Can AlphaFold refine structures for X-ray & Cryo-EM/ET data? Now it can! Great collab with @moalquraishi.bsky.social and @randyjread.bsky.social led by @alisiafadini.bsky.social and @minhuanli.bsky.social. 🧵below. Code to follow...
Enabling better crystal structures & better structure prediction. Can’t wait to see where folks take that! SFCalculator is implemented in PyTorch, TensorFlow, and JAX. Open Source. See biorxiv.org/content/10.1... for more info & github.com/Hekstra-Lab/... to get started. 4/4
With SFCalculator you can also *train* structure prediction / generative models directly on X-ray data. As
James Holton has shown, the data are much more accurate than the models. The result: experiment-based generative models for ensembles (not yet general!) 3/4
We can refine protein structures by searching the latent space of pre-trained generative models. Using a Boltzmann Generator (@franknoe) as an example, doing so yields models with good physics & data fit! 2/4
Crystal structures are *not* God-given truth. They approximate, w/ flaws & errors, X-ray diffraction data. AlphaFold etc. have been trained on structures, not data. SFCalculator now differentiably connects structures to diffraction data. What does this enable? 🧵 1/4 www.biorxiv.org/content/10.1...
Fruit of a close collaboration with Rama Ranganathan's group, where Doeke, Ian (@kiwhite), and Rama first developed EFX, and BoRam worked tirelessly to grow crystals and analyze data. New hardware and software from @HekstraLab were critical for success!
In evolution, members of a protein family are often variations on a theme. The dynamic states resemble stable states of other channels: The sequence of steps of ion permeation is conserved from channel to channel with variations in relative energy. 7/8
Does the channel itself move? Yes! It moves as the ions pass, differently depending on the direction of ion flow. This suggests how rectification (asymmetric currents) can evolve. 6/8
What do we see? K+ ions coming in, hopping, and leaving. We see the K+ ions move, putting on a new “coat” of water molecules as they exit. 5/8
The experiment in simple: a crystal between two electrodes; X-rays coming in from the side: 4/8
Crystals of NaK2K, (H/T Youxing Jiang @ UTSW), form an ideal starting point: all ion channel pores are easily aligned with electric field (E): half of them “up”, half “down”. The red spheres are K+ ions: 3/8
Key is EF-X, a technique in which we apply electric field (EF) pulses to protein crystals and see the resulting motions with X-ray pulses. Physiological electric field, temperature, and timescales are all accessible. 2/8
Now in Cell: K+ ion channels enable electric currents consisting of potassium ions to generate action potentials in heart, brain, and muscle. For the first time, we can now see these currents atom-by-atom. www.cell.com/cell/abstrac... 1/8
Led by Rick Hewitt and Kevin Dalton, the result is Laue-DIALS, hosted by @rs-station.bsky.social at rs-station.github.io/laue-dials/. Wanna try this out but need advice? Please get in touch. Further upgrades coming soon! Read more at pubs.aip.org/aca/sdy/arti... 2/2
X-ray diffraction can access protein dynamics. Why so few datasets? One reason? Lack of powerful pulsed X-ray sources. XFELs are limited. Synchrotrons throw away >99% of photons. Working with Aaron Bewster (DIALS/LBNL) and BioCARS (biocars.uchicago.edu/) to change this! 🧵1/2
Hello World! Catching up after not posting for a long time on Twitter/X/BlueSky (what happened to Mastodon?).
