Literature DB >> 36180044

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

Matthias Dreydoppel1, Mikael Akke2, Ulrich Weininger1.   

Abstract

Aromatic ring flips are a hallmark of protein dynamics. They are experimentally studied by NMR spectroscopy, where recent advances have led to improved characterization across a wide range of time scales. Results on different proteins have been interpreted as continuous diffusive ring rotations or jumplike flips, leading to diverging views of the protein interior as being fluidlike or solidlike, respectively. It is challenging to distinguish between these mechanisms and other types of conformational exchange because chemical-shift-mediated line broadening provides only conclusive evidence for ring flips only if the system can be moved from the slow- to intermediate/fast-exchange regime. Moreover, whenever the chemical shift difference between the two symmetry-related sites is close to zero, it is not generally possible to determine the exchange time scale. Here we resolve these issues by measuring residual dipolar coupling (RDC)-mediated exchange contributions using NMR relaxation dispersion experiments on proteins dissolved in dilute liquid crystalline media. Excellent agreement is found between the experimental difference in RDC between the two symmetry-related sites and the value calculated from high-resolution X-ray structures, demonstrating that dynamics measured for F52 in the B1 domain of protein G reports on distinct, jumplike flips rather than other types of conformational exchange.

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Year:  2022        PMID: 36180044      PMCID: PMC9574926          DOI: 10.1021/acs.jpcb.2c05097

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   3.466


  45 in total

1.  Effect of pressure on the tertiary structure and dynamics of folded basic pancreatic trypsin inhibitor.

Authors:  H Li; H Yamada; K Akasaka
Journal:  Biophys J       Date:  1999-11       Impact factor: 4.033

2.  Ring flips revisited: (13)C relaxation dispersion measurements of aromatic side chain dynamics and activation barriers in basic pancreatic trypsin inhibitor.

Authors:  Ulrich Weininger; Kristofer Modig; Mikael Akke
Journal:  Biochemistry       Date:  2014-07-11       Impact factor: 3.162

3.  Rates and energetics of tyrosine ring flips in yeast iso-2-cytochrome c.

Authors:  B T Nall; E H Zuniga
Journal:  Biochemistry       Date:  1990-08-21       Impact factor: 3.162

4.  A sharp thermal transition of fast aromatic-ring dynamics in ubiquitin.

Authors:  Vignesh Kasinath; Yinan Fu; Kim A Sharp; A Joshua Wand
Journal:  Angew Chem Int Ed Engl       Date:  2014-12-04       Impact factor: 15.336

5.  Analysis of local molecular motions of aromatic sidechains in proteins by 2D and 3D fast MAS NMR spectroscopy and quantum mechanical calculations.

Authors:  Piotr Paluch; Tomasz Pawlak; Agata Jeziorna; Julien Trébosc; Guangjin Hou; Alexander J Vega; Jean-Paul Amoureux; Martin Dracinsky; Tatyana Polenova; Marek J Potrzebowski
Journal:  Phys Chem Chem Phys       Date:  2015-11-21       Impact factor: 3.676

6.  Backbone conformational constraints in a microcrystalline U-15N-labeled protein by 3D dipolar-shift solid-state NMR spectroscopy.

Authors:  W Trent Franks; Benjamin J Wylie; Sara A Stellfox; Chad M Rienstra
Journal:  J Am Chem Soc       Date:  2006-03-15       Impact factor: 15.419

7.  Increased resolution of aromatic cross peaks using alternate 13C labeling and TROSY.

Authors:  Alexander G Milbradt; Haribabu Arthanari; Koh Takeuchi; Andras Boeszoermenyi; Franz Hagn; Gerhard Wagner
Journal:  J Biomol NMR       Date:  2015-05-10       Impact factor: 2.835

8.  1H R relaxation dispersion experiments in aromatic side chains.

Authors:  Matthias Dreydoppel; Roman J Lichtenecker; Mikael Akke; Ulrich Weininger
Journal:  J Biomol NMR       Date:  2021-09-12       Impact factor: 2.835

9.  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

10.  Fractional 13C enrichment of isolated carbons using [1-13C]- or [2- 13C]-glucose facilitates the accurate measurement of dynamics at backbone Calpha and side-chain methyl positions in proteins.

Authors:  Patrik Lundström; Kaare Teilum; Tommy Carstensen; Irina Bezsonova; Silke Wiesner; D Flemming Hansen; Tomasz L Religa; Mikael Akke; Lewis E Kay
Journal:  J Biomol NMR       Date:  2007-06-07       Impact factor: 2.582

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