Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

Keywords

Equipment

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Role of the gates and anchoring residues in enzymes activity and selectivity.

2013/10/E/NZ1/00649

Keywords:

enzyme redesign gating residues anchoring residues selectivity smart library tunnels transport

Descriptors:

  • NZ1_4: Structural biology
  • NZ1_1: Molecular biology
  • NZ1_9: Biotechnology

Panel:

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

Host institution :

Politechnika Śląska, Centrum Biotechnologii

woj. śląskie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr Artur Góra 

Number of co-investigators in the project: 11

Call: SONATA BIS 3 - announced on 2013-06-14

Amount awarded: 1 482 500 PLN

Project start date (Y-m-d): 2014-07-16

Project end date (Y-m-d): 2019-12-15

Project duration:: 65 months (the same as in the proposal)

Project status: Project settled

Equipment purchased [PL]

  1. Stacje robocze oparte o karty graficzne do obliczeń dynamiki molekularnej (100 000 PLN)
  2. Drukarka (3 000 PLN)
  3. Lokalna stacja robocza.
  4. Lokalna stacja robocza (42 000 PLN)

Information in the final report

  • Publication in academic press/journals (10)
  • Articles in post-conference publications (18)
  1. AQUA-DUCT: Analysis of Molecular Dynamics Simulations of Macromolecules with the use of Molecular Probes [Article v1. 0]
    Authors:
    K Mitusińska, A Raczyńska, P Wojsa, M Bzówka, A Góra
    Academic press:
    Living Journal of Computational Molecular Science (rok: 2021, tom: 2, strony: 21383), Wydawca: University of Colorado Boulder
    Status:
    Published
    DOI:
    10.33011/livecoms.2.1.21383 - link to the publication
  2. BALCONY: an R package for MSA and functional compartments of protein variability analysis
    Authors:
    Alicja Płuciennik, Michał Stolarczyk, Maria Bzówka, Agata Raczyńska, Tomasz Magdziarz and Artur Góra
    Academic press:
    BMC Bioinformatics (rok: 2018, tom: 19, strony: 300-308), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1186/s12859-018-2294-z - link to the publication
  3. Modulating D-amino acid oxidase (DAAO) substrate specificity through facilitated solvent access
    Authors:
    Kalyanasundaram Subramanian, Artur Góra, Ruud Spruijt, Karolina Mitusińska, Maria Suarez-Diez, Vitor Martins dos Santos, Peter J. Schaap
    Academic press:
    PLoS One (rok: 2018, tom: 13(6), strony: e0198990), Wydawca: PLoS
    Status:
    Published
    DOI:
    10.1371/journal.pone.0198990 - link to the publication
  4. Applications of water molecules for analysis of macromolecule properties
    Authors:
    Karolina Mitusińska, Agata Raczyńska, Maria Bzówka, Weronika Bagrowska, Artur Góra
    Academic press:
    Computational and Structural Biotechnology Journal (rok: 2020, tom: 18, strony: 355-365), Wydawca: Elsevier B.V.
    Status:
    Published
    DOI:
    10.1016/j.csbj.2020.02.001 - link to the publication
  5. Computational insights into the known inhibitors of human soluble epoxide hydrolase
    Authors:
    Maria Bzówka, Karolina Mitusińska, Katarzyna Hopko, Artur Góra
    Academic press:
    Drug Discovery Today (rok: 2021, tom: XX, strony: XXX), Wydawca: Elsevier
    Status:
    Accepted for publication
    DOI:
    10.1016/j.drudis.2021.05.017 - link to the publication
  6. Distant Non-Obvious Mutations Influence the Activity of a Hyperthermophilic Pyrococcus furiosus Phosphoglucose Isomerase
    Authors:
    Subramanian, K.; Mitusińska, K.; Raedts, J.; Almourfi, F.; Joosten, H.-J.; Hendriks, S.; Sedelnikova, S. E.; Kengen, S. W. M.; Hagen, W. R.; Góra, A.; Martins dos Santos, V. A. P.; Baker, P. J.; van der Oost, J.; Schaap, P. J.
    Academic press:
    Biomolecules (rok: 2019, tom: 9(6), strony: 212), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/biom9060212 - link to the publication
  7. Exploring Solanum tuberosum Epoxide Hydrolase Internal Architecture by Water Molecules Tracking
    Authors:
    Karolina Mitusińska, Tomasz Magdziarz, Maria Bzówka, Agnieszka Stańczak and Artur Góra
