Literature DB >> 25193427

Towards automatic protein backbone assignment using proton-detected 4D solid-state NMR data.

ShengQi Xiang1, Veniamin Chevelkov, Stefan Becker, Adam Lange.   

Abstract

We introduce an efficient approach for sequential protein backbone assignment based on two complementary proton-detected 4D solid-state NMR experiments that correlate Hi(N)/Ni with CAi/COi or CAi-1/COi-1. The resulting 4D spectra exhibit excellent sensitivity and resolution and are amenable to (semi-)automatic assignment approaches. This strategy allows to obtain sequential connections with high confidence as problems related to peak overlap and multiple assignment possibilities are avoided. Non-uniform sampling schemes were implemented to allow for the acquisition of 4D spectra within a few days. Rather moderate hardware requirements enable the successful demonstration of the method on deuterated type III secretion needles using a 600 MHz spectrometer at a spinning rate of 25 kHz.

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Year:  2014        PMID: 25193427     DOI: 10.1007/s10858-014-9859-6

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN: 0925-2738            Impact factor:   2.835


  37 in total

Review 1.  Radial sampling for fast NMR: Concepts and practices over three decades.

Authors:  Brian E Coggins; Ronald A Venters; Pei Zhou
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2010-07-30       Impact factor: 9.795

2.  Toxin-induced conformational changes in a potassium channel revealed by solid-state NMR.

Authors:  Adam Lange; Karin Giller; Sönke Hornig; Marie-France Martin-Eauclaire; Olaf Pongs; Stefan Becker; Marc Baldus
Journal:  Nature       Date:  2006-04-13       Impact factor: 49.962

3.  Ultrahigh resolution in proton solid-state NMR spectroscopy at high levels of deuteration.

Authors:  Veniamin Chevelkov; Kristina Rehbein; Anne Diehl; Bernd Reif
Journal:  Angew Chem Int Ed Engl       Date:  2006-06-02       Impact factor: 15.336

4.  A proton-detected 4D solid-state NMR experiment for protein structure determination.

Authors:  Matthias Huber; Sebastian Hiller; Paul Schanda; Matthias Ernst; Anja Böckmann; René Verel; Beat H Meier
Journal:  Chemphyschem       Date:  2011-02-15       Impact factor: 3.102

5.  Sensitivity gains, linearity, and spectral reproducibility in nonuniformly sampled multidimensional MAS NMR spectra of high dynamic range.

Authors:  Christopher L Suiter; Sivakumar Paramasivam; Guangjin Hou; Shangjin Sun; David Rice; Jeffrey C Hoch; David Rovnyak; Tatyana Polenova
Journal:  J Biomol NMR       Date:  2014-04-22       Impact factor: 2.835

6.  Proton-detected MAS NMR experiments based on dipolar transfers for backbone assignment of highly deuterated proteins.

Authors:  Veniamin Chevelkov; Birgit Habenstein; Antoine Loquet; Karin Giller; Stefan Becker; Adam Lange
Journal:  J Magn Reson       Date:  2014-03-04       Impact factor: 2.229

7.  Automated robust and accurate assignment of protein resonances for solid state NMR.

Authors:  Jakob Toudahl Nielsen; Natalia Kulminskaya; Morten Bjerring; Niels Chr Nielsen
Journal:  J Biomol NMR       Date:  2014-05-10       Impact factor: 2.835

8.  A general Monte Carlo/simulated annealing algorithm for resonance assignment in NMR of uniformly labeled biopolymers.

Authors:  Kan-Nian Hu; Wei Qiang; Robert Tycko
Journal:  J Biomol NMR       Date:  2011-06-28       Impact factor: 2.835

Review 9.  Solid-state NMR studies of amyloid fibril structure.

