Literature DB >> 27489348

Structure of fully protonated proteins by proton-detected magic-angle spinning NMR.

Loren B Andreas1, Kristaps Jaudzems1, Jan Stanek1, Daniela Lalli1, Andrea Bertarello1, Tanguy Le Marchand1, Diane Cala-De Paepe1, Svetlana Kotelovica2, Inara Akopjana2, Benno Knott3, Sebastian Wegner3, Frank Engelke3, Anne Lesage1, Lyndon Emsley4, Kaspars Tars2, Torsten Herrmann1, Guido Pintacuda5.   

Abstract

Protein structure determination by proton-detected magic-angle spinning (MAS) NMR has focused on highly deuterated samples, in which only a small number of protons are introduced and observation of signals from side chains is extremely limited. Here, we show in two fully protonated proteins that, at 100-kHz MAS and above, spectral resolution is high enough to detect resolved correlations from amide and side-chain protons of all residue types, and to reliably measure a dense network of (1)H-(1)H proximities that define a protein structure. The high data quality allowed the correct identification of internuclear distance restraints encoded in 3D spectra with automated data analysis, resulting in accurate, unbiased, and fast structure determination. Additionally, we find that narrower proton resonance lines, longer coherence lifetimes, and improved magnetization transfer offset the reduced sample size at 100-kHz spinning and above. Less than 2 weeks of experiment time and a single 0.5-mg sample was sufficient for the acquisition of all data necessary for backbone and side-chain resonance assignment and unsupervised structure determination. We expect the technique to pave the way for atomic-resolution structure analysis applicable to a wide range of proteins.

Entities:  

Keywords:  NMR spectroscopy; magic-angle spinning; protein structures; proton detection; viral nucleocapsids

Mesh:

Substances:

Year:  2016        PMID: 27489348      PMCID: PMC4995937          DOI: 10.1073/pnas.1602248113

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  73 in total

1.  Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.

Authors:  Torsten Herrmann; Peter Güntert; Kurt Wüthrich
Journal:  J Mol Biol       Date:  2002-05-24       Impact factor: 5.469

2.  Solid-state protein-structure determination with proton-detected triple-resonance 3D magic-angle-spinning NMR spectroscopy.

Authors:  Donghua H Zhou; John J Shea; Andrew J Nieuwkoop; W Trent Franks; Benjamin J Wylie; Charles Mullen; Dennis Sandoz; Chad M Rienstra
Journal:  Angew Chem Int Ed Engl       Date:  2007       Impact factor: 15.336

3.  Optimum levels of exchangeable protons in perdeuterated proteins for proton detection in MAS solid-state NMR spectroscopy.

Authors:  Umit Akbey; Sascha Lange; W Trent Franks; Rasmus Linser; Kristina Rehbein; Anne Diehl; Barth-Jan van Rossum; Bernd Reif; Hartmut Oschkinat
Journal:  J Biomol NMR       Date:  2009-08-22       Impact factor: 2.835

4.  Characterization of different water pools in solid-state NMR protein samples.

Authors:  Anja Böckmann; Carole Gardiennet; René Verel; Andreas Hunkeler; Antoine Loquet; Guido Pintacuda; Lyndon Emsley; Beat H Meier; Anne Lesage
Journal:  J Biomol NMR       Date:  2009-11       Impact factor: 2.835

5.  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

6.  Recommendations of the wwPDB NMR Validation Task Force.

Authors:  Gaetano T Montelione; Michael Nilges; Ad Bax; Peter Güntert; Torsten Herrmann; Jane S Richardson; Charles D Schwieters; Wim F Vranken; Geerten W Vuister; David S Wishart; Helen M Berman; Gerard J Kleywegt; John L Markley
Journal:  Structure       Date:  2013-09-03       Impact factor: 5.006

7.  Proton-detected solid-state NMR reveals intramembrane polar networks in a seven-helical transmembrane protein proteorhodopsin.

Authors:  Meaghan E Ward; Lichi Shi; Evelyn Lake; Sridevi Krishnamurthy; Howard Hutchins; Leonid S Brown; Vladimir Ladizhansky
Journal:  J Am Chem Soc       Date:  2011-10-07       Impact factor: 15.419

8.  Solid-state NMR and SAXS studies provide a structural basis for the activation of alphaB-crystallin oligomers.

Authors:  Stefan Jehle; Ponni Rajagopal; Benjamin Bardiaux; Stefan Markovic; Ronald Kühne; Joseph R Stout; Victoria A Higman; Rachel E Klevit; Barth-Jan van Rossum; Hartmut Oschkinat
Journal:  Nat Struct Mol Biol       Date:  2010-08-29       Impact factor: 15.369

9.  Calculation of symmetric multimer structures from NMR data using a priori knowledge of the monomer structure, co-monomer restraints, and interface mapping: The case of leucine zippers.

