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  1. Article: Towards Elucidating Structure-Spectra Relationships in Rhamnogalacturonan II: Computational Protocols for Accurate

    Bharadwaj, Vivek S / Westawker, Luke P / Crowley, Michael F

    Frontiers in molecular biosciences

    2022  Volume 8, Page(s) 756219

    Abstract: Apiose is a naturally occurring, uncommon branched-chain pentose found in plant cell walls as part of the complex polysaccharide Rhamnogalacturonan II (RG-II). The structural elucidation of the three-dimensional structure of RG-II by nuclear magnetic ... ...

    Abstract Apiose is a naturally occurring, uncommon branched-chain pentose found in plant cell walls as part of the complex polysaccharide Rhamnogalacturonan II (RG-II). The structural elucidation of the three-dimensional structure of RG-II by nuclear magnetic resonance (NMR) spectroscopy is significantly complicated by the ability of apiose to cross-link
    Language English
    Publishing date 2022-01-24
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2814330-9
    ISSN 2296-889X
    ISSN 2296-889X
    DOI 10.3389/fmolb.2021.756219
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  2. Article ; Online: Molecular simulation of lignin-related aromatic compound permeation through gram-negative bacterial outer membranes.

    Vermaas, Josh V / Crowley, Michael F / Beckham, Gregg T

    The Journal of biological chemistry

    2022  Volume 298, Issue 12, Page(s) 102627

    Abstract: Lignin, an abundant aromatic heteropolymer in secondary plant cell walls, is the single largest source of renewable aromatics in the biosphere. Leveraging this resource for renewable bioproducts through targeted microbial action depends on lignin ... ...

    Abstract Lignin, an abundant aromatic heteropolymer in secondary plant cell walls, is the single largest source of renewable aromatics in the biosphere. Leveraging this resource for renewable bioproducts through targeted microbial action depends on lignin fragment uptake by microbial hosts and subsequent enzymatic action to obtain the desired product. Recent computational work has emphasized that bacterial inner membranes are permeable to many aromatic compounds expected from lignin depolymerization processes. In this study, we expand on these findings through simulations for 42 lignin-related compounds across a gram-negative bacterial outer membrane model. Unbiased simulation trajectories indicate that spontaneous crossing for the full outer membrane is relatively rare at molecular simulation timescales, primarily due to preferential membrane partitioning and slow diffusion within the lipopolysaccharide layer within the outer membrane. Membrane partitioning and permeability coefficients were determined through replica exchange umbrella sampling simulations to overcome sampling limitations. We find that the glycosylated lipopolysaccharides found in the outer membrane increase the permeation barrier to many lignin-related compounds, particularly the most hydrophobic compounds. However, the effect is relatively modest; at industrially relevant concentrations, uncharged lignin-related compounds will readily diffuse across the outer membrane without the need for specific porins. Together, our results provide insight into the permeability of the bacterial outer membrane for assessing lignin fragment uptake and the future production of renewable bioproducts.
    Language English
    Publishing date 2022-10-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1016/j.jbc.2022.102627
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  3. Article ; Online: Atomistic, macromolecular model of the

    Addison, Bennett / Bu, Lintao / Bharadwaj, Vivek / Crowley, Meagan F / Harman-Ware, Anne E / Crowley, Michael F / Bomble, Yannick J / Ciesielski, Peter N

    Science advances

    2024  Volume 10, Issue 1, Page(s) eadi7965

    Abstract: Plant secondary cell walls (SCWs) are composed of a heterogeneous interplay of three major biopolymers: cellulose, hemicelluloses, and lignin. Details regarding specific intermolecular interactions and higher-order architecture of the SCW superstructure ... ...

