Manfredonia A.J.* and Kraut D.A. (2022) The 26S Proteasome Switches Between ATP-Dependent and -Independent Mechanisms in Response to Substrate Ubiquitination. Biomolecules 12:750.

Hurley C.M., Kraut D.A. (2021) Determination of Proteasomal Unfolding Ability. In: Cacace A.M., Hickey C.M., Békés M. (eds) Targeted Protein Degradation. Methods in Molecular Biology, 2365:217-244. Humana, New York, NY. doi:10.1007/978-1-0716-1665-9_12

Cresti JR*, Manfredonia AJ*, Bragança CE, Boscia IV JA, Hurley CM, Cundiff MD & Kraut DA (2021). Proteasomal Conformation Controls Unfolding Ability. Proc Natl Acad Sci USA 118:e2101004118. 10.1073/pnas.2101004118.

Zhai T., Zhang F., Haider S., Kraut D. and Huang Z. (2021). An Integrated Computational and Experimental Approach to Identifying Inhibitors for SARS-CoV-2 3CL Protease. Front Mol Biosci. 8:267. doi:10.3389/fmolb.2021.661424.

Bragança C.E. & Kraut D.A. (2020). Mode of Targeting to the Proteasome Determines GFP Fate. J Biol Chem, 295:15892-15901. doi:10.1074/jbc.RA120.015235.

Cundiff M.D.*, Hurley C.M.*, Wong J.D., Bashyal A., Rosenberg J., Reichard E.L., Nassif N.D., Brodbelt J.S., & Kraut D.A. (2019). Ubiquitin Receptors are Required for Substrate-Mediated Activation of the Proteasome’s Unfolding Ability. Scientific Reports 9:14506. doi: 10.1038/s41598-019-50857-y.

Reichard, E.L., Chirico, G.G., Dewey, W.J., Nassif, N.D., Bard, K.E.,Millas, N.E., & Kraut D.A. (2016). Substrate Ubiquitination Controls the Unfolding Ability of the ProteasomeJ Biol Chem291:18547-18561. doi: 10.1074/jbc.M116.720151.

Nassif, N.D., Cambray, S.E., & Kraut D.A. (2014). Slipping up: Partial Substrate Degradation by ATP-Dependent ProteasesIUBMB Life66:309-317. doi:10.1002/iub.1271.

Fuxreiter M., Tóth-Petróczy A., Kraut D.A., Matouschek A.T., Lim R.Y., Xue B., Kurgan L., Uversky V.N. (2014). Disordered Proteinaceous MachinesChemical Reviews114:6806-43. doi:10.1021/cr4007329

Kraut, D.A. (2013). Slippery substrates impair ATP-dependent protease function by slowing unfoldingJournal of Biological Chemistry288:34729-34735. doi: 10.1074/jbc.M113.512533 

Kraut, D.A., Israeli, E., Schrader, E.K., Patil, A., Nakai, K., Nanavati, D., Inobe, T., & Matouschek, A. (2012). Sequence- and Species Dependence of Proteasomal ProcessivityACS Chemical Biology7(8):1444–1453. doi:10.1021/cb3001155. PubmedCentral Link

Kraut, D.A., & Matouschek, A. (2011). Proteasomal degradation from internal sites favors partial proteolysis via remote domain stabilizationACS Chemical Biology6(10), 1087–1095. doi:10.1021/cb2002285. PubmedCentral Link

Kraut, D.A., Yu, H., & Matouschek, A. (2011). How ClpX unfolds GFP in stages by pullingJournal of Molecular Biology413(1), 1–3. doi:10.1016/j.jmb.2011.08.007 (Commentary)

Kraut, D.A., & Matouschek, A. (2010). Pup grows up: in vitro characterization of the degradation of pupylated proteinsThe EMBO Journal29(7), 1163–1164. doi:10.1038/emboj.2010.40 (Commentary)

Kraut, D.A., Sigala, P.A., Fenn, T.D., & Herschlag, D. (2010). Dissecting the paradoxical effects of hydrogen bond mutations in the ketosteroid isomerase oxyanion holeProceedings of the National Academy of Sciences107(5):1960–1965. doi:10.1073/pnas.0911168107

Schwans, J.P., Kraut, D.A., & Herschlag, D. (2009). Determining the catalytic role of remote substrate binding interactions in ketosteroid isomeraseProceedings of the National Academy of Sciences106(34):14271–14275. doi:10.1073/pnas.0901032106

Koodathingal, P., Jaffe, N.E., Kraut, D.A., Prakash, S., Fishbain, S., Herman, C., & Matouschek, A. (2009). ATP-dependent proteases differ substantially in their ability to unfold globular proteinsThe Journal of Biological Chemistry284(28):18674–18684. doi:10.1074/jbc.M900783200