CheB chemotaxis coding sequence (protein glutamate methylesterase)
CheB is part of the chemotaxis pathway in E. coli.
Usage and Biology
When phosphorylated by CheA, CheB demethylates the Aspartate receptors. This is part of the chemoattractant-concentration detection process.
Sequence and Features
- 10COMPATIBLE WITH RFC
- 12COMPATIBLE WITH RFC
- 21COMPATIBLE WITH RFC
- 23COMPATIBLE WITH RFC
- 25Illegal AgeI site found at 841
- 1000COMPATIBLE WITH RFC
In Silico Validation
2017 Team NYU-Abu Dhabi ran an in silico experiment of part BBa_C0024 which is the CheB chemotaxis coding sequence for the protein glutamate methylesterase. The MD simulations were run using GROMACS with the CHARMM36 forcefield. We ran an energy minimization for 500 ps using the steepest descent minimization algorithm with a stopping condition of maximum force less than 1000 kJ/mol/nm. We found that the energy was minimized in this time frame as shown by the steady convergence of the potential energy (Figure 1)
The minimized structure was solvated with water >12 A away from the protein surface. Potassium and chlorine atoms were added to neutralize the system and mimic experimental conditions of approximately 30 mM concentrations. We equilibrated in two phases, first under an NVT ensemble and then under an NPT ensemble. Both were found to equilibrate within 150 ps as shown in Figures 2 and 3, respectively. These adjusted the volume to 1 bar and temperature to 300K with restraints on the solutes. "" ""
The last frame of the NPT equilibration was extracted to start NVT simulations. A short animation of the protein run for 1 ns is attached. RMSD and radius of gyration analyses were run in order to determine the stability of the protein. The RMSD plot (Figure 4) shows the RMSD of the backbone does not fluctuate dramatically over the 1 ns run, indicating that the structure is stable. The 0.05 nm difference in backbone RMSD over the whole run indicate that the structure at 1 ns is slightly different from the initial structure, due to the energy minimization. ""
The radius of gyration, which measures a protein’s compactness, indicates that the protein is stably folded over the 1 ns production run. The plot shows reasonable variation and, along with the RMSD plots, show that this protein is very stable in explicit solvent solution (Figure 5). ""