Literature DB >> 26451400

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

Piotr Paluch1, Tomasz Pawlak1, Agata Jeziorna1, Julien Trébosc2, Guangjin Hou3, Alexander J Vega3, Jean-Paul Amoureux4, Martin Dracinsky5, Tatyana Polenova3, Marek J Potrzebowski1.   

Abstract

We report a new multidimensional magic angle spinning NMR methodology, which provides an accurate and detailed probe of molecular motions occurring on timescales of nano- to microseconds, in sidechains of proteins. The approach is based on a 3D CPVC-RFDR correlation experiment recorded under fast MAS conditions (ν(R) = 62 kHz), where (13)C-(1)H CPVC dipolar lineshapes are recorded in a chemical shift resolved manner. The power of the technique is demonstrated in model tripeptide Tyr-(d)Ala-Phe and two nanocrystalline proteins, GB1 and LC8. We demonstrate that, through numerical simulations of dipolar lineshapes of aromatic sidechains, their detailed dynamic profile, i.e., the motional modes, is obtained. In GB1 and LC8 the results unequivocally indicate that a number of aromatic residues are dynamic, and using quantum mechanical calculations, we correlate the molecular motions of aromatic groups to their local environment in the crystal lattice. The approach presented here is general and can be readily extended to other biological systems.

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Year:  2015        PMID: 26451400      PMCID: PMC4890705          DOI: 10.1039/c5cp04475h

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  39 in total

1.  Generalized Gradient Approximation Made Simple.

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Review 2.  Molecular dynamics simulations of biomolecules.

Authors:  Martin Karplus; J Andrew McCammon
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Review 3.  Long-timescale molecular dynamics simulations of protein structure and function.

Authors:  John L Klepeis; Kresten Lindorff-Larsen; Ron O Dror; David E Shaw
Journal:  Curr Opin Struct Biol       Date:  2009-04-08       Impact factor: 6.809

4.  An analysis of phase-modulated heteronuclear dipolar decoupling sequences in solid-state nuclear magnetic resonance.

Authors:  Rajendra Singh Thakur; Narayanan D Kurur; P K Madhu
Journal:  J Magn Reson       Date:  2008-04-23       Impact factor: 2.229

5.  Solid-state NMR measurements of asymmetric dipolar couplings provide insight into protein side-chain motion.

Authors:  Paul Schanda; Matthias Huber; Jérôme Boisbouvier; Beat H Meier; Matthias Ernst
Journal:  Angew Chem Int Ed Engl       Date:  2011-09-14       Impact factor: 15.336

6.  A double-component Anderson-Weiss approach for describing NMR signals of mobile SIn units: application to constant-time DIPSHIFT experiments.

Authors:  Marcio Fernando Cobo; Detlef Reichert; Kay Saalwächter; Eduardo Ribeiro deAzevedo
Journal:  J Magn Reson       Date:  2014-09-28       Impact factor: 2.229

7.  Theoretical study of CP-VC: a simple, robust and accurate MAS NMR method for analysis of dipolar C-H interactions under rotation speeds faster than ca. 60 kHz.

Authors:  P Paluch; J Trébosc; Y Nishiyama; M J Potrzebowski; M Malon; J P Amoureux
Journal:  J Magn Reson       Date:  2015-01-14       Impact factor: 2.229

Review 8.  Advanced solid-state NMR approaches for structure determination of membrane proteins and amyloid fibrils.

Authors:  Ming Tang; Gemma Comellas; Chad M Rienstra
Journal:  Acc Chem Res       Date:  2013-05-10       Impact factor: 22.384

9.  Crystal polymorphism of protein GB1 examined by solid-state NMR spectroscopy and X-ray diffraction.

Authors:  Heather L Frericks Schmidt; Lindsay J Sperling; Yi Gui Gao; Benjamin J Wylie; John M Boettcher; Scott R Wilson; Chad M Rienstra
Journal:  J Phys Chem B       Date:  2007-12-04       Impact factor: 2.991

10.  Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding.

Authors:  Luciano A Abriata; Matteo Dal Peraro
Journal:  Sci Rep       Date:  2015-05-29       Impact factor: 4.379

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  7 in total

Review 1.  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

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

Authors:  Diego F Gauto; Pavel Macek; Alessandro Barducci; Hugo Fraga; Audrey Hessel; Tsutomu Terauchi; David Gajan; Yohei Miyanoiri; Jerome Boisbouvier; Roman Lichtenecker; Masatsune Kainosho; Paul Schanda
Journal:  J Am Chem Soc       Date:  2019-07-05       Impact factor: 15.419

3.  HIV-1 Capsid Function Is Regulated by Dynamics: Quantitative Atomic-Resolution Insights by Integrating Magic-Angle-Spinning NMR, QM/MM, and MD.

Authors:  Huilan Zhang; Guangjin Hou; Manman Lu; Jinwoo Ahn; In-Ja L Byeon; Christopher J Langmead; Juan R Perilla; Ivan Hung; Peter L Gor'kov; Zhehong Gan; William W Brey; David A Case; Klaus Schulten; Angela M Gronenborn; Tatyana Polenova
Journal:  J Am Chem Soc       Date:  2016-10-18       Impact factor: 15.419

4.  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

5.  Phenyl-Ring Dynamics in Amyloid Fibrils and Proteins: The Microscopic-Order-Macroscopic-Disorder Perspective.

Authors:  Eva Meirovitch; Zhichun Liang; Jack H Freed
Journal:  J Phys Chem B       Date:  2018-09-10       Impact factor: 2.991

6.  Improving dipolar recoupling for site-specific structural and dynamics studies in biosolids NMR: windowed RN-symmetry sequences.

Authors:  Xingyu Lu; Huilan Zhang; Manman Lu; Alexander J Vega; Guangjin Hou; Tatyana Polenova
Journal:  Phys Chem Chem Phys       Date:  2016-01-18       Impact factor: 3.676

7.  Dynamic Nuclear Polarization Enhanced MAS NMR Spectroscopy for Structural Analysis of HIV-1 Protein Assemblies.

Authors:  Rupal Gupta; Manman Lu; Guangjin Hou; Marc A Caporini; Melanie Rosay; Werner Maas; Jochem Struppe; Christopher Suiter; Jinwoo Ahn; In-Ja L Byeon; W Trent Franks; Marcella Orwick-Rydmark; Andrea Bertarello; Hartmut Oschkinat; Anne Lesage; Guido Pintacuda; Angela M Gronenborn; Tatyana Polenova
Journal:  J Phys Chem B       Date:  2016-01-12       Impact factor: 2.991

  7 in total

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