Literature DB >> 29189927

Solvent saturation transfer to proteins (SSTP) for structural and functional characterization of proteins.

Pushpa Mishra1, C Ashley Barnes1, Madeleine Strickland1, Nico Tjandra2,3.   

Abstract

Protein structure determination using NMR is dependent on experimentally acquired distance restraints. Often, however, an insufficient number of these restraints are available for determining a protein's correct fold, much less its detailed three-dimensional structure. In consideration of this problem, we propose a simple means to acquire supplemental structural restraints from protein surface accessibilities using solvent saturation transfer to proteins (SSTP), based on the principles of paramagnetic chemical-exchange saturation transfer. Here, we demonstrate the utility of SSTP in structure calculations of two proteins, TSG101 and ubiquitin. The observed SSTP was found to be directly proportional to solvent accessibility. Since SSTP does not involve the direct excitation of water, which compromises the analysis of protein protons entangled in the breadth of the water resonance, it has an advantage over conventional water-based magnetization transfers. Inclusion of structural restraints derived from SSTP improved both the precision and accuracy of the final protein structures in comparison to those determined by traditional approaches, when using minimal amounts of additional structural data. Furthermore, we show that SSTP can detect weak protein-protein interactions which are unobservable by chemical shift perturbations.

Entities:  

Keywords:  CSP; NMR; ParaCEST; Structure refinements; TSG101; Ubiquitin; Yb-DOTAM

Mesh:

Substances:

Year:  2017        PMID: 29189927      PMCID: PMC5820130          DOI: 10.1007/s10858-017-0151-4

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


  17 in total

1.  Structure and functional interactions of the Tsg101 UEV domain.

Authors:  Owen Pornillos; Steven L Alam; Rebecca L Rich; David G Myszka; Darrell R Davis; Wesley I Sundquist
Journal:  EMBO J       Date:  2002-05-15       Impact factor: 11.598

2.  The Xplor-NIH NMR molecular structure determination package.

Authors:  Charles D Schwieters; John J Kuszewski; Nico Tjandra; G Marius Clore
Journal:  J Magn Reson       Date:  2003-01       Impact factor: 2.229

3.  Structure of human TSG101 UEV domain.

Authors:  Andres Palencia; Jose C Martinez; Pedro L Mateo; Irene Luque; Ana Camara-Artigas
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2006-03-18

Review 4.  Using chemical shift perturbation to characterise ligand binding.

Authors:  Mike P Williamson
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2013-03-21       Impact factor: 9.795

5.  The amide protons of an ytterbium(III) dota tetraamide complex act as efficient antennae for transfer of magnetization to bulk water.

Authors:  Shanrong Zhang; Lydie Michaudet; Shawn Burgess; A Dean Sherry
Journal:  Angew Chem Int Ed Engl       Date:  2002-06-03       Impact factor: 15.336

6.  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

7.  Investigations into whole water, prototropic and amide proton exchange in lanthanide(III) DOTA-tetraamide chelates.

Authors:  Mark Woods; Azhar Pasha; Piyu Zhao; Gyula Tircso; Somdatta Chowdhury; Garry Kiefer; Donald E Woessner; A Dean Sherry
Journal:  Dalton Trans       Date:  2011-05-31       Impact factor: 4.390

8.  Chemical exchange saturation transfer (CEST): what is in a name and what isn't?

Authors:  Peter C M van Zijl; Nirbhay N Yadav
Journal:  Magn Reson Med       Date:  2011-02-17       Impact factor: 4.668

9.  Parameterization of solvent-protein interaction and its use on NMR protein structure determination.

Authors:  Yu Wang; Charles D Schwieters; Nico Tjandra
Journal:  J Magn Reson       Date:  2012-06-07       Impact factor: 2.229

10.  Site-resolved measurement of water-protein interactions by solution NMR.

Authors:  Nathaniel V Nucci; Maxim S Pometun; A Joshua Wand
Journal:  Nat Struct Mol Biol       Date:  2011-01-02       Impact factor: 15.369

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  1 in total

1.  Simultaneous measurement of 1HC/N-R2's for rapid acquisition of backbone and sidechain paramagnetic relaxation enhancements (PREs) in proteins.

Authors:  C Ashley Barnes; Mary R Starich; Nico Tjandra; Pushpa Mishra
Journal:  J Biomol NMR       Date:  2021-02-24       Impact factor: 2.835

  1 in total

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