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Article: Expanding the ligandable proteome by paralog hopping with covalent probes.

Zhang, Yuanjin / Liu, Zhonglin / Hirschi, Marsha / Brodsky, Oleg / Johnson, Eric / Won, Sang Joon / Nagata, Asako / Petroski, Matthew D / Majmudar, Jaimeen D / Niessen, Sherry / VanArsdale, Todd / Gilbert, Adam M / Hayward, Matthew M / Stewart, Al E / Nager, Andrew R / Melillo, Bruno / Cravatt, Benjamin

bioRxiv : the preprint server for biology

2024

Abstract: More than half of the ~20,000 protein-encoding human genes have at least one paralog. Chemical proteomics has uncovered many electrophile-sensitive cysteines that are exclusive to a subset of paralogous proteins. Here, we explore whether such covalent ... ...

Abstract	More than half of the ~20,000 protein-encoding human genes have at least one paralog. Chemical proteomics has uncovered many electrophile-sensitive cysteines that are exclusive to a subset of paralogous proteins. Here, we explore whether such covalent compound-cysteine interactions can be used to discover ligandable pockets in paralogs that lack the cysteine. Leveraging the covalent ligandability of C109 in the cyclin CCNE2, we mutated the corresponding residue in paralog CCNE1 to cysteine (N112C) and found through activity-based protein profiling (ABPP) that this mutant reacts stereoselectively and site-specifically with tryptoline acrylamides. We then converted the tryptoline acrylamide-N112C-CCNE1 interaction into a NanoBRET-ABPP assay capable of identifying compounds that reversibly inhibit both N112C- and WT-CCNE1:CDK2 complexes. X-ray crystallography revealed a cryptic allosteric pocket at the CCNE1:CDK2 interface adjacent to N112 that binds the reversible inhibitors. Our findings thus provide a roadmap for leveraging electrophile-cysteine interactions to extend the ligandability of the proteome beyond covalent chemistry.
Language	English
Publishing date	2024-01-19
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.01.18.576274
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Article: Spherical Aberration of Cataractous Eyes and Its Relationship With Age, Ocular Biometry, and Various IOL Platforms.

Hirabayashi, Matthew T / Gharabagi, Areiss P / Hesemann, Nathan P / Johnson, Sandra M / Webel, Aaron D / Petroski, Gregory F / Davis, Geetha R

Journal of refractive surgery (Thorofare, N.J. : 1995)

2023 Volume 39, Issue 2, Page(s) 89–94

Abstract: Purpose: To determine the median spherical aberration (SA) of the cataractous population, how it relates to biometry, and the theoretical effect of different intraocular lens (IOL) platforms.: Methods: A retrospective chart review of patients ... ...

Abstract	Purpose: To determine the median spherical aberration (SA) of the cataractous population, how it relates to biometry, and the theoretical effect of different intraocular lens (IOL) platforms. Methods: A retrospective chart review of patients undergoing cataract surgery evaluation with a high quality Pentacam (Oculus Optikgeräte GmbH) were included. Age, gender, Q-value, mean total SA, higher order aberration root mean square wavefront error, and equivalent keratometry were collected from the Holladay report and axial length and anterior chamber depth (ACD) from the IOLMaster 700 (Carl Zeiss Meditec AG). Results: Data from 1,725 eyes of 999 patients were collected. SA had a median of 0.37 µm (95% confidence interval: 0.36 to 0.38. Age ( Conclusions: SA is not normally distributed, suggesting that there may be no "average" SA that IOLs should aim to correct. Patients might benefit from tailoring IOL choice to individual SA. Without access to SA data, eyes with steeper average keratometry or younger patients may have less SA, which could influence IOL choice.
MeSH term(s)	Humans ; Retrospective Studies ; Lenses, Intraocular ; Cataract Extraction ; Vision, Ocular ; Biometry ; Refraction, Ocular
Language	English
Publishing date	2023-02-01
Publishing country	United States
Document type	Journal Article
ISSN	1081-597X
ISSN	1081-597X
DOI	10.3928/1081597X-20221207-01
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Article ; Online: Mechanism-based neddylation inhibitor.

