ArticleJournal of biomolecular NMR2013
Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.
Article in Journal of biomolecular NMR, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33 citing papers in PubMed.
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- Contribution of protein conformational heterogeneity to NMR lineshapes at cryogenic temperatures.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Distinguishing Different Hydrogen-Bonded Helices in Proteins by EfficientBiochemistry · 2024Article
- The Stabilization of S100A9 Structure by Calcium Inhibits the Formation of Amyloid Fibrils.International journal of molecular sciences · 2023Article
- Transient RNA Interactions Leave a Covalent Imprint on a Viral Capsid Protein.Journal of the American Chemical Society · 2022Article
- Selective observation of semi-rigid non-core residues in dynamically complex mutant huntingtin protein fibrils.Journal of structural biology: X · 2022Article
- POKY software tools encapsulating assignment strategies for solution and solid-state protein NMR data.Journal of structural biology: X · 2022Article
- Molecular conformations and dynamics in the extracellular matrix of mammalian structural tissues: Solid-state NMR spectroscopy approaches.Matrix biology plus · 2021Review
- Real-time observation of structure and dynamics during the liquid-to-solid transition of FUS LC.Biophysical journal · 2021Article
- Structural Arrangement within a Peptide Fibril Derived from the Glaucoma-Associated Myocilin Olfactomedin Domain.The journal of physical chemistry. B · 2021Article
- Regulatory inter-domain interactions influence Hsp70 recruitment to the DnaJB8 chaperone.Nature communications · 2021Article
- Solid-state NMR spectroscopy.Nature reviews. Methods primers · 2021Article
- Solid-state NMR investigation of the involvement of the P2 region in tau amyloid fibrils.Scientific reports · 2020Article
- Out-of-Register Parallel β-Sheets and Antiparallel β-Sheets Coexist in 150-kDa Oligomers Formed by Amyloid-β(1-42).Journal of molecular biology · 2020Article
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Abstract
We introduce a Python-based program that utilizes the large database of (13)C and (15)N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D (13)C-(13)C, (15)N-(13)C, or 3D (15)N-(13)C-(13)C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D (13)C-(13)C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the Cα and Cβ chemical shifts, the highest-ranked PLUQ assignments were 40-60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO-Cα-Cβ or N-Cα-Cβ), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination.
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