Protein structure and dynamics at the Swedish NMR Center

Dnr:

SNIC 2016/5-61

Type:

SNAC Small

Principal Investigator:

Vladislav Orekhov

Affiliation:

Göteborgs universitet

Start Date:

2017-01-01

End Date:

2018-01-01

Primary Classification:

10601: Strukturbiologi

Webpage:

http://www.nmr.gu.se/

Allocation

Abstract

The Swedish NMR Centre (SNC) is a national facility funded by the University of Gothenburg, the Knut and Alice Wallenberg Foundation, the Swedish Research Council and SciLifeLab. SNC provides access to state of art NMR equipment and methodology for Swedish, Scandinavian, and European scientists. We are involved in a number of local and collaboration projects in the fields of molecular structural biology, metabolomics, material sciences, etc. Usage of the cluster during 2013-2016 was highly valuable and was acknowledged in a number of scientific publications. The actual usage of the NCS cluster significantly increased at the end of 2016 and exceeded the allocated value of 3 000 hours/month. In 2017, we plan to routinely use heavy calculations and will need at least 5 000 hours/month on average with peak demand up to 15 000 hours/month. We apply for a renewal of the time allocation on the NCS cluster to be able to calculate structures of proteins using, well established programs such as Matlab, CS-Rosetta [1], CYANA [2], CNS[4], and newly introduced program YASARA as well as to perform advanced signal processing using our own implementations of compressed sensing and parallel factor analysis algorithms in software MddNMR [3]. YASARA, which is the most computationally demanding program, is of great use in our structural biology projects. MddNMR is a publicly available program, which is being developed at the Swedish NMR Centre over ten years. It is designed to make the best use of the NMR spectrometer time and for automation of the spectra analysis. By using of novel signal processing algorithms, we can reduce the experiment time 10-100 times relative to the traditional approach. The software also saves large amount of manual work on the spectra analysis. These results come, however, with significant amount of calculations. 1. Consistent blind protein structure generation from NMR chemical shift data Yang Shen, Oliver Lange, Frank Delaglio, et al. Proc Natl Acad Sci USA, (2008) 105, 4685-4690 2. Herrmann, T., Güntert, P. & Wüthrich, K. Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J. Mol. Biol. 319, 209–227 (2002) 3. Orekhov, V.Y. and V.A. Jaravine, Analysis of non-­uniformly sampled spectra with Multi-­Dimensional Decomposition. Progress in Nuclear Magnetic Resonance Spectroscopy, 2011. 59: p. 271-292. 4. A.T. Brunger, Version 1.2 of the Crystallography and NMR System, Nature Protocols 2, 2728-2733 (2007).