‘Towards new applications of NMR spectroscopy in chemical and

biomolecular structural studies’ Project supported by Foundation for Polish Science – TEAM Programme

Project duration: 2010, December – 2014, November

Discipline: NMR spectroscopy

Head of the TEAM: prof. Wiktor Koźmiński

Location: Faculty of Chemistry, University of Warsaw

Project goals

The main goal of the project is development of new experimental techniques and processing methods aimed at precise determination of spectral parameters, like chemical shifts, scalar and residual dipolar couplings from multidimensional NMR spectra. We will focus attention on the emerging field of biomolecules like proteins and nucleic acids, however new application for small and medium size organic compounds (as for example polyprenols and steroids [12]) are also considered. The new methods should provide access to precise values of NMR parameters which are not presently obtainable, but would enable faster and more exact determination of high resolution 3D structures of larger biomolecules.

One of not satisfactorily solved problems of nonlinearly sampled NMR data sets are artifacts. Artifacts in the spectra of low dynamic range of signal intensities are tolerable (for example in experiments for protein backbone assignment), however they may obscure weak signals in the case of NOESY spectra featuring wider range of peak intensities. Therefore, one of important project goals will be improvement of MFT-based processing procedures eliminating artifacts.

The practical aim of the project is better utilization of existing NMR hardware, and dissemination of DASP (Digital Alias-free Signal Processing) methodology in different fields of science and technology. The economical aspect is crucial here. The employment of new methods developed in the project would contribute to more efficient use of expensive NMR equipment.

The development of NMR methodology, essential for the project, will be conducted in Structural Research Laboratory of Chemistry Department University of Warsaw, where we are primary users of 700 MHz Varian NMR Systems spectrometer. Experiments developed until now (and listed above) have been tested on standard samples. Presently, we use three standard samples of proteins: human ubiquitin (¹³C,¹⁵N labeled) and Maltose Binding Protein (MBP, both ¹³C,¹⁵N and ²H,¹³C,¹⁵N labeled). All of them are very useful for testing purposes: ubiquitin is small (76 residues) protein with well know NMR spectra and is used for initial testing of the new methods, MBP on the other hand, is example of large protein (370 residues), and we use it to prove applicability of new experiments to large, slowly tumbling molecules. NMR measurements on different, non-standard samples with employment of MFT approach have been performed in the past thank to cooperation with various foreign partners (listed above, mostly from Slovenia and Ukraine). Foreign partners reaped the benefits of random sampling in NMR, while we had an opportunity to check the applicability of the approach to collection of data needed for explanation of real biological mechanisms.

We believe that this model of cooperation will still provide mutual benefits and can be successfully continued. Moreover, we believe that young researchers from our lab could gather very useful knowledge exploiting the experience of our foreign partners in various fields of structural biology. This would allow us to extend the area of activities performed in our laboratory and establish a genuine structural research there. Foreign partners will provide access to their well-equipped facilities, sharing access to specialized instrumentation (like cryogenically cooled probes) that is not available in Warsaw. Access to spectrometers of different vendors would also help us to develop instrument specific software. Additionally, the cooperation in protein expression and purification is planned, in order to obtain other interesting samples. We also plan to purchase additional commercially available protein standards of different sizes and co-solvents for RDC measurements.

Foreign partners

· prof. Martin Billeter – Department of Chemistry, Swedish NMR Center, University of Göteborg, Göteborg, Sweden

· prof. Janez Plavec – Slovenian NMR Center, National Institute of Chemistry, Ljubljana, Slovenia

· prof. Vladimír Sklenář – National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic

· dr. Andrzej Tarczyński – School of Informatics University of Westminster, London, England

Recruitment procedure

The project aim is to engage the best students and postdocs from Poland and abroad, and provide them an opportunity to work in team on interesting and perspective project with important potential theoretical and practical goals. The research tasks will be distributed between the team members according to their individual skills and interest. Successful candidates will obtain status of MSc and PhD students, or staff (postdocs) of Chemistry Department University of Warsaw, according to internal regulations. During conducting the project, students should obtain MSc and PhD diplomas, while the postdocs would have an opportunity to start their independent research which should be a first step to obtain habilitation in a short time. Postdoc positions will be offered for 12 or 24 months with the option to extend for another period. All candidates should be strongly interested in work in the emerging field of methodology of modern NMR spectroscopy. The most important recruitment criterion is a outstanding motivation.

Criteria for Ph.D. students:

- diploma in chemistry or biophysics

- understanding of NMR spectroscopy

- basic programming skills

- written and oral English

- experience in operating of NMR spectrometers would an advantage

- motivation to conduct PhD studies on high scientific level

Criteria for students:

- background in chemistry or biophysics

- some experience with NMR spectroscopy

- basic programming skills

- written English

- motivation to obtain MSc diploma solving important scientific problems

Benefits:

PhD students	students
monthly income of 3500 PLN (non-taxed)	monthly income of 1000 PLN (non-taxed)

Candidates are asked to provide:

- Cover letter, describing Candidate motivation

- Curriculum Vitae (CV)

- Academic transcripts (students)

- Degree certificates with academic transcripts (Ph. D. students)

- Ph. D. certificate (postdocs)

- One or more letters of recommendation from a scientist who is familiar with the Candidate, submitted directly to program laureate

- Information about scientific publications, scholarships, prizes and awards or other relevant documents demonstrating the excellence of Candidate (if applicable)

- A list of attended conferences with titles and authors of presentations

Candidates should send application documents by 3-th June 2013 to team.kozminski@chem.uw.edu.pl