Literature DB >> 31560199

Extreme Nonuniform Sampling for Protein NMR Dynamics Studies in Minimal Time.

Gregory Jameson1,2, Alexandar L Hansen3, Dawei Li3, Lei Bruschweiler-Li3, Rafael Brüschweiler1,2,3,4.   

Abstract

NMR spectroscopy is an extraordinarily rich source of quantitative dynamics of proteins in solution using spin relaxation or chemical exchange saturation transfer (CEST) experiments. However, 15N-CEST measurements require prolonged multidimensional, so-called pseudo-3D HSQC experiments where the pseudo dimension is a radio frequency offset Δω of a weak 15N saturation field. Nonuniform sampling (NUS) approaches have the potential to significantly speed up these measurements, but they also carry the risk of introducing serious artifacts and the systematic optimization of nonuniform sampling schedules has remained elusive. It is demonstrated here how this challenge can be addressed by using fitted cross-peaks of a reference 2D HSQC experiment as footprints, which are subsequently used to reconstruct cross-peak amplitudes of a pseudo-3D data set as a function of Δω by a linear least-squares fit. It is shown for protein Im7 how the approach can yield highly accurate CEST profiles based on an absolutely minimally sampled (AMS) data set allowing a speed-up of a factor 20-30. Spectrum-specific optimized nonuniform sampling (SONUS) schemes based on the Cramer-Rao lower bound metric were critical to achieve such a performance, revealing also more general properties of optimal sampling schedules. This is the first systematic exploration and optimization of NUS schedules for the dramatic speed-up of quantitative multidimensional NMR measurements that minimize unwanted errors.

Entities:  

Year:  2019        PMID: 31560199      PMCID: PMC6953986          DOI: 10.1021/jacs.9b08032

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


  31 in total

1.  NMR characterization of the dynamics of biomacromolecules.

Authors:  Arthur G Palmer
Journal:  Chem Rev       Date:  2004-08       Impact factor: 60.622

2.  Studying "invisible" excited protein states in slow exchange with a major state conformation.

Authors:  Pramodh Vallurupalli; Guillaume Bouvignies; Lewis E Kay
Journal:  J Am Chem Soc       Date:  2012-05-03       Impact factor: 15.419

3.  Sensitivity of nonuniform sampling NMR.

Authors:  Melissa R Palmer; Christopher L Suiter; Geneive E Henry; James Rovnyak; Jeffrey C Hoch; Tatyana Polenova; David Rovnyak
Journal:  J Phys Chem B       Date:  2015-05-18       Impact factor: 2.991

4.  Quantitative lid dynamics of MDM2 reveals differential ligand binding modes of the p53-binding cleft.

Authors:  Scott A Showalter; Lei Bruschweiler-Li; Eric Johnson; Fengli Zhang; Rafael Brüschweiler
Journal:  J Am Chem Soc       Date:  2008-04-25       Impact factor: 15.419

5.  Probing Invisible, Excited Protein States by Non-Uniformly Sampled Pseudo-4D CEST Spectroscopy.

Authors:  Dong Long; Frank Delaglio; Ashok Sekhar; Lewis E Kay
Journal:  Angew Chem Int Ed Engl       Date:  2015-07-15       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

Review 7.  Applications of non-uniform sampling and processing.

Authors:  Sven G Hyberts; Haribabu Arthanari; Gerhard Wagner
Journal:  Top Curr Chem       Date:  2012

8.  Fast multidimensional NMR spectroscopy using compressed sensing.

Authors:  Daniel J Holland; Mark J Bostock; Lynn F Gladden; Daniel Nietlispach
Journal:  Angew Chem Int Ed Engl       Date:  2011-06-06       Impact factor: 15.336

9.  Rapid Determination of Fast Protein Dynamics from NMR Chemical Exchange Saturation Transfer Data.

Authors:  Yina Gu; Alexandar L Hansen; Yu Peng; Rafael Brüschweiler
Journal:  Angew Chem Int Ed Engl       Date:  2016-01-28       Impact factor: 15.336

10.  Comprehensive analysis of NMR data using advanced line shape fitting.

Authors:  Markus Niklasson; Renee Otten; Alexandra Ahlner; Cecilia Andresen; Judith Schlagnitweit; Katja Petzold; Patrik Lundström
Journal:  J Biomol NMR       Date:  2017-10-17       Impact factor: 2.835

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