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  1. Article ; Online: Potential of mean force conformational energy maps for disaccharide linkages of the Burkholderia multivorans exopolysaccharide C1576 in aqueous solution.

    Jou, Ining A / Yoo, Andrew S / Dionne, Elyssa V / Brady, John W

    Carbohydrate research

    2023  Volume 524, Page(s) 108741

    Abstract: Potential of Mean Force Ramachandran energy maps in aqueous solution have been prepared for all of the glycosidic linkages found in the C1576 exopolysaccharide from the biofilms of the bacterial species Burkholderia multivorans, a member of the ... ...

    Abstract Potential of Mean Force Ramachandran energy maps in aqueous solution have been prepared for all of the glycosidic linkages found in the C1576 exopolysaccharide from the biofilms of the bacterial species Burkholderia multivorans, a member of the Burkholderia cepacian complex that was isolated from a cystic fibrosis patient. C1576 is a rhamnomannan with a tetrasaccharide repeat unit. In general, for the four linkage types in this polymer, hydration did not produce dramatic changes in the Ramachandran energy surfaces, with the 3-methyl-α-d-rhamnopyranose-(1→3)-α-d-rhamnopyranose case exhibiting the greatest hydration change, with the global minimum energy conformation shifting by more than 80° in ψ. However, hydration did reduce the rigidity of all the linkages, increasing the overall flexibility of this polysaccharide.
    MeSH term(s) Humans ; Disaccharides ; Burkholderia ; Molecular Conformation ; Biofilms
    Chemical Substances Disaccharides
    Language English
    Publishing date 2023-01-18
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1435-7
    ISSN 1873-426X ; 0008-6215
    ISSN (online) 1873-426X
    ISSN 0008-6215
    DOI 10.1016/j.carres.2023.108741
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  2. Article ; Online: Water structuring above solutes with planar hydrophobic surfaces.

    Schnupf, Udo / Brady, John W

    Physical chemistry chemical physics : PCCP

    2017  Volume 19, Issue 19, Page(s) 11851–11863

    Abstract: Many important biological solutes possess not only polar and hydrogen bonding functionalities, but also weakly-hydrating, or hydrophobic, surfaces. Theories of the hydration of such surfaces predict that their solvent interactions will change from a ... ...

    Abstract Many important biological solutes possess not only polar and hydrogen bonding functionalities, but also weakly-hydrating, or hydrophobic, surfaces. Theories of the hydration of such surfaces predict that their solvent interactions will change from a wetting type interaction to a dewetting regime as a function of the solute size, with a gradual transition in behavior taking place around characteristic lengths of ∼1 nm. Aggregations of non-polar species over this size range will undergo a transition from being dominated by entropy to being dominated by enthalpy. These transitions can be understood in part in terms of the geometries required of the solvating water molecules. We report here a series of simulations in aqueous solution of organic molecules with planar faces of increasing size, ranging from cyclopropane to circumcircumcoronene, in order to explore the transition in behavior for such solutes as their size increases. For this series, the dewetting transition occurred gradually, converging asymptotically to a limiting separation value for first layer water molecules of around 3.3 Å, while the transition in hydrogen bonding orientational structure occurred between cyclopropane and cyclopentadene. Water immediately adjacent to the largest planar hydrophobic surfaces oriented in ways that resembled on average the structural organization of the basal planes of ice.
    Language English
    Publishing date 2017-05-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/c7cp00179g
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  3. Article ; Online: Microscopy and modelling investigations on the morphology of the biofilm exopolysaccharide produced by Burkholderia multivorans strain C1576.

    Cacioppo, Michele / De Zorzi, Rita / Syrgiannis, Zois / Bellich, Barbara / Bertoncin, Paolo / Jou, Ining A / Brady, John W / Rizzo, Roberto / Cescutti, Paola

    International journal of biological macromolecules

    2023  Volume 253, Issue Pt 6, Page(s) 127294

    Abstract: Bacteria form very often biofilms where they embed in a self-synthesized matrix exhibiting a gel-like appearance. Matrices offer several advantages, including defence against external threats and the easiness of intercellular communication. In infections, ...

