Joachim Frank

American Academy of Arts & Science Member

National Academy of Sciences Member

2017 Nobel Prize in Chemistry

Cryo-electron microscopy and single-particle reconstruction , studying the mechanism of protein biosynthesis and other molecular processes in the cell.

Additional Website: https://joachimfranklab.org

We investigate the mechanism of translation on the ribosome by using cryo-electron microscopy and single-particle reconstruction aiming at the highest resolution. We are continuing the development of cryo-EM technology, and in the past 10 years have focused on time-resolved methods using microfluidic chips, as well as mapping the energy landscape of molecules from single-particle images by machine-learning. These methods can be used to study the structure and dynamics of a wide range of macromolecular complexes at close-to-atomic resolutions.

Our laboratory conducts research on the mechanism of translation by the ribosome and on other processes involving molecular machines in the cell. The primary method of structural research is cryo-electron microscopy, based on the principle of forming a three-dimensional image by collecting and combining thousands of projections of the molecules embedded in a thin layer of ice. This method of “single-particle reconstruction” was pioneered in our lab (1975 to 1986) while still at the Wadsworth Center in Albany and is now widely used to study macromolecular interactions in a large range of biological systems.

Well-characterized, functionally active molecular complexes are prepared in vitro. They are stalled by chemical means (antibiotics, GTP nonhydrolyzable analogs, etc.), placed on a grid, and rapidly frozen by immersion into liquid ethane at liquid-nitrogen temperature. Single molecule projections are recorded by means of single-electron recording detectors. The resulting electronic images are subsequently processed in the computer using a number of software systems including Relion and cryoSpark, resulting in three-dimensional density maps that used as the basis for atomic modeling.

Time-resolved cryo-EM, as implemented in our lab, can follow the progress of reactions of biomolecules and determine the structures of reaction intermediates in the time range of 5 to 1000 millisecond. To this end, we have developed microfluidic chips in which reaction components are rapidly mixed, allowed to react for a set time, and the product is sprayed onto the EM grid before the grid is immersed in the cryogen.  We have studied reaction intermediates in translation initiation, termination and recycling both in bacteria and eukaryotes.

• Bhattacharjee, S., Feng, X., Maji, S., Dadhwal, P., Zhang, Z., Brown, Z.P., and Frank, J. (2024). Time resolution in cryo-EM using a PDMS-based microfluidic chip assembly and its application to the study of HflX-mediated ribosome recycling. Cell 187, 782–796.

• Brown, Z.P., Abaeva, I.S., De, S., Hellen, C.U.T., Pestova, T.V., and Frank, J. (2022). Molecular architecture of 40S translation initiation complexes on the hepatitis C virus IRES. EMBO J. 41. doi: 10.15252/embj.2022110581.

• Sztain, T., Ahn, S.-H., Bogetti, A.T., Casalino, L., Goldsmith, J.A., Seitz, E., McCool, R.S., Kearns, F.L., Acosta-Reyes, F., Maji, S., Mashayekhi, G., McCammon, J.A., Ourmazd, A., Frank, J., McLellan, J.S., Chong, L.T., and Amaro, R.E. (2021). A glycan gate controls opening of the SARS-CoV-2 spike protein. Nat. Chem. 13, 963–968.

• Dashti, A., Mashayekhi, G., Shekhar, M., Hail, D.B., Salah, S., Schwander, P., des Georges, A., Singharoy, A., Frank, J., and Ourmazd, A. (2020). Retrieving functional pathways of biomolecules from single-particle snapshots. Nat. Comm. 11, 4734.

• Kaledhonkar, S., Fu, Z., Caban, K., Li, W., Chen, B., Sun, M., Gonzales, R.L., and Frank, J. (2019). Late steps in bacterial translation initiation visualized using time-resolved cryo-EM. Nature 570, 400-404.

• Fu, Z., Indrisiunaite, G., Kaledhonkar, S., Shah, B., Sun, M., Chen, B., Grassucci, R.A., Ehrenberg, M., and Frank, J. (2019). The structural basis for release factor activation during translation termination revealed by time-resolved cryogenic electron microscopy. Nat. Comm. 10, 2579.