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Yeast Models for Amyloids and Prions: Environmental Modulation and Drug Discovery.

Chernova TA, Chernoff YO, Wilkinson KD.

Molecules. 2019 Sep 18;24(18). pii: E3388. doi: 10.3390/molecules24183388. Review.


Prion-based memory of heat stress in yeast.

Chernova TA, Chernoff YO, Wilkinson KD.

Prion. 2017 May 4;11(3):151-161. doi: 10.1080/19336896.2017.1328342. Epub 2017 May 19.


Yeast Short-Lived Actin-Associated Protein Forms a Metastable Prion in Response to Thermal Stress.

Chernova TA, Kiktev DA, Romanyuk AV, Shanks JR, Laur O, Ali M, Ghosh A, Kim D, Yang Z, Mang M, Chernoff YO, Wilkinson KD.

Cell Rep. 2017 Jan 17;18(3):751-761. doi: 10.1016/j.celrep.2016.12.082.


Prions, Chaperones, and Proteostasis in Yeast.

Chernova TA, Wilkinson KD, Chernoff YO.

Cold Spring Harb Perspect Biol. 2017 Feb 1;9(2). pii: a023663. doi: 10.1101/cshperspect.a023663. Review.


Wss1 metalloprotease partners with Cdc48/Doa1 in processing genotoxic SUMO conjugates.

Balakirev MY, Mullally JE, Favier A, Assard N, Sulpice E, Lindsey DF, Rulina AV, Gidrol X, Wilkinson KD.

Elife. 2015 Sep 8;4. doi: 10.7554/eLife.06763.


Quantitative analysis of protein-protein interactions.

Eletr ZM, Wilkinson KD.

Methods Mol Biol. 2015;1278:23-37. doi: 10.1007/978-1-4939-2425-7_2.


Stress-dependent proteolytic processing of the actin assembly protein Lsb1 modulates a yeast prion.

Ali M, Chernova TA, Newnam GP, Yin L, Shanks J, Karpova TS, Lee A, Laur O, Subramanian S, Kim D, McNally JG, Seyfried NT, Chernoff YO, Wilkinson KD.

J Biol Chem. 2014 Oct 3;289(40):27625-39. doi: 10.1074/jbc.M114.582429. Epub 2014 Aug 20.


Physiological and environmental control of yeast prions.

Chernova TA, Wilkinson KD, Chernoff YO.

FEMS Microbiol Rev. 2014 Mar;38(2):326-44. doi: 10.1111/1574-6976.12053. Epub 2013 Dec 4. Review.


BAP1 is phosphorylated at serine 592 in S-phase following DNA damage.

Eletr ZM, Yin L, Wilkinson KD.

FEBS Lett. 2013 Dec 11;587(24):3906-11. doi: 10.1016/j.febslet.2013.10.035. Epub 2013 Nov 5.


Regulation of proteolysis by human deubiquitinating enzymes.

Eletr ZM, Wilkinson KD.

Biochim Biophys Acta. 2014 Jan;1843(1):114-28. doi: 10.1016/j.bbamcr.2013.06.027. Epub 2013 Jul 9. Review.


Two ZnF-UBP domains in isopeptidase T (USP5).

Avvakumov GV, Walker JR, Xue S, Allali-Hassani A, Asinas A, Nair UB, Fang X, Zuo X, Wang YX, Wilkinson KD, Dhe-Paganon S.

Biochemistry. 2012 Feb 14;51(6):1188-98. doi: 10.1021/bi200854q. Epub 2012 Feb 3.


Structure and recognition of polyubiquitin chains of different lengths and linkage.

Fushman D, Wilkinson KD.

F1000 Biol Rep. 2011;3:26. doi: 10.3410/B3-26. Epub 2011 Dec 1.


Prion induction by the short-lived, stress-induced protein Lsb2 is regulated by ubiquitination and association with the actin cytoskeleton.

Chernova TA, Romanyuk AV, Karpova TS, Shanks JR, Ali M, Moffatt N, Howie RL, O'Dell A, McNally JG, Liebman SW, Chernoff YO, Wilkinson KD.

Mol Cell. 2011 Jul 22;43(2):242-52. doi: 10.1016/j.molcel.2011.07.001.


An emerging model for BAP1's role in regulating cell cycle progression.

Eletr ZM, Wilkinson KD.

Cell Biochem Biophys. 2011 Jun;60(1-2):3-11. doi: 10.1007/s12013-011-9184-6. Review.


Polyubiquitin binding and cross-reactivity in the USP domain deubiquitinase USP21.

Ye Y, Akutsu M, Reyes-Turcu F, Enchev RI, Wilkinson KD, Komander D.

EMBO Rep. 2011 Apr;12(4):350-7. doi: 10.1038/embor.2011.17. Epub 2011 Mar 11.


Distribution and paralogue specificity of mammalian deSUMOylating enzymes.

Kolli N, Mikolajczyk J, Drag M, Mukhopadhyay D, Moffatt N, Dasso M, Salvesen G, Wilkinson KD.

Biochem J. 2010 Sep 1;430(2):335-44. doi: 10.1042/BJ20100504.


