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Article ; Online: Structure of

Shaw, Gary X / Fan, Lixin / Cherry, Scott / Shi, Genbin / Tropea, Joseph E / Ji, Xinhua

Current research in structural biology

2023 Volume 5, Page(s) 100095

Abstract: Dihydroneopterin aldolase (DHNA) is essential for folate biosynthesis in microorganisms. Without a counterpart in mammals, DHNA is an attractive target for antimicrobial agents. ...

Abstract	Dihydroneopterin aldolase (DHNA) is essential for folate biosynthesis in microorganisms. Without a counterpart in mammals, DHNA is an attractive target for antimicrobial agents.
Language	English
Publishing date	2023-01-30
Publishing country	Netherlands
Document type	Journal Article
ISSN	2665-928X
ISSN (online)	2665-928X
DOI	10.1016/j.crstbi.2023.100095
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Article ; Online: P1' specificity of the S219V/R203G mutant tobacco etch virus protease.

Golda, Mária / Hoffka, Gyula / Cherry, Scott / Tropea, Joseph E / Lountos, George T / Waugh, David S / Wlodawer, Alexander / Tőzsér, József / Mótyán, János András

Proteins

2024

Abstract: Proteases that recognize linear amino acid sequences with high specificity became indispensable tools of recombinant protein technology for the removal of various fusion tags. Due to its stringent sequence specificity, the catalytic domain of the nuclear ...

Abstract	Proteases that recognize linear amino acid sequences with high specificity became indispensable tools of recombinant protein technology for the removal of various fusion tags. Due to its stringent sequence specificity, the catalytic domain of the nuclear inclusion cysteine protease of tobacco etch virus (TEV PR) is also a widely applied reagent for enzymatic removal of fusion tags. For this reason, efforts have been made to improve its stability and modify its specificity. For example, P1' autoproteolytic cleavage-resistant mutant (S219V) TEV PR was found not only to be nearly impervious to self-inactivation, but also exhibited greater stability and catalytic efficiency than the wild-type enzyme. An R203G substitution has been reported to further relax the P1' specificity of the enzyme, however, these results were obtained from crude intracellular assays. Until now, there has been no rigorous comparison of the P1' specificity of the S219V and S219V/R203G mutants in vitro, under carefully controlled conditions. Here, we compare the P1' amino acid preferences of these single and double TEV PR mutants. The in vitro analysis was performed by using recombinant protein substrates representing 20 P1' variants of the consensus TENLYFQ*SGT cleavage site, and synthetic oligopeptide substrates were also applied to study a limited set of the most preferred variants. In addition, the enzyme-substrate interactions were analyzed in silico. The results indicate highly similar P1' preferences for both enzymes, many side-chains can be accommodated by the S1' binding sites, but the kinetic assays revealed lower catalytic efficiency for the S219V/R203G than for the S219V mutant.
Language	English
Publishing date	2024-04-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	806683-8
ISSN	1097-0134 ; 0887-3585
ISSN (online)	1097-0134
ISSN	0887-3585
DOI	10.1002/prot.26693
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Article ; Online: Structural basis for cell type specific DNA binding of C/EBPβ: The case of cell cycle inhibitor p15INK4b promoter.

Lountos, George T / Cherry, Scott / Tropea, Joseph E / Wlodawer, Alexander / Miller, Maria

Journal of structural biology

2022 Volume 214, Issue 4, Page(s) 107918

Abstract: C/EBPβ is a key regulator of numerous cellular processes, but it can also contribute to tumorigenesis and viral diseases. It binds to specific DNA sequences (C/EBP sites) and interacts with other transcription factors to control expression of multiple ... ...

