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Article ; Online: A glycal-based photoaffinity probe that enriches sialic acid binding proteins.

Thuy-Boun, Peter S / Wolan, Dennis W

Bioorganic & medicinal chemistry letters

2019 Volume 29, Issue 18, Page(s) 2609–2612

Abstract: To identify sialic acid binding proteins from complex proteomes, three photocrosslinking affinity-based probes were constructed using Neu5Ac (5 and 6) and Neu5Ac2en (7) scaffolds. Kinetic inhibition assays and Western blotting revealed the Neu5Ac2en- ... ...

Abstract	To identify sialic acid binding proteins from complex proteomes, three photocrosslinking affinity-based probes were constructed using Neu5Ac (5 and 6) and Neu5Ac2en (7) scaffolds. Kinetic inhibition assays and Western blotting revealed the Neu5Ac2en-based 7 to be an effective probe for the labeling of a purified gut microbial sialidase (BDI_2946) and a purified human sialic acid binding protein (hCD33). Additionally, LC-MS/MS affinity-based protein profiling verified the ability of 7 to enrich a low-abundance sialic acid binding protein (complement factor H) from human serum thus validating the utility of this probe in a complex context.
MeSH term(s)	Dose-Response Relationship, Drug ; Enzyme Inhibitors/chemical synthesis ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/pharmacology ; Humans ; Molecular Probes/chemical synthesis ; Molecular Probes/chemistry ; Molecular Probes/pharmacology ; Molecular Structure ; N-Acetylneuraminic Acid/chemical synthesis ; N-Acetylneuraminic Acid/chemistry ; N-Acetylneuraminic Acid/pharmacology ; Neuraminidase/antagonists & inhibitors ; Neuraminidase/metabolism ; Sialic Acid Binding Ig-like Lectin 3/antagonists & inhibitors ; Sialic Acid Binding Ig-like Lectin 3/isolation & purification ; Sialic Acid Binding Ig-like Lectin 3/metabolism ; Structure-Activity Relationship
Chemical Substances	CD33 protein, human ; Enzyme Inhibitors ; Molecular Probes ; Sialic Acid Binding Ig-like Lectin 3 ; Neuraminidase (EC 3.2.1.18) ; N-Acetylneuraminic Acid (GZP2782OP0)
Language	English
Publishing date	2019-08-01
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1063195-1
ISSN	1464-3405 ; 0960-894X
ISSN (online)	1464-3405
ISSN	0960-894X
DOI	10.1016/j.bmcl.2019.07.054
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Article ; Online: A photoaffinity probe that targets folate-binding proteins.

Takamura, Akihiro / Thuy-Boun, Peter S / Kitamura, Seiya / Han, Zhen / Wolan, Dennis W

Bioorganic & medicinal chemistry letters

2021 Volume 40, Page(s) 127903

Abstract: Folate and related derivatives are essential small molecules required for survival. Of significant interest is the biological role and necessity of folate in the crosstalk between commensal organisms and their respective hosts, including the tremendously ...

Abstract	Folate and related derivatives are essential small molecules required for survival. Of significant interest is the biological role and necessity of folate in the crosstalk between commensal organisms and their respective hosts, including the tremendously complex human distal gut microbiome. Here, we designed a folate-based probe consisting of a photo-crosslinker to detect and quantitate folate-binding proteins from proteomic samples. We demonstrate the selectivity of our probe for the well-established human folate-binding protein dihydrofolate reductase and show no promiscuous labeling occurs with human caspase-3 or bovine serum albumin, which served as negative controls. Affinity-based enrichment of folate-binding proteins from an E. coli lysate in combination with mass spectrometry proteomics verified the ability of our probe to isolate low-abundance folate-dependent proteins. We envision that our probe will serve as a tool to elucidate the roles of commensal microbial folate-binding proteins in health and microbiome-related diseases.
MeSH term(s)	Caspase 3/chemistry ; Chromatography, High Pressure Liquid ; Cross-Linking Reagents/chemistry ; Escherichia coli/chemistry ; Folic Acid/chemistry ; Folic Acid Transporters/analysis ; Humans ; Microbiota/physiology ; Molecular Probes/chemistry ; Photochemical Processes ; Proteomics ; Serum Albumin, Bovine/metabolism ; Tandem Mass Spectrometry ; Tetrahydrofolate Dehydrogenase/chemistry
Chemical Substances	Cross-Linking Reagents ; Folic Acid Transporters ; Molecular Probes ; Serum Albumin, Bovine (27432CM55Q) ; Folic Acid (935E97BOY8) ; Tetrahydrofolate Dehydrogenase (EC 1.5.1.3) ; Caspase 3 (EC 3.4.22.-)
Language	English
Publishing date	2021-03-11
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1063195-1
ISSN	1464-3405 ; 0960-894X
ISSN (online)	1464-3405
ISSN	0960-894X
DOI	10.1016/j.bmcl.2021.127903
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Article ; Online: Identification of an N-acetylneuraminic acid-presenting bacteria isolated from a human microbiome.

