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Cao Y, Cheung NA, Giustini D, LeDue J, Murphy TH. Scholar Metrics Scraper (SMS): automated retrieval of citation and author data. Front Res Metr Anal 2024; 9:1335454. [PMID: 38456123 PMCID: PMC10917922 DOI: 10.3389/frma.2024.1335454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/06/2024] [Indexed: 03/09/2024] Open
Abstract
Academic departments, research clusters and evaluators analyze author and citation data to measure research impact and to support strategic planning. We created Scholar Metrics Scraper (SMS) to automate the retrieval of bibliometric data for a group of researchers. The project contains Jupyter notebooks that take a list of researchers as an input and exports a CSV file of citation metrics from Google Scholar (GS) to visualize the group's impact and collaboration. A series of graph outputs are also available. SMS is an open solution for automating the retrieval and visualization of citation data.
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Affiliation(s)
- Yutong Cao
- Department of Psychiatry, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
| | - Nicole A. Cheung
- Department of Psychiatry, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
| | - Dean Giustini
- Biomedical Branch Library, University of British Columbia, Vancouver, BC, Canada
| | - Jeffrey LeDue
- Department of Psychiatry, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
| | - Timothy H. Murphy
- Department of Psychiatry, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
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Cheung NA, Song M, Sue CK, Clubb RT. Quantifying the Kinetics of Pilus-Specific Sortase-Catalyzed Crosslinking Using High-Performance Liquid Chromatography. Methods Mol Biol 2024; 2727:135-143. [PMID: 37815714 DOI: 10.1007/978-1-0716-3491-2_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Gram-positive bacteria display pili whose protein components (pilins) are covalently crosslinked by pilus-specific sortase enzymes. These cysteine transpeptidase enzymes catalyze a transpeptidation reaction that joins the pilins together via lysine isopeptide bonds. The crosslinking reaction that builds the SpaA pilus in Corynebacterium diphtheriae is mediated by the SrtA sortase (CdSrtA) and has been reconstituted in vitro. Here, we present a protocol that can be used to measure the kinetics of CdSrtA-catalyzed crosslinking using high-performance liquid chromatography (HPLC). In principle, this biochemical procedure can be used to measure the in vitro crosslinking activity of any pilus-specific sortase.
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Affiliation(s)
- Nicole A Cheung
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Mabel Song
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Christopher K Sue
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Robert T Clubb
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.
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Sue CK, Cheung NA, Mahoney BJ, McConnell SA, Scully JM, Fu JY, Chang C, Ton-That H, Loo JA, Clubb RT. The basal and major pilins in the Corynebacterium diphtheriae SpaA pilus adopt similar structures that competitively react with the pilin polymerase. Biopolymers 2024; 115:e23539. [PMID: 37227047 DOI: 10.1002/bip.23539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/12/2023] [Accepted: 04/24/2023] [Indexed: 05/26/2023]
Abstract
Many species of pathogenic gram-positive bacteria display covalently crosslinked protein polymers (called pili or fimbriae) that mediate microbial adhesion to host tissues. These structures are assembled by pilus-specific sortase enzymes that join the pilin components together via lysine-isopeptide bonds. The archetypal SpaA pilus from Corynebacterium diphtheriae is built by the Cd SrtA pilus-specific sortase, which crosslinks lysine residues within the SpaA and SpaB pilins to build the shaft and base of the pilus, respectively. Here, we show that Cd SrtA crosslinks SpaB to SpaA via a K139(SpaB)-T494(SpaA) lysine-isopeptide bond. Despite sharing only limited sequence homology, an NMR structure of SpaB reveals striking similarities with the N-terminal domain of SpaA (N SpaA) that is also crosslinked by Cd SrtA. In particular, both pilins contain similarly positioned reactive lysine residues and adjacent disordered AB loops that are predicted to be involved in the recently proposed "latch" mechanism of isopeptide bond formation. Competition experiments using an inactive SpaB variant and additional NMR studies suggest that SpaB terminates SpaA polymerization by outcompeting N SpaA for access to a shared thioester enzyme-substrate reaction intermediate.
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Affiliation(s)
- Christopher K Sue
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California, USA
| | - Nicole A Cheung
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California, USA
- Molecular Biology Institute, University of California, Los Angeles, California, USA
| | - Brendan J Mahoney
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California, USA
| | - Scott A McConnell
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California, USA
| | - Jack M Scully
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California, USA
| | - Janine Y Fu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California, USA
| | - Chungyu Chang
- Molecular Biology Institute, University of California, Los Angeles, California, USA
- Division of Oral and Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, California, USA
| | - Hung Ton-That
- Molecular Biology Institute, University of California, Los Angeles, California, USA
- Division of Oral and Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, California, USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California, USA
- Molecular Biology Institute, University of California, Los Angeles, California, USA
| | - Robert T Clubb
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California, USA
- Molecular Biology Institute, University of California, Los Angeles, California, USA
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Sue CK, Cheung NA, Mahoney BJ, McConnell SA, Scully JM, Fu JY, Chang C, Ton-That H, Loo JA, Clubb RT. The Basal and Major Pilins in the Corynebacterium diphtheriae SpaA Pilus Adopt Similar Structures that Competitively React with the Pilin Polymerase. bioRxiv 2023:2023.02.23.529612. [PMID: 36865106 PMCID: PMC9980135 DOI: 10.1101/2023.02.23.529612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Many species of pathogenic gram-positive bacteria display covalently crosslinked protein polymers (called pili or fimbriae) that mediate microbial adhesion to host tissues. These structures are assembled by pilus-specific sortase enzymes that join the pilin components together via lysine-isopeptide bonds. The archetypal SpaA pilus from Corynebacterium diphtheriae is built by the Cd SrtA pilus-specific sortase, which crosslinks lysine residues within the SpaA and SpaB pilins to build the shaft and base of the pilus, respectively. Here, we show that Cd SrtA crosslinks SpaB to SpaA via a K139(SpaB)-T494(SpaA) lysine-isopeptide bond. Despite sharing only limited sequence homology, an NMR structure of SpaB reveals striking similarities with the N-terminal domain of SpaA ( N SpaA) that is also crosslinked by Cd SrtA. In particular, both pilins contain similarly positioned reactive lysine residues and adjacent disordered AB loops that are predicted to be involved in the recently proposed "latch" mechanism of isopeptide bond formation. Competition experiments using an inactive SpaB variant and additional NMR studies suggest that SpaB terminates SpaA polymerization by outcompeting N SpaA for access to a shared thioester enzyme-substrate reaction intermediate.
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