Literature DB >> 31199882

Aromatic Ring Dynamics, Thermal Activation, and Transient Conformations of a 468 kDa Enzyme by Specific 1H-13C Labeling and Fast Magic-Angle Spinning NMR.

Diego F Gauto1, Pavel Macek1, Alessandro Barducci2, Hugo Fraga1,3,4, Audrey Hessel1, Tsutomu Terauchi5,6, David Gajan7, Yohei Miyanoiri8,9, Jerome Boisbouvier1, Roman Lichtenecker10, Masatsune Kainosho5,9, Paul Schanda1.   

Abstract

Aromatic residues are located at structurally important sites of many proteins. Probing their interactions and dynamics can provide important functional insight but is challenging in large proteins. Here, we introduce approaches to characterize the dynamics of phenylalanine residues using 1H-detected fast magic-angle spinning (MAS) NMR combined with a tailored isotope-labeling scheme. Our approach yields isolated two-spin systems that are ideally suited for artifact-free dynamics measurements, and allows probing motions effectively without molecular weight limitations. The application to the TET2 enzyme assembly of ∼0.5 MDa size, the currently largest protein assigned by MAS NMR, provides insights into motions occurring on a wide range of time scales (picoseconds to milliseconds). We quantitatively probe ring-flip motions and show the temperature dependence by MAS NMR measurements down to 100 K. Interestingly, favorable line widths are observed down to 100 K, with potential implications for DNP NMR. Furthermore, we report the first 13C R1ρ MAS NMR relaxation-dispersion measurements and detect structural excursions occurring on a microsecond time scale in the entry pore to the catalytic chamber and at a trimer interface that was proposed as the exit pore. We show that the labeling scheme with deuteration at ca. 50 kHz MAS provides superior resolution compared to 100 kHz MAS experiments with protonated, uniformly 13C-labeled samples.

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Year:  2019        PMID: 31199882      PMCID: PMC7302935          DOI: 10.1021/jacs.9b04219

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  92 in total

1.  Structure and backbone dynamics of a microcrystalline metalloprotein by solid-state NMR.

Authors:  Michael J Knight; Andrew J Pell; Ivano Bertini; Isabella C Felli; Leonardo Gonnelli; Roberta Pierattelli; Torsten Herrmann; Lyndon Emsley; Guido Pintacuda
Journal:  Proc Natl Acad Sci U S A       Date:  2012-06-21       Impact factor: 11.205

2.  Crystal structure of TET protease reveals complementary protein degradation pathways in prokaryotes.

Authors:  Ljudmila Borissenko; Michael Groll
Journal:  J Mol Biol       Date:  2005-01-16       Impact factor: 5.469

Review 3.  Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy.

Authors:  Arthur G Palmer; Francesca Massi
Journal:  Chem Rev       Date:  2006-05       Impact factor: 60.622

4.  Accurate measurement of one-bond H-X heteronuclear dipolar couplings in MAS solid-state NMR.

Authors:  Paul Schanda; Beat H Meier; Matthias Ernst
Journal:  J Magn Reson       Date:  2011-03-21       Impact factor: 2.229

5.  Site-specific measurement of slow motions in proteins.

Authors:  Józef R Lewandowski; Hans Jürgen Sass; Stephan Grzesiek; Martin Blackledge; Lyndon Emsley
Journal:  J Am Chem Soc       Date:  2011-10-03       Impact factor: 15.419

6.  Alternative SAIL-Trp for robust aromatic signal assignment and determination of the χ(2) conformation by intra-residue NOEs.

Authors:  Yohei Miyanoiri; Mitsuhiro Takeda; JunGoo Jee; Akira M Ono; Kosuke Okuma; Tsutomu Terauchi; Masatsune Kainosho
Journal:  J Biomol NMR       Date:  2011-09-23       Impact factor: 2.835

7.  Microsecond Protein Dynamics from Combined Bloch-McConnell and Near-Rotary-Resonance R1p Relaxation-Dispersion MAS NMR.

Authors:  Dominique Marion; Diego F Gauto; Isabel Ayala; Karine Giandoreggio-Barranco; Paul Schanda
Journal:  Chemphyschem       Date:  2018-12-20       Impact factor: 3.102

8.  Dynamics of amino acid side chains in membrane proteins by high field solid state deuterium nuclear magnetic resonance spectroscopy. Phenylalanine, tyrosine, and tryptophan.

Authors:  R A Kinsey; A Kintanar; E Oldfield
Journal:  J Biol Chem       Date:  1981-09-10       Impact factor: 5.157

9.  Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association.

Authors:  Robert B Best; Wenwei Zheng; Jeetain Mittal
Journal:  J Chem Theory Comput       Date:  2014-10-16       Impact factor: 6.006

10.  Limits of Resolution and Sensitivity of Proton Detected MAS Solid-State NMR Experiments at 111 kHz in Deuterated and Protonated Proteins.

Authors:  Kai Xue; Riddhiman Sarkar; Carina Motz; Sam Asami; Diana C Rodriguez Camargo; Venita Decker; Sebastian Wegner; Zdenek Tosner; Bernd Reif
Journal:  Sci Rep       Date:  2017-08-07       Impact factor: 4.379

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  7 in total

1.  Bioactive scaffolds with enhanced supramolecular motion promote recovery from spinal cord injury.

Authors:  Z Álvarez; A N Kolberg-Edelbrock; I R Sasselli; J A Ortega; R Qiu; Z Syrgiannis; P A Mirau; F Chen; S M Chin; S Weigand; E Kiskinis; S I Stupp
Journal:  Science       Date:  2021-11-11       Impact factor: 47.728

2.  Characterizing Fast Conformational Exchange of Aromatic Rings Using Residual Dipolar Couplings: Distinguishing Jumplike Flips from Other Exchange Mechanisms.

Authors:  Matthias Dreydoppel; Mikael Akke; Ulrich Weininger
Journal:  J Phys Chem B       Date:  2022-09-30       Impact factor: 3.466

Review 3.  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

Review 4.  From Angstroms to Nanometers: Measuring Interatomic Distances by Solid-State NMR.

Authors:  Alexander A Shcherbakov; João Medeiros-Silva; Nhi Tran; Martin D Gelenter; Mei Hong
Journal:  Chem Rev       Date:  2021-10-25       Impact factor: 72.087

5.  Visualizing protein breathing motions associated with aromatic ring flipping.

Authors:  Laura Mariño Pérez; Francesco S Ielasi; Luiza M Bessa; Damien Maurin; Jaka Kragelj; Martin Blackledge; Nicola Salvi; Guillaume Bouvignies; Andrés Palencia; Malene Ringkjøbing Jensen
Journal:  Nature       Date:  2022-02-16       Impact factor: 69.504

6.  Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR.

Authors:  Diego F Gauto; Pavel Macek; Duccio Malinverni; Hugo Fraga; Matteo Paloni; Iva Sučec; Audrey Hessel; Juan Pablo Bustamante; Alessandro Barducci; Paul Schanda
Journal:  Nat Commun       Date:  2022-04-08       Impact factor: 17.694

7.  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

  7 in total

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