RIP is the only molecular dynamics (MD) protocol that can generate
artificially large conformational changes,
without the need for any
form of constraints. It generates true local perturbations.
microsecond long MD
are common-place now (damn you rich supercomputer centers), you can't
actually see much going on in these simulations. You certainly don't see
surface loop motions of more than 5 Ångstroms.
Before RIP, to see large motions in a protein, you typically need to use
MD protocols such as high-temperature annealing, or replica-exchange,
which apply high temperatures to specific regions in the protein. If you
don't want the rest of the protein to unravel, you need to put
constraints on the rest of the protein. Unfortunately, as these
constraints must be manually applied, these methods can't be used
automatically on a arbitrary protein.
So four 4 years ago, I started working in the
lab, on improving an elegant technique
called the Anistropic Thermal Diffusion developed by previous postdoc,
Noboyuki Ota. He came up with the idea of cooling down a protein in
simulation, and then applying a thermometer on one single residue. By
watching the residue knock around neighboring residues, he could follow
the energy diffusion through the protein.
In order to get it working, Nobu had to put artificial constraints on
all the backbone atoms, and all the surface atoms. My project in the
Agard lab was basically working on how to heat a residue without the
need for constraints. When I got to the lab, I was told Nobu had
implemented ATD as a hack to the source-code to XPLOR and that the code
was to be found in an unplugged Silicon Graphics machine that was
gathering dust in the corner of the lab. It took 6 months of hell before
I could reproduce it using a salad of Python scripts and AMBER.
Eventually I worked out how to heat a sidechain in a local way without
the need for backbone constraints. The solution was to only apply heat
to the sidechain degrees of freedom. As the heating is applied to the
rotameric sidechian chi-angles, which does not affect the backbone at
all, I called it the Rotamerically Induced Perturbation. At first, I was
mimicking Ota's studies but then one day, I decided to crank up the
perturbation, and to my absolute astonishment, I say a coherent 10
Ångstrom motion of an α-helix in a 10 ps simulation.
That's when I realized I could use this method to explore large surface
motions of proteins. Anyway, the rest of the project involved testing
RIP against a
whole bunch of
proteins with well-studied
dynamics, and figuring out how to interpret the simulations. The studies
are done, published, and unlike the ATD, the code is not sitting on an
obsolete machine in the back of the room. It has been
released into the wild.