Han, Zhen / Thuy-Boun, Peter S / Pfeiffer, Wayne / Vartabedian, Vincent F / Torkamani, Ali / Teijaro, John R / Wolan, Dennis W

Scientific reports

2021 Volume 11, Issue 1, Page(s) 4763

Abstract: N-Acetylneuraminic acid is the most abundant sialic acid (SA) in humans and is expressed as the terminal sugar on intestinal mucus glycans. Several pathogenic bacteria harvest and display host SA on their own surfaces to evade Siglec-mediated host ... ...

Abstract	N-Acetylneuraminic acid is the most abundant sialic acid (SA) in humans and is expressed as the terminal sugar on intestinal mucus glycans. Several pathogenic bacteria harvest and display host SA on their own surfaces to evade Siglec-mediated host immunity. While previous studies have identified bacterial enzymes associated with SA catabolism, no reported methods permit the selective labeling, tracking, and quantitation of SA-presenting microbes within complex multi-microbial systems. We combined metabolic labeling, click chemistry, 16S rRNA gene, and whole-genome sequencing to track and identify SA-presenting microbes from a cultured human fecal microbiome. We isolated a new strain of Escherichia coli that incorporates SA onto its own surface and encodes for the nanT, neuA, and neuS genes necessary for harvesting and presenting SA. Our method is applicable to the identification of SA-presenting bacteria from human, animal, and environmental microbiomes, as well as providing an entry point for the investigation of surface-expressed SA-associated structures.
MeSH term(s)	Bacteria/chemistry ; Bacteria/genetics ; Bacteria/isolation & purification ; Bacteria/metabolism ; Escherichia coli/chemistry ; Escherichia coli/genetics ; Escherichia coli/isolation & purification ; Escherichia coli/metabolism ; Feces/microbiology ; Genes, Bacterial ; Humans ; Microbiota ; N-Acetylneuraminic Acid/analysis ; N-Acetylneuraminic Acid/genetics ; N-Acetylneuraminic Acid/metabolism
Chemical Substances	N-Acetylneuraminic Acid (GZP2782OP0)
Language	English
Publishing date	2021-02-26
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-83875-w
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Article ; Online: Quantitative Metaproteomics and Activity-based Protein Profiling of Patient Fecal Microbiome Identifies Host and Microbial Serine-type Endopeptidase Activity Associated With Ulcerative Colitis.

Thuy-Boun, Peter S / Wang, Ana Y / Crissien-Martinez, Ana / Xu, Janice H / Chatterjee, Sandip / Stupp, Gregory S / Su, Andrew I / Coyle, Walter J / Wolan, Dennis W

Molecular & cellular proteomics : MCP

2022 Volume 21, Issue 3, Page(s) 100197

Abstract: The gut microbiota plays an important yet incompletely understood role in the induction and propagation of ulcerative colitis (UC). Organism-level efforts to identify UC-associated microbes have revealed the importance of community structure, but less is ...

