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Team:EPF-Lausanne/Modeling overview
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==Goal== | ==Goal== | ||
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| + | 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 in the light activated state (so called light state) and the ground state (so called dark state), calculate atoms and residues movements of particular LOV domain region, and finally deduce which residue could be mutated to stabilize the light activated state of this LOV domain. | ||
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| + | Then, simulation of complete LOVTAP protein with selected mutations could give us insights about the behavior of our protein in its environement. | ||
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==Starting material== | ==Starting material== | ||
Both LOV domain crystallography files were obtained from [http://www.rcsb.org/pdb/home/home.do RCSB]: | Both LOV domain crystallography files were obtained from [http://www.rcsb.org/pdb/home/home.do RCSB]: | ||
Revision as of 09:44, 21 September 2009
Contents |
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 in the light activated state (so called light state) and the ground state (so called dark state), calculate atoms and residues movements of particular LOV domain region, 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:
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.
Steps
Minimization
Equilibration
Analysis and validation
Simulation
Atom movement analysis
