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  1. Article ; Online: Finding priority bacterial ribosomes for future structural and antimicrobial research based upon global RNA and protein sequence analysis.

    Cooper, Helena B / Krause, Kurt L / Gardner, Paul P

    PeerJ

    2023  Volume 11, Page(s) e14969

    Abstract: Ribosome-targeting antibiotics comprise over half of antibiotics used in medicine, but our fundamental knowledge of their binding sites is derived primarily from ribosome structures of non-pathogenic species. These ... ...

    Abstract Ribosome-targeting antibiotics comprise over half of antibiotics used in medicine, but our fundamental knowledge of their binding sites is derived primarily from ribosome structures of non-pathogenic species. These include
    MeSH term(s) RNA/analysis ; Phylogeny ; Ribosomes/genetics ; Anti-Bacterial Agents/analysis ; Escherichia coli/genetics ; Bacteria/genetics ; Sequence Analysis, Protein
    Chemical Substances RNA (63231-63-0) ; Anti-Bacterial Agents
    Language English
    Publishing date 2023-03-22
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2703241-3
    ISSN 2167-8359 ; 2167-8359
    ISSN (online) 2167-8359
    ISSN 2167-8359
    DOI 10.7717/peerj.14969
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Finding priority bacterial ribosomes for future structural and antimicrobial research based upon global RNA and protein sequence analysis

    Helena B. Cooper / Kurt L. Krause / Paul P. Gardner

    PeerJ, Vol 11, p e

    2023  Volume 14969

    Abstract: Ribosome-targeting antibiotics comprise over half of antibiotics used in medicine, but our fundamental knowledge of their binding sites is derived primarily from ribosome structures of non-pathogenic species. These include Thermus thermophilus, ... ...

    Abstract Ribosome-targeting antibiotics comprise over half of antibiotics used in medicine, but our fundamental knowledge of their binding sites is derived primarily from ribosome structures of non-pathogenic species. These include Thermus thermophilus, Deinococcus radiodurans and the archaean Haloarcula marismortui, as well as the commensal and sometimes pathogenic organism, Escherichia coli. Advancements in electron cryomicroscopy have allowed for the determination of more ribosome structures from pathogenic bacteria, with each study highlighting species-specific differences that had not been observed in the non-pathogenic structures. These observed differences suggest that more novel ribosome structures, particularly from pathogens, are required for a more accurate understanding of the level of diversity of the entire bacterial ribosome, with the potential of leading to innovative advancements in antibiotic research. In this study, high accuracy covariance and hidden Markov models were used to annotate ribosomal RNA and protein sequences respectively from genomic sequence, allowing us to determine the underlying ribosomal sequence diversity using phylogenetic methods. This analysis provided evidence that the current non-pathogenic ribosome structures are not sufficient representatives of some pathogenic bacteria, such as Campylobacter pylori, or of whole phyla such as Bacteroidota (Bacteroidetes).
    Keywords Ribosomes ; Structure ; Homology ; Antibiotic resistance ; Evolution ; Phylogeny ; Medicine ; R ; Biology (General) ; QH301-705.5
    Subject code 540
    Language English
    Publishing date 2023-03-01T00:00:00Z
    Publisher PeerJ Inc.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Optimisation of Neuraminidase Expression for Use in Drug Discovery by Using HEK293-6E Cells.

    Campbell, Ashley C / Tanner, John J / Krause, Kurt L

    Viruses

    2021  Volume 13, Issue 10

    Abstract: Influenza virus is a highly contagious virus that causes significant human mortality and morbidity annually. The most effective drugs for treating influenza are the neuraminidase inhibitors, but resistance to these inhibitors has emerged, and additional ... ...