Abstract	C/EBPβ is a key regulator of numerous cellular processes, but it can also contribute to tumorigenesis and viral diseases. It binds to specific DNA sequences (C/EBP sites) and interacts with other transcription factors to control expression of multiple eukaryotic genes in a tissue and cell-type dependent manner. A body of evidence has established that cell-type-specific regulatory information is contained in the local DNA sequence of the binding motif. In human epithelial cells, C/EBPβ is an essential cofactor for TGFβ signaling in the case of Smad2/3/4 and FoxO-dependent induction of the cell cycle inhibitor, p15INK4b. In the TGFβ-responsive region 2 of the p15INK4b promoter, the Smad binding site is flanked by a C/EBP site, CTTAA•GAAAG, which differs from the canonical, palindromic ATTGC•GCAAT motif. The X-ray crystal structure of C/EBPβ bound to the p15INK4b promoter fragment shows how GCGC-to-AAGA substitution generates changes in the intermolecular interactions in the protein-DNA interface that enhances C/EBPβ binding specificity, limits possible epigenetic regulation of the promoter, and generates a DNA element with a unique pattern of methyl groups in the major groove. Significantly, CT/GA dinucleotides located at the 5'ends of the double stranded element maintain local narrowing of the DNA minor groove width that is necessary for DNA recognition. Our results suggest that C/EBPβ would accept all forms of modified cytosine in the context of the CpT site. This contrasts with the effect on the consensus motif, where C/EBPβ binding is modestly increased by cytosine methylation, but substantially decreased by hydroxymethylation.
MeSH term(s)	Humans ; CCAAT-Enhancer-Binding Protein-beta/genetics ; Epigenesis, Genetic ; Cell Cycle ; Cytosine ; DNA/genetics
Chemical Substances	CCAAT-Enhancer-Binding Protein-beta ; Cytosine (8J337D1HZY) ; DNA (9007-49-2)
Language	English
Publishing date	2022-11-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1032718-6
ISSN	1095-8657 ; 1047-8477
ISSN (online)	1095-8657
ISSN	1047-8477
DOI	10.1016/j.jsb.2022.107918
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Article ; Online: Successful clozapine rechallenge in a patient with suspected drug induced lupus.

Pathak, Suraj / Cherry, Scott / Samad, Samreen / Aftab, Ambreen

BMJ case reports

2019 Volume 12, Issue 4

Abstract: Clozapine is the most effective treatment for patients with refractory schizophrenia. Clozapine is also associated with serious and potentially lethal side effects including drug induced lupus (DIL). There have been four previous published case reports ... ...

Abstract	Clozapine is the most effective treatment for patients with refractory schizophrenia. Clozapine is also associated with serious and potentially lethal side effects including drug induced lupus (DIL). There have been four previous published case reports describing clozapine inducing a lupus-like syndrome including one previous case where a clozapine rechallenge was attempted without success. This case report describes a successful clozapine rechallenge in a patient with suspected DIL.
MeSH term(s)	Antipsychotic Agents/adverse effects ; Clozapine/adverse effects ; Humans ; Lupus Erythematosus, Systemic/chemically induced ; Schizophrenia/drug therapy
Chemical Substances	Antipsychotic Agents ; Clozapine (J60AR2IKIC)
Language	English
Publishing date	2019-04-03
Publishing country	England
Document type	Case Reports ; Journal Article
ISSN	1757-790X
ISSN (online)	1757-790X
DOI	10.1136/bcr-2018-228574
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Article: Clinical course of 12 patients on a Covid-19 dementia isolation ward.

Kerslake, Richard / Cherry, Scott / Buckle, Jessica / Harris, Richard / Caplan, Richard

BJPsych bulletin

2020 Volume 44, Issue 6, Page(s) 288–290

Language	English
Publishing date	2020-11-19
Publishing country	England
Document type	Journal Article
ZDB-ID	2816886-0
ISSN	2056-4708 ; 2056-4694
ISSN (online)	2056-4708
ISSN	2056-4694
DOI	10.1192/bjb.2020.109
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Article ; Online: Investigating the relationship between worker demographics and nature of injury on Federal Department of Defense workers' compensation injury rates and costs from 2000 to 2008.

