Literature DB >> 23831612

An introduction to biological NMR spectroscopy.

Dominique Marion1.   

Abstract

NMR spectroscopy is a powerful tool for biologists interested in the structure, dynamics, and interactions of biological macromolecules. This review aims at presenting in an accessible manner the requirements and limitations of this technique. As an introduction, the history of NMR will highlight how the method evolved from physics to chemistry and finally to biology over several decades. We then introduce the NMR spectral parameters used in structural biology, namely the chemical shift, the J-coupling, nuclear Overhauser effects, and residual dipolar couplings. Resonance assignment, the required step for any further NMR study, bears a resemblance to jigsaw puzzle strategy. The NMR spectral parameters are then converted into angle and distances and used as input using restrained molecular dynamics to compute a bundle of structures. When interpreting a NMR-derived structure, the biologist has to judge its quality on the basis of the statistics provided. When the 3D structure is a priori known by other means, the molecular interaction with a partner can be mapped by NMR: information on the binding interface as well as on kinetic and thermodynamic constants can be gathered. NMR is suitable to monitor, over a wide range of frequencies, protein fluctuations that play a crucial role in their biological function. In the last section of this review, intrinsically disordered proteins, which have escaped the attention of classical structural biology, are discussed in the perspective of NMR, one of the rare available techniques able to describe structural ensembles. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 16 MCP).

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Year:  2013        PMID: 23831612      PMCID: PMC3820920          DOI: 10.1074/mcp.O113.030239

Source DB:  PubMed          Journal:  Mol Cell Proteomics        ISSN: 1535-9476            Impact factor:   5.911


  54 in total

1.  Automated assignment of ambiguous nuclear overhauser effects with ARIA.

Authors:  J P Linge; S I O'Donoghue; M Nilges
Journal:  Methods Enzymol       Date:  2001       Impact factor: 1.600

2.  RefDB: a database of uniformly referenced protein chemical shifts.

Authors:  Haiyan Zhang; Stephen Neal; David S Wishart
Journal:  J Biomol NMR       Date:  2003-03       Impact factor: 2.835

3.  Automated NMR structure calculation with CYANA.

Authors:  Peter Güntert
Journal:  Methods Mol Biol       Date:  2004

Review 4.  Macromolecular NMR spectroscopy for the non-spectroscopist.

Authors:  Ann H Kwan; Mehdi Mobli; Paul R Gooley; Glenn F King; Joel P Mackay
Journal:  FEBS J       Date:  2011-01-28       Impact factor: 5.542

Review 5.  Weak alignment NMR: a hawk-eyed view of biomolecular structure.

Authors:  Ad Bax; Alexander Grishaev
Journal:  Curr Opin Struct Biol       Date:  2005-10       Impact factor: 6.809

6.  Protein backbone angle restraints from searching a database for chemical shift and sequence homology.

Authors:  G Cornilescu; F Delaglio; A Bax
Journal:  J Biomol NMR       Date:  1999-03       Impact factor: 2.835

7.  A two-dimensional nuclear Overhauser enhancement (2D NOE) experiment for the elucidation of complete proton-proton cross-relaxation networks in biological macromolecules.

Authors:  A Kumar; R R Ernst; K Wüthrich
Journal:  Biochem Biophys Res Commun       Date:  1980-07-16       Impact factor: 3.575

8.  Side chain dynamics in unfolded protein states: an NMR based 2H spin relaxation study of delta131delta.

Authors:  Wing-Yiu Choy; David Shortle; Lewis E Kay
Journal:  J Am Chem Soc       Date:  2003-02-19       Impact factor: 15.419

9.  Probing chemical shifts of invisible states of proteins with relaxation dispersion NMR spectroscopy: how well can we do?

Authors:  D Flemming Hansen; Pramodh Vallurupalli; Patrik Lundström; Philipp Neudecker; Lewis E Kay
Journal:  J Am Chem Soc       Date:  2008-02-01       Impact factor: 15.419

10.  Dynamics induced by β-lactam antibiotics in the active site of Bacillus subtilis L,D-transpeptidase.

Authors:  Lauriane Lecoq; Catherine Bougault; Jean-Emmanuel Hugonnet; Carole Veckerlé; Ombeline Pessey; Michel Arthur; Jean-Pierre Simorre
Journal:  Structure       Date:  2012-05-09       Impact factor: 5.006

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  32 in total

1.  Progress in protein crystallography.

Authors:  Zbigniew Dauter; Alexander Wlodawer
Journal:  Protein Pept Lett       Date:  2016       Impact factor: 1.890

2.  Biophysics & Structural Biology at Synchrotrons BSBS 2019 Biological NMR Session.

Authors:  Frances Separovic
Journal:  Biophys Rev       Date:  2019-05-23

Review 3.  Metabolomics in the study of spontaneous animal diseases.

Authors:  Helena Tran; Malcolm McConville; Panayiotis Loukopoulos
Journal:  J Vet Diagn Invest       Date:  2020-08-18       Impact factor: 1.279

4.  Maintaining and Enhancing Diversity of Sampled Protein Conformations in Robotics-Inspired Methods.

Authors:  Jayvee R Abella; Mark Moll; Lydia E Kavraki
Journal:  J Comput Biol       Date:  2017-10-16       Impact factor: 1.479

5.  Confirmation of intersubunit connectivity and topology of designed protein complexes by native MS.

Authors:  Aniruddha Sahasrabuddhe; Yang Hsia; Florian Busch; William Sheffler; Neil P King; David Baker; Vicki H Wysocki
Journal:  Proc Natl Acad Sci U S A       Date:  2018-01-19       Impact factor: 11.205

6.  Digested disorder, Quarterly intrinsic disorder digest (October-November-December, 2013).

Authors:  Shelly DeForte; Krishna D Reddy; Vladimir N Uversky
Journal:  Intrinsically Disord Proteins       Date:  2015-03-09

Review 7.  Label-Free Physical Techniques and Methodologies for Proteins Detection in Microfluidic Biosensor Structures.

Authors:  Georgii Konoplev; Darina Agafonova; Liubov Bakhchova; Nikolay Mukhin; Marharyta Kurachkina; Marc-Peter Schmidt; Nikolay Verlov; Alexander Sidorov; Aleksandr Oseev; Oksana Stepanova; Andrey Kozyrev; Alexander Dmitriev; Soeren Hirsch
Journal:  Biomedicines       Date:  2022-01-18

8.  Structure of S. pombe telomerase protein Pof8 C-terminal domain is an xRRM conserved among LARP7 proteins.

Authors:  Ritwika Basu; Catherine D Eichhorn; Ryan Cheng; Robert D Peterson; Juli Feigon
Journal:  RNA Biol       Date:  2020-11-01       Impact factor: 4.652

Review 9.  Mixing omics: combining genetics and metabolomics to study rheumatic diseases.

Authors:  Cristina Menni; Jonas Zierer; Ana M Valdes; Tim D Spector
Journal:  Nat Rev Rheumatol       Date:  2017-02-02       Impact factor: 20.543

Review 10.  Techniques for Detection of Clinical Used Heparins.

Authors:  Binjie Li; Huimin Zhao; Mingjia Yu
Journal:  Int J Anal Chem       Date:  2021-05-06       Impact factor: 1.885

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