    Abstract Influenza virus is a highly contagious virus that causes significant human mortality and morbidity annually. The most effective drugs for treating influenza are the neuraminidase inhibitors, but resistance to these inhibitors has emerged, and additional drug discovery research on neuraminidase and other targets is needed. Traditional methods of neuraminidase production from embryonated eggs are cumbersome, while insect cell derived protein is less reflective of neuraminidase produced during human infection. Herein we describe a method for producing neuraminidase from a human cell line, HEK293-6E, and demonstrate the method by producing the neuraminidase from the 1918 H1N1 pandemic influenza strain. This method produced high levels of soluble neuraminidase expression (>3000 EU/mL), was enhanced by including a secretion signal from a viral chemokine binding protein, and does not require co-expression of additional proteins. The neuraminidase produced was of sufficient quantity and purity to support high resolution crystal structure determination. The structure solved using this protein conformed to the previously reported structure. Notably the glycosylation at three asparagine residues was superior in quality to that from insect cell derived neuraminidase. This method of production of neuraminidase should prove useful in further studies, such as the characterisation of inhibitor binding.
    MeSH term(s) Antiviral Agents/pharmacology ; Drug Discovery/methods ; Drug Resistance, Viral ; Enzyme Inhibitors/pharmacology ; HEK293 Cells ; Humans ; Influenza A Virus, H1N1 Subtype/drug effects ; Influenza A Virus, H1N1 Subtype/enzymology ; Influenza, Human/drug therapy ; Molecular Conformation ; Neuraminidase/genetics ; Protein Binding ; Viral Proteins/metabolism
    Chemical Substances Antiviral Agents ; Enzyme Inhibitors ; Viral Proteins ; Neuraminidase (EC 3.2.1.18)
    Language English
    Publishing date 2021-09-22
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v13101893
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: The Immune Response to SARS-CoV-2 and Variants of Concern.

    Torbati, Elham / Krause, Kurt L / Ussher, James E

    Viruses

    2021  Volume 13, Issue 10

    Abstract: At the end of 2019 a newly emerged betacoronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the cause of an outbreak of severe pneumonia, subsequently termed COVID-19, in a number of patients in Wuhan, China. ... ...

    Abstract At the end of 2019 a newly emerged betacoronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the cause of an outbreak of severe pneumonia, subsequently termed COVID-19, in a number of patients in Wuhan, China. Subsequently, SARS-CoV-2 rapidly spread globally, resulting in a pandemic that has to date infected over 200 million individuals and resulted in more than 4.3 million deaths. While SARS-CoV-2 results in severe disease in 13.8%, with increasing frequency of severe disease with age, over 80% of infections are asymptomatic or mild. The immune response is an important determinant of outcome following SARS-CoV-2 infection. While B cell and T cell responses are associated with control of infection and protection against subsequent challenge with SARS-CoV-2, failure to control viral replication and the resulting hyperinflammation are associated with severe COVID-19. Towards the end of 2020, several variants of concern emerged that demonstrate increased transmissibility and/or evasion of immune responses from prior SARS-CoV-2 infection. This article reviews what is known about the humoral and cellular immune responses to SARS-CoV-2 and how mutation and structural/functional changes in the emerging variants of concern impact upon the immune protection from prior infection or vaccination.
    MeSH term(s) COVID-19/immunology ; Humans ; Immunity/immunology ; Pandemics/prevention & control ; SARS-CoV-2/immunology
    Language English
    Publishing date 2021-09-23
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v13101911
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Detection of D-glutamate production from the dual Function enzyme, 4-amino-4-deoxychorismate Lyase/D-amino Acid Transaminase, in

    Opel-Reading, Helen K / Mortuza, Roman / Krause, Kurt L

    Bio-protocol

    2019  Volume 9, Issue 1, Page(s) e3135

    Abstract: D-amino acid transaminase (D-AAT) is able to synthesize both D-glutamate and D-alanine, according to the following reaction: D-alanine + α-ketoglutarate ⇌ D-glutamate + pyruvate. These two D-amino acids are essential components of the peptidoglycan layer ...

