On the problem of resonance assignments in solid state NMR of uniformly ¹⁵N,¹³C-labeled proteins

Journal of Magnetic Resonance
Robert Tycko

Abstract

Determination of accurate resonance assignments from multidimensional chemical shift correlation spectra is one of the major problems in biomolecular solid state NMR, particularly for relative large proteins with less-than-ideal NMR linewidths. This article investigates the difficulty of resonance assignment, using a computational Monte Carlo/simulated annealing (MCSA) algorithm to search for assignments from artificial three-dimensional spectra that are constructed from the reported isotropic (15)N and (13)C chemical shifts of two proteins whose structures have been determined by solution NMR methods. The results demonstrate how assignment simulations can provide new insights into factors that affect the assignment process, which can then help guide the design of experimental strategies. Specifically, simulations are performed for the catalytic domain of SrtC (147 residues, primarily β-sheet secondary structure) and the N-terminal domain of MLKL (166 residues, primarily α-helical secondary structure). Assuming unambiguous residue-type assignments and four ideal three-dimensional data sets (NCACX, NCOCX, CONCA, and CANCA), uncertainties in chemical shifts must be less than 0.4 ppm for assignments for SrtC to be unique, and less...Continue Reading

References

May 1, 1997·Journal of Chemical Information and Computer Sciences·K B Li, B C Sanctuary
Mar 1, 1997·Journal of Magnetic Resonance·N E BuchlerR A Goldstein
Jan 1, 1997·Annual Review of Physical Chemistry·J N OnuchicP G Wolynes
Dec 7, 2000·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·C Bailey-KelloggB R Donald
Apr 15, 2004·Journal of the American Chemical Society·Simon SharpeRobert Tycko
Apr 22, 2004·Journal of the American Chemical Society·Tatyana I IgumenovaAnn E McDermott
Mar 7, 2006·Journal of Biomolecular NMR·Ansgar B SiemerBeat H Meier
Feb 7, 2007·Journal of the American Chemical Society·Amir GoldbourtAnn E McDermott
Aug 10, 2007·Journal of Biomolecular NMR·W Trent FranksChad M Rienstra
Aug 19, 2007·Journal of the American Chemical Society·Lingling ChenLeonard J Mueller
Apr 26, 2008·Proceedings of the National Academy of Sciences of the United States of America·Jonathan J HelmusChristopher P Jaroniec
May 7, 2008·Journal of Biomolecular NMR·Alexander LemakMiguel Llinás
Feb 27, 2009·Journal of Molecular Biology·Lichi ShiVladimir Ladizhansky
Aug 2, 2011·Journal of Biomolecular NMR·Birgit HabensteinAnja Böckmann
Nov 10, 2011·Biophysical Journal·Kan-Nian HuRobert Tycko
Jul 17, 2012·Journal of the American Chemical Society·Elena Schmidt, Peter Güntert
Jul 19, 2012·Journal of Biomolecular NMR·Jonas FredrikssonMartin Billeter
May 22, 2013·Journal of Biomolecular NMR·Elena SchmidtPeter Güntert
Dec 29, 2013·Journal of Molecular Biology·Marvin J BayroRobert Tycko
May 13, 2014·Journal of Biomolecular NMR·Jakob Toudahl NielsenNiels Chr Nielsen
Aug 8, 2014·Journal of the American Chemical Society·Emeline Barbet-MassinGuido Pintacuda
Sep 7, 2014·Journal of Biomolecular NMR·ShengQi XiangAdam Lange
Sep 16, 2014·Structure·Lijing SuJosep Rizo

❮ Previous
Next ❯

Citations

Apr 27, 2021·Journal of the American Chemical Society·Blake D FondaDylan T Murray
Aug 10, 2021·Nature Reviews. Methods Primers·Bernd ReifMei Hong

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.