Structural Biology
Using single particle cryo-electron microcscopy, the Davis lab determines the high-resolution structures of large, macromolecular complexes and uses this information to determine their assembly mechanisms. We also develop new computational tools to facilitate these efforts.
Critically, MIT has made significant investments in this exciting technology, including the purchase of two new microscopes (a Titan Krios/K3 and Talos Arctica/Falcon III) that are housed in the MIT.nano building. We have also recently installed a cryo-FIB-SEM (the Aquilos), which enables preparation of lamella for in situ structural studies. Members of our lab learn to: plunge-freeze samples using the vitrobot, the chameleon, and a series of home-built plungers; load and clip grids; and acquire and analyze data independently on these high-performance microscopes.
Additionally, through the MIT Structural Biology Core facility, our group accesses a well-established pipeline to crystallize and determine the structure of proteins of interest.
Mass spectrometry
Our lab owns and operates a top-of-the line HF-X orbitrap mass spectrometer coupled to a Ultimate 3000 nanoflow UHPLC , which is housed in a dedicated mass spectrometry facility. Using this instrument, we can quantitatively determine the composition of large cellular machines, measure the kinetics of their assembly and disassembly and, through the use of cross-linking, gain insights into their overall architecture. In contrast to typical biochemistry groups, Davis lab members have the opportunity to become mass spec experts and run these experiments completely independently.
Biochemistry and Biophysics
The Davis lab is well-equipped to purify endogenous macromolecular complexes from yeast and mammalian cell lines as well as to clone, heterologously express and purify proteins of interest in a variety of expression systems. Additionally, we have access to an extensive array of biophysical instruments through the MIT-BIF and the MIT-MicroBio Center including high throughput liquid handling robotics, next-generation sequencing services and analytical equipment such as circular dichroism spectrometers, micro-scale calorimeters, mass photometry, and analytical ultracentrifuges.
Computation
We own and operate a series of local high performance workstations for our methods development efforts, and to process our cryo-EM and mass spectrometry datasets.
Additionally, we are superusers of the recently constructed satori research computing facility, which provides access to high-performance nodes each equipped with 4xV100 GPUs, and 1TB working memory…cryoDRGN go brrr…
Finally, in collaboration with the Drennan lab, we have constructed and operate a purpose-built cryo-EM processing server, housed at the MGHPCC.