    Academic press:
    Biomolecules (rok: 2018, tom: 8, strony: 143), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/biom8040143 - link to the publication
  8. AQUA-DUCT a ligands tracking tool
    Authors:
    Tomasz Magdziarz, Karolina Mitusińska, Sandra Gołdowska, Alicja Płuciennik, Michał Stolarczyk, Magdalena Ługowska, Artur Góra
    Academic press:
    Bioinformatics (rok: 2017, tom: 33, strony: 2045–2046), Wydawca: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btx125 - link to the publication
  9. Structural and Evolutionary Analysis Indicate That the SARS-CoV-2 Mpro Is a Challenging Target for Small-Molecule Inhibitor Design
    Authors:
    Maria Bzówka, Karolina Mitusińska, Agata Raczyńska, Aleksandra Samol, Jack A. Tuszyński, Artur Góra
    Academic press:
    International Journal of Molecular Sciences (rok: 2020, tom: 21(9), strony: 3099-3116), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms21093099 - link to the publication
  10. AQUA-DUCT 1.0: structural and functional analysis of macromolecules from an intramolecular voids perspective
    Authors:
    Magdziarz, T.; Mitusińska, K.; Bzówka, M.; Raczyńska, A.; Stańczak, A.; Banas, M.; Bagrowska, W.; Góra, A.
    Academic press:
    Bioinformatics (rok: 2020, tom: 36(8), strony: 2599–2601), Wydawca: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btz946 - link to the publication
  1. Evolution of functionally important compartments of proteins – what can we learn from studying epoxide hydrolases?
    Authors:
    M. Bzówka , T. Magdziarz, K. Mitusinska, A. Stanczak, A. Raczynska, A. Góra
    Conference:
    18th European Congress on Biotechnology (rok: 2018, ), Wydawca: Elsevier - New Biotechnology
    Data:
    konferencja 1-4 lipiec
    Status:
    Published
  2. Influence of the missing loop refinement for substrate access to the active site in Aspergillus Niger epoxide hydrolase
    Authors:
    Karolina Markowska, Artur Góra
    Conference:
    XIXth Gliwice Scientific Meetings 2015 (rok: 2015, ), Wydawca: Association for the Support of Cancer Research
    Data:
    konferencja 20-21.11
    Status:
    Published
  3. PROTEIN HOT SPOTS IDENTIFICATION CAN WE REPLACE LONG SIMULATIONS BY SERIES OF SHORT RUNS?
    Authors:
    Aleksandra Samol, Karolina Mitusińsla, Maria Bzówka, Tomasz Magdziarz, Artur Góra
    Conference:
    XXII nd Gliwice Scientific Meetings 2018 (rok: 2018, ), Wydawca: Association for the Support of Cancer Research
    Data:
    konferencja 16-17.11
    Status:
    Published
  4. VALIDATION OF THE USABILITY OF VARIOUS CLUSTERIZATIO N AND TRIMMING METHODS FOR OBJECTS DISPERSED SPHERICALLY IN THREE DIMENSIONAL SPACE – EXTENSIVE ANALYSIS OF WATER FLOW THROUGH PROTEIN CORE
    Authors:
    Agata Raczyńska, Tomasz Magdziarz, Karolina Mitusińska, Artur Góra
    Conference:
    XXI st Gliwice Scientific Meetings 2017 (rok: 2017, ), Wydawca: Association for the Support of Cancer Research
    Data:
    konferencja 17-18.11
    Status:
    Published
  5. AQUADUCT - a water tracking tool
    Authors:
    Tomasz Magdziarz, Karolina Markowska, Artur Góra
    Conference:
    EMBO conference The biochemistry and chemistry of biocatalysis: From understanding to design (rok: 2016, ), Wydawca: EMBOpress
    Data:
    konferencja 12-15.06
    Status:
    Published
  6. PANTA RHEI: analysis of solvent flow in MD simulations
    Authors:
    Tomasz Magdziarz, Karolina Markowska, Sandra Gołdowska, Artur Góra
    Conference:
    BIT16 (rok: 2016, ), Wydawca: Uniwersytet Mikołaja Kopernika W Toruniu.
    Data:
    konferencja 16-18.06
    Status:
    Published
  7. MODIFICATION OF THE HUMAN SOLUBLE EPOXIDE HYDROLASE ACTIVE SITE ACCESSIBILITY BY ENGINEERING OF ITS ENTRANCE TUNNEL
    Authors:
    Sandra GOŁDOWSKA, Karolina MARKOWSKA, Alicja PŁUCIENNIK, Artur GÓRA
    Conference:
    8th Central European Conference Chemistry towards Biology (rok: 2016, ), Wydawca: University of Veterinary and Pharmaceutical Sciences Brno, Czech Republic, ISBN 978-80-7305-777-0
