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  1. Article ; Online: Reliable

    Crean, Rory M / Pudney, Christopher R / Cole, David K / van der Kamp, Marc W

    Journal of chemical information and modeling

    2022  Volume 62, Issue 3, Page(s) 577–590

    Abstract: Accurate and ... ...

    Abstract Accurate and efficient
    MeSH term(s) Entropy ; Humans ; Ligands ; Molecular Dynamics Simulation ; Protein Binding ; Proteins/chemistry
    Chemical Substances Ligands ; Proteins
    Language English
    Publishing date 2022-01-20
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.1c00765
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1230: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  2. Article: Active Site Loop Engineering Abolishes Water Capture in Hydroxylating Sesquiterpene Synthases.

    Srivastava, Prabhakar L / Johns, Sam T / Walters, Rebecca / Miller, David J / Van der Kamp, Marc W / Allemann, Rudolf K

    ACS catalysis

    2023  Volume 13, Issue 21, Page(s) 14199–14204

    Abstract: Terpene synthases (TS) catalyze complex reactions to produce a diverse array of terpene skeletons from linear isoprenyl diphosphates. Patchoulol synthase (PTS) ... ...

    Abstract Terpene synthases (TS) catalyze complex reactions to produce a diverse array of terpene skeletons from linear isoprenyl diphosphates. Patchoulol synthase (PTS) from
    Language English
    Publishing date 2023-10-20
    Publishing country United States
    Document type Journal Article
    ISSN 2155-5435
    ISSN 2155-5435
    DOI 10.1021/acscatal.3c03920
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Path to Actinorhodin: Regio- and Stereoselective Ketone Reduction by a Type II Polyketide Ketoreductase Revealed in Atomistic Detail.

    Serapian, Stefano A / Crosby, John / Crump, Matthew P / van der Kamp, Marc W

    JACS Au

    2022  Volume 2, Issue 4, Page(s) 972–984

    Abstract: In type II polyketide synthases (PKSs), which typically biosynthesize several antibiotic and antitumor compounds, the substrate is a growing polyketide chain, shuttled between individual PKS enzymes, while covalently tethered to an acyl carrier protein ( ... ...

    Abstract In type II polyketide synthases (PKSs), which typically biosynthesize several antibiotic and antitumor compounds, the substrate is a growing polyketide chain, shuttled between individual PKS enzymes, while covalently tethered to an acyl carrier protein (ACP): this requires the ACP interacting with a series of different enzymes in succession. During biosynthesis of the antibiotic actinorhodin, produced by
    Language English
    Publishing date 2022-04-07
    Publishing country United States
    Document type Journal Article
    ISSN 2691-3704
    ISSN (online) 2691-3704
    DOI 10.1021/jacsau.2c00086
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Antimicrobial Resistance Conferred by OXA-48 β-Lactamases: Towards a Detailed Mechanistic Understanding.

    Hirvonen, Viivi H A / Spencer, James / van der Kamp, Marc W

    Antimicrobial agents and chemotherapy

    2021  Volume 65, Issue 6

    Abstract: OXA-48-type β-lactamases are now routinely encountered in bacterial infections caused by carbapenem- ... ...

    Abstract OXA-48-type β-lactamases are now routinely encountered in bacterial infections caused by carbapenem-resistant
    MeSH term(s) Anti-Bacterial Agents/pharmacology ; Cephalosporins ; Drug Resistance, Bacterial ; beta-Lactamase Inhibitors/pharmacology ; beta-Lactamases/genetics
    Chemical Substances Anti-Bacterial Agents ; Cephalosporins ; beta-Lactamase Inhibitors ; beta-Lactamases (EC 3.5.2.6)
    Language English
    Publishing date 2021-05-18
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 217602-6
    ISSN 1098-6596 ; 0066-4804
    ISSN (online) 1098-6596
    ISSN 0066-4804
    DOI 10.1128/AAC.00184-21
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 809: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)
    Einzelsignatur: Show issues

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  5. Article ; Online: Correction to "Loop Dynamics and Enzyme Catalysis in Protein Tyrosine Phosphatases".

