SECONDARY AND TERTIARY STRUCTURE OF HUMAN a1-ACID GLYCOPROTEIN BY HOMOLOGY MODELING AND VIBRATIONAL SPECTROSCOPY
V. Kopecký Jr.1,2, R. Ettrich3, K. Hofbauerová2,4, V. Baumruk1 and V. Karpenko4
1Institute of Physics, Charles University, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
2Department of Biochemistry, Faculty of Sciences, Charles University, Albertov 2030, 128 40 Prague 2, Czech Republic, e-mail: firstname.lastname@example.org
3 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
4Department of Physical and Macromolecular Chemistry, Faculty of Sciences, Charles University, Albertov 2030, 128 40 Prague 2, Czech Republic
Human a1-acid glycoprotein (AGP), also known as orosomucoid, is a 41-kDa single polypeptide formed of 183 amino acids. It contains 42% carbohydrate in weight and has up to 16 sialic acids 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 .
The aim of our work was to predict and verify the three-dimensional structure of AGP. A structural model, using available lipocalin structures as templates, was constructed by means of the Modeller program . The model shows that AGP folds as a highly symmetrical all-b protein dominated by a single eight-stranded antiparallel b-sheet. For the first time secondary and tertiary structures of AGP have been studied by infrared and Raman spectroscopy. Vibrational spectroscopy confirmed details of the secondary structure predicted by modeling, i.e. 15% a-helices, 41% b-sheets, 12% b-turns, 8% b-bands and 24% unordered structure at pH 7.4. Thermal dynamics in the range 20–70 °C monitored by Raman spectroscopy and analyzed by principle component analysis revealed full reversibility of the protein motion upon heating dominated by decreasing of b-sheets, probably thermal “breathing” of the b-barrel.
Docking of progesterone into the binding pocket of our model was explored with the AutoDock program . Then Raman difference spectroscopy confirmed the predicted proximity of Trp122 to the progesterone binding pocket. We can conclude that our model was verified in so many details by vibrational spectroscopy that it can represent a valuable contribution to understanding the role and behavior of AGP .
The support by the Grant Agency of the Charles University (No. 220/2000/B-CH) and Ministry of Education of the Czech Republic (No. MSM113100001, No. MSM113200001, No. MSM123100001) is acknowledged.
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