Publications

Publications

2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2009 | 2008 | 2007 | 2006 | 2003

Preprints

  1. Steinkühler, J., Abrahamson, C. H., Agudo-Canalejo, J., Golestanian, R., Tullman-Ercek, D., Kamat, N. P. (2022). Enzymatically-Active Bacterial Microcompartments Follow Substrate Gradients and Are Protected from Aggregation in a Cell-Free System. bioRxiv. DOI: 10.1101/2022.05.16.492142
  1. Brauer, D.D., Santiago, C.B., Merz, Z.N., McCarthy, E., Tullman-Ercek, D., Francis, M.B. (2021). Comprehensive Fitness Landscape of a Multi-Geometry Protein Capsid Informs Machine Learning Models of Assembly. bioRxiv. DOI: 10.1101/2021.12.21.473721

2023

  1. Waltmann, C., Kennedy, N.W., Mills, C.E., Roth, E.W., Ikonomova, S.P., Tullman-Ercek, D., Olvera de la Cruz, M. (2023). Kinetic Growth of Multicomponent Microcompartment Shells. ACS Nano. DOI: 10.1021/acsnano.3c03353
  1. Abrahamson, C. H., Palmero, B. J., Kennedy, N. W., Tullman-Ercek, D. (2023). Theoretical and Practical Aspects of Multienzyme Organization and Encapsulation. Annual Review of Biophysics. DOI: 10.1146/annurev-biophys-092222-020832
  1. Liang, J. M., Burdette, L. A., Wong, H. T., Tullman-Ercek, D. (2023). Construction of a Constitutively Active Type III Secretion System for Heterologous Protein Secretion. Applied Microbiology and Biotechnology. DOI: 10.1007/s00253-023-12411-9
  1. Ikwuagwu, B., Hartman, E., Mills, C. E., Tullman-Ercek, D. (2023). Systematic Engineering of Virus-like Particles to Identify Self-Assembly Rules for Shifting Particle Size. Virology. DOI: 10.1016/J.VIROL.2023.01.002
  1. Griffith, J. E., Chen, Y., Liu, Q., Wang, Q., Richards, J. J., Tullman-Ercek, D., Shull, K.R., Wang, M. (2023). Quantitative High-Throughput Measurement of Bulk Mechanical Properties Using Commonly Available Equipment. Materials Horizons. 10 (1), 97–106. DOI: 10.1039/D2MH01064J

2022

  1. Ikwuagwu, B., Tullman-Ercek, D. (2022). Virus-like particles for drug delivery: a review of methods and applications. Current Opinion in Biotechnology. 78, 102785. DOI: 10.1016/J.COPBIO.2022.102785
  1. Mills, C. E., Waltmann, C., Archer, A. G., Kennedy, N. W., Abrahamson, C. H., Jackson, A. D., Roth, E. W., Shirman, S., Jewett, M. C., Mangan, N. M., Olvera De La Cruz, M., Tullman-Ercek, D. (2022). Vertex Protein PduN Tunes Encapsulated Pathway Performance by Dictating Bacterial Metabolosome Morphology. Nature Communications. 13 (3746). DOI: 10.1038/s41467-022-31279-3
  1. Kennedy, N. W., Mills, C. E., Abrahamson, C. H., Archer, A. G., Shirman, S., Jewett, M. C., Mangan, N. M., Tullman-Ercek, D. (2022). Linking the Salmonella Enterica 1,2-Propanediol Utilization Bacterial Microcompartment Shell to the Enzymatic Core via the Shell Protein PduB. Journal of Bacteriology. DOI: 10.1128/JB.00576-21
  1. Waltmann, C., Mills, C. E., Wang, J., Qiao, B., Torkelson, J. M., Tullman-Ercek, D., de la Cruz, M. O. (2022). Functional Enzyme–Polymer Complexes. Proceedings of the National Academy of Sciences. 119 (13). DOI: 10.1073/PNAS.2119509119
  1. Berger, O., Battistella, C., Chen, Y., Oktawiec, J., Siwicka, Z. E., Tullman-Ercek, D., Wang, M., Gianneschi, N. C. (2022). Mussel Adhesive-Inspired Proteomimetic Polymer. Journal of the American Chemical Society. 144 (10), 4383–4392. DOI: 10.1021/jacs.1c10936
  1. McFarland, A. G., Kennedy, N. W., Mills, C. E., Tullman-Ercek, D., Huttenhower, C., Hartmann, E. M. (2022). Density-Based Binning of Gene Clusters to Infer Function or Evolutionary History Using GeneGrouper. Bioinformatics. 38 (3), 612–620. DOI: 10.1093/bioinformatics/btab752

