Literature DB >> 28317074

Probing conformational dynamics in biomolecules via chemical exchange saturation transfer: a primer.

Pramodh Vallurupalli1, Ashok Sekhar2, Tairan Yuwen2, Lewis E Kay3,4.   

Abstract

Although Chemical Exchange Saturation Transfer (CEST) type NMR experiments have been used to study chemical exchange processes in molecules since the early 1960s, there has been renewed interest in the past several years in using this approach to study biomolecular conformational dynamics. The methodology is particularly powerful for the study of sparsely populated, transiently formed conformers that are recalcitrant to investigation using traditional biophysical tools, and it is complementary to relaxation dispersion and magnetization transfer experiments that have traditionally been used to study chemical exchange processes. Here we discuss the concepts behind the CEST experiment, focusing on practical aspects as well, we review some of the pulse sequences that have been developed to characterize protein and RNA conformational dynamics, and we discuss a number of examples where the CEST methodology has provided important insights into the role of dynamics in biomolecular function.

Keywords:  CEST; Excited conformational states; Molecular dynamics; Slow conformational exchange

Mesh:

Substances:

Year:  2017        PMID: 28317074     DOI: 10.1007/s10858-017-0099-4

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


  117 in total

1.  A 2D ¹³C-CEST experiment for studying slowly exchanging protein systems using methyl probes: an application to protein folding.

Authors:  Guillaume Bouvignies; Lewis E Kay
Journal:  J Biomol NMR       Date:  2012-06-12       Impact factor: 2.835

2.  The energy landscapes and motions of proteins.

Authors:  H Frauenfelder; S G Sligar; P G Wolynes
Journal:  Science       Date:  1991-12-13       Impact factor: 47.728

Review 3.  Alzheimer's disease.

Authors:  Henry W Querfurth; Frank M LaFerla
Journal:  N Engl J Med       Date:  2010-01-28       Impact factor: 91.245

4.  Analysis of non-uniformly sampled spectra with multi-dimensional decomposition.

Authors:  Vladislav Yu Orekhov; Victor A Jaravine
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2011-02-24       Impact factor: 9.795

Review 5.  Hydrogen exchange: the modern legacy of Linderstrøm-Lang.

Authors:  S W Englander; L Mayne; Y Bai; T R Sosnick
Journal:  Protein Sci       Date:  1997-05       Impact factor: 6.725

Review 6.  Protein folding dynamics: the diffusion-collision model and experimental data.

Authors:  M Karplus; D L Weaver
Journal:  Protein Sci       Date:  1994-04       Impact factor: 6.725

7.  Carbonyl carbon transverse relaxation dispersion measurements and ms-micros timescale motion in a protein hydrogen bond network.

Authors:  Rieko Ishima; James Baber; John M Louis; Dennis A Torchia
Journal:  J Biomol NMR       Date:  2004-06       Impact factor: 2.835

8.  Backbone dynamics of a free and phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation.

Authors:  N A Farrow; R Muhandiram; A U Singer; S M Pascal; C M Kay; G Gish; S E Shoelson; T Pawson; J D Forman-Kay; L E Kay
Journal:  Biochemistry       Date:  1994-05-17       Impact factor: 3.162

Review 9.  A century of Alzheimer's disease.

Authors:  Michel Goedert; Maria Grazia Spillantini
Journal:  Science       Date:  2006-11-03       Impact factor: 47.728

10.  Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch.

Authors:  Yi Xue; Brant Gracia; Daniel Herschlag; Rick Russell; Hashim M Al-Hashimi
Journal:  Nat Commun       Date:  2016-06-13       Impact factor: 14.919

View more
  42 in total

1.  Probing the excited-state chemical shifts and exchange parameters by nitrogen-decoupled amide proton chemical exchange saturation transfer (HNdec-CEST).

Authors:  Qinglin Wu; Benjamin A Fenton; Jessica L Wojtaszek; Pei Zhou
Journal:  Chem Commun (Camb)       Date:  2017-07-27       Impact factor: 6.222

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

Authors:  Gregory Jameson; Alexandar L Hansen; Dawei Li; Lei Bruschweiler-Li; Rafael Brüschweiler
Journal:  J Am Chem Soc       Date:  2019-10-14       Impact factor: 15.419

3.  Allosteric Mechanisms of Nonadditive Substituent Contributions to Protein-Ligand Binding.

Authors:  Stephen Boulton; Katherine Van; Bryan VanSchouwen; Jerry Augustine; Madoka Akimoto; Giuseppe Melacini
Journal:  Biophys J       Date:  2020-08-15       Impact factor: 4.033

4.  Adding Substituent Nonadditivity in Protein Allostery by NMR.

Authors:  Mary C Clay; Charalampos G Kalodimos
Journal:  Biophys J       Date:  2020-08-15       Impact factor: 4.033

5.  Binding kinetics and substrate selectivity in HIV-1 protease-Gag interactions probed at atomic resolution by chemical exchange NMR.

Authors:  Lalit Deshmukh; Vitali Tugarinov; John M Louis; G Marius Clore
Journal:  Proc Natl Acad Sci U S A       Date:  2017-10-30       Impact factor: 11.205

6.  Revisiting 1HN CPMG relaxation dispersion experiments: a simple modification can eliminate large artifacts.

Authors:  Tairan Yuwen; Lewis E Kay
Journal:  J Biomol NMR       Date:  2019-10-23       Impact factor: 2.835

Review 7.  Emerging solution NMR methods to illuminate the structural and dynamic properties of proteins.

Authors:  Haribabu Arthanari; Koh Takeuchi; Abhinav Dubey; Gerhard Wagner
Journal:  Curr Opin Struct Biol       Date:  2019-07-19       Impact factor: 6.809

8.  15N CEST data and traditional model-free analysis capture fast internal dynamics of DJ-1.

Authors:  Jonathan Catazaro; Tessa Andrews; Nicole M Milkovic; Jiusheng Lin; Austin J Lowe; Mark A Wilson; Robert Powers
Journal:  Anal Biochem       Date:  2017-11-21       Impact factor: 3.365

9.  Effects of maturation on the conformational free-energy landscape of SOD1.

Authors:  Robert M Culik; Ashok Sekhar; Jayashree Nagesh; Harmeen Deol; Jessica A O Rumfeldt; Elizabeth M Meiering; Lewis E Kay
Journal:  Proc Natl Acad Sci U S A       Date:  2018-02-26       Impact factor: 11.205

10.  Probing excited conformational states of nucleic acids by nitrogen CEST NMR spectroscopy.

Authors:  Bo Zhao; Jared T Baisden; Qi Zhang
Journal:  J Magn Reson       Date:  2019-11-11       Impact factor: 2.229

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.