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  1. Article ; Online: Impact of the T296S mutation in P450 GcoA for aryl-O-demethylation

    Sonia F. G. Santos / Rajesh Reddy Bommareddy / Gary W. Black / Warispreet Singh

    Frontiers in Chemistry, Vol

    a QM/MM study

    2024  Volume 11

    Abstract: Lignin, a complex plant cell wall component, holds promise as a renewable aromatic carbon feedstock. p-Vanillin is a key product of lignin depolymerization and a precursor of protocatechuic acid (PCA) that has tremendous potential for biofuel production. ...

    Abstract Lignin, a complex plant cell wall component, holds promise as a renewable aromatic carbon feedstock. p-Vanillin is a key product of lignin depolymerization and a precursor of protocatechuic acid (PCA) that has tremendous potential for biofuel production. While the GcoAB enzyme, native to Amycolatopsis sp., naturally catalyzes aryl-O-demethylation toward guaiacol, recent research introduced a single mutation, T296S, into the GcoAP450 enzyme, enabling it to catalyze aryl-O-demethylation of p-vanillin. This structural modification increases the efficiency of GcoAP450 for the natural substrate while being active for p-vanillin. This study reveals the increased flexibility of p-vanillin and its ability to adapt a favorable conformation by aligning the methoxy group in close proximity to Fe(IV) = O of Cpd I in the active site of the T296S variant. The QM/MM calculations in accordance with the experimental data validated that the rate-limiting step for the oxidation of p-vanillin is hydrogen atom abstraction and provided a detailed geometric structure of stationary and saddle points for the oxidation of p-vanillin.
    Keywords catalysis ; aryl-O-demethylation ; Cytochrome P450 ; molecular dynamics ; QM/MM ; Chemistry ; QD1-999
    Subject code 540
    Language English
    Publishing date 2024-01-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Fungal β-glucan-facilitated cross-feeding activities between Bacteroides and Bifidobacterium species

    Pedro Fernandez-Julia / Gary W. Black / William Cheung / Douwe Van Sinderen / Jose Munoz-Munoz

    Communications Biology, Vol 6, Iss 1, Pp 1-

    2023  Volume 14

    Abstract: Abstract The human gut microbiota (HGM) is comprised of a very complex network of microorganisms, which interact with the host thereby impacting on host health and well-being. β-glucan has been established as a dietary polysaccharide supporting growth of ...

    Abstract Abstract The human gut microbiota (HGM) is comprised of a very complex network of microorganisms, which interact with the host thereby impacting on host health and well-being. β-glucan has been established as a dietary polysaccharide supporting growth of particular gut-associated bacteria, including members of the genera Bacteroides and Bifidobacterium, the latter considered to represent beneficial or probiotic bacteria. However, the exact mechanism underpinning β-glucan metabolism by gut commensals is not fully understood. We show that mycoprotein represents an excellent source for β-glucan, which is consumed by certain Bacteroides species as primary degraders, such as Bacteroides cellulosilyticus WH2. The latter bacterium employs two extracellular, endo-acting enzymes, belonging to glycoside hydrolase families 30 and 157, to degrade mycoprotein-derived β-glucan, thereby releasing oligosaccharides into the growth medium. These released oligosaccharides can in turn be utilized by other gut microbes, such as Bifidobacterium and Lactiplantibacillus, which thus act as secondary degraders. We used a cross-feeding approach to track how both species are able to grow in co-culture.
    Keywords Biology (General) ; QH301-705.5
    Subject code 590
    Language English
    Publishing date 2023-05-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article: The effect of Maillard reaction products and yeast strain on the synthesis of key higher alcohols and esters in beer fermentations

    Dack, Rachael E / Gary W. Black / Georgios Koutsidis / St. John Usher

    Food chemistry. 2017 Oct. 01, v. 232

    2017  

    Abstract: The effect of Maillard reaction products (MRPs), formed during the production of dark malts, on the synthesis of higher alcohols and esters in beer fermentations was investigated by headspace solid-phase microextraction GC–MS. Higher alcohol levels were ... ...

    Abstract The effect of Maillard reaction products (MRPs), formed during the production of dark malts, on the synthesis of higher alcohols and esters in beer fermentations was investigated by headspace solid-phase microextraction GC–MS. Higher alcohol levels were significantly (p<0.05) higher in dark malt fermentations, while the synthesis of esters was inhibited, due to possible suppression of enzyme activity and/or gene expression linked to ester synthesis. Yeast strain also affected flavour synthesis with Saccharomyces cerevisiae strain A01 producing considerably lower levels of higher alcohols and esters than S288c and L04. S288c produced approximately double the higher alcohol levels and around twenty times more esters compared to L04. Further investigations into malt type-yeast strain interactions in relation to flavour development are required to gain better understanding of flavour synthesis that could assist in the development of new products and reduce R&D costs for the industry.
    Keywords alcohols ; beers ; esters ; fermentation ; flavor ; gas chromatography-mass spectrometry ; gene expression ; headspace analysis ; industry ; Maillard reaction products ; malt ; new products ; research and development ; Saccharomyces cerevisiae ; solid phase microextraction ; yeasts
    Language English
    Dates of publication 2017-1001
    Size p. 595-601.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 243123-3
    ISSN 1873-7072 ; 0308-8146
    ISSN (online) 1873-7072
    ISSN 0308-8146
    DOI 10.1016/j.foodchem.2017.04.043
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