Abstract	The gut microbiota plays an important yet incompletely understood role in the induction and propagation of ulcerative colitis (UC). Organism-level efforts to identify UC-associated microbes have revealed the importance of community structure, but less is known about the molecular effectors of disease. We performed 16S rRNA gene sequencing in parallel with label-free data-dependent LC-MS/MS proteomics to characterize the stool microbiomes of healthy (n = 8) and UC (n = 10) patients. Comparisons of taxonomic composition between techniques revealed major differences in community structure partially attributable to the additional detection of host, fungal, viral, and food peptides by metaproteomics. Differential expression analysis of metaproteomic data identified 176 significantly enriched protein groups between healthy and UC patients. Gene ontology analysis revealed several enriched functions with serine-type endopeptidase activity overrepresented in UC patients. Using a biotinylated fluorophosphonate probe and streptavidin-based enrichment, we show that serine endopeptidases are active in patient fecal samples and that additional putative serine hydrolases are detectable by this approach compared with unenriched profiling. Finally, as metaproteomic databases expand, they are expected to asymptotically approach completeness. Using ComPIL and de novo peptide sequencing, we estimate the size of the probable peptide space unidentified ("dark peptidome") by our large database approach to establish a rough benchmark for database sufficiency. Despite high variability inherent in patient samples, our analysis yielded a catalog of differentially enriched proteins between healthy and UC fecal proteomes. This catalog provides a clinically relevant jumping-off point for further molecular-level studies aimed at identifying the microbial underpinnings of UC.
MeSH term(s)	Chromatography, Liquid ; Colitis, Ulcerative/diagnosis ; Colitis, Ulcerative/microbiology ; Endopeptidases ; Feces/microbiology ; Humans ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Serine ; Tandem Mass Spectrometry
Chemical Substances	RNA, Ribosomal, 16S ; Serine (452VLY9402) ; Endopeptidases (EC 3.4.-)
Language	English
Publishing date	2022-01-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2075924-1
ISSN	1535-9484 ; 1535-9476
ISSN (online)	1535-9484
ISSN	1535-9476
DOI	10.1016/j.mcpro.2022.100197
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Article ; Online: Triflic Acid Treatment Enables LC-MS/MS Analysis of Insoluble Bacterial Biomass.

Wang, Ana Y / Thuy-Boun, Peter S / Stupp, Gregory S / Su, Andrew I / Wolan, Dennis W

Journal of proteome research

2018 Volume 17, Issue 9, Page(s) 2978–2986

Abstract: The lysis and extraction of soluble bacterial proteins from cells is a common practice for proteomics analyses, but insoluble bacterial biomasses are often left behind. Here, we show that with triflic acid treatment, the insoluble bacterial biomass of ... ...

Abstract	The lysis and extraction of soluble bacterial proteins from cells is a common practice for proteomics analyses, but insoluble bacterial biomasses are often left behind. Here, we show that with triflic acid treatment, the insoluble bacterial biomass of Gram
MeSH term(s)	Bacillus subtilis/chemistry ; Bacillus subtilis/genetics ; Bacillus subtilis/metabolism ; Bacterial Proteins/isolation & purification ; Chromatography, Liquid ; Complex Mixtures/chemistry ; Gastrointestinal Microbiome/genetics ; Humans ; Jurkat Cells ; Membrane Proteins/isolation & purification ; Mesylates/chemistry ; Metagenome ; Proteomics/methods ; Pseudomonas aeruginosa/chemistry ; Pseudomonas aeruginosa/genetics ; Pseudomonas aeruginosa/metabolism ; Sonication/methods ; Tandem Mass Spectrometry
Chemical Substances	Bacterial Proteins ; Complex Mixtures ; Membrane Proteins ; Mesylates ; trifluoromethanesulfonic acid (JE2SY203E8)
Language	English
Publishing date	2018-08-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.8b00166
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Article ; Online: Identification of an N-acetylneuraminic acid-presenting bacteria isolated from a human microbiome

Zhen Han / Peter S. Thuy-Boun / Wayne Pfeiffer / Vincent F. Vartabedian / Ali Torkamani / John R. Teijaro / Dennis W. Wolan

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 12

Abstract: Abstract N-Acetylneuraminic acid is the most abundant sialic acid (SA) in humans and is expressed as the terminal sugar on intestinal mucus glycans. Several pathogenic bacteria harvest and display host SA on their own surfaces to evade Siglec-mediated ... ...

