Team:EPF-Lausanne/Modeling

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. 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

• when electrostatic charges are present, we add the Coulomb force, where Q1, Q2 are the charges and ϵ0 is the permittivity of free space

The bonded interactions:

Angles, bonds and dihedral angles have to be taken into account

To understand a bit more, you can see the following article: Introduction to Molecular Dynamics Simulation - Michael P. Allen

Steps

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