Modeling

To do

- Model allosteric interactions between LOVTAP & TrpR

What will be done:

- Model of LOVTAP in dark phase

- Model of LOVTAP in light phase

- Characterize how the J-alpha helix changes

- Model sturctural changes that enhance the switch feature of LOVTAP e.g. in dark phase: really weak interaction between LOVTAP and the corresponding DNA sequence, in light phase: strong binding of LOVTAP on DNA.

We will follow the following article protocol:
Freddolino, P.L., Dittrich M., Schulten K., Dynamic Switching Mechanisms in LOV1 and LOV2 Domains of Plant Phototropins. Biophysical Journal, 91, 3630-3639, 2006 (Pubmed)

- Model the fusion of LOV domain with other transcription factors

Implementation of the simulation

We generated all the files needed to do the simulation, thanks to the tutorial of NAMD, which can be found on the following page:
http://www.ks.uiuc.edu/Training/Tutorials/

Steps are explained in a little bit more detail on this page:

Simulation

The protein move thanks to different forces, namely the following ones:

• the Lennard-Jones potential, which take into account the Van der Waals forces. It represents the non-bonded forces and the total potential energy can be calculated from the sum of energy contributions between pairs of atoms.

Lennard Jones potential

• another force is the well-known Coulomb force

To envisage

- Molecular mutationnal assay

Already done

Here is our first movie from the modeling, showing the behavior of the protein in the dark state condition: Dark State

After having modified some parameters in the parameter files, here is our second movie, concerning the light state of the protein this time, with the FMN: Light State with FMN without water