Mallon, Timothy M / Cherry, Scott E

Journal of occupational and environmental medicine

2015 Volume 57 Suppl 3, Page(s) S27–30

Abstract: Objective: This is the first study of workers' compensation injuries and costs in Department of Defense workers that examined whether any demographic factors including age, sex, occupation, and nature of injury altered the risks or costs of an injury or ...

Abstract	Objective: This is the first study of workers' compensation injuries and costs in Department of Defense workers that examined whether any demographic factors including age, sex, occupation, and nature of injury altered the risks or costs of an injury or illness over time. Methods: Department of Defense Workers' Compensation claims for period 2000 to 2008 were analyzed (n = 142,115) using Defense Portal Analysis and Defense Manpower Data Center to calculate injury rates and costs. Regression analysis was done using SPSS to examine the change in the risk of injury or illness over time from 2000 to 2008. Results: The age group of 30 to 34 years had the lowest costs per claim and highest claims rate, 332 per 10,000. The age group of 65 to 70 years had the lowest claims rate of 188 per 10,000 but the highest costs per claim. Claims cost increased $69 for each 5-year group, and older workers had a threefold increase in costs per claim. Conclusion: Younger workers get hurt more often, but older workers tend to have more expensive claims.
MeSH term(s)	Adolescent ; Adult ; Age Factors ; Aged ; Cross-Sectional Studies ; Female ; Humans ; Insurance Claim Review ; Male ; Middle Aged ; Occupational Diseases/economics ; Occupational Injuries/economics ; Occupational Injuries/etiology ; Occupations ; Sex Factors ; United States ; United States Department of Defense/economics ; United States Department of Defense/statistics & numerical data ; Workers' Compensation/economics ; Workers' Compensation/statistics & numerical data ; Young Adult
Language	English
Publishing date	2015-03
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1223932-x
ISSN	1536-5948 ; 1076-2752
ISSN (online)	1536-5948
ISSN	1076-2752
DOI	10.1097/JOM.0000000000000416
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Article ; Online: Characterization of a broadly specific cadaverine N-hydroxylase involved in desferrioxamine B biosynthesis in Streptomyces sviceus.

Giddings, Lesley-Ann / Lountos, George T / Kim, Kang Woo / Brockley, Matthew / Needle, Danielle / Cherry, Scott / Tropea, Joseph E / Waugh, David S

PloS one

2021 Volume 16, Issue 3, Page(s) e0248385

Abstract: N-hydroxylating flavin-dependent monooxygenases (FMOs) are involved in the biosynthesis of hydroxamate siderophores, playing a key role in microbial virulence. Herein, we report the first structural and kinetic characterization of a novel alkyl diamine N- ...

