Team:EPF-Lausanne/Modeling

                               

Protein domain of interest

Our protein of interest is LOVTAP. This protein was sythetically engineered by Sosnick group. It is a fusion protein between a LOV domain (Avena Sativa phototropin 1) and the E. Coli tryptophan repressor. This protein undergoes changes under light activation as shown by Sosnick et al, in fact when the protein is activated by light it binds DNA and inversely. For more information about LOVTAP protein please click here.

Goal

Starting material

Both LOV domain crystallography files were obtained from RCSB:

Light activated LOV domain

Dark LOV domain

These crystallographies were done by Halavaty et al..

Molecular dynamics: a little theory

Molecular dynamics simulation consists of the numerical, step-by-step, solution of the classical equations of motion. For this purpose we need to be able to calculate the forces acting on the atoms, and these are usually derived from a potential energy.

         Click here to expand

This potential energy can be divided into:

The non-bonded interactions:

The ''Lennard-Jones potential'' is the most commonly used form, with two parameters: σ, the diameter, and ε, the well depth. It takes 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 pair potential showing the r⁻¹² and r⁻⁶ contributions [[Image:lennard_jones_vdw_forces.jpg]] [[Image:Lennard_jones.jpg|300px|center|thumb|Lennard-Jones pair potential showing the r⁻¹² and r⁻⁶ contributions]]

when electrostatic charges are present, we add the ''Coulomb force'', where Q1, Q2 are the charges and ϵ0 is the permittivity of free space [[Image:Coulomb.jpg‎|200px|center]]

The bonded interactions:

Angles, bonds and dihedral angles have to be taken into account [[Image:bonded.jpg‎|400px|center]]

To understand a bit more, you can see the following article: [[Media:Introduction_to_molecular_Dynamics_Simulation.pdf‎ | Introduction to Molecular Dynamics Simulation - Michael P. Allen]]

Steps

Minimization

Equilibration

Analysis and validation

Simulation

Atom movement analysis

References

Analysis methodology

Results

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 structural 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.

- Between Light state and Dark State

- RMS between light state and dark state

- length between the two arms N C

- only cytochrome with interactions in light state and dark state

To envisage

- Molecular mutational assay