Rat NKRP1A and NKRP1B proteins studied by vibrational spectroscopy and molecular modeling
K. Hofbauerová1, 2, V. Kopecký Jr.2, O. Vaněk3, L. Mihók1, R. Ettrich4, K. Bezouška1, 3
1Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4, CZ-14220, Czech Republic
2Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, Prague 2, CZ-12116, Czech Republic
3Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, Prague 2, CZ-12840, Czech Republic
4Laboratory of High Performance Computing, Institute of Physical Biology of USB and Institute of Systems Biology and Ecology of AS CR, Zámek 136, Nové Hrady, CZ-37333, Czech Republic
Lectin-like receptors of the C-type lectin family are important antigens at the surface of immune cells. Natural killer receptor protein 1 (NKRP1) is a lectin-like receptor of a natural killer cell, where NKRP1A is an activating and NKRP1B an inhibitory one. The activating and inhibitory signals launched by these receptors regulate effector functions of natural killer cells such as killing malignantly transformed, viral infected, or stressed cells . NKRP1 proteins are unique for their high affinities for the classical ligands of C-type lectins – carbohydrates. These proteins prefer to bind linear but not branched oligosaccharides . Binding of complex carbohydrates opens a possible way to medical applications.
Therefore, the aim of our study is to characterize structure of NKRP1 proteins and structural changes upon ligand binding. To initiate ligand binding studies, we have prepared soluble forms of rat NKRP1A and B proteins by recombinant expression of their extracellular domains in E. coli followed by in vitro refolding. Structure of the proteins was investigated by infrared, Raman and drop coating deposition Raman spectroscopy. Homology modeling of the proteins was provided as well. It was found that the structure of both proteins is very similar and spectral differences are caused mainly by a different amino acid composition of the peptide chains. However, significant differences exist. The influence of binding of ligands, complex branched oligosaccharides, on the secondary structure as well as on local environments was followed by infrared and Raman difference spectroscopy. Protein behaviour in solution was studied by molecular dynamics simulation. Results from theoretical calculations were critically confronted with experimental measurements, whereas good agreement was reached.
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2. K. Bezouška, Collect. Czech. Chem. Commun., 69, (2004), 535.
The research was supported by Ministry of Education of the Czech Republic (Nos. MSM 0021620835, MSM 0021620808), by the Institutional Research Concept (No. AVOZ 50200510), and by the Grant Agency of the Czech Republic (No. A5020403).