Petroski, Matthew D

Chemistry & biology

2010 Volume 17, Issue 1, Page(s) 6–8

Abstract: Brownell et al. (2010) elucidate the mechanism of action of MLN4924, a NEDD8-activating enzyme inhibitor. MLN4924 requires the activity of the enzyme to generate a NEDD8-adenylate analog that potently and selectively shuts down this posttranslational ... ...

Abstract	Brownell et al. (2010) elucidate the mechanism of action of MLN4924, a NEDD8-activating enzyme inhibitor. MLN4924 requires the activity of the enzyme to generate a NEDD8-adenylate analog that potently and selectively shuts down this posttranslational modification system.
Language	English
Publishing date	2010-01-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	917827-2
ISSN	1879-1301 ; 1074-5521
ISSN (online)	1879-1301
ISSN	1074-5521
DOI	10.1016/j.chembiol.2010.01.002
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Article ; Online: The ubiquitin system, disease, and drug discovery.

Petroski, Matthew D

BMC biochemistry

2008 Volume 9 Suppl 1, Page(s) S7

Abstract: The ubiquitin system of protein modification has emerged as a crucial mechanism involved in the regulation of a wide array of cellular processes. As our knowledge of the pathways in this system has grown, so have the ties between the protein ubiquitin ... ...

Abstract	The ubiquitin system of protein modification has emerged as a crucial mechanism involved in the regulation of a wide array of cellular processes. As our knowledge of the pathways in this system has grown, so have the ties between the protein ubiquitin and human disease. The power of the ubiquitin system for therapeutic benefit blossomed with the approval of the proteasome inhibitor Velcade in 2003 by the FDA. Current drug discovery activities in the ubiquitin system seek to (i) expand the development of new proteasome inhibitors with distinct mechanisms of action and improved bioavailability, and (ii) validate new targets. This review summarizes our current understanding of the role of the ubiquitin system in various human diseases ranging from cancer, viral infection and neurodegenerative disorders to muscle wasting, diabetes and inflammation. I provide an introduction to the ubiquitin system, highlight some emerging relationships between the ubiquitin system and disease, and discuss current and future efforts to harness aspects of this potentially powerful system for improving human health. PUBLICATION HISTORY : Republished from Current BioData's Targeted Proteins database (TPdb; http://www.targetedproteinsdb.com).
MeSH term(s)	Animals ; Cysteine Proteinase Inhibitors/therapeutic use ; Drug Discovery ; Humans ; Inflammation/drug therapy ; Inflammation/metabolism ; Musculoskeletal Diseases/drug therapy ; Musculoskeletal Diseases/metabolism ; Mutation ; Neoplasms/drug therapy ; Neoplasms/metabolism ; Neurodegenerative Diseases/drug therapy ; Neurodegenerative Diseases/metabolism ; Proteasome Endopeptidase Complex/metabolism ; Proteasome Inhibitors ; Tumor Suppressor Protein p53/metabolism ; Ubiquitin/metabolism ; Ubiquitin-Protein Ligases/antagonists & inhibitors ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitination
Chemical Substances	Cysteine Proteinase Inhibitors ; Proteasome Inhibitors ; Tumor Suppressor Protein p53 ; Ubiquitin ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
Language	English
Publishing date	2008-10-21
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2041216-2
ISSN	1471-2091 ; 1471-2091
ISSN (online)	1471-2091
ISSN	1471-2091
DOI	10.1186/1471-2091-9-S1-S7
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Article ; Online: Phosphorylation of SAMHD1 Thr592 increases C-terminal domain dynamics, tetramer dissociation and ssDNA binding kinetics.

Orris, Benjamin / Huynh, Kevin W / Ammirati, Mark / Han, Seungil / Bolaños, Ben / Carmody, Jason / Petroski, Matthew D / Bosbach, Benedikt / Shields, David J / Stivers, James T

Nucleic acids research

2022 Volume 50, Issue 13, Page(s) 7545–7559

Abstract: SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1 (SAMHD1) is driven into its activated tetramer form by binding of GTP activator and dNTP activators/substrates. In addition, the inactive monomeric and dimeric forms of the ... ...

