2019 Fiscal Year Annual Research Report
Enabling NMR studies of sparsely labelled large proteins by automated assignment
| Project/Area Number |
17K07312
|
|---|
| Research Institution | Tokyo Metropolitan University |
|---|
Principal Investigator |
PETER GUENTERT 首都大学東京, 理学研究科, 客員教授 (20392110)
|
|---|
| Co-Investigator(Kenkyū-buntansha) |
池谷 鉄兵 首都大学東京, 理学研究科, 助教 (30457840)
|
|---|
| Project Period (FY) |
2017-04-01 – 2020-03-31
|
| Keywords | protein NMR / in-cell NMR / resonance assignment / automated assignment / methyl groups / isotope labeling |
|---|
| Outline of Annual Research Achievements |
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.
|
-
-
[Journal Article] Automated backbone NMR resonance assignment of large proteins using redundant linking from a single simultaneous acquisition2020
Author(s)
Stanek, J., Schubeis, T., Paluch, P., Guentert, P., Andreas, L. B., Pintacuda, G.
-
Journal Title
Journal of the American Chemical Society
Volume: 142
Pages: 5793-5799
DOI
Peer Reviewed / Int'l Joint Research
-
[Journal Article] Backbone and methyl assignment of bacteriorhodopsin incorporated into nanodiscs2020
Author(s)
Kooijman, L., Ansorge, P., Schuster, M., Baumann, C., Loehr, F., Jurt, S., Guentert, P., Zerbe, O.
-
Journal Title
Journal of Biomolecular NMR
Volume: 74
Pages: 45-60
DOI
Peer Reviewed / Open Access / Int'l Joint Research
-
-
[Journal Article] Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex2019
Author(s)
Gauto, D. F., Estrozi, L. F., Schwieters, C. D., Effantin, G., Macek, P., Sounier, R., Sivertsen, A. C., Schmidt, E., Kerfah, R., Mas, G., Colletier, J.-P., Guentert, P., Favier, A., Schoehn, G., Schanda, P., Boisbouvier, J.
-
Journal Title
Nature Communications
Volume: 10
Pages: 2697
DOI
Peer Reviewed / Open Access / Int'l Joint Research
-
-
-
-
-
