Complex Biomolecular Machines

  • Description of the research topic

    In a wide range of biological activities, from cell locomotion to membrane transport, Nature deploys numerous sophisticated molecular machines which have become highly optimized for performance and controllability. Rational design and engineering of similarly complex biosystems is a very exciting field with a potential to dramatically alter future’s medicine or industrial biochemistry. However, to overcome major challenges in design of artificial enzymes, the precise understanding of control mechanism on key reaction steps by larger molecular scale structure and dynamics is required. FoF1 ATP synthase is interesting as a model system: a delicate molecular machine synthesizing or hydrolyzing ATP utilizing a rotary motor. (1-2) ATP synthase is a member of the RecA-like helicase family, and it is particularly interesting how the structural and residual differences of the same family determine the ATP hydrolysis mechanism and its effect on the overall function of these enzymes. Rad51, RadA and RecA are examples from this group of proteins, which fulfill particularly important roles in cellular functions: the repair of damaged DNA and the maintenance of genomic diversity. Despite the numerous studies, many details are still uncovered, especially the role of ATP hydrolysis and the description of the reaction mechanism at the atomic level. Computational biophysics provides an adequate set of tools to describe the atomic level structural differences and accurate energetics of the system. By using my experience in different quantum mechanical (QM/MM) and molecular dynamics simulations (MD), we would like to expand our current understanding of RecA enzymes, aiming to provide details on the coupling of reaction steps with the large scale motions. (3-4) To combine the theoretical studies with experimental investigation of reaction kinetics and structural characterization of filament formation by using polarized light spectroscopy will be performed in collaboration with Prof. Takahashi Masayuki (Univ. Tokyo).

    Thesis supervisor: Tamás Beke-Somfai

    Required language skills: English
    Recommended language skills: Hungarian

    How to Apply?

    If you are interested apply here: [PhD] György Hevesy Doctoral School of Chemistry – Eötvös Loránd University (elte.hu)

    For more information visite the following website: György Hevesy Doctoral School of Chemistry (elte.hu)

  • Funded: Not Funded

    Master Degree: Required

    Duration: 4 Years

    Full/Part Time: Full Time

    Starting Date: 06 September 2021

    Deadline to Apply: 31 May 2021

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