Literature DB >> 31262947

Combining Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) Spectroscopy for Integrative Structural Biology of Protein-RNA Complexes.

Alexander Leitner1, Georg Dorn2, Frédéric H-T Allain2.   

Abstract

Deciphering complex RNA-protein interactions on a (near-)atomic level is a hurdle that hinders advancing our understanding of fundamental processes in RNA metabolism and RNA-based gene regulation. To overcome challenges associated with individual structure determination methods, structural information derived from complementary biophysical methods can be combined in integrative structural biology approaches. Here, we review recent advances in such hybrid structural approaches with a focus on combining mass spectrometric analysis of cross-linked protein-RNA complexes and nuclear magnetic resonance (NMR) spectroscopy.
Copyright © 2019 Cold Spring Harbor Laboratory Press; all rights reserved.

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Year:  2019        PMID: 31262947      PMCID: PMC6601463          DOI: 10.1101/cshperspect.a032359

Source DB:  PubMed          Journal:  Cold Spring Harb Perspect Biol        ISSN: 1943-0264            Impact factor:   10.005


  85 in total

1.  NMR study of 100 kDa HCV IRES RNA using segmental isotope labeling.

Authors:  Insil Kim; Peter J Lukavsky; Joseph D Puglisi
Journal:  J Am Chem Soc       Date:  2002-08-14       Impact factor: 15.419

2.  Cut and paste RNA for nuclear magnetic resonance, paramagnetic resonance enhancement, and electron paramagnetic resonance structural studies.

Authors:  Olivier Duss; Nana Diarra Dit Konté; Frédéric H-T Allain
Journal:  Methods Enzymol       Date:  2015-06-22       Impact factor: 1.600

3.  Investigation of protein-RNA interactions by mass spectrometry--Techniques and applications.

Authors:  Carla Schmidt; Katharina Kramer; Henning Urlaub
Journal:  J Proteomics       Date:  2012-05-02       Impact factor: 4.044

4.  In vitro transcription: preparative RNA yields in analytical scale reactions.

Authors:  I D Pokrovskaya; V V Gurevich
Journal:  Anal Biochem       Date:  1994-08-01       Impact factor: 3.365

5.  hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1.

Authors:  Yoichiro Sugimoto; Alessandra Vigilante; Elodie Darbo; Alexandra Zirra; Cristina Militti; Andrea D'Ambrogio; Nicholas M Luscombe; Jernej Ule
Journal:  Nature       Date:  2015-03-18       Impact factor: 49.962

Review 6.  The Evolving Contribution of Mass Spectrometry to Integrative Structural Biology.

Authors:  Marco Faini; Florian Stengel; Ruedi Aebersold
Journal:  J Am Soc Mass Spectrom       Date:  2016-04-07       Impact factor: 3.109

Review 7.  The identification and characterization of non-coding and coding RNAs and their modified nucleosides by mass spectrometry.

Authors:  Kirk W Gaston; Patrick A Limbach
Journal:  RNA Biol       Date:  2014       Impact factor: 4.652

Review 8.  Isotope labeling strategies for NMR studies of RNA.

Authors:  Kun Lu; Yasuyuki Miyazaki; Michael F Summers
Journal:  J Biomol NMR       Date:  2009-09-30       Impact factor: 2.835

9.  Modulating the Cascade architecture of a minimal Type I-F CRISPR-Cas system.

Authors:  Daniel Gleditzsch; Hanna Müller-Esparza; Patrick Pausch; Kundan Sharma; Srivatsa Dwarakanath; Henning Urlaub; Gert Bange; Lennart Randau
Journal:  Nucleic Acids Res       Date:  2016-05-23       Impact factor: 16.971

10.  Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins.

Authors:  Katharina Kramer; Timo Sachsenberg; Benedikt M Beckmann; Saadia Qamar; Kum-Loong Boon; Matthias W Hentze; Oliver Kohlbacher; Henning Urlaub
Journal:  Nat Methods       Date:  2014-08-31       Impact factor: 28.547

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  2 in total

1.  Musashi-1: An Example of How Polyalanine Tracts Contribute to Self-Association in the Intrinsically Disordered Regions of RNA-Binding Proteins.

Authors:  Tsai-Chen Chen; Jie-Rong Huang
Journal:  Int J Mol Sci       Date:  2020-03-26       Impact factor: 5.923

Review 2.  Rapidly Growing Protein-Centric Technologies to Extensively Identify Protein-RNA Interactions: Application to the Analysis of Co-Transcriptional RNA Processing.

Authors:  Akio Masuda; Toshihiko Kawachi; Kinji Ohno
Journal:  Int J Mol Sci       Date:  2021-05-18       Impact factor: 5.923

  2 in total

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