Protein structure and dynamics at the Swedish NMR Center
Title: Protein structure and dynamics at the Swedish NMR Center
SNIC Project: SNIC 2013/1-347
Project Type: SNAC Medium
Principal Investigator: Vladislav Orekhov <vladislav.orekhov@nmr.gu.se>
Affiliation: Göteborgs universitet
Duration: 2014-01-01 – 2015-01-01
Classification: 10601 10602 10603
Homepage: http://www.nmr.gu.se/
Keywords:

Abstract

The Swedish NMR Centre is a national and EU funded facility, which 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 was highly valuable and will be acknowledged in several scientific publication. In 2014, we plan to increase (from the current level) use of the computational recourses. 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 CS-Rosetta [1], CYANA [2], and ARIA [3], as well as to perform advanced signal processing using our own implementations of compressed sensing and parallel factor analysis algorithms in software MddNMR [4]. CS Rosetta, which is the most computationally demanding program, will be of great use in our structural biology projects. Already at an early stage, often within a couple of days, we will be able to calculate a preliminary model of protein structure. In many practical cases, the structures produced by Rosetta will be sufficient for answering specific biological questions, for example, for interpreting protein interactions with other molecules. For obtaining the high-resolution structures, we will use CYANA and ARIA. 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. Rieping W., Habeck M., Bardiaux B., Bernard A., Malliavin T.E., Nilges M. (2007) ARIA2: automated NOE assignment and data integration in NMR structure calculation. Bioinformatics 23:381-382. 4. Jaravine, V., I. Ibraghimov and V. Y. Orekhov (2006). "Removal of time barrier for high-resolution multidimensional NMR spectroscopy." Nature Methods 3(8): 605-607.