Figure 1.
3D representation of the sm27/FGF2 complex.
NMR-constraints derived structure of the complex between sm27 and FGF2, used as a starting structure for all simulations and analyses. Red surface represents protein region involved in ligand recognition.
Figure 2.
Comparison between the experimental and calculated S2 values.
The direct comparison between experimental (red) and calculated (black) S2 parameters. Comparison between the two values for the apo (a) and holo (b) systems for S2 calculated over the whole trajectory. Panel c) shows the comparison of experimental (red) S2 parameters with values calculated over the 100 ns trajectory interval (black) that yield the best agreement (200–300 ns).
Figure 3.
Comparison between the experimental and calculated local dynamics.
a) Comparison between local dynamics for the apo system, calculated over the 100 ns trajectory interval yielding the best match (800–900 ns). b) Comparison between local dynamics for the holo system, calculated over the 100 ns trajectory interval yielding the best match (200–300 ns). The insets show a magnification of the graphs to improve clarity.
Figure 4.
Representative structures of the ensemble of the sm27/FGF2 complex that recapitulates calculated and experimental data.
From structural representations of two different orientations of the sm27-FGF2 complex (a and c) it is immediately evident that the ligand can occupy a diverse range of conformations/configurations and the protein dynamically adapts to them. Sm27 molecule is shown in magenta sticks, while protein side-chains involved in interaction (Y33, K35, N36, R53, K128, R129, K134, Q143, K144, A145) are shown as blue lines. In b and d the same views of sm27-FGF2 complex are offered and the position of heparin (yellow sticks) and FGFR1 (dark olive and orange cartoons), deduced from X-ray structure (PDB ID: 1FQ9), are shown.
Figure 5.
Distances between FGF2 binding site aminoacids and sm27.
Histogram of the distance between the COM of the ligand calculated over the 200–300 ns interval.
Figure 6.
FGF2 hydration changes induced by Sm27 binding.
Upper panel: ratio of the normalized intensities observed for holo and apo FGF2 is reported as a function of the residue number as derived from ePHOGSY NOE spectra. Dotted lines delimit intensity variations beyond ±50% upon sm27 binding. Lower panel: Ratio of the mean residence time (MRT) per residue calculated for all atoms over the whole MD trajectories of apo and holo protein. Distance cut-off of 3.5 Å was used. Dashed gray line highlights the binding site regions.
Figure 7.
FGF2 hydration changes induced by sm27 binding.
Residues affected by hydration changes upon sm27 binding, as deduced from MRT analysis (blue) and ePHOGSY NMR data (magenta) are shown as mesh. Residues Y33, K35, N36, R53, K128, R129, K134, Q143, K144, A145, involved on the average in the contact with the ligand (green sticks), are shown as green surface.