Automatic methyl assignment in large proteins by the MAGIC algorithm

Journal of Biomolecular NMR
Yoan R MonneauCharalampos G Kalodimos

Abstract

Selective methyl labeling is an extremely powerful approach to study the structure, dynamics and function of biomolecules by NMR. Despite spectacular progress in the field, such studies remain rather limited in number. One of the main obstacles remains the assignment of the methyl resonances, which is labor intensive and error prone. Typically, NOESY crosspeak patterns are manually correlated to the available crystal structure or an in silico template model of the protein. Here, we propose methyl assignment by graphing inference construct, an exhaustive search algorithm with no peak network definition requirement. In order to overcome the combinatorial problem, the exhaustive search is performed locally, i.e. for a small number of methyls connected through-space according to experimental 3D methyl NOESY data. The local network approach drastically reduces the search space. Only the best local assignments are combined to provide the final output. Assignments that match the data with comparable scores are made available to the user for cross-validation by additional experiments such as methyl-amide NOEs. Several NMR datasets for proteins in the 25-50 kDa range were used during development and for performance evaluation against th...Continue Reading

References

Nov 1, 1995·Journal of Biomolecular NMR·F DelaglioA Bax
Nov 6, 2003·Journal of the American Chemical Society·Vitali Tugarinov, Lewis E Kay
Aug 12, 2004·Chemical Reviews·Andrew R Pickford, Iain D Campbell
Aug 3, 2005·Chembiochem : a European Journal of Chemical Biology·Vitali Tugarinov, Lewis E Kay
Jan 24, 2007·Nature·Remco Sprangers, Lewis E Kay
Nov 29, 2007·Journal of the American Chemical Society·Rivka L IsaacsonStephen Matthews
Dec 31, 2008·Journal of Biomolecular NMR·Isabel AyalaJérôme Boisbouvier
Apr 11, 2009·Proceedings of the National Academy of Sciences of the United States of America·Nataliya PopovychCharalampos G Kalodimos
Sep 29, 2009·Journal of Biomolecular NMR·Amy M Ruschak, Lewis E Kay
Dec 22, 2009·Journal of Biomolecular NMR·Dirk StratmannCarine van Heijenoort
Jun 1, 2011·Journal of Biomolecular NMR·Carlos AmeroJérôme Boisbouvier
Jan 8, 2013·Journal of Biomolecular NMR·Yingqi Xu, Stephen Matthews
Oct 1, 2013·Journal of Biomolecular NMR·Roman J LichteneckerRobert Konrat
May 9, 2014·Science·Tomohide SaioCharalampos G Kalodimos
Jun 11, 2014·Journal of Magnetic Resonance·Fa-An ChaoGianluigi Veglia
Dec 17, 2014·Bioinformatics·Woonghee LeeJohn L Markley
Sep 26, 2015·Current Opinion in Structural Biology·Silke Wiesner, Remco Sprangers
Aug 9, 2016·Nature·Chengdong HuangCharalampos G Kalodimos
Apr 5, 2017·Annual Review of Biophysics·Chengdong Huang, Charalampos G Kalodimos
Jul 12, 2017·Journal of the American Chemical Society·Iva PritišanacAndrew J Baldwin

❮ Previous
Next ❯

Citations

Jan 4, 2020·Journal of Biomolecular NMR·Ricarda TörnerJerome Boisbouvier
Oct 31, 2019·Nature Communications·Iva PritišanacPeter Güntert
Dec 22, 2017·Chemistry : a European Journal·Celestine N ChiBeat Vögeli
Mar 5, 2020·Progress in Nuclear Magnetic Resonance Spectroscopy·Stefan Schütz, Remco Sprangers
Nov 5, 2020·Nature Communications·Soumya P BeheraHaribabu Arthanari
Jan 31, 2021·Nature Communications·Santrupti NerliNikolaos G Sgourakis
Sep 5, 2020·Progress in Nuclear Magnetic Resonance Spectroscopy·Iva PritišanacPeter Güntert
Jun 2, 2018·Methods : a Companion to Methods in Enzymology·Sebastien Alphonse, Ranajeet Ghose
Jul 1, 2018·Methods : a Companion to Methods in Enzymology·Scott D GormanDavid D Boehr
May 15, 2021·Biomolecular NMR Assignments·Ricarda TörnerJerome Boisbouvier
Nov 15, 2021·Journal of Molecular Biology·Tao XieCharalampos G Kalodimos

❮ 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.