Authors:  Robert Tycko
Journal:  Annu Rev Phys Chem       Date:  2011       Impact factor: 12.703

10.  Solid-state NMR studies of HIV-1 capsid protein assemblies.

Authors:  Yun Han; Jinwoo Ahn; Jason Concel; In-Ja L Byeon; Angela M Gronenborn; Jun Yang; Tatyana Polenova
Journal:  J Am Chem Soc       Date:  2010-02-17       Impact factor: 15.419

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  12 in total

1.  Sequential backbone assignment based on dipolar amide-to-amide correlation experiments.

Authors:  ShengQi Xiang; Kristof Grohe; Petra Rovó; Suresh Kumar Vasa; Karin Giller; Stefan Becker; Rasmus Linser
Journal:  J Biomol NMR       Date:  2015-05-15       Impact factor: 2.835

2.  Protein residue linking in a single spectrum for magic-angle spinning NMR assignment.

Authors:  Loren B Andreas; Jan Stanek; Tanguy Le Marchand; Andrea Bertarello; Diane Cala-De Paepe; Daniela Lalli; Magdaléna Krejčíková; Camille Doyen; Carl Öster; Benno Knott; Sebastian Wegner; Frank Engelke; Isabella C Felli; Roberta Pierattelli; Nicholas E Dixon; Lyndon Emsley; Torsten Herrmann; Guido Pintacuda
Journal:  J Biomol NMR       Date:  2015-06-16       Impact factor: 2.835

3.  On the problem of resonance assignments in solid state NMR of uniformly ¹⁵N,¹³C-labeled proteins.

Authors:  Robert Tycko
Journal:  J Magn Reson       Date:  2015-04       Impact factor: 2.229

4.  MAS NMR of HIV-1 protein assemblies.

Authors:  Christopher L Suiter; Caitlin M Quinn; Manman Lu; Guangjin Hou; Huilan Zhang; Tatyana Polenova
Journal:  J Magn Reson       Date:  2015-04       Impact factor: 2.229

Review 5.  1H-Detected Biomolecular NMR under Fast Magic-Angle Spinning.

Authors:  Tanguy Le Marchand; Tobias Schubeis; Marta Bonaccorsi; Piotr Paluch; Daniela Lalli; Andrew J Pell; Loren B Andreas; Kristaps Jaudzems; Jan Stanek; Guido Pintacuda
Journal:  Chem Rev       Date:  2022-05-10       Impact factor: 72.087

6.  Gd3+-chelated lipid accelerates solid-state NMR spectroscopy of seven-transmembrane proteins.

Authors:  Chang Liu; Jing Liu; Xiaojun Xu; ShengQi Xiang; Shenlin Wang
Journal:  J Biomol NMR       Date:  2017-05-30       Impact factor: 2.835

7.  Solid-State NMR H-N-(C)-H and H-N-C-C 3D/4D Correlation Experiments for Resonance Assignment of Large Proteins.

Authors:  Hugo Fraga; Charles-Adrien Arnaud; Diego F Gauto; Maxime Audin; Vilius Kurauskas; Pavel Macek; Carsten Krichel; Jia-Ying Guan; Jerome Boisbouvier; Remco Sprangers; Cécile Breyton; Paul Schanda
Journal:  Chemphyschem       Date:  2017-09-05       Impact factor: 3.102

8.  Bacteriophage Tail-Tube Assembly Studied by Proton-Detected 4D Solid-State NMR.

Authors:  Maximilian Zinke; Pascal Fricke; Camille Samson; Songhwan Hwang; Joseph S Wall; Sascha Lange; Sophie Zinn-Justin; Adam Lange
Journal:  Angew Chem Int Ed Engl       Date:  2017-07-07       Impact factor: 15.336

9.  Rapid access to RNA resonances by proton-detected solid-state NMR at >100 kHz MAS.

Authors:  Alexander Marchanka; Jan Stanek; Guido Pintacuda; Teresa Carlomagno
Journal:  Chem Commun (Camb)       Date:  2018-07-05       Impact factor: 6.222

10.  Atomic-resolution chemical characterization of (2x)72-kDa tryptophan synthase via four- and five-dimensional 1H-detected solid-state NMR.

Authors:  Alexander Klein; Petra Rovó; Varun V Sakhrani; Yangyang Wang; Jacob B Holmes; Viktoriia Liu; Patricia Skowronek; Laura Kukuk; Suresh K Vasa; Peter Güntert; Leonard J Mueller; Rasmus Linser
Journal:  Proc Natl Acad Sci U S A       Date:  2022-01-25       Impact factor: 11.205

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