Abstract	SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1 (SAMHD1) is driven into its activated tetramer form by binding of GTP activator and dNTP activators/substrates. In addition, the inactive monomeric and dimeric forms of the enzyme bind to single-stranded (ss) nucleic acids. During DNA replication SAMHD1 can be phosphorylated by CDK1 and CDK2 at its C-terminal threonine 592 (pSAMHD1), localizing the enzyme to stalled replication forks (RFs) to promote their restart. Although phosphorylation has only a small effect on the dNTPase activity and ssDNA binding affinity of SAMHD1, perturbation of the native T592 by phosphorylation decreased the thermal stability of tetrameric SAMHD1 and accelerated tetramer dissociation in the absence and presence of ssDNA (∼15-fold). In addition, we found that ssDNA binds competitively with GTP to the A1 site. A full-length SAMHD1 cryo-EM structure revealed substantial dynamics in the C-terminal domain (which contains T592), which could be modulated by phosphorylation. We propose that T592 phosphorylation increases tetramer dynamics and allows invasion of ssDNA into the A1 site and the previously characterized DNA binding surface at the dimer-dimer interface. These features are consistent with rapid and regiospecific inactivation of pSAMHD1 dNTPase at RFs or other sites of free ssDNA in cells.
MeSH term(s)	DNA, Single-Stranded ; Guanosine Triphosphate/metabolism ; Kinetics ; Monomeric GTP-Binding Proteins/genetics ; Phosphorylation ; SAM Domain and HD Domain-Containing Protein 1/chemistry ; SAM Domain and HD Domain-Containing Protein 1/metabolism
Chemical Substances	DNA, Single-Stranded ; Guanosine Triphosphate (86-01-1) ; SAM Domain and HD Domain-Containing Protein 1 (EC 3.1.5.-) ; SAMHD1 protein, human (EC 3.1.5.-) ; Monomeric GTP-Binding Proteins (EC 3.6.5.2)
Language	English
Publishing date	2022-07-07
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkac573
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Zs.A 1067: Show issues

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Article ; Online: Lys11- and Lys48-linked ubiquitin chains interact with p97 during endoplasmic-reticulum-associated degradation.

Locke, Matthew / Toth, Julia I / Petroski, Matthew D

The Biochemical journal

2014 Volume 459, Issue 1, Page(s) 205–216

Abstract: The ATPase associated with various cellular activities p97 has a critical function in the cytoplasmic degradation of proteins misfolded in the ER (endoplasmic reticulum) through a mechanism known as ERAD (ER-associated degradation). During this process, ... ...

Abstract	The ATPase associated with various cellular activities p97 has a critical function in the cytoplasmic degradation of proteins misfolded in the ER (endoplasmic reticulum) through a mechanism known as ERAD (ER-associated degradation). During this process, p97 binds polyubiquitinated ERAD substrates and couples ATP hydrolysis to their dislocation from the ER as a prerequisite to destruction by the proteasome. The ubiquitin signals important for this process are not fully understood. In the present paper we report that p97 interacts with Lys11- and Lys48-linked ubiquitin polymers, but not those containing Lys63 linkages. Disruption of p97 through siRNA-mediated depletion, dominant-negative overexpression or chemical inhibition results in the accumulation of Lys11 and Lys48 ubiquitin chains predominantly at the ER membrane, and is associated with ER stress induction. We show that a catalytically inactive deubiquitinating enzyme and p97 cofactor YOD1 enhances the accumulation of Lys11- and Lys48-linked polyubiquitin in the cytoplasm, at the ER membrane and bound to p97. In addition to general effects on p97-associated ubiquitin polymers, the ERAD substrate CD3δ is modified with both Lys11 and Lys48 ubiquitin chains prior to p97-dependent dislocation. Collectively, the results of the present study are consistent with a major role for p97 in the recognition of Lys11 and Lys48 polyubiquitinated proteins before their degradation by the proteasome.
MeSH term(s)	Adenosine Triphosphatases/metabolism ; Animals ; Cell Line ; Endoplasmic Reticulum/metabolism ; HEK293 Cells ; Humans ; Insecta ; Nuclear Proteins/metabolism ; Polyubiquitin/metabolism ; Protein Binding/physiology
Chemical Substances	Nuclear Proteins ; Polyubiquitin (120904-94-1) ; Adenosine Triphosphatases (EC 3.6.1.-) ; p97 ATPase (EC 3.6.1.-)
Language	English
Publishing date	2014-01-13
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2969-5
ISSN	1470-8728 ; 0006-2936 ; 0306-3275 ; 0264-6021
ISSN (online)	1470-8728
ISSN	0006-2936 ; 0306-3275 ; 0264-6021
DOI	10.1042/BJ20120662
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Article ; Online: Adapted ATPase domain communication overcomes the cytotoxicity of p97 inhibitors.

