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BBB seminar: Alexander Schug

Using the computer as a lab: From biomolecular simulations to simulating cancer

Alexander Schug
John von Neumann Institute for Computing, Jülich Supercomputing Centre, Jülich, Germany

Exploring the interrelationship of structure and function is crucial for the understanding of molecular life. Yet despite significant progress of experimental methods, full characterization of functional cycles for proteins and RNA remains an ongoing challenge. In-silico approaches such as biomolecular simulations offer a complementary option. One can use such simulations akin to an atomically resolved microscope to gain insight into the dynamical motion of biomolecules. Examples include tracing the co-evolution of residues [1], which can be exploited in structure prediction tools and is, e.g., sufficient for the blind prediction of proteins and RNA [2]. Similarly, one can use low-resolution experimental information such as small-angle x-ray scattering (SAXS) data to model suitable biomolecular conformations or compare data from simulations directly against experimental measurements such as single-molecule fluorescence energy transfer (smFRET) data [3]. Finally, I will highlight our recent work on the simulation of tissue development [4] and cancer.

References:

[1] Weigt M et al., Proc Natl Acad Sci USA (2009) 106, 67-72; Schug A et al., Proc Natl Acad Sci USA (2009) 106, 22124-9; Morcos F et al., Proc Natl Acad Sci (2011) 108, E1293-301

[2] Dago AE et al., Proc Natl Acad Sci USA (2012), 109, E1733-42; De Leonardis E et al., Nucleic Acids Res (2015) 43, 10444-55; Figliuzzi M et al., Mol Biol Evol (2016) 33, 268-80; Uguzzoni G et al., Proc Natl Acad Sci USA (2017) 114, E2662-71

[3] Reinartz, I et al., J Chem Phys (2018) 148, 123321

[4] Stanganello, E et al., Nat Commun (2015) 6, 5846.; Mattes, B et al., Elife (2018) 7, e36953


Chairperson: Mathias Ziegler, Department of Biomedicine