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.

Stereochemistry Determination by Powder X-Ray Diffraction Analysis and NMR Spectroscopy Residual Dipolar Couplings

2009 ◽  
Vol 48 (31) ◽  
pp. 5670-5674 ◽  
Author(s):  
Manuela E. García ◽  
Silvina Pagola ◽  
Armando Navarro-Vázquez ◽  
Damilola D. Phillips ◽  
Chakicherla Gayathri ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Diffraction Analysis ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings ◽  
X Ray Diffraction ◽  
X Ray

Stereochemistry Determination by Powder X-Ray Diffraction Analysis and NMR Spectroscopy Residual Dipolar Couplings

2009 ◽  
Vol 121 (31) ◽  
pp. 5780-5784 ◽  
Author(s):  
Manuela E. García ◽  
Silvina Pagola ◽  
Armando Navarro-Vázquez ◽  
Damilola D. Phillips ◽  
Chakicherla Gayathri ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Diffraction Analysis ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings ◽  
X Ray Diffraction ◽  
X Ray

scholarly journals Solution Structure of the 128 kDa Enzyme I Dimer fromEscherichia coliand Its 146 kDa Complex with HPr Using Residual Dipolar Couplings and Small- and Wide-Angle X-ray Scattering

2010 ◽  
Vol 132 (37) ◽  
pp. 13026-13045 ◽  
Author(s):  
Charles D. Schwieters ◽  
Jeong-Yong Suh ◽  
Alexander Grishaev ◽  
Rodolfo Ghirlando ◽  
Yuki Takayama ◽  
...  
Keyword(s):  
Solution Structure ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings ◽  
Wide Angle ◽  
X Ray ◽  
X Ray Scattering ◽  
Enzyme I ◽  
Ray Scattering

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.

Characterizing weak protein–protein complexes by NMR residual dipolar couplings

2011 ◽  
Vol 40 (12) ◽  
pp. 1371-1381 ◽  
Author(s):  
Malene Ringkjøbing Jensen ◽  
Jose-Luis Ortega-Roldan ◽  
Loïc Salmon ◽  
Nico van Nuland ◽  
Martin Blackledge
Keyword(s):  
Residual Dipolar Couplings ◽  
Protein Complexes ◽  
Dipolar Couplings ◽  
Nmr Residual Dipolar Couplings
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