    Abstract Bacteria form very often biofilms where they embed in a self-synthesized matrix exhibiting a gel-like appearance. Matrices offer several advantages, including defence against external threats and the easiness of intercellular communication. In infections, biofilm formation enhances bacteria resistance against antimicrobials, causing serious clinical problems for patients' treatments. Biofilm matrices are composed of proteins, extracellular DNA, and polysaccharides, the latter being the major responsible for matrix architecture. The repeating unit of the biofilm polysaccharide synthesized by Burkholderia multivorans strain C1576 contains two mannoses and two sequentially linked rhamnoses, one of them 50 % methylated on C-3. Rhamnose, a 6-deoxysugar, has lower polarity than other common monosaccharides and its methylation further reduces polarity. This suggests a possible role of this polysaccharide in the biofilm matrix; in fact, computer modelling and atomic force microscopy studies evidenced intra- and inter-molecular non-polar interactions both within polysaccharides and with aliphatic molecules. In this paper, the polysaccharide three-dimensional morphology was investigated using atomic force microscopy in both solid and solution states. Independent evidence of the polymer conformation was obtained by transmission electron microscopy which confirmed the formation of globular compact structures. Finally, data from computer dynamic simulations were used to model the three-dimensional structure.
    MeSH term(s) Humans ; Polysaccharides, Bacterial/chemistry ; Burkholderia/metabolism ; Biofilms ; Microscopy, Atomic Force
    Chemical Substances Polysaccharides, Bacterial
    Language English
    Publishing date 2023-10-07
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2023.127294
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  4. Article: Ramachandran conformational energy maps for disaccharide linkages found in Burkholderia multivorans biofilm polysaccharides

    Jou, Ining A / Caterino, Marco / Schnupf, Udo / Rizzo, Roberto / Cescutti, Paola / Brady, John W

    International journal of biological macromolecules. 2020 Jan. 15, v. 143

    2020  

    Abstract: Ramachandran conformational energy maps have been prepared for all of the glycosidic linkages found in the C1576 exopolysaccharide that constitutes the biofilms of the bacterial species Burkholderia multivorans, a member of the Burkholderia cepacian ... ...

    Abstract Ramachandran conformational energy maps have been prepared for all of the glycosidic linkages found in the C1576 exopolysaccharide that constitutes the biofilms of the bacterial species Burkholderia multivorans, a member of the Burkholderia cepacian complex that was isolated from a cystic fibrosis patient. This polysaccharide is a rhamnomannan with a tetrasaccharide repeat unit containing two mannose residues and two rhamnose residues, –[3-α-d-Man-(1→2)-α-d-Man-(1→2)-α-d-Rha-(1→3)-α-d-Rha-(1→]n–, where approximately 50% of the rhamnoses are randomly methylated on their O3 hydroxyl groups, further increasing the overall hydrophobicity of the chains. Because of the methylation, the tetrasaccharide repeat unit actually contains six possible linkages. The conformational energy maps are fully adiabatic relaxed maps in which the energy for each (φ,ψ) grid point on the map represents the lowest possible energy for the molecule in that conformation, considering all the combinations of the other degrees of freedom, such as hydroxyl orientations. Molecular dynamics simulations were used to verify that these maps indeed describe the conformational dynamics of these linkages. All six linkages were found to be quite restricted in possible φ angles, but to exhibit several possible low-energy ψ angles, suggesting that these chains could be quite flexible.
    Keywords Burkholderia multivorans ; biofilm ; cystic fibrosis ; energy ; exopolysaccharides ; glycosidic linkages ; hydrophobicity ; mannose ; methylation ; moieties ; molecular dynamics ; ozone ; rhamnose ; simulation models
    Language English
    Dates of publication 2020-0115
    Size p. 501-509.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2019.11.037
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  5. Book: Introductory food chemistry

    Brady, John W

    2013  

    Title variant Food chemistry
    Author's details John W. Brady
    Keywords Food/Analysis ; Food/Composition
    Language English
    Size XV, 638 S., Ill., graph. Darst., 26 cm
    Publisher Comstock Publ. Associates/Cornell Univ. Press
    Publishing place Ithaca, NY u.a.
    Document type Book
    Note Author: John W. Brady (Professor in the Department of Food Science at Cornell University) ; Includes bibliographical references (p. 621-628) and index
    ISBN 0801450756 ; 9780801450754
    Database Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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  6. Book: Introductory food chemistry

