Christopher W. Akey, Ph.D.
Professor of Physiology & Biophysics
- Title Professor of Physiology & Biophysics
- Office W315A
- Email email@example.com
- Phone (617) 358-8451
- Education B.S. University of Richmond
Ph.D. Cornell University
We are studying the structure and function of macromolecular machines involved in programmed cell death and protein translocation across cell membranes. In our work, we use biochemistry and molecular biology coupled with high resolution cryo-electron microscopy, X-ray crystallography and molecular modeling. This allows us to create snapshots of large assemblies and infer function from structure.
The apoptosome: a cell death signaling platform
In the intrinsic death pathway, cytochrome c binds to Apaf-1 and triggers apoptosome assembly in the presence of dATP. This platform binds procaspase-9, which activates procaspase-3 and other downstream procaspases. To understand this process, we determined a structure of the active pc-9 human apoptosome at near atomic resolution and created a model of this heptameric platform, which contains 49 domains, 7 cytochrome c molecules and 3-4 well ordered pc-9 CARDs. Further studies of the active apoptosome should provide additional insights into the assembly and function of this cell killer, which has a complicated and still mysterious activation program. In parallel studies, we determined a near atomic structure of the Drosophila Apaf-1 related killer (Dark) in the ground state. A comparison of human and Drosophila apoptosome structures provides a possible explanation for their nucleotide preferences.
Nuclear pore complexes
The large size and modular construction of the yeast NPC (~600Å by 1100Å; 55 MDa) requires a multi-scale approach to obtain a complete model of this translocation machine that spans large pores in the nuclear envelope. This work will inform us on the roles of different nucleoporins (Nups) in hierarchical assembly of the spoke-ring scaffold, pore membrane stabilization, spoke dynamics, formation of the central transporter and NPC evolution. Single particle structures are being determined of isolated structural domains, which will be used with a large data base of Nup crosslinks from Mass Spectrometry, and ~25 published Nup domain structures for Integrative Modeling with a density map for the entire 8-fold symmetric NPC.
*Animated NPC gif by Dr. Ignacia Echeverria/ A. Sali group
Video tour of the yeast NPC integrative model 2.0: Part I, Part II, Part III
An Architectural Guide to the Nuclear Pore Complex – NIH Director’s Blog
Nascent secretory proteins are translocated into the lumen of the ER in higher eukaryotes and across the plasma membrane in bacteria. Conversely, membrane proteins are gated laterally into the lipid bilayer by the Sec61 and SecYEG channels. We seek to create a model of the co-translational translocon to understand these processes. Current studies are targeting the bacterial ribosome-channel complex to provide new insights into translocation.
*Opening the lateral gate in the E. coli SecYEG channel
The Type IVb secretion system of Legionella pneumophila
The T4bSS translocates effector proteins into the host eukaryotic cell. This process is required for infectivity by Legionella, a facultative pathogen. When alveolar macrophages are infected, this leads to a severe pneumonia (Legionnaires’ disease), which is particularly deadly in hospital burn units. We are studying the T4bSS with the goal of creating a molecular model of its function. As a first step, we determined the crystal structure of the interacting domains of IcmR-IcmQ (Rm-IcmQ). IcmR is a chaperone for IcmQ which is able to bind to the membrane surface, while the C-terminal Qc domain binds NAD+, presumably through a scorpion motif. This may be part of a signaling process that occurs at the bacterial plasma membrane to sense the metabolic state of Lp cells as they approach stationary phase, when the T4bSS is fully assembled. We are now focusing on other components of this protein translocase.
*Structure of IcmR(Rm)-IcmQ and NAD+ binding to the Qc domain
Kim S.J., Fernandez-Martinez J., Nudelman I., Shi Y., Zhang W., Raveh B., Herricks T., Slaughter B.D., Hogan J.A., Upla P., Chemmama I.E., Pellarin R., Echeverria I., Shivaraju M., Chaudhury A.S., Wang J., Williams R., Unruh J.R., Greenberg C.H., Jacobs E.Y., Yu Z., de la Cruz M.J., Mironska R., Stokes D.L., Aitchison J.D., Jarrold M.F., Gerton J.L., Ludtke S.J., Akey C.W., Chait B.T., Sali A., and Rout M.P. (2018). Integrative structure and functional anatomy of a Nuclear Pore Complex. Nature. 555:475-482. doi: 10.1038/nature26003. PMID: 29539637
Dorstyn L., Akey C.W., and Kumar S. (2018). New insights into apoptosome structure and function. Cell Death Differ. 2018 Jul;25(7):1194-1208. doi: 10.1038/s41418-017-0025-z. Review. PMID: 29765111
Cheng, T.C., Akey, I.V., Yuan, S., Yu, Z., Ludtke, S.J. and Akey, C.W. (2017). A near atomic structure of the Dark apoptosome provides insight into assembly and activation. Structure 25:40-52. doi:10.1016/j.str.2016.11.002. PMID: 27916517
Cheng, T.C., Hong, C., Akey, I.V., Yuan, S. and Akey, C.W. (2016). A near atomic structure of the active human apoptosome. Elife. Oct 4;5. pii: e17755. doi: 10.7554/eLife.17755. PMID: 27697150
Park, E., Ménétret, J. F., Gumbart, J.C., Ludtke, S.J., Li, W., Whynot, A., Rapoport, T. A., and Akey, C. W. (2014). Structure of the SecY channel during initiation of protein translocation. Nature 506, 102-106. PMID: 24153188
Farelli, J.D., Gumbart, J.C., Akey, I.V., Hempstead, A., Amyot, W., McKnight, C.J., Head, J.F., Isberg, R.R. and Akey, C.W. (2013). IcmQ in the Type 4b secretion system contains an NAD+ binding domain. Structure 21,1361-1373. PMID: 23850453