Role of metal ions in DNA recognition by proteins

Project funded by Fundação para a Ciência e a Tecnologia, I.P. (FCT) (FCT_CPCA_2020_01), grant CPCA/A2/4568/2020. Funded amount: EUR 1,507, as stated by the source. Runs 2021-01-01 to 2021-12-31. Keywords: Molecular Dynamics, Quantum Mechanics/Molecular Mechanics, Protein-DNA interactions, Allosteric Transcription Factors, Endonucleases, Engineering and technology. Source: OpenAIRE Graph, from the funder's project data (collected by OpenAIRE on 2026-07-23); national funding data, not CORDIS; selected because its keywords name quantum. Abstract given by the source: In this project, which is a follow-up of past and ongoing projects within our work group, we will study bacterial Transcription Factors (TFs) belonging to the GntR superfamily and develop new programmable TFs. Understanding the allosteric mechanism of TFs is essential for several medical and biochemical applications, given the importance of TFs in the regulation of the natural cell circuits and for the development of new ones. We will use computational chemistry as our main tool. To clarify: the role of Zn2+ ion binding to the effector domain, the mechanism of allosteric regulation in GntR repressors and activators that employ Zn2+ ion, and the conformational changes that affect DNA binding. After a detailed study of these specific TFs, it will be possible to characterize more accurately the metal-binding subfamily of GntR TFs and understand how the substrate specificity can be changed to design new synthetic programmable TFs through computational and experimental methods. Another important aspect that will be studied is the role of metal ions in the conformational changes that allow the DNA cleavage by different endonucleases. Our computational approaches include ion motif parameterization, Molecular Dynamic and Quantum Mechanic/Molecular Mechanic simulations. To complete our project, it is necessary to use a range of highly complex computational approaches with different needs. The software performance used is highly dependent on a constant high computational power.

Original source.

Source: OpenAIRE Graph: projects of national funders, OpenAIRE, from the project data of Fundação para a Ciência e a Tecnologia, I.P. (FCT). Retrieved 2026-10-28. Licence: Creative Commons Attribution 4.0 (OpenAIRE Graph). Selected metadata, adapted presentation; the publisher's record is authoritative. No endorsement by the source is implied. Licence: Creative Commons Attribution 4.0 (CC BY 4.0).

AI-assisted summary: The project, funded by Fundação para a Ciência e a Tecnologia, focuses on studying bacterial Transcription Factors from the GntR superfamily and their allosteric mechanisms using computational chemistry. It runs from January 1, 2021, to December 31, 2021, with a funding amount of EUR 1,507. Suggested technology pillar: simulation. Generated by AI from the public source text; it may contain errors and the original source is authoritative.