Christopher W. Akey, Ph.D.

Research

We are studying the structure and function of macromolecular machines involved in cellular processes that include protein translocation across cell membranes mediated by the Nuclear Pore Complex (NPC), ribosome-channel complexes and the Type IVb secretion system of Legionella pneumophila. We also study apoptosomes that function in programmed cell death. In our work, we use biochemistry and molecular biology, coupled with high resolution cryo-electron microscopy, X-ray crystallography and molecular modeling to create snapshots of nano-machines. In addition, the recent ground breaking prediction of protein structures with deep learning algorithms (cf. Alphafold and Rosettafold) now provides additional “homology” models that are used to improve our structures. This analysis provides medium and high resolution models that allow us to infer the functions of these large machines in their respective cellular pathways.

Towards a comprehensive model of the yeast NPC

The large size, modular construction and dynamic nature of the 8-fold symmetric, yeast NPC (~600Å by 1100Å; 52 MDa) requires a multi-scale approach to obtain a complete model of this translocation machine, which 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 that will be used with a large data base of Nup crosslinks from Mass Spectrometry, published Nup domain structures and Deep learning models for Molecular and Integrative Modeling with composite 3D maps of the NPC. We have extended this analysis in an active collaboration with the Villa laboratory (UCSD) and are thus able to compare structures of contracted and radially expanded conformations in the isolated and in situ yeast NPC.

There are many take home messages from this ongoing work: we now have a better understanding of how these large machines may assemble, how they may flex and adapt to changes in transport by expansion of their central passageway, how Nups have evolved to form 3 different co-axial rings, while some Nups share similar interaction motifs with proteins that help guide cargo through the central channel. Moreover, we have observed multiple types of NPC in the same cell, which reflects the lego-like ability of this assembly to use interchangeable parts to modify the outer rings. This mutability may play a role in adapting these machines for specialized functions at the nuclear periphery.

A detailed understanding of the architecture and mechanics of the NPC will provide an in-depth view of how the nucleus and cell body communicate, which is an important step that may allow rational drug design to prevent serious disease.

This project is a team effort and major collaborators include Michael Rout, PhD and Brian Chait, PhD (Rockefeller University), Javier Fernandez-Martinez, PhD (Basque Foundation of Science); Ignacia Echeverria, PhD and Andrej Sali, PhD (University of California, San Francisco) Steve Ludtke, PhD (Baylor College of Medicine) and Elizabeth Villa, PhD, (University of California, San Diego).

An Architectural Guide to the Nuclear Pore Complex – NIH Director’s Blog (2018)

New Model of Yeast Nuclear Pore Complex Revealed (2022)

[Open Access from Cell] Comprehensive structure and functional adaptations of the yeast nuclear pore complex.

Preview: Megan R. McCarthy and C. Patrick Lusk (2022).
One ring doesn’t rule them all: Distinct nuclear pore complexes in a single cell.

NPC Publications:

Akey CW, Singh D, Ouch C, Echeverria I, Nudelman I, Varberg JM, Yu Z, Fang F, Shi Y, Wang J, Salzberg D, Song K, Xu C, Gumbart JC, Suslov S, Unruh J, Jaspersen SL, Chait BT, Sali A, Fernandez-Martinez J, Ludtke SJ, Villa E, Rout MP. (2021). Comprehensive structure and functional adaptations of the yeast nuclear pore complex. Cell. 2021 Dec 29:S0092-8674(21)01453-7. doi: 10.1016/j.cell.2021.12.015. Online ahead of print. PMID: 34982960

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

Yang, Q., Rout, M.P. and Akey, C.W. (1998). Three-dimensional architecture of the isolated yeast nuclear pore complex: Functional and evolutionary implications. Molec. Cell 1, 223-234. PMID: 9659919

Akey, C.W. and Radermacher, M. (1993). Architecture of the Xenopus Nuclear Pore Complex revealed by three-dimensional cryo-electron microscopy. J. Cell Biol. 122, 1-19. PMID: 8314837

Additional Research Projects in the Lab

The apoptosome: a cell death signaling platform

Ribosome-channel complexes

The Type IVb secretion system of Legionella pneumophila

Links:

PubMed publications list
BU Profile
ResearchGate

Contact Us

Department of Pharmacology, Physiology & Biophysics
Chobanian & Avedisian School of Medicine
700 Albany Street, W315A
Boston MA 02118-2526

Phone:(617) 358-8451
e-mail: cakey@bu.edu