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 tool 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.
Above is a complete view of the movement attributed to every amino acid of a protein. Having all of the curves present at the same time can be quite confusing. The true power of this measurement can be harnessed when amino acids are displayed in smaller clusters. Below is the dynamics of the 25th, 80th, and 90th amino acid of the 6GIX protein.
Functionality
WHAT CAN RMSF ACCOMPLISH
Appendix A
Procedure of data collected in vitro
