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  1. Article ; Online: Celebrating the Next Generation of Women in Computational Chemistry to Increase Diversity, Equity, Inclusion, and Respect.

    Palermo, Giulia

    Journal of chemical information and modeling

    2022  Volume 62, Issue 17, Page(s) 4292–4293

    Language English
    Publishing date 2022-08-24
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.2c01038
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  2. Article ; Online: Celebrating Women of Color in Computational Chemistry.

    Palermo, Giulia

    Journal of chemical information and modeling

    2022  Volume 62, Issue 13, Page(s) 3133–3134

    MeSH term(s) Chemistry ; Computational Chemistry ; Female ; Humans ; Skin Pigmentation
    Language English
    Publishing date 2022-07-27
    Publishing country United States
    Document type Editorial ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.2c00663
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Book ; Online: Multiscale Modeling from Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations

    Tozzini, Valentina / Palermo, Giulia / Dal Peraro, Matteo / Bonvin, Alexandre M. J. J. / Amaro, Rommie E.

    2020  

    Keywords Science: general issues ; multiscale modeling ; molecular dynamics simulations ; advanced sampling methods ; coarse grained models ; macro-biomolecules ; molecular crowding ; system biology ; bioinformatics
    Size 1 electronic resource (235 pages)
    Publisher Frontiers Media SA
    Document type Book ; Online
    Note English ; Open Access
    HBZ-ID HT021230908
    ISBN 9782889661091 ; 2889661091
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  4. Article ; Online: Editorial: Editing DNA and RNA through Computations.

    Palermo, Giulia / Soares, Thereza A

    Journal of chemical information and modeling

    2023  Volume 63, Issue 24, Page(s) 7603–7604

    MeSH term(s) RNA ; DNA/genetics
    Chemical Substances RNA (63231-63-0) ; DNA (9007-49-2)
    Language English
    Publishing date 2023-12-22
    Publishing country United States
    Document type Editorial
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.3c01824
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Structure and Dynamics of the CRISPR-Cas9 Catalytic Complex.

    Palermo, Giulia

    Journal of chemical information and modeling

    2019  Volume 59, Issue 5, Page(s) 2394–2406

    Abstract: CRISPR-Cas9 is a bacterial immune system with exciting applications for genome editing. In spite of extensive experimental characterization, the active site chemistry of the RuvC domain-which performs DNA cleavages-has remained elusive. Its knowledge is ... ...

    Abstract CRISPR-Cas9 is a bacterial immune system with exciting applications for genome editing. In spite of extensive experimental characterization, the active site chemistry of the RuvC domain-which performs DNA cleavages-has remained elusive. Its knowledge is key for structure-based engineering aimed at improving DNA cleavages. Here, we deliver an in-depth characterization by using quantum-classical (QM/MM) molecular dynamics (MD) simulations and a Gaussian accelerated MD method, coupled with bioinformatics analysis. We disclose a two-metal aided architecture in the RuvC active site, which is poised to operate DNA cleavages, in analogy with other DNA/RNA processing enzymes. The conformational dynamics of the RuvC domain further reveals that an "arginine finger" stably contacts the scissile phosphate, with the function of stabilizing the active complex. Remarkably, the formation of a catalytically competent state of the RuvC domain is only observed upon the conformational activation of the other nuclease domain of CRISPR-Cas9-i.e., the HNH domain-such allowing concerted cleavages of double stranded DNA. This structure is in agreement with the available experimental data and remarkably differs from previous models based on classical mechanics, demonstrating also that only quantum mechanical simulations can accurately describe the metal-aided active site in CRISPR-Cas9. This fully catalytic structure-in which both the HNH and RuvC domains are prone to perform DNA cleavages-constitutes a stepping-stone for understanding DNA cleavage and specificity. It calls for novel experimental verifications and offers the structural foundations for engineering efforts aimed at improving the genome editing capability of CRISPR-Cas9.
    MeSH term(s) Biocatalysis ; CRISPR-Cas Systems ; Gene Editing ; Molecular Dynamics Simulation ; Protein Domains ; Quantum Theory
    Language English
    Publishing date 2019-02-27
    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.8b00988
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: The Electronic Structure of Genome Editors from the First Principles.

    Nierzwicki, Łukasz / Ahsan, Mohd / Palermo, Giulia

    Electronic structure (Bristol, England)

    2023  Volume 5, Issue 1

    Abstract: Genome editing based on the CRISPR-Cas9 system has paved new avenues for medicine, pharmaceutics, biotechnology, and beyond. This article reports the role of first-principles (ab-initio) molecular dynamics (MD) in the CRISPR-Cas9 revolution, achieving a ... ...

    Abstract Genome editing based on the CRISPR-Cas9 system has paved new avenues for medicine, pharmaceutics, biotechnology, and beyond. This article reports the role of first-principles (ab-initio) molecular dynamics (MD) in the CRISPR-Cas9 revolution, achieving a profound understanding of the enzymatic function and offering valuable insights for enzyme engineering. We introduce the methodologies and explain the use of ab-initio MD simulations to characterize the two-metal dependent mechanism of DNA cleavage in the RuvC domain of the Cas9 enzyme, and how a second catalytic domain, HNH, cleaves the target DNA with the aid of a single metal ion. A detailed description of how ab-initio MD is combined with free-energy methods - i.e., thermodynamic integration and metadynamics - to break and form chemical bonds is given, explaining the use of these methods to determine the chemical landscape and establish the catalytic mechanism in CRISPR-Cas9. The critical role of classical methods is also discussed, explaining theory and application of constant pH MD simulations, used to accurately predict the catalytic residues' protonation states. Overall, first-principles methods are shown to unravel the electronic structure of the Cas9 enzyme, providing valuable insights that can serve for the design of genome editing tools with improved catalytic efficiency or controllable activity.
    Language English
    Publishing date 2023-02-01
    Publishing country England
    Document type Journal Article
    ISSN 2516-1075
    ISSN (online) 2516-1075
    DOI 10.1088/2516-1075/acb410
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Establishing the fundamental rules for genetic code expansion.