Wei, Yang / Toth, Julia I / Blanco, Gabrielle A / Bobkov, Andrey A / Petroski, Matthew D

The Journal of biological chemistry

2018 Volume 293, Issue 52, Page(s) 20169–20180

Abstract: ... The ... ...

Abstract	The AAA
MeSH term(s)	Adenosine Triphosphatases/antagonists & inhibitors ; Adenosine Triphosphatases/genetics ; Adenosine Triphosphatases/metabolism ; Amino Acid Substitution ; HCT116 Cells ; Humans ; Indoles/pharmacology ; Mutation, Missense ; Protein Domains ; Pyrimidines/pharmacology ; Valosin Containing Protein/antagonists & inhibitors ; Valosin Containing Protein/genetics ; Valosin Containing Protein/metabolism
Chemical Substances	CB-5083 ; Indoles ; Pyrimidines ; Adenosine Triphosphatases (EC 3.6.1.-) ; Valosin Containing Protein (EC 3.6.4.6)
Language	English
Publishing date	2018-10-31
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.RA118.004301
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Article ; Online: Rfu1: stimulus for the ubiquitin economy.

Wolf, Dieter A / Petroski, Matthew D

Cell

2009 Volume 137, Issue 3, Page(s) 397–398

Abstract: During cellular stress, monoubiquitin is in demand due to the accumulation of misfolded proteins that require proteasomal degradation. Kimura et al. (2009) now show in yeast that monoubiquitin levels are bolstered during stress conditions by ... ...

Abstract	During cellular stress, monoubiquitin is in demand due to the accumulation of misfolded proteins that require proteasomal degradation. Kimura et al. (2009) now show in yeast that monoubiquitin levels are bolstered during stress conditions by downregulation of the protein Rfu1, an inhibitor of the deubiquitinating enzyme Doa4.
MeSH term(s)	Allosteric Regulation ; Endopeptidases/genetics ; Endopeptidases/metabolism ; Endosomal Sorting Complexes Required for Transport ; Endosomes/metabolism ; Humans ; Mutation ; Proteasome Endopeptidase Complex/genetics ; Protein Binding ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/antagonists & inhibitors ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Signal Transduction ; Ubiquitin/metabolism ; Ubiquitin Thiolesterase ; Ubiquitin-Protein Ligase Complexes/metabolism
Chemical Substances	DOA4 protein, S cerevisiae ; Endosomal Sorting Complexes Required for Transport ; Saccharomyces cerevisiae Proteins ; Ubiquitin ; Ubiquitin-Protein Ligase Complexes (EC 2.3.2.23) ; Endopeptidases (EC 3.4.-) ; Ubiquitin Thiolesterase (EC 3.4.19.12) ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
Language	English
Publishing date	2009-05-01
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2009.04.032
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Zs.A 1167: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 58: Show issues

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Article ; Online: The cyclomodulin cycle inhibiting factor (CIF) alters cullin neddylation dynamics.

Toro, Tasha B / Toth, Julia I / Petroski, Matthew D

The Journal of biological chemistry

2013 Volume 288, Issue 21, Page(s) 14716–14726

Abstract: The bacterial effector protein cycle inhibiting factor (CIF) converts glutamine 40 of NEDD8 to glutamate (Q40E), causing cytopathic effects and inhibiting cell proliferation. Although these have been attributed to blocking the functions of cullin-RING ... ...

