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Cited by 9Advanced NMR Techniques and ApplicationsProtein Structure and DynamicsMolecular spectroscopy and chirality

Progress toward automated methyl assignments for methyl-TROSY applications

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Clay, Mary C., Saleh, Tamjeed, Kamatham, Samuel, Rossi, Paolo, Kalodimos, Charalampos G.·2022·Structure
DOI 10.1016/j.str.2021.11.009PMC PMC8741727
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Abstract

Methyl-TROSY spectroscopy has extended the reach of solution-state NMR to supra-molecular machineries over 100 kDa in size. Methyl groups are ideal probes for studying structure, dynamics, and protein-protein interactions in quasi-physiological conditions with atomic resolution. Successful implementation of the methodology requires accurate methyl chemical shift assignment, and the task still poses a significant challenge in the field. In this work, we outline the current state of technology for methyl labeling, data collection, data analysis, and nuclear Overhauser effect (NOE)-based automated methyl assignment approaches. We present MAGIC-Act and MAGIC-View, two Python extensions developed as part of the popular NMRFAM-Sparky package, and MAGIC-Net a standalone structure-based network analysis program. MAGIC-Act conducts statistically driven amino acid typing, Leu/Val pairing guided by 3D HMBC-HMQC, and NOESY cross-peak symmetry checking. MAGIC-Net provides model-based NOE statistics to aid in selection of a methyl labeling scheme. The programs provide a versatile, semi-automated framework for rapid methyl assignment.

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  • Methyl side-chain NMR assignments can be obtained using only methyl-methyl NOEs from 3D NMR experiments and atomic coordinates of a structure or AF2 model as input with software such as MAUS, MAGIC, and methylFLYA.

    “Here, NMR assignments for methyl side-chain groups can be obtained using only methyl-methyl NOEs obtained from 3D NMR experiments and the atomic coordinates of a structure (or AF2 predicted structure) as input with software such as MAUS, MAGIC, and methylFLYA91,93,94.”

    From The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins (2024) · cites this paper as [94]

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Authors
Clay, M. C., Saleh, T., Kamatham, S., Rossi, P., & Kalodimos, C. G.
Affiliations
St. Jude Children's Research Hospital (US)
Corresponding author
  • Rossi, Paolo
  • Kalodimos, Charalampos G.
ORCID
Venue
Structure
Publisher
Elsevier BV
Published
2022-01
Volume
30
Issue
1
Pages
69-79.e2
ISSN
0969-2126 (ISSN-L)
DOI
10.1016/j.str.2021.11.009
PMC
PMC8741727
OpenAlex
W4200568296
Cited by
9
References
54
Citations by year
2026: 2 · 2025: 1 · 2024: 2 · 2023: 3 · 2022: 1
FWCI
0.55
Type
journal article
Language
en
Open access
Licence
Locations
  • Structure (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • American Lebanese Syrian Associated Charities
  • National Institutes of Health (R35 GM122462)
Topics
  • Physical Sciences › Chemistry › Spectroscopy › Advanced NMR Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Chemistry › Spectroscopy › Molecular spectroscopy and chirality
Keywords
nuclear Overhauser effect, protein-protein interaction, supramolecular self-assembly
MeSH terms
Algorithms, Amino Acids, Humans, Methylation, Models, Molecular, Protein Binding, Proteins, Nuclear Magnetic Resonance, Biomolecular

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