    Sinha, Souvik / Ahsan, Mohd / Palermo, Giulia

    Nature chemistry

    2023  Volume 15, Issue 7, Page(s) 892–893

    MeSH term(s) Genetic Code ; Amino Acids/genetics
    Chemical Substances Amino Acids
    Language English
    Publishing date 2023-06-30
    Publishing country England
    Document type Journal Article ; Comment
    ZDB-ID 2464596-5
    ISSN 1755-4349 ; 1755-4330
    ISSN (online) 1755-4349
    ISSN 1755-4330
    DOI 10.1038/s41557-023-01243-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Corrigendum: Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules.

    Nierzwicki, Łukasz / Palermo, Giulia

    Frontiers in molecular biosciences

    2021  Volume 8, Page(s) 698735

    Language English
    Publishing date 2021-05-28
    Publishing country Switzerland
    Document type Journal Article ; Published Erratum
    ZDB-ID 2814330-9
    ISSN 2296-889X
    ISSN 2296-889X
    DOI 10.3389/fmolb.2021.698735
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules.

    Nierzwicki, Łukasz / Palermo, Giulia

    Frontiers in molecular biosciences

    2021  Volume 8, Page(s) 641208

    Abstract: Single-particle cryogenic electron microscopy (cryo-EM) has revolutionized the field of the structural biology, providing an access to the atomic resolution structures of large biomolecular complexes in their near-native environment. Today's cryo-EM maps ...

    Abstract Single-particle cryogenic electron microscopy (cryo-EM) has revolutionized the field of the structural biology, providing an access to the atomic resolution structures of large biomolecular complexes in their near-native environment. Today's cryo-EM maps can frequently reach the atomic-level resolution, while often containing a range of resolutions, with conformationally variable regions obtained at 6 Å or worse. Low resolution density maps obtained for protein flexible domains, as well as the ensemble of coexisting conformational states arising from cryo-EM, poses new challenges and opportunities for Molecular Dynamics (MD) simulations. With the ability to describe the biomolecular dynamics at the atomic level, MD can extend the capabilities of cryo-EM, capturing the conformational variability and predicting biologically relevant short-lived conformational states. Here, we report about the state-of-the-art MD procedures that are currently used to refine, reconstruct and interpret cryo-EM maps. We show the capability of MD to predict short-lived conformational states, finding remarkable confirmation by cryo-EM structures subsequently solved. This has been the case of the CRISPR-Cas9 genome editing machinery, whose catalytically active structure has been predicted through both long-time scale MD and enhanced sampling techniques 2 years earlier than cryo-EM. In summary, this contribution remarks the ability of MD to complement cryo-EM, describing conformational landscapes and relating structural transitions to function, ultimately discerning relevant short-lived conformational states and providing mechanistic knowledge of biological function.
    Language English
    Publishing date 2021-04-05
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2814330-9
    ISSN 2296-889X
    ISSN 2296-889X
    DOI 10.3389/fmolb.2021.641208
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Newly scheduled carbamate compounds: A synopsis of their properties and development, and considerations for the scientific community.

    Palermo, Giulia / Kovarik, Zrinka / Hotchkiss, Peter J

    Toxicology

    2022  Volume 480, Page(s) 153322

    Abstract: In November 2019, for the first time in the history of the Chemical Weapons Convention, changes were made to Schedule 1 of the Annex on Chemicals. While there is little in the scientific literature regarding any of these newly scheduled chemicals, the ... ...

    Abstract In November 2019, for the first time in the history of the Chemical Weapons Convention, changes were made to Schedule 1 of the Annex on Chemicals. While there is little in the scientific literature regarding any of these newly scheduled chemicals, the carbamates, specifically, prove to be substantially different, both in terms of their chemical composition and their toxicological effects, from all the other scheduled nerve agents and have yet to be fully reported on in the literature. Herein, we present a literature review of the available information on carbamates included in Schedule 1, as well as analogous other carbamates, and provide a summary of their utility and function as cholinesterase inhibitors in general and their toxicities. Though there is a paucity of studies in the literature related to the detection of these newly scheduled quaternary and bisquaternary carbamates and/or their biomarkers, information available on carbamate pesticides may be a solid starting point to further postulate amenable detection methodologies. Lastly, we note some implications of these newly scheduled carbamates for the nonproliferation and disarmament community.
    MeSH term(s) Carbamates/toxicity ; Cholinesterase Inhibitors/toxicity ; Nerve Agents ; Pesticides/toxicity
    Chemical Substances Carbamates ; Cholinesterase Inhibitors ; Nerve Agents ; Pesticides
    Language English
    Publishing date 2022-09-14
    Publishing country Ireland
    Document type Journal Article ; Review
    ZDB-ID 184557-3
    ISSN 1879-3185 ; 0300-483X
    ISSN (online) 1879-3185
    ISSN 0300-483X
    DOI 10.1016/j.tox.2022.153322
    Database MEDical Literature Analysis and Retrieval System OnLINE

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