    Crean, Rory M / Biler, Michal / Corbella, Marina / Calixto, Ana R / van der Kamp, Marc W / Hengge, Alvan C / Kamerlin, Shina C L

    Journal of the American Chemical Society

    2022  Volume 144, Issue 22, Page(s) 10091–10093

    Language English
    Publishing date 2022-05-24
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.2c04624
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Bonn / Germany

    Z 4' 55/32: Show issues
    Z 7.3: Show issues

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  6. Article ; Online: Enlighten2: molecular dynamics simulations of protein-ligand systems made accessible.

    Zinovjev, Kirill / van der Kamp, Marc W

    Bioinformatics (Oxford, England)

    2020  Volume 36, Issue 20, Page(s) 5104–5106

    Abstract: Motivation: Experimental structural data can allow detailed insight into protein structure and protein-ligand interactions, which is crucial for many areas of bioscience, including drug design and enzyme engineering. Typically, however, little more than ...

    Abstract Motivation: Experimental structural data can allow detailed insight into protein structure and protein-ligand interactions, which is crucial for many areas of bioscience, including drug design and enzyme engineering. Typically, however, little more than a static picture of protein-ligand interactions is obtained, whereas dynamical information is often required for deeper understanding and to assess the effect of mutations. Molecular dynamics (MD) simulations can provide such information, but setting up and running these simulations is not straightforward and requires expert knowledge. There is thus a need for a tool that makes protein-ligand simulation easily accessible to non-expert users.
    Results: We present Enlighten2: efficient simulation protocols for protein-ligand systems alongside a user-friendly plugin to the popular visualization program PyMOL. With Enlighten2, non-expert users can straightforwardly run and visualize MD simulations on protein-ligand models of interest. There is no need to learn new programs and all underlying tools are free and open source.
    Availability and implementation: The Enlighten2 Python package and PyMOL plugin are free to use under the GPL3.0 licence and can be found at https://enlighten2.github.io. We also provide a lightweight Docker image via DockerHub that includes Enlighten2 with all the required utilities.
    MeSH term(s) Drug Design ; Ligands ; Molecular Dynamics Simulation ; Proteins ; Software
    Chemical Substances Ligands ; Proteins
    Language English
    Publishing date 2020-07-16
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btaa643
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2374: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  7. Article: Cooperative Conformational Transitions Underpin the Activation Heat Capacity in the Temperature Dependence of Enzyme Catalysis.

    Walker, Emma J / Hamill, Carlin J / Crean, Rory / Connolly, Michael S / Warrender, Annmaree K / Kraakman, Kirsty L / Prentice, Erica J / Steyn-Ross, Alistair / Steyn-Ross, Moira / Pudney, Christopher R / van der Kamp, Marc W / Schipper, Louis A / Mulholland, Adrian J / Arcus, Vickery L

    ACS catalysis

    2024  Volume 14, Issue 7, Page(s) 4379–4394

    Abstract: Many enzymes display non-Arrhenius behavior with curved Arrhenius plots in the absence of denaturation. There has been significant debate about the origin of this behavior and recently the role of the activation heat capacity ( ... ...

    Abstract Many enzymes display non-Arrhenius behavior with curved Arrhenius plots in the absence of denaturation. There has been significant debate about the origin of this behavior and recently the role of the activation heat capacity (Δ
    Language English
    Publishing date 2024-03-08
    Publishing country United States
    Document type Journal Article
    ISSN 2155-5435
    ISSN 2155-5435
    DOI 10.1021/acscatal.3c05584
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Free energy along drug-protein binding pathways interactively sampled in virtual reality.

    Deeks, Helen M / Zinovjev, Kirill / Barnoud, Jonathan / Mulholland, Adrian J / van der Kamp, Marc W / Glowacki, David R

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 16665

    Abstract: We describe a two-step approach for combining interactive molecular dynamics in virtual reality (iMD-VR) with free energy (FE) calculation to explore the dynamics of biological processes at the molecular level. We refer to this combined approach as iMD- ... ...

