
Dominant Mechanism ◽  
X Ray ◽  
Conformational Selection

RDCs (residual dipolar couplings) in NMR spectroscopy provide information about protein dynamics complementary to NMR relaxation methods, especially in the previously inaccessible time window between the protein correlation time τc and 50 μs. For ubiquitin, new modes of motion of the protein backbone could be detected using RDC-based techniques. An ensemble of ubiquitin based on these RDC values is found to comprise all different conformations that ubiquitin adopts upon binding to different recognition proteins. These conformations in protein–protein complexes had been derived from 46 X-ray structures. Thus, for ubiquitin recognition by other proteins, conformational selection rather than induced fit seems to be the dominant mechanism.

Limited Flexibility of Lactose Detected from Residual Dipolar Couplings Using Molecular Dynamics Simulations and Steric Alignment Methods

2005 ◽  
Vol 127 (10) ◽  
pp. 3589-3595 ◽  
Author(s):  
Manuel Martín-Pastor ◽  
Angeles Canales ◽  
Francisco Corzana ◽  
Juan L. Asensio ◽  
Jesús Jiménez-Barbero
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings ◽  
Dynamics Simulations

scholarly journals Configuration determination by residual dipolar couplings: accessing the full conformational space by molecular dynamics with tensorial constraints

2019 ◽  
Vol 10 (38) ◽  
pp. 8774-8791 ◽  
Author(s):  
Pavleta Tzvetkova ◽  
Ulrich Sternberg ◽  
Thomas Gloge ◽  
Armando Navarro-Vázquez ◽  
Burkhard Luy
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Residual Dipolar Couplings ◽  
Structural Models ◽  
Dipolar Couplings ◽  
Conformational Space ◽  
Flexible Molecules ◽  
Dynamics Simulations

The use of tensorial orientational constraints for NMR-derived residual dipolar couplings (RDCs) in molecular dynamics simulations brings detailed structural models of flexible molecules in solution in reach.

On the Interpretation of Residual Dipolar Couplings as Reporters of Molecular Dynamics

2004 ◽  
Vol 126 (39) ◽  
pp. 12646-12650 ◽  
Author(s):  
Kai Fredriksson ◽  
Martti Louhivuori ◽  
Perttu Permi ◽  
Arto Annila
Keyword(s):  
Molecular Dynamics ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings
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