2021

  1. Tullman-Ercek, D., Warren, M. (2021). Editorial Overview: Bacterial Microcompartments to the Fore as Metabolism Is Put in Its Place. Current Opinion in Microbiology. 64, 159–161. DOI: 10.1016/J.MIB.2021.10.011
  1. Chen, Y., Wang, Q.,  Mills, C. E., Kann, J. G., Shull K. R., Tullman-Ercek, D., & Wang, M. (2021). High-Throughput Screening Test for Adhesion in Soft Materials Using Centrifugation. ACS Central Science.  7 (7), 1135–1143. DOI: 10.1021/acscentsci.1c00414
  1. Burdette, L. A., Wong, H. T., & Tullman-Ercek, D. (2021). An optimized growth medium for increased recombinant protein secretion titer via the type III secretion system. Microbial Cell Factories. 20(1), 1-13. DOI: 10.1186/s12934-021-01536-z
  1. Kennedy, N. W., Mills, C. E., Nichols, T. M., Abrahamson, C. H., & Tullman-Ercek, D. (2021). Bacterial microcompartments: tiny organelles with big potential. Current Opinion in Microbiology. 63, 36-42. DOI: 10.1016/j.mib.2021.05.010
  1. Li, Y., Kennedy, N. W., Li, S., Mills, C. E., Tullman-Ercek, D., & Olvera de la Cruz, M. (2021). Computational and experimental approaches to controlling bacterial microcompartment assembly. ACS Central Science. 7(4), 658-670. DOI: 10.1021/acscentsci.0c01699
  1. Glasscock, C. J., Biggs, B. W., Lazar, J. T., Arnold, J. H., Burdette, L. A., Valdes, A., Kang, M., Tullman-Ercek, D., Tyo, K. E. J., & Lucks, J. B. (2021). Dynamic Control of Gene Expression with Riboregulated Switchable Feedback Promoters. ACS Synthetic Biology. 10(5), 1199-1213. DOI: 10.1021/acssynbio.1c00015
  1. Kennedy, N. W., Ikonomova, S. P., Lee, M. S., Raeder, H. W., & Tullman-Ercek, D. (2021). Self-assembling shell proteins PduA and PduJ have essential and redundant roles in bacterial microcompartment assembly. Journal of Molecular Biology. 433(2), 166721. DOI: 10.1016/j.jmb.2020.11.020

2020

  1. Robinson, S. A., Hartman, E. C., Ikwuagwu, B. C., Francis, M. B., Tullman-Ercek, D. (2020). “Engineering a Virus-like Particle to Display Peptide Insertions Using an Apparent Fitness Landscape.” Biomacromolecules. 21(10): 4194-4204. DOI: 10.1021/acs.biomac.0c00987
  1. Kafader, J. O., Melani, R. D., Durbin, K. R., Ikwuagwu, B., Early, B. P., Fellers, R. T., Beu, S. C., Zabrouskov, V., Makarov, A. A., Maze, J. T., Shinholt, D. L., Yip, P. F., Tullman-Ercek, D., Senko, M. W., Compton, P. D., Kelleher, N. L. (2020). “Multiplexed mass spectrometry of individual ions improves measurement of proteoforms and their complexes.” Nature Methods. 17(4): 391-4. DOI: 10.1038/s41592-020-0764-5
  1. Kennedy, N. W., Hershewe, J. M., Nichols, T. M., Roth, E. W., Wilke, C. D., Mills, C. E., Jewett, M. C., Tullman-Ercek, D. (2020). “Apparent size and morphology of bacterial microcompartments varies with technique.” PLoS One. 15(3). DOI: 10.1371/journal.pone.0226395
  1. Nichols, T. M., Kennedy, N. W, Tullman-Ercek, D. (2020). “A genomic integration platform for heterologous cargo encapsulation in 1,2-propanediol utilization bacterial microcompartments.” Biochemical Engineering Journal. 156. DOI: 10.1016/j.bej.2020.107496

2019

  1. Nichols, T. M., Kennedy, N. W, Tullman-Ercek, D. (2019). “Cargo encapsulation in bacterial microcompartments: Methods and analysis.” Methods in Enzymology. Vol. 617. New York, NY :: Academic, 2019. Metabolons and Supramolecular Enzyme Assemblies. DOI: 10.1016/bs.mie.2018.12.009
  1. Brauer, D. D., Hartman, E. C., Bader, D. L. V., Merz, Z. N., Tullman-Ercek, D., Francis, M. B. (2019). “Systematic engineering of a protein nanocage for high-yield, site-specific modification.” Journal of the American Chemical Society. 141(9): 3875-84. DOI: 10.1021/jacs.8b10734
  1. Hartman, E. C., Lobba, M. J., Favor, A. H., Robinson, S. A., Francis, M. B., Tullman-Ercek, D. (2019). “Experimental evaluation of co-evolution in a self-assembling particle.” Biochemistry. 58(11): 1527-38. DOI: 10.1021/acs.biochem.8b00948
  1. Hartman, E. C., Tullman-Ercek, D. (2019). “Learning from protein fitness landscapes: a review of mutability, epistasis, and evolution.” Current Opinion in Systems Biology. 14: 25-31. DOI: 10.1016/j.coisb.2019.02.006

