Fig. 3

Modeling identifies specific interactions between αvβ3 integrin and 25HC. a Ectodomain structure of αvβ3 integrin containing ‘RGD’’-binding site (site I) (blue) and site-II (red) residues highlighted by a layer of solvent molecule of radius 1.4 Å. The site-II-bound 25HC molecule is presented as a surface model in green and Mn²⁺ ions from metal-ion-dependent ligand-binding site (MIDAS) and adjacent to MIDAS (ADMIDAS) sites of βI domain, β-propeller domain and genu knee region are presented in cyan. b Potential interacting residues for molecular recognition of αvβ3 integrin by 25HC were identified in a docking simulation. H-bonds are highlighted in dashed lines in red. c, d Ser399 of β-propeller (red), Ser162 (blue) and Ala263 (black) of βI domain make stable H-bond interactions with 3- and 25-hydroxyl groups of 25HC, respectively. The H-bond distances (c) and H-bond angles (d) are plotted against MD simulation time (200 ns). e The root-mean-square deviations (RMSD) measured for specificity-determining loop (SDL), α1- and α7 helices during the entire 200 ns long simulation. The SDL region undergoes significant conformational change (RMSD of ~6 Å) upon 25HC binding. f The conformational change in the SDL is accompanied by disruption of H-bond interaction between Tyr122-Thr182 residues, as well as change in the β-propeller blade that interacts with SDL. Movement of the regions from the beginning 0 ns (blue) to the end 200 ns (red) is indicated by arrows. g Correlation matrices (as heat maps) indicating correlated (red) or anti-correlated motions (blue) of α- and β-subunits of αvβ3 integrin in unbound and 25HC-bound states. h, i The distance between the amide NH of Q120 of the β-propeller domain and backbone carbonyl oxygen of P169 of the SDL. Breakage of this electrostatic interaction in the 25HC-bound protein (blue) during the simulation, around ~30 ns simulation causes significant increase in the distance, which remain intact in the unbound protein (magenta) during the entire 200 ns simulation time