Fig 1.
The αβ-tubulin dimer and DAMA-colchicine.
(A) The α-tubulin and β-tubulin heterodimer (PDB ID: 1SA0). α-tubulin is shown in green cyan and β-tubulin is shown in tv_blue color. Regions of colchicine binding pocket are highlighted with different colors; the T5 and T7 loop with orange color, the cylindrical H7 and H8 helices with yellow and red color respectively, and B9 sheet is with magenta color. The GTP and GDP are shown using spacefill models. The white, grey, red, blue and golden yellow colors represent carbon, hydrogen, oxygen, nitrogen and phosphorous atoms, respectively. The DAMA-colchicine has been shown using stick model where green, grey, blue, red and yellow colors represent carbon, hydrogen, nitrogen, oxygen and sulphur atoms respectively (B) Structure of DAMA-colchicine: Ring A and C show trimethoxy benzene and methoxytropone ring and seven member B ring join A and C ring with mercaptoacetyl group.
Fig 2.
Multiple sequence analysis of tubulin 1SA0 and human β-tubulin isotypes.
The isotype βIII shows change of Ala315 to Thr, Cys239 to Ser, and Thr351-to Val, Isotype βII change of Val316 to Ile at the colchicine binding pocket. Region of changed residues at colchicine binding pocket are shown in red color.
Fig 3.
Comparison of crystal structure and docked conformation of DAMA-colchicine in tubulin 1SA0 and human αβ-tubulin isotypes.
Color scheme for α-tubulin is green_cyan and β-tubulin is tv_blue for tubulin 1SA0 tv_red for isotype βII, tv_yellow for isotype βIII and violet for isotype βIV. Crystal structure of DAMA-colchicine is shown in magenta color, while DAMA-colchicine after docking is shown in green color. The oxygen, nitrogen and sulphur atoms of DAMA-colchicine are shown in red, blue and pale yellow color, respectively. The DAMA-colchicine prefers the αβ tubulin interface in tubulin 1SA0 and tubulin isotypes. (A) Tubulin 1SA0-DAMA-colchicine complex. (B) αβII tubulin isotype-DAMA-colchicine complex (C) αβIII tubulin isotype-DAMA-colchicine complex (D) αβIV tubulin isotype-DAMA-colchicine complex.
Table 1.
RMSD of docked DAMA-colchicine relative to crystal structure, binding energy and hydrogen bonding interactions in tubulin 1SA0, and human αβII αβIII and αβIV tubulin isotypes.
Table 2.
Residues present around the 4 Å distances of DAMA-colchicine in tubulin 1SA0, and human αβ tubulin isotypes after docking.
Fig 4.
Root mean square deviations (RMSD) corresponding to tubulin 1SA0 and αβ-tubulin isotypes.
Root mean square deviations (RMSD) correspond to tubulin 1SA0 (black colour), αβII (red colour)), αβIII (green colour) and αβIV (blue colour) of tubulin isotypes for 25ns MD simulations. RMSD was calculated for αβ-tubulin isotypes excluding the C-terminal region starting from amino acid Ala-428. The RMSD analysis suggests that tubulin 1SA0, αβII, αβIII and αβIV deviate to quite some extent from their starting conformations and reached their equilibrium conformations after 15ns, and then retained their stability with fluctuations between 2.2–2.7Å.
Fig 5.
Root mean square fluctuations (RMSF) corresponding to β-tubulin isotypes.
Root mean square fluctuations (RMSF) αβII (red colour), αβIII (green colour) and αβIV (blue colour) tubulin heterodimer for 25ns MD simulations.
Fig 6.
Molecular dynamics (MD) simulated end structures of tubulin 1SA0 and tubulin isotypes.
The positions of DAMA-colchicine before and after simulation are shown for comparison. The colour scheme for αβ-tubulin and DAMA-colchicine is same as for the Fig 3. Initial docked conformation of DAMA-colchicine (before simulation) shown in magenta colour while DAMA-colchicine after simulation is shown in green colour similar to Fig 3. (A) Tubulin 1SA0 and DAMA-colchicine complex. (B) αβII tubulin isotype-DAMA-colchicine complex. (C) αβIII tubulin isotype-DAMA-colchicine complex (D) αβIV tubulin isotype-DAMA-colchicine complex. It is observed after simulation that the DAMA-colchicine moves away from the initial position in αβIII tubulin isotype.
Table 3.
RMSD of DAMA-colchicine relative to docked structure, and hydrogen bonding interactions of DAMA-colchicine, with tubulin 1SA0 and tubulin isotypes after MD simulation.
Table 4.
Residues present around the 4 Å distances of DAMA-colchicine in tubulin 1SA0 and tubulin isotypes after simulation.
Table 5.
Binding free energy of tubulin 1SA0, αβII, αβIII, and αβIV tubulin isotypes with DAMA-colchicine.
Table 6.
RMSD of DAMA-colchicine relative to crystal structure, binding energy and hydrogen bonding interactions of DAMA-colchicine with in-silico mutant structures of αβIII tubulin isotypes after docking.