Abstract	The bacterial effector protein cycle inhibiting factor (CIF) converts glutamine 40 of NEDD8 to glutamate (Q40E), causing cytopathic effects and inhibiting cell proliferation. Although these have been attributed to blocking the functions of cullin-RING ubiquitin ligases, how CIF modulates NEDD8-dependent signaling is unclear. Here we use conditional NEDD8-dependent yeast to explore the effects of CIF on cullin neddylation. Although CIF causes cullin deneddylation and the generation of free NEDD8 Q40E, inhibiting the COP9 signalosome (CSN) allows Q40E to form only on NEDD8 attached to cullins. In the presence of the CSN, NEDD8 Q40E is removed from cullins more rapidly than NEDD8, leading to a decrease in steady-state cullin neddylation. As NEDD8 Q40E is competent for cullin conjugation in the absence of functional CSN and with overexpression of the NEDD8 ligase Dcn1, our data are consistent with NEDD8 deamidation causing enhanced deneddylation of cullins by the CSN. This leads to a dramatic change in the extent of activated cullin-RING ubiquitin ligases.
MeSH term(s)	Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; COP9 Signalosome Complex ; Cullin Proteins/genetics ; Cullin Proteins/metabolism ; Glutamic Acid/genetics ; Glutamic Acid/metabolism ; Glutamine/genetics ; Glutamine/metabolism ; Humans ; Multiprotein Complexes/genetics ; Multiprotein Complexes/metabolism ; NEDD8 Protein ; Peptide Hydrolases/genetics ; Peptide Hydrolases/metabolism ; Protein Processing, Post-Translational ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Ubiquitin-Protein Ligases/genetics ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitins/genetics ; Ubiquitins/metabolism
Chemical Substances	Bacterial Proteins ; Cullin Proteins ; Dcn1 protein, S cerevisiae ; Multiprotein Complexes ; NEDD8 Protein ; NEDD8 protein, human ; Saccharomyces cerevisiae Proteins ; Ubiquitins ; Glutamine (0RH81L854J) ; Glutamic Acid (3KX376GY7L) ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Peptide Hydrolases (EC 3.4.-) ; COP9 Signalosome Complex (EC 3.4.19.12)
Language	English
Publishing date	2013-04-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.M112.448258
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Article ; Online: The ubiquitin system, disease, and drug discovery

Petroski Matthew D

BMC Biochemistry, Vol 9, Iss Suppl 1, p S

2008 Volume 7

Abstract: Abstract The ubiquitin system of protein modification has emerged as a crucial mechanism involved in the regulation of a wide array of cellular processes. As our knowledge of the pathways in this system has grown, so have the ties between the protein ... ...

Abstract	Abstract The ubiquitin system of protein modification has emerged as a crucial mechanism involved in the regulation of a wide array of cellular processes. As our knowledge of the pathways in this system has grown, so have the ties between the protein ubiquitin and human disease. The power of the ubiquitin system for therapeutic benefit blossomed with the approval of the proteasome inhibitor Velcade in 2003 by the FDA. Current drug discovery activities in the ubiquitin system seek to (i) expand the development of new proteasome inhibitors with distinct mechanisms of action and improved bioavailability, and (ii) validate new targets. This review summarizes our current understanding of the role of the ubiquitin system in various human diseases ranging from cancer, viral infection and neurodegenerative disorders to muscle wasting, diabetes and inflammation. I provide an introduction to the ubiquitin system, highlight some emerging relationships between the ubiquitin system and disease, and discuss current and future efforts to harness aspects of this potentially powerful system for improving human health. Publication history Republished from Current BioData's Targeted Proteins database (TPdb; http://www.targetedproteinsdb.com ).
Keywords	Biochemistry ; QD415-436 ; Organic chemistry ; QD241-441 ; Chemistry ; QD1-999 ; Science ; Q ; DOAJ:Biochemistry ; DOAJ:Life Sciences ; DOAJ:Biology and Life Sciences ; Animal biochemistry ; QP501-801
Language	English
Publishing date	2008-10-01T00:00:00Z
Publisher	BioMed Central
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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