Immediate start is possible, or as agreed with the successful applicant.
The Biomolecular self-assembly “Momentum” research group is looking for a post-doctoral fellow to conduct research in the field of theoretical biophysics.
The successful candidate will carry out primarily theoretical simulations employing molecular dynamics (MD) and quantum chemistry (QM, QM/MM) techniques to reveal structural and mechanistic aspects of members in RecA-like helicase family as well as in membrane associated complexes (Band3-hemichrome). The main focus will be on elucidating interactions between the micro- and macroscale within DNA-Protein complexes. In case of the membrane associated complex the aim is to reach an atomic level understanding of the formed complex using simulations relying on experimental data. The candidate will take an active part in designing and performing models and simulations, in data analysis and in writing scientific papers, as well as assist younger students in the lab.
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)
(1) T. Beke-Somfai, P. Lincoln, B. Nordén: Double-lock ratchet mechanism revealing the role of αSER-344 in FoF1 ATP synthase PNAS, 2011, 108, 4828-4833
(2) T. Beke-Somfai, P. Lincoln, B. Nordén: Rate of hydrolysis in ATP synthase is fine-tuned by α-subunit motif controlling active site conformation PNAS, 2013, 110, 2117-2122
(3) A. Reymer, S. Babik, M. Takahashi B. Nordén, T. Beke-Somfai: ATP Hydrolysis in the RecA–DNA Filament Promotes Structural Changes at the Protein–DNA Interface Biochemistry, 2015, 54 (30), pp 4579–4582
(4) A. Reymer, Frederick, K., S. Rocha, T. Beke-Somfai, C. C. Kitts, S. Lindquist, B. Nordén: Orientation of aromatic residues in amyloid cores: Structural insights into prion fiber diversity Proc. Natl. Acad. Sci., U.S.A., 2014, 111, 17158-17163
- PhD in chemistry, physics, biology or in biomedical sciences
- Experience in any of the computational chemistry techniques mentioned above (Coarse-grained, MD, or QM/MM)
- Experience with linux systems
- fluent in English
- Ability to work in a group, as well as alone
- experience in shell scripting or programming
- detailed scientific curriculum vitae
- full list of publications
- motivation letter
- two letters of recommendation
- contact data (phone, e-mail)
Continuous processing, latest April 15., 2017