Abstract	N-hydroxylating flavin-dependent monooxygenases (FMOs) are involved in the biosynthesis of hydroxamate siderophores, playing a key role in microbial virulence. Herein, we report the first structural and kinetic characterization of a novel alkyl diamine N-hydroxylase DesB from Streptomyces sviceus (SsDesB). This enzyme catalyzes the first committed step in the biosynthesis of desferrioxamine B, a clinical drug used to treat iron overload disorders. X-ray crystal structures of the SsDesB holoenzyme with FAD and the ternary complex with bound NADP+ were solved at 2.86 Å and 2.37 Å resolution, respectively, providing a structural view of the active site environment. SsDesB crystallized as a tetramer and the structure of the individual protomers closely resembles the structures of homologous N-hydroxylating FMOs from Erwinia amylovora (DfoA), Pseudomonas aeruginosa (PvdA), and Aspergillus fumigatus (SidA). Using NADPH oxidation, oxygen consumption, and product formation assays, kinetic parameters were determined for various substrates with SsDesB. SsDesB exhibited typical saturation kinetics with substrate inhibition at high concentrations of NAD(P)H as well as cadaverine. The apparent kcat values for NADPH in steady-state NADPH oxidation and oxygen consumption assays were 0.28 ± 0.01 s-1 and 0.24 ± 0.01 s-1, respectively. However, in product formation assays used to measure the rate of N-hydroxylation, the apparent kcat for NADPH (0.034 ± 0.008 s-1) was almost 10-fold lower under saturating FAD and cadaverine concentrations, reflecting an uncoupled reaction, and the apparent NADPH KM was 33 ± 24 μM. Under saturating FAD and NADPH concentrations, the apparent kcat and KM for cadaverine in Csaky assays were 0.048 ± 0.004 s-1 and 19 ± 9 μM, respectively. SsDesB also N-hydroxylated putrescine, spermidine, and L-lysine substrates but not alkyl (di)amines that were branched or had fewer than four methylene units in an alkyl chain. These data demonstrate that SsDesB has wider substrate scope compared to other well-studied ornithine and lysine N-hydroxylases, making it an amenable biocatalyst for the production of desferrioxamine B, derivatives, and other N-substituted products.
MeSH term(s)	Bacterial Proteins/metabolism ; Biocatalysis ; Cadaverine/metabolism ; Catalytic Domain ; Deferoxamine/metabolism ; Dinitrocresols/metabolism ; Flavin-Adenine Dinucleotide/metabolism ; Flavins/metabolism ; Holoenzymes/metabolism ; Hydroxylation ; Kinetics ; Mixed Function Oxygenases/biosynthesis ; Mixed Function Oxygenases/chemistry ; Mixed Function Oxygenases/metabolism ; NADP/metabolism ; Ornithine/metabolism ; Oxidation-Reduction ; Siderophores/biosynthesis ; Streptomyces/enzymology
Chemical Substances	Bacterial Proteins ; Dinitrocresols ; Flavins ; Holoenzymes ; Siderophores ; Flavin-Adenine Dinucleotide (146-14-5) ; 4,6-dinitro-o-cresol (1604ZJR09T) ; NADP (53-59-8) ; Ornithine (E524N2IXA3) ; Mixed Function Oxygenases (EC 1.-) ; lysine monooxygenase (EC 1.13.12.2) ; Deferoxamine (J06Y7MXW4D) ; Cadaverine (L90BEN6OLL)
Language	English
Publishing date	2021-03-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0248385
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Article ; Online: Removal of Affinity Tags with TEV Protease.

Raran-Kurussi, Sreejith / Cherry, Scott / Zhang, Di / Waugh, David S

Methods in molecular biology (Clifton, N.J.)

2017 Volume 1586, Page(s) 221–230

Abstract: Although affinity tags are highly effective tools for the expression and purification of recombinant proteins, they generally need to be removed prior to structural and functional studies. This chapter describes a simple method for overproducing a ... ...

Abstract	Although affinity tags are highly effective tools for the expression and purification of recombinant proteins, they generally need to be removed prior to structural and functional studies. This chapter describes a simple method for overproducing a soluble form of a stable variant of tobacco etch virus (TEV) protease in Escherichia coli and a protocol for purifying it to homogeneity so that it can be used as a reagent for removing affinity tags from recombinant proteins by site-specific endoproteolysis. Further, we cleave a model substrate protein (MBP-NusG) in vitro using the purified TEV protease to illustrate a protease cleavage protocol that can be employed for simple pilot experiments and large-scale protein preparations.
MeSH term(s)	Chromatography, Affinity/methods ; Cloning, Molecular/methods ; Endopeptidases/genetics ; Endopeptidases/isolation & purification ; Endopeptidases/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Maltose-Binding Proteins/genetics ; Maltose-Binding Proteins/metabolism ; Peptide Elongation Factors/genetics ; Peptide Elongation Factors/metabolism ; Potyvirus/enzymology ; Proteolysis ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/isolation & purification ; Recombinant Fusion Proteins/metabolism ; Solubility ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Up-Regulation
Chemical Substances	Escherichia coli Proteins ; Maltose-Binding Proteins ; NusG protein, E coli ; Peptide Elongation Factors ; Recombinant Fusion Proteins ; Transcription Factors ; Endopeptidases (EC 3.4.-) ; TEV protease (EC 3.4.-)
Language	English
Publishing date	2017-04-25
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-6887-9_14
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Article ; Online: Unique Structural Fold of LonBA Protease from