    Brady, John W

    2013  

    Author's details John W. Brady
    Keywords Food/Analysis. ; Food/Composition.
    Language English
    Size xv, 638 p. :, ill. (some col.) ;, 26 cm.
    Publisher Comstock Pub. Associates
    Publishing place Ithaca
    Document type Book
    ISBN 9780801450754 ; 0801450756
    Database NAL-Catalogue (AGRICOLA)

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  7. Article ; Online: Physico-chemical properties of aqueous drug solutions: From the basic thermodynamics to the advanced experimental and simulation results.

    Bellich, Barbara / Gamini, Amelia / Brady, John W / Cesàro, Attilio

    International journal of pharmaceutics

    2018  Volume 540, Issue 1-2, Page(s) 65–77

    Abstract: The physical chemical properties of aqueous solutions of model compounds are illustrated in relation to hydration and solubility issues by using three perspectives: thermodynamic, spectroscopic and molecular dynamics simulations. The thermodynamic survey ...

    Abstract The physical chemical properties of aqueous solutions of model compounds are illustrated in relation to hydration and solubility issues by using three perspectives: thermodynamic, spectroscopic and molecular dynamics simulations. The thermodynamic survey of the fundamental backgrounds of concentration dependence and experimental solubility results show some peculiar behavior of aqueous solutions with several types of similar solutes. Secondly, the use of a variety of experimental spectroscopic devices, operating under different experimental conditions of dimension and frequency, has produced a large amount of structural and dynamic data on aqueous solutions showing the richness of the information produced, depending on where and how the experiment is carried out. Finally, the use of molecular dynamics computational work is presented to highlight how the different types of solute functional groups and surface topologies organize adjacent water molecules differently. The highly valuable contribution of computer simulation studies in providing molecular explanations for experimental deductions, either of a thermodynamic or spectroscopic nature, is shown to have changed the current knowledge of many aqueous solution processes. While this paper is intended to provide a collective view on the latest literature results, still the presentation aims at a tutorial explanation of the potentials of the three methodologies in the field of aqueous solutions of pharmaceutical molecules.
    MeSH term(s) Drug Compounding ; Models, Chemical ; Molecular Dynamics Simulation ; Pharmaceutical Preparations/chemistry ; Solubility ; Spectrum Analysis ; Technology, Pharmaceutical/methods ; Temperature ; Thermodynamics ; Water/chemistry
    Chemical Substances Pharmaceutical Preparations ; Water (059QF0KO0R)
    Language English
    Publishing date 2018-02-02
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 428962-6
    ISSN 1873-3476 ; 0378-5173
    ISSN (online) 1873-3476
    ISSN 0378-5173
    DOI 10.1016/j.ijpharm.2018.01.042
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  8. Article: The biofilm of Burkholderia cenocepacia H111 contains an exopolysaccharide composed of l-rhamnose and l-mannose: Structural characterization and molecular modelling

    Bellich, Barbara / Jou, Ining A / Buriola, Claudia / Ravenscroft, Neil / Brady, John W / Fazli, Mustafa / Tolker-Nielsen, Tim / Rizzo, Roberto / Cescutti, Paola

    Carbohydrate research. 2021 Jan., v. 499

    2021  

    Abstract: Burkholderia cenocepacia belongs to the Burkholderia Cepacia Complex, a group of 22 closely related species both of clinical and environmental origin, infecting cystic fibrosis patients. B. cenocepacia accounts for the majority of the clinical isolates, ... ...