Authors:  S I O'Donoghue; G F King; M Nilges
Journal:  J Biomol NMR       Date:  1996-09       Impact factor: 2.835

10.  High-sensitivity observation of dipolar exchange and NOEs between exchangeable protons in proteins by 3D solid-state NMR spectroscopy.

Authors:  Eric K Paulson; Corey R Morcombe; Vadim Gaponenko; Barbara Dancheck; R Andrew Byrd; Kurt W Zilm
Journal:  J Am Chem Soc       Date:  2003-11-26       Impact factor: 15.419

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  67 in total

1.  Expanding the horizons for structural analysis of fully protonated protein assemblies by NMR spectroscopy at MAS frequencies above 100 kHz.

Authors:  Jochem Struppe; Caitlin M Quinn; Manman Lu; Mingzhang Wang; Guangjin Hou; Xingyu Lu; Jodi Kraus; Loren B Andreas; Jan Stanek; Daniela Lalli; Anne Lesage; Guido Pintacuda; Werner Maas; Angela M Gronenborn; Tatyana Polenova
Journal:  Solid State Nucl Magn Reson       Date:  2017-07-03       Impact factor: 2.293

2.  Structural and molecular basis of cross-seeding barriers in amyloids.

Authors:  Asen Daskalov; Denis Martinez; Virginie Coustou; Nadia El Mammeri; Mélanie Berbon; Loren B Andreas; Benjamin Bardiaux; Jan Stanek; Abdelmajid Noubhani; Brice Kauffmann; Joseph S Wall; Guido Pintacuda; Sven J Saupe; Birgit Habenstein; Antoine Loquet
Journal:  Proc Natl Acad Sci U S A       Date:  2021-01-05       Impact factor: 11.205

Review 3.  Structural biology of supramolecular assemblies by magic-angle spinning NMR spectroscopy.

Authors:  Caitlin M Quinn; Tatyana Polenova
Journal:  Q Rev Biophys       Date:  2017-01       Impact factor: 5.318

4.  Fast MAS 1H-13C correlation NMR for structural investigations of plant cell walls.

Authors:  Pyae Phyo; Mei Hong
Journal:  J Biomol NMR       Date:  2019-09-18       Impact factor: 2.835

5.  Dynamic Nuclear Polarization Magic-Angle Spinning Nuclear Magnetic Resonance Combined with Molecular Dynamics Simulations Permits Detection of Order and Disorder in Viral Assemblies.

Authors:  Rupal Gupta; Huilan Zhang; Manman Lu; Guangjin Hou; Marc Caporini; Melanie Rosay; Werner Maas; Jochem Struppe; Jinwoo Ahn; In-Ja L Byeon; Hartmut Oschkinat; Kristaps Jaudzems; Emeline Barbet-Massin; Lyndon Emsley; Guido Pintacuda; Anne Lesage; Angela M Gronenborn; Tatyana Polenova
Journal:  J Phys Chem B       Date:  2019-06-11       Impact factor: 2.991

6.  1H detection of heteronuclear dipolar oscillations with water suppression in single crystal peptide and oriented protein samples.

Authors:  Zheng Long; Stanley J Opella
Journal:  J Magn Reson       Date:  2020-07-18       Impact factor: 2.229

Review 7.  Insights into protein misfolding and aggregation enabled by solid-state NMR spectroscopy.

Authors:  Patrick C A van der Wel
Journal:  Solid State Nucl Magn Reson       Date:  2017-10-04       Impact factor: 2.293

8.  Progress in proton-detected solid-state NMR (SSNMR): Super-fast 2D SSNMR collection for nano-mole-scale proteins.

Authors:  Yoshitaka Ishii; Ayesha Wickramasinghe; Isamu Matsuda; Yuki Endo; Yuji Ishii; Yusuke Nishiyama; Takahiro Nemoto; Takayuki Kamihara
Journal:  J Magn Reson       Date:  2017-11-28       Impact factor: 2.229

9.  Exact distance measurements for structure and dynamics in solid proteins by fast-magic-angle-spinning NMR.

Authors:  Kristof Grohe; Evgeny Nimerovsky; Himanshu Singh; Suresh K Vasa; Benedikt Söldner; Beat Vögeli; Chad M Rienstra; Rasmus Linser
Journal:  Chem Commun (Camb)       Date:  2019-06-14       Impact factor: 6.222

10.  Fast electron paramagnetic resonance magic angle spinning simulations using analytical powder averaging techniques.

Authors:  Edward P Saliba; Alexander B Barnes
Journal:  J Chem Phys       Date:  2019-09-21       Impact factor: 3.488

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