Identification and developmental expression of Xenopus laevis SUMO proteases.

Wang Y, Mukhopadhyay D, Mathew S, Hasebe T, Heimeier RA, Azuma Y, Kolli N, Shi YB, Wilkinson KD, Dasso M.

PLoS One. 2009 Dec 24;4(12):e8462. doi: 10.1371/journal.pone.0008462.


DUBs at a glance.

Wilkinson KD.

J Cell Sci. 2009 Jul 15;122(Pt 14):2325-9. doi: 10.1242/jcs.041046. Review. No abstract available.


Regulation and cellular roles of ubiquitin-specific deubiquitinating enzymes.

Reyes-Turcu FE, Ventii KH, Wilkinson KD.

Annu Rev Biochem. 2009;78:363-97. doi: 10.1146/annurev.biochem.78.082307.091526. Review.


Molecular discrimination of structurally equivalent Lys 63-linked and linear polyubiquitin chains.

Komander D, Reyes-Turcu F, Licchesi JD, Odenwaelder P, Wilkinson KD, Barford D.

EMBO Rep. 2009 May;10(5):466-73. doi: 10.1038/embor.2009.55. Epub 2009 Apr 17.


Beta-arrestin-dependent signaling and trafficking of 7-transmembrane receptors is reciprocally regulated by the deubiquitinase USP33 and the E3 ligase Mdm2.

Shenoy SK, Modi AS, Shukla AK, Xiao K, Berthouze M, Ahn S, Wilkinson KD, Miller WE, Lefkowitz RJ.

Proc Natl Acad Sci U S A. 2009 Apr 21;106(16):6650-5. doi: 10.1073/pnas.0901083106. Epub 2009 Apr 10.


Polyubiquitin binding and disassembly by deubiquitinating enzymes.

Reyes-Turcu FE, Wilkinson KD.

Chem Rev. 2009 Apr;109(4):1495-508. doi: 10.1021/cr800470j. Review. No abstract available.


Evidence for bidentate substrate binding as the basis for the K48 linkage specificity of otubain 1.

Wang T, Yin L, Cooper EM, Lai MY, Dickey S, Pickart CM, Fushman D, Wilkinson KD, Cohen RE, Wolberger C.

J Mol Biol. 2009 Mar 6;386(4):1011-23. doi: 10.1016/j.jmb.2008.12.085. Epub 2009 Jan 13.


Burkholderia mallei tssM encodes a putative deubiquitinase that is secreted and expressed inside infected RAW 264.7 murine macrophages.

Shanks J, Burtnick MN, Brett PJ, Waag DM, Spurgers KB, Ribot WJ, Schell MA, Panchal RG, Gherardini FC, Wilkinson KD, Deshazer D.

Infect Immun. 2009 Apr;77(4):1636-48. doi: 10.1128/IAI.01339-08. Epub 2009 Jan 21.


Dynamic compartmentalization of base excision repair proteins in response to nuclear and mitochondrial oxidative stress.

Griffiths LM, Swartzlander D, Meadows KL, Wilkinson KD, Corbett AH, Doetsch PW.

Mol Cell Biol. 2009 Feb;29(3):794-807. doi: 10.1128/MCB.01357-08. Epub 2008 Nov 24.


Nucleolar protein B23/nucleophosmin regulates the vertebrate SUMO pathway through SENP3 and SENP5 proteases.

Yun C, Wang Y, Mukhopadhyay D, Backlund P, Kolli N, Yergey A, Wilkinson KD, Dasso M.

J Cell Biol. 2008 Nov 17;183(4):589-95. doi: 10.1083/jcb.200807185.


BRCA1-associated protein-1 is a tumor suppressor that requires deubiquitinating activity and nuclear localization.

Ventii KH, Devi NS, Friedrich KL, Chernova TA, Tighiouart M, Van Meir EG, Wilkinson KD.

Cancer Res. 2008 Sep 1;68(17):6953-62. doi: 10.1158/0008-5472.CAN-08-0365.


Protein partners of deubiquitinating enzymes.

Ventii KH, Wilkinson KD.

Biochem J. 2008 Sep 1;414(2):161-75. doi: 10.1042/BJ20080798. Review.


Positional-scanning fluorigenic substrate libraries reveal unexpected specificity determinants of DUBs (deubiquitinating enzymes).

Drag M, Mikolajczyk J, Bekes M, Reyes-Turcu FE, Ellman JA, Wilkinson KD, Salvesen GS.

Biochem J. 2008 Nov 1;415(3):367-75. doi: 10.1042/BJ20080779.


DeTEKting ubiquitination of APC/C substrates.

Haas AL, Wilkinson KD.

Cell. 2008 May 16;133(4):570-2. doi: 10.1016/j.cell.2008.04.034.


Recognition of polyubiquitin isoforms by the multiple ubiquitin binding modules of isopeptidase T.

Reyes-Turcu FE, Shanks JR, Komander D, Wilkinson KD.

J Biol Chem. 2008 Jul 11;283(28):19581-92. doi: 10.1074/jbc.M800947200. Epub 2008 May 15.


Characterization of ubiquitin and ubiquitin-like-protein isopeptidase activities.

