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.

scholarly journals Probing the dynamic stalk region of the ribosome using solution NMR

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Xiaolin Wang ◽  
John P. Kirkpatrick ◽  
Hélène M. M. Launay ◽  
Alfonso de Simone ◽  
Daniel Häussinger ◽  
...  
Keyword(s):  
Residual Dipolar Couplings ◽  
Nmr Relaxation ◽  
Structural Refinement ◽  
Functional Regions ◽  
Chain Complexes ◽  
Relaxation Measurements ◽  
Nascent Chain ◽  
Alignment Strategy ◽  
Dynamic Regions ◽  
Structural Ensemble

Abstract We 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 mobile C-terminal domain (CTD) of the stalk protein bL12. A structural refinement of this domain using the observed RDCs did not show large changes relative to the isolated protein in the absence of the ribosome, and we also found that alignment of the CTD was almost independent of the presence of the core ribosome particle, indicating that the inter-domain linker has significant flexibility. The nature of this linker was subsequently probed in more detail using a paramagnetic alignment strategy, which revealed partial propagation of alignment between neighbouring domains, providing 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.

Structure of Thermally Modified Wood Studied by Liquid State NMR Measurements

Holzforschung ◽  
2002 ◽  
Vol 56 (5) ◽  
pp. 522-528 ◽  
Author(s):  
S. Hietala ◽  
S. L. Maunu ◽  
F. Sundholm ◽  
S. Jämsä ◽  
P. Viitaniemi
Keyword(s):  
Relaxation Times ◽  
Nmr Relaxation ◽  
Spectroscopic Techniques ◽  
H Nmr ◽  
Yield Information ◽  
Cell Dimensions ◽  
Relaxation Measurements ◽  
Nmr Methods ◽  
Thermally Modified Wood ◽  
Pfg Nmr

Summary Thermal modification is a technique to produce wood with increased dimensional stability and lower equilibrium moisture content. 2H NMR relaxation measurements and pulsed field gradient (PFG-NMR) methods are non-invasive spectroscopic techniques that can be used to measure the response of liquid confined in porous materials and yield information on the size and distribution of the pores. These methods were used to study the structure and changes in structure of thermally modified Scots pine wood. The 2H longitudinal relaxation measurements of wood samples at different moisture contents showed different relaxation times and relaxation time distribution in the thermally treated samples. The effect of the thermal treatments on the cell size in wood samples was studied by PFG-NMR measurements with different dwell times. The PFG-NMR measurements showed no clear change in the cell dimensions of the thermally modified samples compared with control samples taken from the same log.

scholarly journals Computer-Assisted 3D Structure Elucidation of Natural Products using Residual Dipolar Couplings

2017 ◽  
Vol 129 (13) ◽  
pp. 3714-3718 ◽  
Author(s):  
Eduardo Troche-Pesqueira ◽  
Clemens Anklin ◽  
Roberto R. Gil ◽  
Armando Navarro-Vázquez
Keyword(s):  
Natural Products ◽  
Structure Elucidation ◽  
Residual Dipolar Couplings ◽  
3D Structure ◽  
Dipolar Couplings ◽  
Computer Assisted

scholarly journals Computer-Assisted 3D Structure Elucidation of Natural Products using Residual Dipolar Couplings

2017 ◽  
Vol 56 (13) ◽  
pp. 3660-3664 ◽  
Author(s):  
Eduardo Troche-Pesqueira ◽  
Clemens Anklin ◽  
Roberto R. Gil ◽  
Armando Navarro-Vázquez
Keyword(s):  
Natural Products ◽  
Structure Elucidation ◽  
Residual Dipolar Couplings ◽  
3D Structure ◽  
Dipolar Couplings ◽  
Computer Assisted

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.

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

NMR spectroscopy in the conformational analysis of peptides: an overview

2020 ◽  
Vol 27 ◽  
Author(s):  
Marian Vincenzi ◽  
Flavia Anna Mercurio ◽  
Marilisa Leone
Keyword(s):  
Nmr Spectroscopy ◽  
Protein Interactions ◽  
3D Structure ◽  
Theoretical Background ◽  
Triple Resonance ◽  
Protein Protein Interactions ◽  
Nmr Studies ◽  
Conformational Preferences ◽  
Dynamic Perspective ◽  
Nmr Methods

Background: NMR spectroscopy is one of the most powerful tools to study the structure and interaction properties of peptides and proteins from a dynamic perspective. Knowing the bioactive conformations of peptides is crucial in the drug discovery field to design more efficient analogue ligands and inhibitors of protein-protein interactions targeting therapeutically relevant systems. Objective: This review provides a toolkit to investigate peptide conformational properties by NMR. Methods: Articles cited herein, related to NMR studies of peptides and proteins were mainly searched through Pubmed and the web. More recent and old books on NMR spectroscopy written by eminent scientists in the field were consulted as well. Results: The review is mainly focused on NMR tools to gain the 3D structure of small unlabeled peptides. It is more application-oriented as it is beyond its goal to deliver a profound theoretical background. However, the basic principles of 2D homonuclear and heteronuclear experiments are briefly described. Protocols to obtain isotopically labeled peptides and principal triple resonance experiments needed to study them, are discussed as well. Conclusion: NMR is a leading technique in the study of conformational preferences of small flexible peptides whose structure can be often only described by an ensemble of conformations. Although NMR studies of peptides can be easily and fast performed by canonical protocols established a few decades ago, more recently we have assisted to tremendous improvements of NMR spectroscopy to investigate instead large systems and overcome its molecular weight limit.

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