    Abstract D-amino acid transaminase (D-AAT) is able to synthesize both D-glutamate and D-alanine, according to the following reaction: D-alanine + α-ketoglutarate ⇌ D-glutamate + pyruvate. These two D-amino acids are essential components of the peptidoglycan layer of bacteria. In our recently published work, MSMEG_5795 from
    Language English
    Publishing date 2019-01-05
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2833269-6
    ISSN 2331-8325 ; 2331-8325
    ISSN (online) 2331-8325
    ISSN 2331-8325
    DOI 10.21769/BioProtoc.3135
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: The Immune Response to SARS-CoV-2 and Variants of Concern

    Torbati, Elham / Krause, Kurt L. / Ussher, James E.

    Viruses. 2021 Sept. 23, v. 13, no. 10

    2021  

    Abstract: At the end of 2019 a newly emerged betacoronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the cause of an outbreak of severe pneumonia, subsequently termed COVID-19, in a number of patients in Wuhan, China. ... ...

    Abstract At the end of 2019 a newly emerged betacoronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the cause of an outbreak of severe pneumonia, subsequently termed COVID-19, in a number of patients in Wuhan, China. Subsequently, SARS-CoV-2 rapidly spread globally, resulting in a pandemic that has to date infected over 200 million individuals and resulted in more than 4.3 million deaths. While SARS-CoV-2 results in severe disease in 13.8%, with increasing frequency of severe disease with age, over 80% of infections are asymptomatic or mild. The immune response is an important determinant of outcome following SARS-CoV-2 infection. While B cell and T cell responses are associated with control of infection and protection against subsequent challenge with SARS-CoV-2, failure to control viral replication and the resulting hyperinflammation are associated with severe COVID-19. Towards the end of 2020, several variants of concern emerged that demonstrate increased transmissibility and/or evasion of immune responses from prior SARS-CoV-2 infection. This article reviews what is known about the humoral and cellular immune responses to SARS-CoV-2 and how mutation and structural/functional changes in the emerging variants of concern impact upon the immune protection from prior infection or vaccination.
    Keywords B-lymphocytes ; COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; T-lymphocytes ; disease severity ; immune response ; mutation ; pandemic ; pneumonia ; vaccination ; virus replication ; China
    Language English
    Dates of publication 2021-0923
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2516098-9
    ISSN 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v13101911
    Database NAL-Catalogue (AGRICOLA)

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  7. Article ; Online: Optimisation of Neuraminidase Expression for Use in Drug Discovery by Using HEK293-6E Cells

    Ashley C. Campbell / John J. Tanner / Kurt L. Krause

    Viruses, Vol 13, Iss 1893, p

    2021  Volume 1893

    Abstract: Influenza virus is a highly contagious virus that causes significant human mortality and morbidity annually. The most effective drugs for treating influenza are the neuraminidase inhibitors, but resistance to these inhibitors has emerged, and additional ... ...

    Abstract Influenza virus is a highly contagious virus that causes significant human mortality and morbidity annually. The most effective drugs for treating influenza are the neuraminidase inhibitors, but resistance to these inhibitors has emerged, and additional drug discovery research on neuraminidase and other targets is needed. Traditional methods of neuraminidase production from embryonated eggs are cumbersome, while insect cell derived protein is less reflective of neuraminidase produced during human infection. Herein we describe a method for producing neuraminidase from a human cell line, HEK293-6E, and demonstrate the method by producing the neuraminidase from the 1918 H1N1 pandemic influenza strain. This method produced high levels of soluble neuraminidase expression (>3000 EU/mL), was enhanced by including a secretion signal from a viral chemokine binding protein, and does not require co-expression of additional proteins. The neuraminidase produced was of sufficient quantity and purity to support high resolution crystal structure determination. The structure solved using this protein conformed to the previously reported structure. Notably the glycosylation at three asparagine residues was superior in quality to that from insect cell derived neuraminidase. This method of production of neuraminidase should prove useful in further studies, such as the characterisation of inhibitor binding.
    Keywords neuraminidase ; structural biology ; eukaryotic protein expression ; influenza ; protein purification ; transient transfection ; Microbiology ; QR1-502
    Subject code 572
    Language English
    Publishing date 2021-09-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article: Synthesis and Biological Evaluation of Aurachin D Analogues as Inhibitors of

    Lawer, Aggie / Tyler, Chelsea / Hards, Kiel / Keighley, Laura M / Cheung, Chen-Yi / Kierek, Fabian / Su, Simon / Matikonda, Siddharth S / McInnes, Tyler / Tyndall, Joel D A / Krause, Kurt L / Cook, Gregory M / Gamble, Allan B

    ACS medicinal chemistry letters

    2022  Volume 13, Issue 10, Page(s) 1663–1669

    Abstract: A revised total synthesis of aurachin D ( ...

