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Human Vitamin K Epoxide Reductase (hVKORC1): Search for the Functional Conformational States
Nolan CHATRON1,2, Bernard CHALMOND1, Alain TROUVE1, Etienne BENOIT2, Virginie LATTARD2, Luba TCHERTANOV1 1
Centre de Mathématiques et de Leurs Applications, Ecole Normale Supérieure de Cachan CMLA - UMR 8536 CNRS, Université Paris-Saclay, 94235 Cachan, France
2
INRA – VetAgro Sup, USC 1233, Ecole Nationale Vétérinaire de Lyon 69280 Marcy l’Etoile, France
Introduction VKDPs
Human Vitamin K Epoxide Reductase (hVKORC1): - a reticulum endoplasmic membrane protein, activating coagulation process through vitamin K recycling; - a leading target for anti-coagulation therapies, especially based on Vitamin K Agonists (VKAs) oral administration.
COAGULATION
quinone
epoxide
R
R
VKORC1
Problems: - hVKORC1 mutations catalytic disorders or VKAs resistance (left panel); - no crystallographic data available for hVKORC1; - contradictory experimental/theoretical data distinct membrane topology models: 3 TM-helices, 4 TM-helices (right panel), and 5 TM-helices models.
Mutations
Goals: - design a relevant hVKORC1 structural model; - describe hVKORC1 conformational space; - unravel hVKORC1 catalytic mechanism.
R=
Homology modeling
MD simulations & analysis 60,000 atoms 5 x 100 ns 2 x 500 ns 1 µs
hVKORC1 bacterial homolog (left), used as a template to build a hVKORC1 3D model (right).
Active site: C132xxC135 C43 C51
C132
C135
C51 C135
C132
PCA - First eigenvector
DSSP
VKAs
Biological data: either a direct activation of C132 and C135; or an electron transfer from C43 and C51 to C132 and C135.
Residue
PCA - Second eigenvector 90°
Cysteine residues in our model are protonated. Proton donor is considered as an external source.
ConfiScan
I
C132-C135
II
C43-C51 C132-C135
III
C51-C132
IV
V
C51-C132
C51-C132
I III II
IV V
Conclusions - Perspectives hVKORC1 3D model: - 4 TM helices - protonated cysteine residues conformational space exploration MD trajectories: - 5 x 100 ns; 2 x 500 ns 1 µs - secondary structures preservation - highly flexible luminal loop (carrying C43 and C51)
ConfiScan: - similar conformations identification - free energy estimation - minimum energy conformations highlighting identification of biologically relevant conformations concept of hVKORC1 catalytic mechanism, consistent with experimental data (scheme), suggesting an electron transfer from C43 and C51 to C132 and C135.
Ongoing and future work: MD simulations extending (until 1 µs), hVKORC1-vitamin K complexes MD simulations, the binding free energy calculations
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