Literature DB >> 25563704

A minor conformation of a lanthanide tag on adenylate kinase characterized by paramagnetic relaxation dispersion NMR spectroscopy.

Mathias A S Hass1, Wei-Min Liu, Roman V Agafonov, Renee Otten, Lien A Phung, Jesika T Schilder, Dorothee Kern, Marcellus Ubbink.   

Abstract

NMR relaxation dispersion techniques provide a powerful method to study protein dynamics by characterizing lowly populated conformations that are in dynamic exchange with the major state. Paramagnetic NMR is a versatile tool for investigating the structures and dynamics of proteins. These two techniques were combined here to measure accurate and precise pseudocontact shifts of a lowly populated conformation. This method delivers valuable long-range structural restraints for higher energy conformations of macromolecules in solution. Another advantage of combining pseudocontact shifts with relaxation dispersion is the increase in the amplitude of dispersion profiles. Lowly populated states are often involved in functional processes, such as enzyme catalysis, signaling, and protein/protein interactions. The presented results also unveil a critical problem with the lanthanide tag used to generate paramagnetic relaxation dispersion effects in proteins, namely that the motions of the tag can interfere severely with the observation of protein dynamics. The two-point attached CLaNP-5 lanthanide tag was linked to adenylate kinase. From the paramagnetic relaxation dispersion only motion of the tag is observed. The data can be described accurately by a two-state model in which the protein-attached tag undergoes a 23° tilting motion on a timescale of milliseconds. The work demonstrates the large potential of paramagnetic relaxation dispersion and the challenge to improve current tags to minimize relaxation dispersion from tag movements.

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Year:  2015        PMID: 25563704     DOI: 10.1007/s10858-014-9894-3

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


  44 in total

1.  Validation of a lanthanide tag for the analysis of protein dynamics by paramagnetic NMR spectroscopy.

Authors:  Mathias A S Hass; Peter H J Keizers; Anneloes Blok; Yoshitaka Hiruma; Marcellus Ubbink
Journal:  J Am Chem Soc       Date:  2010-07-28       Impact factor: 15.419

2.  Simultaneous determination of protein backbone structure and dynamics from residual dipolar couplings.

Authors:  Guillaume Bouvignies; Phineus Markwick; Rafael Brüschweiler; Martin Blackledge
Journal:  J Am Chem Soc       Date:  2006-11-29       Impact factor: 15.419

3.  Measurement of bond vector orientations in invisible excited states of proteins.

Authors:  Pramodh Vallurupalli; D Flemming Hansen; Elliott Stollar; Eva Meirovitch; Lewis E Kay
Journal:  Proc Natl Acad Sci U S A       Date:  2007-11-15       Impact factor: 11.205

4.  Time-averaged nuclear Overhauser effect distance restraints applied to tendamistat.

Authors:  A E Torda; R M Scheek; W F van Gunsteren
Journal:  J Mol Biol       Date:  1990-07-05       Impact factor: 5.469

5.  Measurement of signs of chemical shift differences between ground and excited protein states: a comparison between H(S/M)QC and R1rho methods.

Authors:  Renate Auer; D Flemming Hansen; Philipp Neudecker; Dmitry M Korzhnev; D Ranjith Muhandiram; Robert Konrat; Lewis E Kay
Journal:  J Biomol NMR       Date:  2009-12-22       Impact factor: 2.835

6.  How reliable are pseudocontact shifts induced in proteins and ligands by mobile paramagnetic metal tags? A modelling study.

Authors:  Dmitry Shishmarev; Gottfried Otting
Journal:  J Biomol NMR       Date:  2013-05-08       Impact factor: 2.835

7.  NMRPipe: a multidimensional spectral processing system based on UNIX pipes.

Authors:  F Delaglio; S Grzesiek; G W Vuister; G Zhu; J Pfeifer; A Bax
Journal:  J Biomol NMR       Date:  1995-11       Impact factor: 2.835

Review 8.  Expanding the utility of NMR restraints with paramagnetic compounds: background and practical aspects.

Authors:  Julia Koehler; Jens Meiler
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2011-05-27       Impact factor: 9.795

9.  Design, synthesis, and evaluation of a lanthanide chelating protein probe: CLaNP-5 yields predictable paramagnetic effects independent of environment.

Authors:  Peter H J Keizers; Athanasios Saragliadis; Yoshitaka Hiruma; Mark Overhand; Marcellus Ubbink
Journal:  J Am Chem Soc       Date:  2008-10-01       Impact factor: 15.419

10.  Disulfide bond isomerization in basic pancreatic trypsin inhibitor: multisite chemical exchange quantified by CPMG relaxation dispersion and chemical shift modeling.

Authors:  Michael J Grey; Chunyu Wang; Arthur G Palmer
Journal:  J Am Chem Soc       Date:  2003-11-26       Impact factor: 15.419

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  4 in total

1.  Lanthanoid tagging via an unnatural amino acid for protein structure characterization.

Authors:  Wen-Xue Jiang; Xin-Hua Gu; Xu Dong; Chun Tang
Journal:  J Biomol NMR       Date:  2017-04-01       Impact factor: 2.835

Review 2.  Characterizing conformational ensembles of multi-domain proteins using anisotropic paramagnetic NMR restraints.

Authors:  Xue-Ni Hou; Hidehito Tochio
Journal:  Biophys Rev       Date:  2022-01-11

3.  Structure determination of high-energy states in a dynamic protein ensemble.

Authors:  John B Stiller; Renee Otten; Daniel Häussinger; Pascal S Rieder; Douglas L Theobald; Dorothee Kern
Journal:  Nature       Date:  2022-03-02       Impact factor: 69.504

Review 4.  Paramagnetic Chemical Probes for Studying Biological Macromolecules.

Authors:  Qing Miao; Christoph Nitsche; Henry Orton; Mark Overhand; Gottfried Otting; Marcellus Ubbink
Journal:  Chem Rev       Date:  2022-01-27       Impact factor: 72.087

  4 in total

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