Valentino, IM, Llivicota-Guaman, JG, Dao, TP, Mulvey, EO, Lehman, AM, Galagadera, SKK, Mallon, EL, Catañeda, CA and Kraut DA (2024). Phase separation of polyubiquitinated proteins in UBQLN2 condensates controls substrate fate. Proc Natl Acad Sci USA 121, e2405964121.
Dottor, C.A., Iosue, C.L., Loshnowsky, A.M., Hopkins, R.A., Stauffer, P.L., Ugras, J.M., Spagnula, J.C., Kraut, D.A. and Wykoff, D.D. (2024). Regulation of THI and PDC genes by Pdc2 in Nakaseomyces glabratus (Candida glabrata) is complex. G3 Genes|Genomes|Genetics, jkae132.
Ragwan, E.R., Kisker, F.M., Morning, A.R., Weiser, K.R., Lago, A.V., Kraut, D.A. (2024). Slippery sequences stall the 26S proteasome at multiple points along the translocation pathway. Protein Sci 33, e5034. 10.1002/pro.5034
Stanton, D.A., Ellis, E.A., Cruse, M.R., Jedlinski, R and Kraut, D.A. (2023). The importance of proteasome grip depends on substrate stability. Biochem Biophys Res Com 677:162-167. 10.1016/j.bbrc.2023.08.025.
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.
10.3390/biom12060750.
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 Proteasome. J Biol Chem, 291:18547-18561. doi: 10.1074/jbc.M116.720151.
Nassif, N.D., Cambray, S.E., & Kraut D.A. (2014). Slipping up: Partial Substrate Degradation by ATP-Dependent Proteases. IUBMB Life, 66:309-317. 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 Machines. Chemical Reviews, 114:6806-43. doi:10.1021/cr4007329
Kraut, D.A. (2013). Slippery substrates impair ATP-dependent protease function by slowing unfolding. Journal of Biological Chemistry, 288:34729-34735. 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 Processivity. ACS Chemical Biology, 7(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 stabilization. ACS Chemical Biology, 6(10), 1087–1095. doi:10.1021/cb2002285. PubmedCentral Link
Kraut, D.A., Yu, H., & Matouschek, A. (2011). How ClpX unfolds GFP in stages by pulling. Journal of Molecular Biology, 413(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 proteins. The EMBO Journal, 29(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 hole. Proceedings of the National Academy of Sciences, 107(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 isomerase. Proceedings of the National Academy of Sciences, 106(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 proteins. The Journal of Biological Chemistry, 284(28):18674–18684. doi:10.1074/jbc.M900783200