Team:Calgary/iGAM
Inspiration
What needs to be addressed?
The modification of proteins can often be a daunting ordeal. For each single amino acid change there are 23 different possibilities to be considered. iGEM Calgary has generated a toolbox to allow iGEM teams make informed decisions on the modification of their proteins.
https://github.com/ReverendSymes/iGAM
iGAM
the international genetic algorithm machine
To assist in the dynamic characterization by other teams we looked to develop a methodology that allows for the calculation and aggregation of Brownian motion measurements for each amino acid in a sequence. The Brownian motion measurement chosen was the Root Mean Square Fluctuation(RMSF) calculated for every atom of a protein in ten picosecond intervals.
The RMSF data was calculated from a nanosecond Molecular Dynamic Simulation(MDS) completed within GROMACS, an industrial MDS software. These values were then averaged over each amino acid, this ensured that the unit of measurement was observed on a scale that was modifiable by teams. This resulted in a series of curves that quantitatively expressed the dynamics for each amino acid.
Access
How to access iGAM
To access the iGAM tools please visit https://github.com/ReverendSymes/iGAM and download the R package project.
Appendix A
Procedure of data collected in vitro
