Doktorské studium

Studijní obor Biomolekulární chemie

Název práce: Metodologie určování struktur excitovaných stavů proteinů pomocí NMR spektroskopie

Školitel: doc. RNDr. Radovan Fiala, CSc.

Předběžné zadání:
Intramolecular motions are crucial for the function of many biomolecules. The structural variability of proteins allows them to adapt their conformation during the process of interaction with biding partners, enzymatic product release, it is involved in biological process activity regulation (for example allostery), etc. The motional modes most interesting from the biological point of view often occure within microsecond to millisecond time window. These motions include conformation switches between a major state of a protein and its low populated excited state. The protein motions can be studied by specialized NMR methods via analysis of NMR relaxation rates. Pioneering studies showed that analysis can provide even the structures of proteins whose populations are very low (around 1%), yet important and biological relevant. The present project focuses on a development of the protocols for measurement and analysis of NMR data to allow the structure determination of the excited states of proteins. The methods will be tested with proteins known to undergo a motion within the given range of timescales to prove the practical applicability of the designed experiments.
CAVANAGH, John. Protein NMR spectroscopy : principles and practice. 2nd ed. Amsterdam: Elsevier, 2007. xxv, 885. ISBN 9780121644918.
Further reading Vallurupalli P, Bouvignies G, Kay LE (2012) Studying "Invisible" Excited Protein States in Slow with a Major State Conformation, J. Am. Chem. Soc.134: 8148-8161 Hansen DF, Vallurupalli P, Kay LE (2008) Quantifying Two-Bond 1HN-13CO and One-Bond 1H-13C Dipolar Couplings of Invisible Protein States by Spin-State Selective Relaxation Dispersion NMR Spectroscopy. J. Am. Chem. Soc. 130: 8397-8405 As the project requires understanding the theory of nuclear relaxation, the candidate should have a solid background in physics.

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