Abstract	Abstract N-Acetylneuraminic acid is the most abundant sialic acid (SA) in humans and is expressed as the terminal sugar on intestinal mucus glycans. Several pathogenic bacteria harvest and display host SA on their own surfaces to evade Siglec-mediated host immunity. While previous studies have identified bacterial enzymes associated with SA catabolism, no reported methods permit the selective labeling, tracking, and quantitation of SA-presenting microbes within complex multi-microbial systems. We combined metabolic labeling, click chemistry, 16S rRNA gene, and whole-genome sequencing to track and identify SA-presenting microbes from a cultured human fecal microbiome. We isolated a new strain of Escherichia coli that incorporates SA onto its own surface and encodes for the nanT, neuA, and neuS genes necessary for harvesting and presenting SA. Our method is applicable to the identification of SA-presenting bacteria from human, animal, and environmental microbiomes, as well as providing an entry point for the investigation of surface-expressed SA-associated structures.
Keywords	Medicine ; R ; Science ; Q
Subject code	540
Language	English
Publishing date	2021-02-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
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Article ; Online: Metaproteomics Analysis of SARS-CoV-2-Infected Patient Samples Reveals Presence of Potential Coinfecting Microorganisms.

Thuy-Boun, Peter S / Mehta, Subina / Gruening, Bjoern / McGowan, Thomas / Nguyen, An / Rajczewski, Andrew T / Johnson, James E / Griffin, Timothy J / Wolan, Dennis W / Jagtap, Pratik D

Journal of proteome research

2021 Volume 20, Issue 2, Page(s) 1451–1454

Abstract: In this Letter, we reanalyze published mass spectrometry data sets of clinical samples with a focus on determining the coinfection status of individuals infected with SARS-CoV-2 coronavirus. We demonstrate the use of ComPIL 2.0 software along with a ... ...

Abstract	In this Letter, we reanalyze published mass spectrometry data sets of clinical samples with a focus on determining the coinfection status of individuals infected with SARS-CoV-2 coronavirus. We demonstrate the use of ComPIL 2.0 software along with a metaproteomics workflow within the Galaxy platform to detect cohabitating potential pathogens in COVID-19 patients using mass spectrometry-based analysis. From a sample collected from gargling solutions, we detected
MeSH term(s)	Acinetobacter/isolation & purification ; Bacterial Infections/complications ; Bacterial Infections/diagnosis ; Bacterial Infections/microbiology ; COVID-19/complications ; COVID-19/diagnosis ; COVID-19/virology ; Coinfection/microbiology ; Coinfection/virology ; Humans ; Mass Spectrometry/methods ; Nasopharynx/microbiology ; Nasopharynx/virology ; Proteomics/methods ; Pseudomonas/isolation & purification ; SARS-CoV-2/metabolism ; SARS-CoV-2/physiology ; Streptococcus pneumoniae/isolation & purification
Language	English
Publishing date	2021-01-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.0c00822
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Article ; Online: ComPIL 2.0: An Updated Comprehensive Metaproteomics Database.

Park, Sung Kyu Robin / Jung, Titus / Thuy-Boun, Peter S / Wang, Ana Y / Yates, John R / Wolan, Dennis W

Journal of proteome research

2019 Volume 18, Issue 2, Page(s) 616–622

Abstract: We designed a metaproteomic analysis method (ComPIL) to accommodate the ever-increasing number of sequences against which experimental shotgun proteomics spectra could be accurately and rapidly queried. Our objective was to create these large databases ... ...

Abstract	We designed a metaproteomic analysis method (ComPIL) to accommodate the ever-increasing number of sequences against which experimental shotgun proteomics spectra could be accurately and rapidly queried. Our objective was to create these large databases for the analysis of complex metasamples with unknown composition, including those derived from human, animal, and environmental microbiomes. The amount of high-throughput sequencing data has substantially increased since our original database was assembled in 2014. Here, we present a rebuild of the ComPIL libraries comprised of updated publicly disseminated sequence data as well as a modified version of the search engine ProLuCID-ComPIL optimized for querying experimental spectra. ComPIL 2.0 consists of 113 million protein records and roughly 4.8 billion unique tryptic peptide sequences and is 2.3 times the size of our original version. We searched a data set collected on a healthy human gut microbiome proteomic sample and compared the results to demonstrate that ComPIL 2.0 showed a substantial increase in the number of unique identified peptides and proteins compared to the first ComPIL version. The high confidence of protein identification and accuracy demonstrated by the use of ComPIL 2.0 may encourage the method's application for large-scale proteomic annotation of complex protein systems.
MeSH term(s)	Amino Acid Sequence ; Animals ; Bacterial Proteins/analysis ; Complex Mixtures/analysis ; Databases, Protein ; Gastrointestinal Microbiome ; Humans ; Peptides/analysis ; Proteomics/methods ; Search Engine
Chemical Substances	Bacterial Proteins ; Complex Mixtures ; Peptides
Language	English
Publishing date	2019-01-14
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.8b00722
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Article ; Online: Asymmetric dimerization of adenosine deaminase acting on RNA facilitates substrate recognition.