    Abstract Burkholderia cenocepacia belongs to the Burkholderia Cepacia Complex, a group of 22 closely related species both of clinical and environmental origin, infecting cystic fibrosis patients. B. cenocepacia accounts for the majority of the clinical isolates, comprising the most virulent and transmissible strains. The capacity to form biofilms is among the many virulence determinants of B. cenocepacia, a characteristic that confers enhanced tolerance to some antibiotics, desiccation, oxidizing agents, and host defenses. Exopolysaccharides are a major component of biofilm matrices, particularly providing mechanical stability to biofilms. Recently, a water-insoluble exopolysaccharide produced by B. cenocepacia H111 in biofilm was characterized. In the present study, a water-soluble exopolysaccharide was extracted from B. cenocepacia H111 biofilm, and its structure was determined by GLC-MS, NMR and ESI-MS. The repeating unit is a linear rhamno-tetrasaccharide with 50% replacement of a 3-α-L-Rha with a α-3-L-Man.[2)-α-L-Rhap-(1→3)-α-L-[Rhap or Manp]-(1→3)-α-L-Rhap-(1→2)-α-L-Rhap-(1→]ₙMolecular modelling was used to obtain information about local structural motifs which could give information about the polysaccharide conformation.
    Keywords Burkholderia cenocepacia ; biofilm ; cystic fibrosis ; exopolysaccharides ; mannose ; research ; rhamnose ; virulence ; water solubility
    Language English
    Dates of publication 2021-01
    Publishing place Elsevier Ltd
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 1435-7
    ISSN 1873-426X ; 0008-6215
    ISSN (online) 1873-426X
    ISSN 0008-6215
    DOI 10.1016/j.carres.2020.108231
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  9. Article ; Online: Inter-residual Hydrogen Bonding in Carbohydrates Unraveled by NMR Spectroscopy and Molecular Dynamics Simulations.

    Rönnols, Jerk / Engström, Olof / Schnupf, Udo / Säwén, Elin / Brady, John W / Widmalm, Göran

    Chembiochem : a European journal of chemical biology

    2019  Volume 20, Issue 19, Page(s) 2519–2528

    Abstract: Carbohydrates, also known as glycans in biological systems, are omnipresent in nature where they as glycoconjugates occur as oligo- and polysaccharides linked to lipids and proteins. Their three-dimensional structure is defined by two or three torsion ... ...

    Abstract Carbohydrates, also known as glycans in biological systems, are omnipresent in nature where they as glycoconjugates occur as oligo- and polysaccharides linked to lipids and proteins. Their three-dimensional structure is defined by two or three torsion angles at each glycosidic linkage. In addition, transglycosidic hydrogen bonding between sugar residues may be important. Herein we investigate the presence of these inter-residue interactions by NMR spectroscopy in D
    MeSH term(s) Carbohydrate Conformation ; Carbohydrates/chemistry ; Disaccharides/chemistry ; Hydrogen Bonding ; Magnetic Resonance Spectroscopy/methods ; Models, Molecular ; Molecular Dynamics Simulation ; Thermodynamics
    Chemical Substances Carbohydrates ; Disaccharides
    Language English
    Publishing date 2019-08-28
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2020469-3
    ISSN 1439-7633 ; 1439-4227
    ISSN (online) 1439-7633
    ISSN 1439-4227
    DOI 10.1002/cbic.201900301
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  10. Article ; Online: Ramachandran conformational energy maps for disaccharide linkages found in Burkholderia multivorans biofilm polysaccharides.

    Jou, Ining A / Caterino, Marco / Schnupf, Udo / Rizzo, Roberto / Cescutti, Paola / Brady, John W

    International journal of biological macromolecules

    2019  Volume 143, Page(s) 501–509

    Abstract: Ramachandran conformational energy maps have been prepared for all of the glycosidic linkages found in the C1576 exopolysaccharide that constitutes the biofilms of the bacterial species Burkholderia multivorans, a member of the Burkholderia cepacian ... ...

    Abstract Ramachandran conformational energy maps have been prepared for all of the glycosidic linkages found in the C1576 exopolysaccharide that constitutes the biofilms of the bacterial species Burkholderia multivorans, a member of the Burkholderia cepacian complex that was isolated from a cystic fibrosis patient. This polysaccharide is a rhamnomannan with a tetrasaccharide repeat unit containing two mannose residues and two rhamnose residues, -[3-α-d-Man-(1→2)-α-d-Man-(1→2)-α-d-Rha-(1→3)-α-d-Rha-(1→]
    MeSH term(s) Biofilms ; Burkholderia/chemistry ; Burkholderia/physiology ; Carbohydrate Conformation ; Disaccharides/chemistry ; Polysaccharides, Bacterial/chemistry
    Chemical Substances Disaccharides ; Polysaccharides, Bacterial
    Language English
    Publishing date 2019-11-28
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2019.11.037
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