研究課題
Proteins that are large, membrane-bound, or studied in living cells by in-cell NMR can in general not be assigned by the conventional solution NMR method that relies on uniform 13C/15N-labeling because the resonance lines become too broad and overlapping. Sparse labeling, in particular of methyl groups is an approach to restore interpretable spectra by drastically reducing relaxation rates and the number of signals. However, it remains difficult to establish resonance assignments, even if the three-dimensional structure of the protein is already known. In this project we develop computational methods to assign the spectra of sparsely labeled difficult proteins by structure-based automated assignment. On the basis of our existing FLYA algorithm for the assignment of uniformly labeled proteins, a new automated assignment method has been developed that can assign large proteins using methyl group labeling or other sparse labeling techniques, and NOESY spectra in conjunction with a known three-dimensional structure. The FLYA algorithm finds assignments by optimizing a mapping between the expected peaks, which one anticipates to see based on the protein sequence, and the measured peaks, which have been identified by peak picking. The general design of the algorithm makes it possible to exploit peak lists from virtually any type of NMR spectrum. In particular, we could show that FLYA is able to assign proteins using as input exclusively NOESY spectra. The new approach has been applied to large proteins up to 468 kDa size and to proteins in living cells.
すべて 2020 2019 その他
すべて 雑誌論文 (6件) (うち国際共著 6件、 査読あり 6件、 オープンアクセス 5件) 学会発表 (3件) (うち国際学会 2件、 招待講演 3件) 備考 (1件)
Progress in NMR Spectroscopy
巻: 118-119 ページ: 54-73
10.1016/j.pnmrs.2020.04.001
Journal of the American Chemical Society
巻: 142 ページ: 5793-5799
10.1021/jacs.0c00251
Journal of Biomolecular NMR
巻: 74 ページ: 45-60
10.1007/s10858-019-00289-7
Nature Communications
巻: 10 ページ: 4922
10.1038/s41467-019-12837-8
巻: 10 ページ: 2697
10.1038/s41467-019-10490-9
International Journal of Molecular Science
巻: 20 ページ: 2442
10.3390/ijms20102442
http://www.cyana.org/
