THE BINDING OF SELECTED LIGANDS TO HUMAN a1-ACID GLYCOPROTEIN STUDIED BY COMBINED APPROACH OF MOLECULAR MODELING AND VIBRATIONAL SPECTROSCOPY
V.
Kopecký Jr.,1 R. Ettrich,2 L. Lüley,2
K. Hofbauerová,3,4 V. Baumruk,1
1Institute of Physics, Faculty of Mathematics
and Physics, Charles University, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
2 Laboratory of
High Performance Computing, Institute of Physical Biology USB and Institute of
Landscape Ecology AS CR, University of South Bohemia, Zámek 136, 373 33 Nové Hrady, Czech
Republic, e-mail: luley@greentech.cz
3Department of Biochemistry, Faculty of
Sciences, Charles University, Albertov 2030, 128 40 Prague 2, Czech Republic
4 Institute of Microbiology, Academy of Sciences of the Czech Republic,
Vídeňská 1083, Prague 4, CZ-14220, Czech Republic
Human a1-acid glycoprotein (AGP), also known as orosomucoid, is a 41-kDa single polypeptide consisting of 183 amino acids. It contains 42% carbohydrate in weight and has up to 16 sialic acid residues. AGP, a human blood plasma protein, belongs to the lipocalin family of proteins, a heterogeneous group of proteins that bind a variety of small hydrophobic ligands. It is known that AGP plays a role under inflammatory or other pathophysiological conditions and is able to bind basic drugs and certain steroid hormones such as progesterone. However, its biological function and 3D structure remains unknown [1].
Three-dimensional structure of AGP has been predicted recently [2] by an approach that combines molecular modeling and vibrational spectroscopy [3]. The model shows that AGP folds as a highly symmetrical all-b protein dominated by a single eight-stranded antiparallel b-sheet. The Raman difference spectroscopy confirmed docking predicted binding pocket for progesterone [2].
Here we present critical assessment of binding of several ligands with different physico-chemical properties to AGP (e.g. progesterone, propranolol, warfarin). In silico docking of ligands into the binding pocket of our model was explored with AutoDock program [4] and followed by molecular dynamics studies in Gromacs software package. In vitro binding of ligands was studied by means of Raman difference spectroscopy that clearly confirmed presence of Trp122 in the binding pocket for all the ligands. It supports computed results that AGP has only one binding site for presented ligands. Thermal dynamics in the range of 20–70 °C monitored by Raman spectroscopy and Fourier-transform infrared spectroscopy and analyzed by homo- and hetero-spectral 2D-correlation analysis [5] revealed full reversibility of the protein motion upon heating dominated by thermal “breathing” of the b-barrel which points at high stability of protein itself but mostly at stability of binding pocket which is localized insight the b-barrel.
Ministry
of Education of the Czech Republic (No. MSM 0021620835, No. MSM6007665808) and
the Academy of Science of the Czech Republic (No. AVOZ60870520) are gratefully
acknowledged for support.
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