Nicholson B, Leach CA, Goldenberg SJ, Francis DM, Kodrasov MP, Tian X, Shanks J, Sterner DE, Bernal A, Mattern MR, Wilkinson KD, Butt TR.

Protein Sci. 2008 Jun;17(6):1035-43. doi: 10.1110/ps.083450408. Epub 2008 Apr 18.


OTU takes the chains OUT.

Balakirev MY, Wilkinson KD.

Nat Chem Biol. 2008 Apr;4(4):227-8. doi: 10.1038/nchembio0408-227. No abstract available.


Structural basis for ubiquitin recognition by the Otu1 ovarian tumor domain protein.

Messick TE, Russell NS, Iwata AJ, Sarachan KL, Shiekhattar R, Shanks JR, Reyes-Turcu FE, Wilkinson KD, Marmorstein R.

J Biol Chem. 2008 Apr 18;283(16):11038-49. doi: 10.1074/jbc.M704398200. Epub 2008 Feb 12.


Proteolytic processing and deubiquitinating activity of papain-like proteases of human coronavirus NL63.

Chen Z, Wang Y, Ratia K, Mesecar AD, Wilkinson KD, Baker SC.

J Virol. 2007 Jun;81(11):6007-18. Epub 2007 Mar 28.


Effects of ubiquitin system alterations on the formation and loss of a yeast prion.

Allen KD, Chernova TA, Tennant EP, Wilkinson KD, Chernoff YO.

J Biol Chem. 2007 Feb 2;282(5):3004-13. Epub 2006 Dec 1.


SUSP1 antagonizes formation of highly SUMO2/3-conjugated species.

Mukhopadhyay D, Ayaydin F, Kolli N, Tan SH, Anan T, Kametaka A, Azuma Y, Wilkinson KD, Dasso M.

J Cell Biol. 2006 Sep 25;174(7):939-49.


The ubiquitin binding domain ZnF UBP recognizes the C-terminal diglycine motif of unanchored ubiquitin.

Reyes-Turcu FE, Horton JR, Mullally JE, Heroux A, Cheng X, Wilkinson KD.

Cell. 2006 Mar 24;124(6):1197-208.


Doa1 is a Cdc48 adapter that possesses a novel ubiquitin binding domain.

Mullally JE, Chernova T, Wilkinson KD.

Mol Cell Biol. 2006 Feb;26(3):822-30.


The discovery of ubiquitin-dependent proteolysis.

Wilkinson KD.

Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15280-2. Epub 2005 Oct 17.


Structure and mechanisms of the proteasome-associated deubiquitinating enzyme USP14.

Hu M, Li P, Song L, Jeffrey PD, Chenova TA, Wilkinson KD, Cohen RE, Shi Y.

EMBO J. 2005 Nov 2;24(21):3747-56. Epub 2005 Oct 6.


The ubiquitin signal: assembly, recognition and termination. Symposium on ubiquitin and signaling.

Wilkinson KD, Ventii KH, Friedrich KL, Mullally JE.

EMBO Rep. 2005 Sep;6(9):815-20. Review. No abstract available.


Deubiquitinating enzyme purification, assay inhibitors, and characterization.

Russell NS, Wilkinson KD.

Methods Mol Biol. 2005;301:207-19.


Ubiquitin-proteasome degradation of KLF5 transcription factor in cancer and untransformed epithelial cells.

Chen C, Sun X, Ran Q, Wilkinson KD, Murphy TJ, Simons JW, Dong JT.

Oncogene. 2005 May 5;24(20):3319-27.


Ubiquitin: a Nobel protein.

Wilkinson KD.

Cell. 2004 Dec 17;119(6):741-5. No abstract available.


Structure of a complex between Nedd8 and the Ulp/Senp protease family member Den1.

Reverter D, Wu K, Erdene TG, Pan ZQ, Wilkinson KD, Lima CD.

J Mol Biol. 2005 Jan 7;345(1):141-51.


Varshavsky's contributions.

Baumeister W, Bachmair A, Chau V, Cohen R, Coffino P, Demartino G, Deshaies R, Dohmen J, Emr S, Finley D, Hampton R, Hill C, Hochstrasser M, Huber R, Jackson P, Jentsch S, Johnson E, Kwon YT, Pagano M, Pickart C, Rechsteiner M, Scheffner M, Sommer T, Tansey W, Tyers M, Vierstra R, Weissman A, Wilkinson KD, Wolf D.

Science. 2004 Nov 19;306(5700):1290-2. No abstract available.


Hsp70 chaperones as modulators of prion life cycle: novel effects of Ssa and Ssb on the Saccharomyces cerevisiae prion [PSI+].

Allen KD, Wegrzyn RD, Chernova TA, Müller S, Newnam GP, Winslett PA, Wittich KB, Wilkinson KD, Chernoff YO.

Genetics. 2005 Mar;169(3):1227-42. Epub 2004 Nov 15.


Modulating huntingtin half-life alters polyglutamine-dependent aggregate formation and cell toxicity.

Kaytor MD, Wilkinson KD, Warren ST.

J Neurochem. 2004 May;89(4):962-73.

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