Ferdiemar started in our graduate program in January, 2014. He already completed a lot of work before he became an official graduate student!
Here is a movie of an SMD simulation: A sodium ion is non-covalently bound to a peptide helix, fixed at the opposite end. The sodium ion is being pulled to investigate how the helix unwinds. Vacuum simulation using NAMD.
The three helices in 1sse. We want a helix that has a CYS N-terminal, but without the CYS. You used helix 616, which has a CYS in the middle.
Helix 598 is easiest, as the CYS is exactly N-terminal. Helix 301 might work, even with both CYS intact. Otherwise, you can mutate CYS 303 -> ALA. (The arrows indicate the direction of the helical dipole.)
Here is a movie of an SMD simulation: A sodium ion is non-covalently bound to a peptide helix, fixed at the opposite end. The sodium ion is being pulled to investigate how the helix unwinds. Vacuum simulation using NAMD.
The three helices in 1sse. We want a helix that has a CYS N-terminal, but without the CYS. You used helix 616, which has a CYS in the middle.
Helix 598 is easiest, as the CYS is exactly N-terminal. Helix 301 might work, even with both CYS intact. Otherwise, you can mutate CYS 303 -> ALA. (The arrows indicate the direction of the helical dipole.)