Tubulin with Tails Extended

I have been doing runs with tubulin heterodimers in the presence of external electric fields (EEFs), over a range of strengths, to see how the dimer’s motion changes in response. In all of them so far, I’ve started with an equilibrated tubulin with tails (C-termini) lying flat along the surface of the dimer. They reached this position at the end of a 50ns MD run; at the start, the tails had been extended (I added them with Modeller).

Because the tails are dynamic, and the movement between an extended and a contracted state along the dimer likely influence the movement of kinesis along the microtubule, it seemed worthwhile to try extending them for the start of a simulation and see what effects it might have during the run.

Setup

The equilibrated molecule was first added to a much larger solvation box, 125x125x125Ang, and the tails were pulled outwards using SMD between the CA of the last residue on each tail and two water molecules outwards from the dimer. Each water molecule was chosen for its positioning outwards from the center of dimer.

The EEF was applied upon the direction of the dimers dipole at the start of the simulation (red arrow). Each run was repeated once for each field strength for 50ns. The first 5 ns were discarded from the bar plots below.

Results

The results of this run suggest that EEFs of sufficient strength can keep the tails in the extended state, whereas they will contract without any EEF, or if the EEF is insufficient (exceeding 20kV/cm). While the observation of keeping the tails extended is, to my knowledge, new, the threshold for EEFs to have an observable effect during an MD run is not (English, 2015).

In an attempt to quantify the degree of “extension” by the tubulin C-termini, I took the dot product of the normalized EEF vector and the vector formed between the first and last CA of the C-termini. The results of this heuristic are below. Again, nothing seems noticeably different until the field exceeds 20kV/cm, after which there is a noticeable increase in the degree of extension in the direction of the field.

Finally, one observation that has informed a future simulation, is the change in bend angle of the free-floating dimer. While most the runs saw the tubulin floating around 6 degrees, in keeping with the results observed by a PMF experiment by Peng, 2014, the dimer exposed to 200kV/cm was more linear, with a bend angle less than 4 degrees. When I have time I’ll follow up on this.

Conclusion

It is not surprising that EEFs can keep the tails extended since they are very negatively charged (each with, at most, -9 unit charges). Their ultimate charge is determined by post-translational modifications, like polyglutamylation and polyglycylation. An extension of this simulation, pun intended, would be to increase the padding and salinity to see whether the results are robust, even in the presence of strong dipole screening.