2018

  1. Burdette, L. A., Leach, S. A., Wong, H. T., Tullman-Ercek, D. (2018). “Developing Gram-negative bacteria for the secretion of heterologous proteins.” Microbial Cell Factories. 17(196). DOI: 10.1186/s12934-018-1041-5
  1. Metcalf, K. J., Lee, M. F. S., Jakobson, C. M., Tullman-Ercek, D. (2018). “An estimate is worth about a thousand experiments: using order-of-magnitude estimates to identify cellular engineering targets.” Microbial Cell Factories. 17(135). DOI: 10.1186/s12934-018-0979-7
  1. Basler, G., Thompson, M., Tullman-Ercek, D., Keasling, J. (2018). “A Pseudomonas putida efflux pump acts on short-chain alcohols.” Biotechnology for Biofuels. 11(136). DOI: 10.1186/s13068-018-1133-9
  1. Jakobson, C. M., Tullman-Ercek, D., Mangan, N. M. (2018). “Spatially organizing biochemistry: choosing a strategy to translate synthetic biology to the factory.” Scientific Reports. 8(1): 8196. DOI: 10.1038/s41598-018-26399-0
  1. Kang, M. K, Tullman-Ercek, D. (2018). “Engineering expression and function of membrane proteins.” Methods. 135(1385). DOI: 10.1016/j.ymeth.2018.04.014
  1. Hartman, E. C.,  Jakobson, C. M., Favor, A. H., Lobba, M. J., Benedicto, E. A., Francis ,M. B., Tullman-Ercek, D. (2018). “Quantitative characterization of all single amino acid variants of a viral capsid-based drug delivery vehicle.” Nature Communications. 9(1385). DOI: 10.1038/s41467-018-03783-y
  1. Davis López, S. A., Griffith, D. A., Choi, B., Cate, J. H., Tullman-Ercek D. (2018). “Evolutionary engineering improves tolerance for medium-chain alcohols in Saccharomyces cerevisiae.” Biotechnology for Biofuels. 11(90). DOI: 10.1186/s13068-018-1089-9
  1. Azam Glasgow, A., Tullman-Ercek, D. (2018). “Type III Secretion Filaments as Templates for Metallic Nanostructure Synthesis.” In: Protein Scaffolds. Methods in Molecular Biology, vol 1798. Humana Press, New York, NY. DOI: 10.1016/j.ymeth.2018.04.014

2017

  1. Slininger-Lee, M. F., Tullman-Ercek, D. (2017). “Practical considerations for the encapsulation of multi-enzyme cargos within the bacterial microcompartment for metabolic engineering.” Current Opinion in Systems Biology. 5(1). DOI: 10.1016/j.coisb.2017.05.017
  1. Slininger, M. F., Jakobson, C. M., Tullman-Ercek, D. (2017). “Evidence for Improved Encapsulated Pathway Behavior in a Bacterial Microcompartment through Shell Protein Engineering.” ACS Synthetic Biology. 6(10):1880-1891. DOI: 10.1021/acssynbio.7b00042
  1. Jakobson, C. M., Tullman-Ercek, D., Slininger, M. F., Mangan, N. M. (2017). “A systems-level model reveals that 1,2-Propanediol utilization microcompartments enhance pathway flux through intermediate sequestration.” PLoS Computational Biology. 13(5). DOI: 10.1371/journal.pcbi.1005525 
  1. Azam Glasgow, A., Wong, H. T., Tullman-Ercek, D. (2017). “A Secretion-Amplification Role for Salmonella enterica Translocon Protein SipD.” ACS Synthetic Biology. 6(6). DOI: 10.1021/acssynbio.6b00335 
  1. Jakobson, C. M., Slininger-Lee, M. F., Tullman-Ercek, D. (2017). “De novo design of signal sequences to localize cargo to the 1,2-propanediol utilization microcompartment.” Protein Science. 26(5). DOI: 10.1002/pro.3144
  1. Metcalf, K. J., Tullman-Ercek, D. (2017). “Use of Transcriptional Control to Increase Secretion of Heterologous Proteins in T3S Systems.” In: Type 3 Secretion Systems. Methods in Molecular Biology, vol 1531 (71-79). Humana Press, New York, NY. DOI: 10.1007/978-1-4939-6649-3_6