    Data:
    konferencja 28.08-1.09
    Status:
    Published
  8. THE OPENING AND CLOSING MOVEMENTS OF LOOP REGULATING THE ACCESS TO THE ACTIVE SITE
    Authors:
    Karolina Mitusińska , Tomasz Magdziarz, Artur Góra
    Conference:
    XXI st Gliwice Scientific Meetings 2017 (rok: 2017, ), Wydawca: Association for the Support of Cancer Research
    Data:
    konferencja 17-18.11
    Status:
    Published
  9. The evolutionary glance at tunnels in proteins
    Authors:
    Alicja Płuciennik, Michał Stolarczyk, Sandra Gołdowska, Magdalena Ługowska, Tomasz Magdziarz, Artur Góra
    Conference:
    BIT16 (rok: 2016, ), Wydawca: Uniwersytet Mikołaja Kopernika W Toruniu.
    Data:
    konferencja 16-18.06
    Status:
    Published
  10. Identification of gates in humane soluble epoxide hydrolase
    Authors:
    Sandra Gołdowska, Karolina Markowska, Artur Góra
    Conference:
    XIXth Gliwice Scientific Meetings 2015 (rok: 2015, ), Wydawca: Association for the Support of Cancer Research
    Data:
    konferencja 20-21.11
    Status:
    Published
  11. Modification of the accessibility of the human soluble epoxide hydrolase active site, in silico study
    Authors:
    Sandra Gołdowska, Karolina Markowska, Alicja Płuciennik, Artur Góra
    Conference:
    BIT16 (rok: 2016, ), Wydawca: Uniwersytet Mikołaja Kopernika W Toruniu.
    Data:
    konferencja 16-18.06
    Status:
    Published
    DOI:
    link to the publication
  12. THE IMPORTANCE OF LIGANDS PRESENCE IN ENZYME CRYSTAL STRUCTURES FOR MOLECULAR DYNAMICS STUDY
    Authors:
    Weronika Bagrowska, Karolina Mitusińska, Tomasz Magdziarz, Artur Góra
    Conference:
    XXII nd Gliwice Scientific Meetings 2018 (rok: 2018, ), Wydawca: Association for the Support of Cancer Research
    Data:
    konferencja 16-17.11
    Status:
    Published
  13. Water tracing as an alternative method for tunnels exploration in macromolecules
    Authors:
    A. Raczynska, T. Magdziarz, K. Mitusinska, A. Góra
    Conference:
    18th European Congress On Biotechnology (rok: 2018, ), Wydawca: Elsevier - New Biotechnology
    Data:
    konferencja 1-4 lipca
    Status:
    Published
  14. BALCONY - Better Alignment Consensus Analysis
    Authors:
    Alicja Płuciennik, Michał Stolarczyk, Tomasz Magdziarz, Artur Góra
    Conference:
    XIXth Gliwice Scientific Meetings 2015 (rok: 2015, ), Wydawca: Association for the Support of Cancer Research
    Data:
    konferencja 20-21.11
    Status:
    Published
  15. Finding of proteins 'breathing motions' through the analysis of water flow
    Authors:
    Maria Bzówka, Karolina Mitusińska, Tomasz Magdziarz, Artur Góra
    Conference:
    Artificial Water Channels: Faraday Discussion (rok: 2018, ), Wydawca: RSC
    Data:
    konferencja 25-27.06
    Status:
    Published
  16. How does the missing loop refillment influence on the substrate access to the catalytic pocket in Aspergillus Niger epoxide hydrolase?
    Authors:
    Mariusz Wiecha, Karolina Markowska, Artur Góra
    Conference:
    XIXth Gliwice Scientific Meetings 2015 (rok: 2015, ), Wydawca: Association for the Support of Cancer Research
    Data:
    konferencja 20-21.11
    Status:
    Published
  17. Influence of binding pocket reshaping on the access to the active site in Limonene-1,2-epoxide hydrolase from Rhodococcus Erythropolis
    Authors:
    Magdalena Ługowska, Karolina Markowska, Artur Góra
    Conference:
    XIXth Gliwice Scientific Meetings 2015 (rok: 2015, ), Wydawca: Association for the Support of Cancer Research
    Data:
    konferencja 20-21.11
    Status:
    Published
  18. SEARCHING FOR THE ALPHA-1,6-FUCOSYLOTRANSFERASE INHIBITORS
    Authors:
    Weronika Bagrowska, Katarzyna Hopko, Karolina Mitusińska, Radosław Kitel, Anna Kasprzycka, Artur Góra
    Conference:
    XXIII rd Gliwice Scientific Meetings 2019 (rok: 2019, ), Wydawca: Association for the Support of Cancer Research
    Data:
    konferencja 22-23.11
    Status:
    Published

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