An Efficient Combination of BEST and NUS Methods in Multidimensional NMR Spectroscopy for High Throughput Analysis of Proteins

Overview

Journal RSC Adv

Publisher Royal Society of Chemistry

Specialty Chemistry

Date 2022 May 11

PMID 35542095

Authors

Veera Mohana Rao Kakita

Mandar Bopardikar

Vaibhav Kumar Shukla

Kavitha Rachineni

Priyatosh Ranjan

Jai Shankar Singh

Ramakrishna V Hosur

Affiliations

Soon will be listed here.

Abstract

Application of Non Uniform Sampling (NUS) along with Band-selective Excitation Short-Transient (BEST) NMR experiments has been demonstrated for obtaining the important residue-specific atomic level backbone chemical shift values in short durations of time. This application has been demonstrated with both well-folded (ubiquitin) and unfolded (α-synuclein) proteins alike. With this strategy, the experiments required for determining backbone chemical shifts can be performed very rapidly, , in ∼2 hours of spectrometer time, and this data can be used to calculate the backbone folds of proteins using well established algorithms. This will be of great value for structural proteomic investigations on one hand, where the speed of structure determination is a limiting factor and for application in the study of slow kinetic processes involving proteins, such as fibrillization, on the other hand.

Citing Articles

Experimental methods to study the structure and dynamics of intrinsically disordered regions in proteins.

Maiti S, Singh A, Maji T, Saibo N, De S Curr Res Struct Biol. 2024; 7:100138.

PMID: 38707546 PMC: 11068507. DOI: 10.1016/j.crstbi.2024.100138.

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

Arthanari H, Takeuchi K, Dubey A, Wagner G Curr Opin Struct Biol. 2019; 58:294-304.

PMID: 31327528 PMC: 6778509. DOI: 10.1016/j.sbi.2019.06.005.

References

Orekhov V, Jaravine V . Analysis of non-uniformly sampled spectra with multi-dimensional decomposition. Prog Nucl Magn Reson Spectrosc. 2011; 59(3):271-92. DOI: 10.1016/j.pnmrs.2011.02.002. View

Schanda P, Van Melckebeke H, Brutscher B . Speeding up three-dimensional protein NMR experiments to a few minutes. J Am Chem Soc. 2006; 128(28):9042-3. DOI: 10.1021/ja062025p. View

Chen J, Nietlispach D, Shaka A, Mandelshtam V . Ultra-high resolution 3D NMR spectra from limited-size data sets. J Magn Reson. 2004; 169(2):215-24. DOI: 10.1016/j.jmr.2004.04.017. View

Kim S, Szyperski T . GFT NMR, a new approach to rapidly obtain precise high-dimensional NMR spectral information. J Am Chem Soc. 2003; 125(5):1385-93. DOI: 10.1021/ja028197d. View

Szyperski T, Atreya H . Principles and applications of GFT projection NMR spectroscopy. Magn Reson Chem. 2006; 44 Spec No:S51-60. DOI: 10.1002/mrc.1817. View

Volles M, Lansbury Jr P . Relationships between the sequence of alpha-synuclein and its membrane affinity, fibrillization propensity, and yeast toxicity. J Mol Biol. 2007; 366(5):1510-22. PMC: 1868670. DOI: 10.1016/j.jmb.2006.12.044. View

Hashimoto M, Masliah E . Alpha-synuclein in Lewy body disease and Alzheimer's disease. Brain Pathol. 1999; 9(4):707-20. PMC: 8098211. DOI: 10.1111/j.1750-3639.1999.tb00552.x. View

Chugh J, Kumar D, Hosur R . Tuning the HNN experiment: generation of serine-threonine check points. J Biomol NMR. 2007; 40(2):145-52. DOI: 10.1007/s10858-007-9217-z. View

Kupce E, Freeman R . Projection-reconstruction technique for speeding up multidimensional NMR spectroscopy. J Am Chem Soc. 2004; 126(20):6429-40. DOI: 10.1021/ja049432q. View

10.

Hiller S, Fiorito F, Wuthrich K, Wider G . Automated projection spectroscopy (APSY). Proc Natl Acad Sci U S A. 2005; 102(31):10876-81. PMC: 1182451. DOI: 10.1073/pnas.0504818102. View

11.

Vallurupalli P, Bouvignies G, Kay L . Increasing the exchange time-scale that can be probed by CPMG relaxation dispersion NMR. J Phys Chem B. 2011; 115(49):14891-900. DOI: 10.1021/jp209610v. View

12.

Polymeropoulos M, Lavedan C, Leroy E, Ide S, Dehejia A, Dutra A . Mutation in the alpha-synuclein gene identified in families with Parkinson's disease. Science. 1997; 276(5321):2045-7. DOI: 10.1126/science.276.5321.2045. View

13.

Deschamps M, Campbell I . Cooling overall spin temperature: protein NMR experiments optimized for longitudinal relaxation effects. J Magn Reson. 2005; 178(2):206-11. DOI: 10.1016/j.jmr.2005.09.011. View

14.

Cavalli A, Salvatella X, Dobson C, Vendruscolo M . Protein structure determination from NMR chemical shifts. Proc Natl Acad Sci U S A. 2007; 104(23):9615-20. PMC: 1887584. DOI: 10.1073/pnas.0610313104. View

15.

Winner B, Jappelli R, Maji S, Desplats P, Boyer L, Aigner S . In vivo demonstration that alpha-synuclein oligomers are toxic. Proc Natl Acad Sci U S A. 2011; 108(10):4194-9. PMC: 3053976. DOI: 10.1073/pnas.1100976108. View

16.

Isaksson L, Mayzel M, Saline M, Pedersen A, Rosenlow J, Brutscher B . Highly efficient NMR assignment of intrinsically disordered proteins: application to B- and T cell receptor domains. PLoS One. 2013; 8(5):e62947. PMC: 3647075. DOI: 10.1371/journal.pone.0062947. View

17.

Panchal S, Bhavesh N, Hosur R . Improved 3D triple resonance experiments, HNN and HN(C)N, for HN and 15N sequential correlations in (13C, 15N) labeled proteins: application to unfolded proteins. J Biomol NMR. 2001; 20(2):135-47. DOI: 10.1023/a:1011239023422. View

18.

Schanda P, Kupce E, Brutscher B . SOFAST-HMQC experiments for recording two-dimensional heteronuclear correlation spectra of proteins within a few seconds. J Biomol NMR. 2005; 33(4):199-211. DOI: 10.1007/s10858-005-4425-x. View

19.

Chakraborty S, Paul S, Hosur R . Simultaneous acquisition of 13Cα-15N and 1H-15N-15N sequential correlations in proteins: application of dual receivers in 3D HNN. J Biomol NMR. 2011; 52(1):5-10. DOI: 10.1007/s10858-011-9596-z. View

20.

Wishart D . Interpreting protein chemical shift data. Prog Nucl Magn Reson Spectrosc. 2011; 58(1-2):62-87. DOI: 10.1016/j.pnmrs.2010.07.004. View