nanobioreactors | protein secretion | biochemical efflux pump

Our focus is to control the transport of all types of materials, from electrons to macromolecules, across cellular membranes. Proteins are the principal “gatekeepers” of the cell but are in relatively complex formations, and therefore we rely heavily on protein engineering and synthetic biology strategies to achieve our goals. Notably, this permits us to engineer not only lipid-based membrane systems but also those membranes that are composed entirely of proteins. Such work has broad application, from the production of biochemical to the development of living batteries.



We seek to engineer bacterial microcompartments and the MS2 viral capsid for the creation of custom nanobioreactors. These custom sub-cellular microenvironments can enable and improve diverse biosynthetic pathways.

Asensio, M., Morella, N., Jakobson, C., Hartman, E., Glasgow, J., Sankaran, B., Zwart, P., and Tullman-Ercek, D. (2016) “A Selection for Assembly Reveals That a Single Amino Acid Mutant of the Bacteriophage MS2 Coat Protein Forms a Smaller Virus-like Particle.” Nano Letters. DOI: 10.1021/acs.nanolett.6b02948

Jakobson, C., Chen, Y., Slininger, M., Valdivia, E., Kim, E., and Tullman-Ercek, D. (2016) “Tuning the Catalytic Activity of Subcellular Nanoreactors.” Journal of Molecular Biology. DOI: 10.1016/j.jmb.2016.07.006

Glasgow, J., Asensio, M., Jakobson, C., Francis, M., and Tullman-Ercek, D. (2015) “The Influence of Electrostatics on Small Molecule Flux through a Protein Nanoreactor.” ACS Synthetic Biology. DOI: 10.1021/acssynbio.5b00037

Kim, E., Slininger, M., and Tullman-Ercek, D. (2014) “The effects of time, temperature, and pH on the stability of Pdu bacterial microcompartments.” Protein Science. DOI: 10.1002/pro.2527

Glasgow, J., Capehart, S., Francis, M., and Tullman-Ercek, D. (2012) “Osmolyte-Mediated Encapsulation of Proteins inside MS2 Viral Capsids.” ACS Nano. DOI: 10.1021/nn302183h


Protein secretion

Secretion of recombinant proteins from a bacterial host can improve production of proteins that are not stably expressed. We make protein-based materials by secreting the protein monomers from an engineered a type III secretion system.

Azam, A. and Tullman-Ercek, D. (2016) “Type-III secretion filaments as scaffolds for inorganic nanostructures.” Journal of the Royal Society Interface. DOI: 10.1098/rsif.2015.0938

Azam, A., Li, C., Metcalf, K., and Tullman-Ercek, D. (2015) “Type III secretion as a generalizable strategy for the production of full-length biopolymer-forming proteins.” Biotechnology and Bioengineering. DOI: 10.1002/bit.25656

Metcalf, K., Finnerty, C., Azam, A., Valdivia, E., Tullman-Ercek, D. (2014) “Using transcriptional control to increase titer of secreted heterologous proteins by the type III secretion system.” Applied and Environmental Microbiology. DOI: 10.1128/AEM.01330-14


Biochemical efflux pumps

One promising solution to problems of biochemical toxicity and recovery is to use efflux pumps to secrete inhibitory chemicals and fuels from the cell, thus increasing both microbial tolerance and fuel titer. We seek to characterize naturally occurring efflux pumps in the context of commodity biochemicals and natural products, and to engineer and optimize such pumps for the extrusion of biochemicals and relevant inhibitors of high interest.

Boyarskiy, S., López, S.D., Kong, N., and Tullman-Ercek, D. (2015) “Transcriptional feedback regulation of efflux protein expression for increased tolerance to and production of n-butanol.” Metabolic Engineering. DOI: 10.1016/j.ymben.2015.11.005

Fisher, M., Boyarskiy, S., Yamada, M., Kong, N., Bauer, S., and Tullman-Ercek, D. (2013) “Enhancing tolerance to short-chain alcohols by engineering the Escherichia coli AcrB efflux pump to secrete the non-native substrate n-butanol.” ACS Synthetic Biology. DOI: 10.1021/sb400065q