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Molecular origins of mechanisms governing biological functions of enzymes with buried actives sites: substrate inhibition, cooperativity, and interference between transport of substrates and products.

2017/26/E/NZ1/00548

Keywords

Descriptors

  • NZ1_3: Biofizyka
  • NZ1_4: Biologia strukturalna
  • NZ2_7: Bioinformatyka

Panel

NZ1 – Molecular biology, structural biology, biotechnology: molecular biology, structural biology, biotechnology

Host institution

Uniwersytet im. Adama Mickiewicza w Poznaniu, Wydział Biologii

Voivodeship: wielkopolskie

Other projects carried out by the institution »

Principal investigator (from the host institution)

dr hab. Jan Brezovsky

Number of co-investigators in the project: 6

Call

SONATA BIS 7 – announced on 2017-06-14

Amount awarded
2 326 000 PLN
Project start date
2018-07-23
Project end date
2025-07-22
Project duration
84 months (the same as in the proposal)
Project status
Project settled

Project description

Download the project description in a pdf file

Note — project descriptions were prepared by the authors of the applications themselves and placed in the system in an unchanged form.

Information in the final report

Publication in academic press/journals (8)

  1. Impact of water models on the structure and dynamics of enzyme tunnels

    Authors:
    Sethi A, Agrawal N, Brezovsky J
    Academic press:
    Computational and Structural Biotechnology Journal (year: 2024, volume: 23, pages: 3946-3954), Publisher: ELSEVIER
    Status:
    Published
    DOI:
    10.1016/j.csbj.2024.10.051 – link to the publication

  2. Water migration through enzyme tunnels is sensitive to choice of explicit water model

    Authors:
    Thirunavukarasu AS, Szleper K, Tanriver G, Marchlewski I, Mitusinska K, Gora A, Brezovsky J
    Academic press:
    Journal of Chemical Information and Modeling (year: 2025, volume: 65, pages: 326–337), Publisher: AMERICAN CHEMICAL SOCIETY
    Status:
    Published
    DOI:
    10.1021/acs.jcim.4c01177 – link to the publication

  3. Dynamics, a Powerful Component of Current and Future in Silico Approaches for Protein Design and Engineering

    Authors:
    Surpeta B, Sequeiros-Borja CE, Brezovsky J
    Academic press:
    International Journal of Molecular Sciences (year: 2020, volume: 21(8), pages: 2713), Publisher: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms21082713 – link to the publication

  4. TransportTools: a library for high-throughput analyses of internal voids in biomolecules and ligand transport through them

    Authors:
    Brezovsky J, Thirunavukarasu AS, Surpeta B, Sequeiros-Borja CE, Mandal N, Sarkar DK, Dongmo Foumthuim CJ, Agrawal N
    Academic press:
    Bioinformatics (year: 2022, volume: 38, pages: 1752-1753), Publisher: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btab872 – link to the publication

  5. Recent advances in user-friendly computational tools to engineer protein function

    Authors:
    Sequeiros-Borja CE, Surpeta B, Brezovsky J
    Academic press:
    Briefings in Bioinformatics (year: 2020, volume: brak, pages: brak), Publisher: OXFORD UNIV PRESS
    Status:
    Published
    DOI:
    10.1093/bib/bbaa150 – link to the publication

  6. Water will find its way: transport through narrow tunnels in hydrolases

    Authors:
    Sequeiros-Borja C, Bartlomiej Surpeta, Thirunavukarasu AS, Dongmo Foumthuim CJ, Marchlewski I, Brezovsky J
    Academic press:
    Journal of Chemical Information and Modeling (year: 2024, volume: 64, pages: 6014-6025), Publisher: AMERICAN CHEMICAL SOCIETY
    Status:
    Published
    DOI:
    10.1021/acs.jcim.4c00094 – link to the publication

  7. Reinforcing Tunnel Network Exploration in Proteins using Gaussian Accelerated Molecular Dynamics

    Authors:
    Mandal N, Surpeta B, Brezovsky J
    Academic press:
    Journal of Chemical Information and Modeling (year: 2024, volume: 64, pages: 6623-6635), Publisher: AMERICAN CHEMICAL SOCIETY
    Status:
    Published
    DOI:
    10.1021/acs.jcim.4c00966 – link to the publication

  8. Incorporating prior knowledge in the seeds of adaptive sampling molecular dynamics simulations of ligand transport in enzymes with buried active sites

    Authors:
    Sarkar DK, Surpeta B, Brezovsky J
    Academic press:
    Journal of Chemical Theory and Computation (year: 2024, volume: 20, pages: 5807-5819), Publisher: AMERICAN CHEMICAL SOCIETY
    Status:
    Published
    DOI:
    10.1021/acs.jctc.4c00452 – link to the publication

Articles in post-conference publications (2)

  1. Deciphering rare opening of gates in ligandtransport tunnels of enzymes using enhanced molecular dynamics simulations

    Authors:
    Mandal N, Surpeta B, Brezovsky J
    Conference:
    The Biochemistry Global Summit 25th IUBMB Congress, 46th FEBS Congress, 15th PABMB Congress (year: 2022, pages: 249), Publisher: FEBS Press
    Date:
    conference 9–14 Lipiec 2022r.
    Status:
    Published

  2. Analysis of substrate exchange between bulk solvent and buried enzyme active site via multiple molecular tunnels using high-throughput simulations

    Authors:
    Sarkar DK, Brezovsky J
    Conference:
    45th FEBS Congress, Molecules of Life: Towards New Horizons (year: 2021, pages: 353), Publisher: FEBS Press
    Date:
    conference 3-8 Lipiec
    Status:
    Published

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