Molecular Docking – Isoprene and RoxA

Computer simulation and analysis are good scientific tools for understanding enzymatic processes. Molecular docking is one of this tools which predicts the structure of protein-ligand complexes.1,2 Since RoxA has just one solved structure in Protein Data Bank that does not have any ligand bounded (PDB: 4B2N), we thought about doing a molecular docking of polyisoprene in RoxA structure. The first step was to analyze RoxA structure in search for its substrate (polyisoprene) binding site. Since, this structure was obtained by RoxA crystals without substrate, its binding site was really tight which suggests that protein must undergo conformational changes to fit polyisoprene. Then we did some manual conformational modifications on residues of RoxA ligand biding site. We based this conformational changes on the comparison of binding sites of RoxA and CcpA (PDB: 3HQ6) which has a same signature motif and share a common ancestry to RoxA.3 We did an alignment of corresponding heme group of each protein using a tool named LigAlign4 installed in PyMOL. The alignment result is shows in Figure 1.

Figure 1 shows the difference between both protein structures, but no significant space available can be seen in CcpA ligand biding site.

After this, we used another PyMOL tool, named Sculpt, to modify the conformation of RoxA biding site residues. The advantage of this tool is that it does not generate conformational absurd and adapts structures around the manual modification (Figure 2).

Figure 2. Use of Sculpt PyMOL tool in the modification of residues.

We preferred to modify residue with bulky side chain to get more space in binding site. We can see the difference between protein before and after modification in Figure 3.

Figure 3. Binding site residues conformational changes; in blue, structure before modifications; in green, structure after modifications.

Then we could compare the surface of each structures (before and after).

References

1. http://www.annualreviews.org/doi/pdf/10.1146/annurev.biophys.32.110601.142532
2. http://ac.els-cdn.com/S0959440X96800613/1-s2.0-S0959440X96800613-main.pdf?_tid=435386ca-5cc0-11e5-911a-00000aacb35d&acdnat=1442441833_e1287cde3c61836ef0017416241540f8
3. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3752256/
4. http://compbio.cs.toronto.edu/ligalign/index.html