    Abstract A revised total synthesis of aurachin D (
    Language English
    Publishing date 2022-09-26
    Publishing country United States
    Document type Journal Article
    ISSN 1948-5875
    ISSN 1948-5875
    DOI 10.1021/acsmedchemlett.2c00401
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: New Zealand glowworm (Arachnocampa luminosa) bioluminescence is produced by a firefly-like luciferase but an entirely new luciferin.

    Watkins, Oliver C / Sharpe, Miriam L / Perry, Nigel B / Krause, Kurt L

    Scientific reports

    2018  Volume 8, Issue 1, Page(s) 3278

    Abstract: The New Zealand glowworm, Arachnocampa luminosa, is well-known for displays of blue-green bioluminescence, but details of its bioluminescent chemistry have been elusive. The glowworm is evolutionarily distant from other bioluminescent creatures studied ... ...

    Abstract The New Zealand glowworm, Arachnocampa luminosa, is well-known for displays of blue-green bioluminescence, but details of its bioluminescent chemistry have been elusive. The glowworm is evolutionarily distant from other bioluminescent creatures studied in detail, including the firefly. We have isolated and characterised the molecular components of the glowworm luciferase-luciferin system using chromatography, mass spectrometry and
    MeSH term(s) Animals ; Firefly Luciferin/chemistry ; Luciferases, Firefly/chemistry ; Luminescent Agents/chemistry ; Luminescent Measurements ; Nematocera/enzymology ; New Zealand
    Chemical Substances Luminescent Agents ; Firefly Luciferin (5TBB02N29K) ; Luciferases, Firefly (EC 1.13.12.7)
    Language English
    Publishing date 2018-02-19
    Publishing country England
    Document type Journal Article ; 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/s41598-018-21298-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Crystal Structure of Inhibitor-Bound GII.4 Sydney 2012 Norovirus 3C-Like Protease.

    Eruera, Alice-Roza / McSweeney, Alice M / McKenzie-Goldsmith, Geena M / Opel-Reading, Helen K / Thomas, Simone X / Campbell, Ashley C / Stubbing, Louise / Siow, Andrew / Hubert, Jonathan G / Brimble, Margaret A / Ward, Vernon K / Krause, Kurt L

    Viruses

    2023  Volume 15, Issue 11

    Abstract: Norovirus is the leading cause of viral gastroenteritis worldwide, and there are no approved vaccines or therapeutic treatments for chronic or severe norovirus infections. The structural characterisation of the norovirus protease and drug development has ...

    Abstract Norovirus is the leading cause of viral gastroenteritis worldwide, and there are no approved vaccines or therapeutic treatments for chronic or severe norovirus infections. The structural characterisation of the norovirus protease and drug development has predominantly focused upon GI.1 noroviruses, despite most global outbreaks being caused by GII.4 noroviruses. Here, we determined the crystal structures of the GII.4 Sydney 2012 ligand-free norovirus protease at 2.79 Å and at 1.83 Å with a covalently bound high-affinity (IC
    MeSH term(s) Humans ; Peptide Hydrolases/metabolism ; Norovirus/metabolism ; Endopeptidases/metabolism ; Catalytic Domain ; Anti-HIV Agents/metabolism ; Genotype ; Caliciviridae Infections ; Phylogeny
    Chemical Substances Peptide Hydrolases (EC 3.4.-) ; Endopeptidases (EC 3.4.-) ; Anti-HIV Agents
    Language English
    Publishing date 2023-10-31
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v15112202
    Database MEDical Literature Analysis and Retrieval System OnLINE

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