    Abstract We describe a two-step approach for combining interactive molecular dynamics in virtual reality (iMD-VR) with free energy (FE) calculation to explore the dynamics of biological processes at the molecular level. We refer to this combined approach as iMD-VR-FE. Stage one involves using a state-of-the-art 'human-in-the-loop' iMD-VR framework to generate a diverse range of protein-ligand unbinding pathways, benefitting from the sophistication of human spatial and chemical intuition. Stage two involves using the iMD-VR-sampled pathways as initial guesses for defining a path-based reaction coordinate from which we can obtain a corresponding free energy profile using FE methods. To investigate the performance of the method, we apply iMD-VR-FE to investigate the unbinding of a benzamidine ligand from a trypsin protein. The binding free energy calculated using iMD-VR-FE is similar for each pathway, indicating internal consistency. Moreover, the resulting free energy profiles can distinguish energetic differences between pathways corresponding to various protein-ligand conformations (e.g., helping to identify pathways that are more favourable) and enable identification of metastable states along the pathways. The two-step iMD-VR-FE approach offers an intuitive way for researchers to test hypotheses for candidate pathways in biomolecular systems, quickly obtaining both qualitative and quantitative insight.
    MeSH term(s) Humans ; Protein Binding ; Ligands ; Proteins ; Molecular Dynamics Simulation ; Virtual Reality
    Chemical Substances Ligands ; Proteins
    Language English
    Publishing date 2023-10-04
    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/s41598-023-43523-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Structurally Informed Mutagenesis of a Stereochemically Promiscuous Aldolase Produces Mutants That Catalyze the Diastereoselective Syntheses of All Four Stereoisomers of 3-Deoxy-hexulosonic Acid.

    Royer, Sylvain F / Gao, Xuan / Groleau, Robin R / van der Kamp, Marc W / Bull, Steven D / Danson, Michael J / Crennell, Susan J

    ACS catalysis

    2022  Volume 12, Issue 18, Page(s) 11444–11455

    Abstract: A 2-keto-3-deoxygluconate aldolase from the ... ...

    Abstract A 2-keto-3-deoxygluconate aldolase from the hyperthermophile
    Language English
    Publishing date 2022-09-06
    Publishing country United States
    Document type Journal Article
    ISSN 2155-5435
    ISSN 2155-5435
    DOI 10.1021/acscatal.2c03285
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Multiscale Simulations Identify Origins of Differential Carbapenem Hydrolysis by the OXA-48 β-Lactamase.

    Hirvonen, Viivi H A / Weizmann, Tal Moshe / Mulholland, Adrian J / Spencer, James / van der Kamp, Marc W

    ACS catalysis

    2022  Volume 12, Issue 8, Page(s) 4534–4544

    Abstract: OXA-48 β-lactamases are frequently encountered in bacterial infections caused by carbapenem-resistant Gram-negative bacteria. Due to the importance of carbapenems in the treatment of healthcare-associated infections and the increasingly wide ... ...

    Abstract OXA-48 β-lactamases are frequently encountered in bacterial infections caused by carbapenem-resistant Gram-negative bacteria. Due to the importance of carbapenems in the treatment of healthcare-associated infections and the increasingly wide dissemination of OXA-48-like enzymes on plasmids, these β-lactamases are of high clinical significance. Notably, OXA-48 hydrolyzes imipenem more efficiently than other commonly used carbapenems, such as meropenem. Here, we use extensive multiscale simulations of imipenem and meropenem hydrolysis by OXA-48 to dissect the dynamics and to explore differences in the reactivity of the possible conformational substates of the respective acylenzymes. Quantum mechanics/molecular mechanics (QM/MM) simulations of the deacylation reaction for both substrates demonstrate that deacylation is favored when the 6α-hydroxyethyl group is able to hydrogen bond to the water molecule responsible for deacylation but disfavored by the increasing hydration of either oxygen of the carboxylated Lys73 general base. Differences in free energy barriers calculated from the QM/MM simulations correlate well with the experimentally observed differences in hydrolytic efficiency between meropenem and imipenem. We conclude that the impaired breakdown of meropenem, compared to imipenem, which arises from a subtle change in the hydrogen bonding pattern between the deacylating water molecule and the antibiotic, is most likely induced by the meropenem 1β-methyl group. In addition to increased insights into carbapenem breakdown by OXA β-lactamases, which may aid in future efforts to design antibiotics or inhibitors, our approach exemplifies the combined use of atomistic simulations in determining the possible different enzyme-substrate substates and their influence on enzyme reaction kinetics.
    Language English
    Publishing date 2022-04-04
    Publishing country United States
    Document type Journal Article
    ISSN 2155-5435
    ISSN 2155-5435
    DOI 10.1021/acscatal.1c05694
    Database MEDical Literature Analysis and Retrieval System OnLINE

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