Team:EPF-Lausanne/Modeling overview

                               

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

Sosnick et al. found that LOVTAP is not stable. After light excitation the LOV domain returns in its ground state (non light activated state) very fastly.

So, the aim of the molecular dynamics simulation is to simulate the LOV domain in its environment under light activation (so called light state) and without light activation (ground state so called dark state), calculate atoms and residues movements of particular/interesting LOV domain regions, and finally deduce which residue could be mutated to stabilize the light activated state of this LOV domain.

Then, simulation of complete LOVTAP protein with selected mutations could give us insights about the behavior of our protein in its environement.

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.

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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

Minimization

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Equilibration

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Analysis and validation

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Simulation

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Atom movement analysis

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