    Abstract Plant secondary cell walls (SCWs) are composed of a heterogeneous interplay of three major biopolymers: cellulose, hemicelluloses, and lignin. Details regarding specific intermolecular interactions and higher-order architecture of the SCW superstructure remain ambiguous. Here, we use solid-state nuclear magnetic resonance (ssNMR) measurements to infer refined details about the structural configuration, intermolecular interactions, and relative proximity of all three major biopolymers within air-dried
    MeSH term(s) Populus ; Cellulose ; Magnetic Resonance Spectroscopy ; Biopolymers ; Plants ; Cell Wall
    Chemical Substances Cellulose (9004-34-6) ; Biopolymers
    Language English
    Publishing date 2024-01-03
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2810933-8
    ISSN 2375-2548 ; 2375-2548
    ISSN (online) 2375-2548
    ISSN 2375-2548
    DOI 10.1126/sciadv.adi7965
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  4. Article ; Online: Diffusion in intact secondary cell wall models of plants at different equilibrium moisture content.

    Sarkar, Daipayan / Bu, Lintao / Jakes, Joseph E / Zieba, Jacob K / Kaufman, Isaiah D / Crowley, Michael F / Ciesielski, Peter N / Vermaas, Josh V

    Cell surface (Amsterdam, Netherlands)

    2023  Volume 9, Page(s) 100105

    Abstract: Secondary plant cell walls are composed of carbohydrate and lignin polymers, and collectively represent a significant renewable resource. Leveraging these resources depends in part on a mechanistic understanding for diffusive processes within plant cell ... ...

    Abstract Secondary plant cell walls are composed of carbohydrate and lignin polymers, and collectively represent a significant renewable resource. Leveraging these resources depends in part on a mechanistic understanding for diffusive processes within plant cell walls. Common wood protection treatments and biomass conversion processes to create biorefinery feedstocks feature ion or solvent diffusion within the cell wall. X-ray fluorescence microscopy experiments have determined that ionic diffusion rates are dependent on cell wall hydration as well as the ionic species through non-linear relationships. In this work, we use classical molecular dynamics simulations to map the diffusion behavior of different plant cell wall components (cellulose, hemicellulose, lignin), ions (Na
    Language English
    Publishing date 2023-03-25
    Publishing country Netherlands
    Document type Journal Article
    ISSN 2468-2330
    ISSN (online) 2468-2330
    DOI 10.1016/j.tcsw.2023.100105
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  5. Article ; Online: The reaction mechanism of the Ideonella sakaiensis PETase enzyme.

    Burgin, Tucker / Pollard, Benjamin C / Knott, Brandon C / Mayes, Heather B / Crowley, Michael F / McGeehan, John E / Beckham, Gregg T / Woodcock, H Lee

    Communications chemistry

    2024  Volume 7, Issue 1, Page(s) 65

    Abstract: Polyethylene terephthalate (PET), the most abundantly produced polyester plastic, can be depolymerized by the Ideonella sakaiensis PETase enzyme. Based on multiple PETase crystal structures, the reaction has been proposed to proceed via a two-step serine ...

    Abstract Polyethylene terephthalate (PET), the most abundantly produced polyester plastic, can be depolymerized by the Ideonella sakaiensis PETase enzyme. Based on multiple PETase crystal structures, the reaction has been proposed to proceed via a two-step serine hydrolase mechanism mediated by a serine-histidine-aspartate catalytic triad. To elucidate the multi-step PETase catalytic mechanism, we use transition path sampling and likelihood maximization to identify optimal reaction coordinates for the PETase enzyme. We predict that deacylation is likely rate-limiting, and the reaction coordinates for both steps include elements describing nucleophilic attack, ester bond cleavage, and the "moving-histidine" mechanism. We find that the flexibility of Trp185 promotes the reaction, providing an explanation for decreased activity observed in mutations that restrict Trp185 motion. Overall, this study uses unbiased computational approaches to reveal the detailed reaction mechanism necessary for further engineering of an important class of enzymes for plastics bioconversion.
    Language English
    Publishing date 2024-03-27
    Publishing country England
    Document type Journal Article
    ZDB-ID 2929562-2
    ISSN 2399-3669 ; 2399-3669
    ISSN (online) 2399-3669
    ISSN 2399-3669
    DOI 10.1038/s42004-024-01154-x
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  6. Article ; Online: Catalytic Mechanism of Aryl-Ether Bond Cleavage in Lignin by LigF and LigG.

