Literature DB >> 35494416

A Chemical Biology Primer for NMR Spectroscopists.

Evan T Clark1,2, Elanor E Sievers1, Galia T Debelouchina1.   

Abstract

Among structural biology techniques, NMR spectroscopy offers unique capabilities that enable the atomic resolution studies of dynamic and heterogeneous biological systems under physiological and native conditions. Complex biological systems, however, often challenge NMR spectroscopists with their low sensitivity, crowded spectra or large linewidths that reflect their intricate interaction patterns and dynamics. While some of these challenges can be overcome with the development of new spectroscopic approaches, chemical biology can also offer elegant and efficient solutions at the sample preparation stage. In this tutorial, we aim to present several chemical biology tools that enable the preparation of selectively and segmentally labeled protein samples, as well as the introduction of site-specific spectroscopic probes and post-translational modifications. The four tools covered here, namely cysteine chemistry, inteins, native chemical ligation, and unnatural amino acid incorporation, have been developed and optimized in recent years to be more efficient and applicable to a wider range of proteins than ever before. We briefly introduce each tool, describe its advantages and disadvantages in the context of NMR experiments, and offer practical advice for sample preparation and analysis. We hope that this tutorial will introduce beginning researchers in the field to the possibilities chemical biology can offer to NMR spectroscopists, and that it will inspire new and exciting applications in the quest to understand protein function in health and disease.

Entities:  

Keywords:  genetic code expansion; intein; post-translational modification; protein engineering; segmental labeling

Year:  2022        PMID: 35494416      PMCID: PMC9053072          DOI: 10.1016/j.jmro.2022.100044

Source DB:  PubMed          Journal:  J Magn Reson Open        ISSN: 2666-4410


  112 in total

1.  Amino acids for Diels-Alder reactions in living cells.

Authors:  Tilman Plass; Sigrid Milles; Christine Koehler; Jędrzej Szymański; Rainer Mueller; Manfred Wiessler; Carsten Schultz; Edward A Lemke
Journal:  Angew Chem Int Ed Engl       Date:  2012-03-30       Impact factor: 15.336

2.  Unprecedented rates and efficiencies revealed for new natural split inteins from metagenomic sources.

Authors:  Patricia Carvajal-Vallejos; Roser Pallissé; Henning D Mootz; Stefan R Schmidt
Journal:  J Biol Chem       Date:  2012-06-28       Impact factor: 5.157

3.  A facile system for encoding unnatural amino acids in mammalian cells.

Authors:  Peng R Chen; Dan Groff; Jiantao Guo; Weijia Ou; Susan Cellitti; Bernhard H Geierstanger; Peter G Schultz
Journal:  Angew Chem Int Ed Engl       Date:  2009       Impact factor: 15.336

4.  A mesophilic cysteine-less split intein for protein trans-splicing applications under oxidizing conditions.

Authors:  Maniraj Bhagawati; Tobias M E Terhorst; Friederike Füsser; Simon Hoffmann; Tim Pasch; Shmuel Pietrokovski; Henning D Mootz
Journal:  Proc Natl Acad Sci U S A       Date:  2019-10-14       Impact factor: 11.205

5.  EPR Distance Measurements in Native Proteins with Genetically Encoded Spin Labels.

Authors:  Moritz J Schmidt; Artem Fedoseev; Dennis Bücker; Julia Borbas; Christine Peter; Malte Drescher; Daniel Summerer
Journal:  ACS Chem Biol       Date:  2015-10-06       Impact factor: 5.100

6.  Paramagnetic relaxation enhancement of membrane proteins by incorporation of the metal-chelating unnatural amino acid 2-amino-3-(8-hydroxyquinolin-3-yl)propanoic acid (HQA).

Authors:  Sang Ho Park; Vivian S Wang; Jasmina Radoicic; Anna A De Angelis; Sabrina Berkamp; Stanley J Opella
Journal:  J Biomol NMR       Date:  2014-11-28       Impact factor: 2.835

7.  A Genetically Encoded F-19 NMR Probe Reveals the Allosteric Modulation Mechanism of Cannabinoid Receptor 1.

Authors:  Xiaoyan Wang; Dongsheng Liu; Ling Shen; Fahui Li; Yongze Li; Lingyun Yang; Tiandan Xu; Houchao Tao; Deqiang Yao; Lijie Wu; Kunio Hirata; Laura M Bohn; Alexandros Makriyannis; Xiaohong Liu; Tian Hua; Zhi-Jie Liu; Jiangyun Wang
Journal:  J Am Chem Soc       Date:  2021-10-01       Impact factor: 15.419

8.  Residue-by-Residue View of In Vitro FUS Granules that Bind the C-Terminal Domain of RNA Polymerase II.

Authors:  Kathleen A Burke; Abigail M Janke; Christy L Rhine; Nicolas L Fawzi
Journal:  Mol Cell       Date:  2015-10-08       Impact factor: 17.970

Review 9.  Easy Synthesis of Complex Biomolecular Assemblies: Wheat Germ Cell-Free Protein Expression in Structural Biology.

Authors:  Marie-Laure Fogeron; Lauriane Lecoq; Laura Cole; Matthias Harbers; Anja Böckmann
Journal:  Front Mol Biosci       Date:  2021-03-25

10.  Single-particle cryo-EM at atomic resolution.

Authors:  Takanori Nakane; Abhay Kotecha; Andrija Sente; Greg McMullan; Simonas Masiulis; Patricia M G E Brown; Ioana T Grigoras; Lina Malinauskaite; Tomas Malinauskas; Jonas Miehling; Tomasz Uchański; Lingbo Yu; Dimple Karia; Evgeniya V Pechnikova; Erwin de Jong; Jeroen Keizer; Maarten Bischoff; Jamie McCormack; Peter Tiemeijer; Steven W Hardwick; Dimitri Y Chirgadze; Garib Murshudov; A Radu Aricescu; Sjors H W Scheres
Journal:  Nature       Date:  2020-10-21       Impact factor: 69.504

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  1 in total

1.  DNP-enhanced solid-state NMR spectroscopy of chromatin polymers.

Authors:  Nesreen Elathram; Bryce E Ackermann; Galia T Debelouchina
Journal:  J Magn Reson Open       Date:  2022-03-26
  1 in total

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