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.

Implementation of the simulation

LOV domains are the light-sensitive portion of phototropins. They absorb light through a flavin cofactor, photo-chemicaly form a covalent bond between the chromophore and a cysteine residue in the protein, and proceed to mediate activation of an attached kinase domain.

Generating input files

First we need a compatible .pdb in addition to parameter and topology files. Steps to generate all the input files are explained in detail on this page How to generate input files. This is a kind of summary of the tuto.

.conf parameters

We should explain here what are the keywords we use in the .conf.

Run a complete simulation

We start from .pdb, .psf, .rtf generated in the previous section. Complete process is on a separate page How to run a simulation.

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