    Prates, Erica Teixeira / Crowley, Michael F / Skaf, Munir S / Beckham, Gregg T

    The journal of physical chemistry. B

    2019  Volume 123, Issue 48, Page(s) 10142–10151

    Abstract: Given the abundance of lignin in nature, multiple enzyme systems have been discovered to cleave the β-O-4 bonds, the most prevalent intermonomer linkage. In particular, stereospecific cleavage of lignin oligomers by ... ...

    Abstract Given the abundance of lignin in nature, multiple enzyme systems have been discovered to cleave the β-O-4 bonds, the most prevalent intermonomer linkage. In particular, stereospecific cleavage of lignin oligomers by glutathione
    MeSH term(s) Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Biocatalysis ; Catalytic Domain ; Coenzymes/chemistry ; Coenzymes/metabolism ; Glutathione/chemistry ; Glutathione/metabolism ; Glycoconjugates/chemistry ; Glycoconjugates/metabolism ; Hydrolysis ; Kinetics ; Lignin/chemistry ; Lignin/metabolism ; Lyases/chemistry ; Lyases/metabolism ; Molecular Dynamics Simulation ; Oxidoreductases/chemistry ; Oxidoreductases/metabolism ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Structure, Secondary ; Quantum Theory ; Sphingomonas/chemistry ; Sphingomonas/enzymology ; Stereoisomerism ; Substrate Specificity ; Thermodynamics
    Chemical Substances Bacterial Proteins ; Coenzymes ; Glycoconjugates ; Lignin (9005-53-2) ; Oxidoreductases (EC 1.-) ; aryl ether cleaving enzyme (EC 1.-) ; Lyases (EC 4.-) ; Glutathione (GAN16C9B8O)
    Language English
    Publishing date 2019-11-19
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.9b06243
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  7. Article ; Online: Reply to Cosgrove: Non-enzymatic action of expansins.

    Bharadwaj, Vivek S / Knott, Brandon C / Ståhlberg, Jerry / Beckham, Gregg T / Crowley, Michael F

    The Journal of biological chemistry

    2020  Volume 295, Issue 19, Page(s) 6783

    MeSH term(s) Cellulase ; Glycosyltransferases ; Hydrolysis ; Plant Proteins
    Chemical Substances Plant Proteins ; Glycosyltransferases (EC 2.4.-) ; Cellulase (EC 3.2.1.4)
    Language English
    Publishing date 2020-05-08
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1074/jbc.RL120.013432
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  8. Article ; Online: Mechanism and Reaction Energy Landscape for Apiose Cross-Linking by Boric Acid in Rhamnogalacturonan II.

    Bharadwaj, Vivek S / Crowley, Michael F / Peña, Maria J / Urbanowicz, Breeanna / O'Neill, Malcolm

    The journal of physical chemistry. B

    2020  Volume 124, Issue 45, Page(s) 10117–10125

    Abstract: Rhamnogalacturonan II (RG-II)-the most complex polysaccharide known in nature-exists as a borate cross-linked dimer in the plant primary cell wall. Boric acid facilitates the formation of this cross-link on the apiosyl residues of RG-II's side chain A. ... ...

    Abstract Rhamnogalacturonan II (RG-II)-the most complex polysaccharide known in nature-exists as a borate cross-linked dimer in the plant primary cell wall. Boric acid facilitates the formation of this cross-link on the apiosyl residues of RG-II's side chain A. Here, we detail the reaction mechanism for the cross-linking process with ab initio calculations coupled with transition state theory. We determine the formation of the first ester linkage to be the rate-limiting step of the mechanism. Our findings demonstrate that the regio- and stereospecific nature of subsequent steps in the reaction itinerary presents four distinct energetically plausible reaction pathways. This has significant implications for the overall structure of the cross-linked RG-II dimer assembly. Our transition state and reaction path analyses reveal key geometric insights that corroborate previous experimental hypotheses on borate ester formation reactions.
    MeSH term(s) Boric Acids ; Cell Wall ; Pectins ; Pentoses
    Chemical Substances Boric Acids ; Pentoses ; rhamnogalacturonan II ; Pectins (89NA02M4RX) ; apiose (E59T26TCEC) ; boric acid (R57ZHV85D4)
    Language English
    Publishing date 2020-10-28
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.0c06920
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  9. Article ; Online: The hydrolysis mechanism of a GH45 cellulase and its potential relation to lytic transglycosylase and expansin function.