    Z 3634: Show issues

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  4. Article ; Online: Structural Insights from Molecular Dynamics Simulations of Tryptophan 7‑Halogenase and Tryptophan 5‑Halogenase

    Jon Ainsley / Adrian J. Mulholland / Gary W. Black / Olivier Sparagano / Christo Z. Christov / Tatyana G. Karabencheva-Christova

    ACS Omega, Vol 3, Iss 5, Pp 4847-

    2018  Volume 4859

    Keywords Chemistry ; QD1-999
    Language English
    Publishing date 2018-05-01T00:00:00Z
    Publisher American Chemical Society
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article: Antidiabetic “gliptins” affect biofilm formation by Streptococcus mutans

    De, Arpan / Arianna Pompilio / Dezemona Petrelli / Gary W. Black / Giulio Lupidi / Iain C. Sutcliffe / Jenifer Francis / Luca A. Vitali

    Microbiological research. 2018 Apr., v. 209

    2018  

    Abstract: Streptococcus mutans, a dental caries causing odontopathogen, produces X-prolyl dipeptidyl peptidase (Sm-XPDAP, encoded by pepX), a serine protease known to have a nutritional role. Considering the potential of proteases as therapeutic targets in ... ...

    Abstract Streptococcus mutans, a dental caries causing odontopathogen, produces X-prolyl dipeptidyl peptidase (Sm-XPDAP, encoded by pepX), a serine protease known to have a nutritional role. Considering the potential of proteases as therapeutic targets in pathogens, this study was primarily aimed at investigating the role of Sm-XPDAP in contributing to virulence-related traits. Dipeptidyl peptidase (DPP IV), an XPDAP analogous enzyme found in mammalian tissues,is a well known therapeutic target in Type II diabetes. Based on the hypothesis that gliptins, commonly used as anti-human-DPP IV drugs, may affect bacterial growth upon inhibition of Sm-XPDAP, we have determined their ex vivo antimicrobial and anti-biofilm activity towards S. mutans. All three DPP IV drugs tested reduced biofilm formation as determined by crystal violet staining. To link the observed biofilm inhibition to the human-DPP IV analogue present in S. mutans UA159, a pepX isogenic mutant was generated. In addition to reduced biofilm formation, CLSM studies of the biofilm formed by the pepX isogenic mutant showed these were comparable to those formed in the presence of saxagliptin, suggesting a probable role of this enzyme in biofilm formation by S. mutans UA159. The effects of both pepX deletion and DPP IV drugs on the proteome were studied using LC–MS/MS. Overall, this study highlights the potential of Sm-XPDAP as a novel anti-biofilm target and suggests a template molecule to synthesize lead compounds effective against this enzyme.
    Keywords antimicrobial properties ; biofilm ; confocal laser scanning microscopy ; dental caries ; drugs ; gentian violet ; mammals ; microbial growth ; mutants ; noninsulin-dependent diabetes mellitus ; pathogens ; proteome ; serine proteinases ; staining ; Streptococcus mutans
    Language English
    Dates of publication 2018-04
    Size p. 79-85.
    Publishing place Elsevier GmbH
    Document type Article
    ZDB-ID 1189614-0
    ISSN 1618-0623 ; 0944-5013
    ISSN (online) 1618-0623
    ISSN 0944-5013
    DOI 10.1016/j.micres.2018.02.005
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

    Z 1148: Show issues

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  6. Article ; Online: Conformational effects on the circular dichroism of Human Carbonic Anhydrase II

    Tatyana G Karabencheva-Christova / Uno Carlsson / Kia Balali-Mood / Gary W Black / Christo Z Christov

    PLoS ONE, Vol 8, Iss 2, p e

    a multilevel computational study.

    2013  Volume 56874

    Abstract: Circular Dichroism (CD) spectroscopy is a powerful method for investigating conformational changes in proteins and therefore has numerous applications in structural and molecular biology. Here a computational investigation of the CD spectrum of the Human ...

    Abstract Circular Dichroism (CD) spectroscopy is a powerful method for investigating conformational changes in proteins and therefore has numerous applications in structural and molecular biology. Here a computational investigation of the CD spectrum of the Human Carbonic Anhydrase II (HCAII), with main focus on the near-UV CD spectra of the wild-type enzyme and it seven tryptophan mutant forms, is presented and compared to experimental studies. Multilevel computational methods (Molecular Dynamics, Semiempirical Quantum Mechanics, Time-Dependent Density Functional Theory) were applied in order to gain insight into the mechanisms of interaction between the aromatic chromophores within the protein environment and understand how the conformational flexibility of the protein influences these mechanisms. The analysis suggests that combining CD semi empirical calculations, crystal structures and molecular dynamics (MD) could help in achieving a better agreement between the computed and experimental protein spectra and provide some unique insight into the dynamic nature of the mechanisms of chromophore interactions.
    Keywords Medicine ; R ; Science ; Q
    Subject code 612
    Language English
    Publishing date 2013-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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