2016

  1. Metcalf, K. J., Bevington, J. L., Rosales, S. L., Burdette, L. A., Valdivia, E., Tullman-Ercek, D. (2016). “Proteins adopt functionally active conformations after type III secretion.” Microbial Cell Factories. 15(1):213. DOI: 10.1186/s12934-016-0606-4
  1. 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
  1. 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
  1. Jakobson, C. and Tullman-Ercek, D. (2016). “Dumpster Diving in the Gut: Bacterial Microcompartments as Part of a Host-Associated Lifestyle.” PLoS Pathogens. DOI: 10.1371/journal.ppat.1005558
  1. 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

2015

  1. 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
  1. Jakobson, C., Kim, E., Slininger, M. Chien, A., and Tullman-Ercek, D. (2015). “Localization of Proteins to the 1,2-Propanediol Utilization Microcompartment by Non-native Signal Sequences Is Mediated by a Common Hydrophobic Motif.” The Journal of Biological Chemistry. DOI: 10.1074/jbc.M115.651919
  1. 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
  1. 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

2014

  1. Kim, E.*, Jakobson, C.*, and Tullman-Ercek, D. (2014). “Engineering transcriptional regulation to control Pdu microcompartment formation.” PLoS ONE. DOI: 10.1371/journal.pone.0113814
    (* denotes equal contributions)
  1. 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
  1. 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.0133-14
  1. Glasgow, J. and Tullman-Ercek, D. (2014). “Production and applications of engineered viral capsids.” Applied Microbiology and Biotechnology. DOI: 10.1007/s00253-014-5787-3

2013

  1. Kim, E. and Tullman-Ercek, D. (2013). “A rapid flow cytometry assay for the relative quantification of protein encapsulation into bacterial microcompartments.” Biotechnology Journal. DOI: 10.1002/biot.201300391
  1. Reyes-Ortiz, V., Heins, R.A., Cheng, G., Kim, E.Y., Vernon, B.C., Elandt, R.B., Adams, P.D., Sale, K.L., Hadi, M.Z., Simmons, B.A., Kent, M.S., Tullman-Ercek, D. (2013). “Addition of a carbohydrate-binding module enhances cellulase penetration into cellulose substrates.” Biotechnology for Biofuels. DOI: 10.1186/1754-6834-6-93
  1. 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
  1. Fisher, M. and Tullman-Ercek, D. (2013). “Change, exchange, and rearrange: protein engineering for the biotechnological production of fuels, pharmaceuticals, and other chemicals.” Current Opinion in Biotechnology. DOI: 10.1016/j.copbio.2013.02.027

2012

  1. Kim, E. and Tullman-Ercek, D. (2012). “Engineering nanoscale protein compartments for synthetic organelles.” Current Opinion in Biotechnology. DOI: 10.1016/j.copbio.2012.11.012
  1. 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

2011

  1. Bokinsky, G., Peralta-Yahya, P. P., George, A., Holmes, B. M., Steen, E. J., Dietrich, J., Soon Lee, T., Tullman-Ercek, D., Voigt, C. A., Simmons, B. A., and Keasling, J. (2011). “Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered Escherichia coli.” Proceedings of the National Academy of Sciences. USA. DOI: 10.1073/pnas.1106958108

2009

  1. Widmaier, D. W., Tullman-Ercek, D., Mirsky, E. A., Temme, K. T., Govindarajan, S., Minshull, J., Voigt, C. A. (2009). “Engineering the Salmonella type III secretion system to export spider silk monomers.” Molecular Systems Biology. DOI: 10.1038/msb.2009.62

2008

  1. Fisher, A. C., Kim, J. Y., Tullman-Ercek, D., Henderson, L. A., DeLisa, M. P. (2008). “Exploration of the bacterial twin-arginine translocation system for expression and purification of properly folded proteins in Escherichia coli.” Microbial Biotechnology. DOI: 10.1111/j.1751-7915.2008.00041.x
  1. Temme, K. T., Salis, H., Tullman-Ercek, D., Levskaya, A., Hong, S. H., Voigt, C. A. (2008). “Induction and relaxation dynamics of the regulatory network controlling the type III secretion system encoded within Salmonella pathogenicity island I.” Journal of Molecular Biology. DOI: 10.1016/j.jmb.2007.12.044

2007

  1. Tullman-Ercek, D., DeLisa, M. P., Kawarasaki, Y., Iranpour, P., Ribnicky, B., Palmer, T., Georgiou, G. (2007). “Export pathway selectivity of Escherichia coli twin-arginine translocation signal peptides.” Journal of Biological Chemistry. DOI: 10.1074/jbc.M610507200

2006

  1. Lee, P. A., Tullman-Ercek, D., Georgiou, G. (2006). “The bacterial twin-arginine translocation pathway.” Annual Review of Microbiology. DOI: 10.1146/annurev.micro.60.080805.142212

2003

  1. DeLisa, M. P., Tullman, D., Georgiou, G. (2003) “Folding quality control in the export of proteins by the bacterial twin-arginine translocation pathway.” Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0937838100