    Bharadwaj, Vivek S / Knott, Brandon C / Ståhlberg, Jerry / Beckham, Gregg T / Crowley, Michael F

    The Journal of biological chemistry

    2020  Volume 295, Issue 14, Page(s) 4477–4487

    Abstract: Family 45 glycoside hydrolases (GH45) are endoglucanases that are integral to cellulolytic secretomes, and their ability to break down cellulose has been successfully exploited in textile and detergent industries. In addition to their industrial ... ...

    Abstract Family 45 glycoside hydrolases (GH45) are endoglucanases that are integral to cellulolytic secretomes, and their ability to break down cellulose has been successfully exploited in textile and detergent industries. In addition to their industrial relevance, understanding the molecular mechanism of GH45-catalyzed hydrolysis is of fundamental importance because of their structural similarity to cell wall-modifying enzymes such as bacterial lytic transglycosylases (LTs) and expansins present in bacteria, plants, and fungi. Our understanding of the catalytic itinerary of GH45s has been incomplete because a crystal structure with substrate spanning the -1 to +1 subsites is currently lacking. Here we constructed and validated a putative Michaelis complex
    MeSH term(s) Catalytic Domain ; Cellulase/chemistry ; Cellulase/genetics ; Cellulase/metabolism ; Fungal Genus Humicola/enzymology ; Fungal Proteins/chemistry ; Fungal Proteins/genetics ; Fungal Proteins/metabolism ; Glycosyltransferases/metabolism ; Hydrolysis ; Kinetics ; Molecular Dynamics Simulation ; Mutagenesis, Site-Directed ; Protein Structure, Tertiary ; Quantum Theory ; Substrate Specificity
    Chemical Substances Fungal Proteins ; Glycosyltransferases (EC 2.4.-) ; murein transglycosylase (EC 2.4.99.-) ; Cellulase (EC 3.2.1.4)
    Language English
    Publishing date 2020-02-13
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1074/jbc.RA119.011406
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: PolyID: Artificial Intelligence for Discovering Performance-Advantaged and Sustainable Polymers.

    Wilson, A Nolan / St John, Peter C / Marin, Daniela H / Hoyt, Caroline B / Rognerud, Erik G / Nimlos, Mark R / Cywar, Robin M / Rorrer, Nicholas A / Shebek, Kevin M / Broadbelt, Linda J / Beckham, Gregg T / Crowley, Michael F

    Macromolecules

    2023  Volume 56, Issue 21, Page(s) 8547–8557

    Abstract: A necessary transformation for a sustainable economy is the transition from fossil-derived plastics to polymers derived from biomass and waste resources. While renewable feedstocks can enhance material performance through unique chemical moieties, ... ...

    Abstract A necessary transformation for a sustainable economy is the transition from fossil-derived plastics to polymers derived from biomass and waste resources. While renewable feedstocks can enhance material performance through unique chemical moieties, probing the vast material design space by experiment alone is not practically feasible. Here, we develop a machine-learning-based tool, PolyID, to reduce the design space of renewable feedstocks to enable efficient discovery of performance-advantaged, biobased polymers. PolyID is a multioutput, graph neural network specifically designed to increase accuracy and to enable quantitative structure-property relationship (QSPR) analysis for polymers. It includes a novel domain-of-validity method that was developed and applied to demonstrate how gaps in training data can be filled to improve accuracy. The model was benchmarked with both a 20% held-out subset of the original training data and 22 experimentally synthesized polymers. A mean absolute error for the glass transition temperatures of 19.8 and 26.4 °C was achieved for the test and experimental data sets, respectively. Predictions were made on polymers composed of monomers from four databases that contain biologically accessible small molecules: MetaCyc, MINEs, KEGG, and BiGG. From 1.4 × 10
    Language English
    Publishing date 2023-10-19
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3436-8
    ISSN 0024-9297
    ISSN 0024-9297
    DOI 10.1021/acs.macromol.3c00994
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