Thuy-Boun, Alexander S / Thomas, Justin M / Grajo, Herra L / Palumbo, Cody M / Park, SeHee / Nguyen, Luan T / Fisher, Andrew J / Beal, Peter A

Nucleic acids research

2020 Volume 48, Issue 14, Page(s) 7958–7972

Abstract: Adenosine deaminases acting on RNA (ADARs) are enzymes that convert adenosine to inosine in duplex RNA, a modification that exhibits a multitude of effects on RNA structure and function. Recent studies have identified ADAR1 as a potential cancer ... ...

Abstract	Adenosine deaminases acting on RNA (ADARs) are enzymes that convert adenosine to inosine in duplex RNA, a modification that exhibits a multitude of effects on RNA structure and function. Recent studies have identified ADAR1 as a potential cancer therapeutic target. ADARs are also important in the development of directed RNA editing therapeutics. A comprehensive understanding of the molecular mechanism of the ADAR reaction will advance efforts to develop ADAR inhibitors and new tools for directed RNA editing. Here we report the X-ray crystal structure of a fragment of human ADAR2 comprising its deaminase domain and double stranded RNA binding domain 2 (dsRBD2) bound to an RNA duplex as an asymmetric homodimer. We identified a highly conserved ADAR dimerization interface and validated the importance of these sequence elements on dimer formation via gel mobility shift assays and size exclusion chromatography. We also show that mutation in the dimerization interface inhibits editing in an RNA substrate-dependent manner for both ADAR1 and ADAR2.
MeSH term(s)	Adenosine Deaminase/chemistry ; Adenosine Deaminase/genetics ; Adenosine Deaminase/metabolism ; Crystallography, X-Ray ; Humans ; Models, Molecular ; Mutation ; Protein Binding ; Protein Domains ; Protein Multimerization ; RNA Editing ; RNA, Double-Stranded/chemistry ; RNA, Double-Stranded/metabolism ; RNA-Binding Proteins/chemistry ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism
Chemical Substances	RNA, Double-Stranded ; RNA-Binding Proteins ; ADARB1 protein, human (EC 3.5.4.4) ; Adenosine Deaminase (EC 3.5.4.4)
Language	English
Publishing date	2020-06-29
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
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/gkaa532
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Article ; Online: Palladium-catalyzed ortho-selective C-H deuteration of arenes: evidence for superior reactivity of weakly coordinated palladacycles.

Ma, Sandy / Villa, Giorgio / Thuy-Boun, Peter S / Homs, Anna / Yu, Jin-Quan

Angewandte Chemie (International ed. in English)

2014 Volume 53, Issue 3, Page(s) 734–737

Abstract: We disclose a protocol for the palladium-catalyzed ortho-selective C-H deuteration of arenes. Phenylacetic acids and benzoic acids are suitable substrates for this reaction. This reaction offers a catalytic route to ortho-deuterated phenylacetic acids ... ...

Abstract	We disclose a protocol for the palladium-catalyzed ortho-selective C-H deuteration of arenes. Phenylacetic acids and benzoic acids are suitable substrates for this reaction. This reaction offers a catalytic route to ortho-deuterated phenylacetic acids and benzoic acids and demonstrates the sharp difference in reactivity of palladacycle intermediates held together by weak and strong coordination.
MeSH term(s)	Benzoates/chemistry ; Carbon/chemistry ; Catalysis ; Deuterium/chemistry ; Hydrogen/chemistry ; Palladium/chemistry ; Phenylacetates/chemistry
Chemical Substances	Benzoates ; Phenylacetates ; Palladium (5TWQ1V240M) ; Carbon (7440-44-0) ; Hydrogen (7YNJ3PO35Z) ; Deuterium (AR09D82C7G)
Language	English
Publishing date	2014-01-13
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2011836-3
ISSN	1521-3773 ; 1433-7851
ISSN (online)	1521-3773
ISSN	1433-7851
DOI	10.1002/anie.201305388
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