Gustchina, Alla / Li, Mi / Andrianova, Anna G / Kudzhaev, Arsen M / Lountos, George T / Sekula, Bartosz / Cherry, Scott / Tropea, Joseph E / Smirnov, Ivan V / Wlodawer, Alexander / Rotanova, Tatyana V

International journal of molecular sciences

2022 Volume 23, Issue 19

Abstract: ATP-dependent Lon proteases are key participants in the quality control system that supports the homeostasis of the cellular proteome. Based on their unique structural and biochemical properties, Lon proteases have been assigned in the MEROPS database to ...

Abstract	ATP-dependent Lon proteases are key participants in the quality control system that supports the homeostasis of the cellular proteome. Based on their unique structural and biochemical properties, Lon proteases have been assigned in the MEROPS database to three subfamilies (A, B, and C). All Lons are single-chain, multidomain proteins containing an ATPase and protease domains, with different additional elements present in each subfamily. LonA and LonC proteases are soluble cytoplasmic enzymes, whereas LonBs are membrane-bound. Based on an analysis of the available sequences of Lon proteases, we identified a number of enzymes currently assigned to the LonB subfamily that, although presumably membrane-bound, include structural features more similar to their counterparts in the LonA subfamily. This observation was confirmed by the crystal structure of the proteolytic domain of the enzyme previously assigned as
MeSH term(s)	ATP-Dependent Proteases/metabolism ; Adenosine Triphosphatases/metabolism ; Adenosine Triphosphate/metabolism ; Bacillus subtilis/genetics ; Bacillus subtilis/metabolism ; Peptide Hydrolases/metabolism ; Protease La/genetics ; Protease La/metabolism ; Proteome/metabolism
Chemical Substances	Proteome ; Adenosine Triphosphate (8L70Q75FXE) ; Peptide Hydrolases (EC 3.4.-) ; ATP-Dependent Proteases (EC 3.4.21.-) ; Protease La (EC 3.4.21.53) ; Adenosine Triphosphatases (EC 3.6.1.-)
Language	English
Publishing date	2022-09-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms231911425
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Article ; Online: Fever, confusion, acute kidney injury: is this atypical neuroleptic malignant syndrome following polypharmacy with clozapine and risperidone?

Cherry, Scott / Siskind, Dan / Spivak, Valeria / Wysoczanski, Daniel / Halangoda, Priyangika

Australasian psychiatry : bulletin of Royal Australian and New Zealand College of Psychiatrists

2016 Volume 24, Issue 6, Page(s) 602–603

Abstract: Objective: Clozapine is the gold-standard antipsychotic medication for treatment-refractory schizophrenia (TRS). However, one potentially lethal side effect of clozapine, as with other antipsychotics, is neuroleptic malignant syndrome (NMS) which could ... ...

Abstract	Objective: Clozapine is the gold-standard antipsychotic medication for treatment-refractory schizophrenia (TRS). However, one potentially lethal side effect of clozapine, as with other antipsychotics, is neuroleptic malignant syndrome (NMS) which could present differently in clozapine therapy. 'Atypical NMS' is a recognised variant of NMS with less rigidity and delayed elevation of creatine kinase; this variant is associated with clozapine. Method: A case from the author's clinical practice was reviewed. Results: A 67-year-old man with TRS was treated with clozapine. Unfortunately, his physical condition deteriorated and he presented with atypical NMS, which initially was treated as presumable urinary tract infection. Conclusions: Atypical NMS is associated with clozapine. This case exposes the potential difficulties in diagnosis, and highlights the importance of considering less common diagnoses in acutely unwell psychiatric patients.
Language	English
Publishing date	2016-12
Publishing country	England
Document type	Journal Article
ZDB-ID	2213198-X
ISSN	1440-1665 ; 1039-8562
ISSN (online)	1440-1665
ISSN	1039-8562
DOI	10.1177/1039856216649768
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