1. Molecular Dynamics Simulations for Alpha-Synuclein: Can that molecule show FRET effect?
In that study, we wanted to see weather if the truncated model of alpha-synuclein will show motions to promote FRET effect or not;
After graphing the distance throughout each end of alpha-synuclein, we observed that the motions of alpha-synuclein might behave in FRET range,
2. Molecular Dynamics Simulations for anti-METH scFv antibody: Can one piece of this protein have enough affinity to hold methamphetamine for another piece?
In that study, we applied molecular dynamics simulations for each chain of anti-METH antibody with methamphetamine to show that affinity of the hydrophobic surface of each chain is enough to hold methamphetamine for integration of the other chain;
After the molecular dynamics simulations, distance of the methamphetamine against each chain graphed. Results are given below which shows methamphetamine stays same distance to the surface as simulation time goes;
Graph that shows distance change of methamphetamine and chain A (or C1)
Graph that shows distance change of methamphetamine and chain A (or C1). Note that shift in the graph probably caused by the change in the orientation of labeled side-chain atom of methamphetamine
3. Preliminary wet-lab results
For our DNA samples that codes our anti-METH antibody design, we were not so lucky.
But for alpha-synuclein, things started giving hope;
After the cut and ligate procedure of obtained alpha-synuclein DNA, we applied transformation to the DH5alpha cells, amplified our plasmid and then continue to obtain our alpha-synuclein sequence for cloning to pET28a vector. By the time that wiki-freeze arrived, our studies were continuing.