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Accessing protein dynamics across scales

Biomolecular systems exhibit hierarchical structural dynamics on timescales from picoseconds to minutes. While it is widely accepted that protein structure plays a major role in defining their function, it becomes more and more evident that protein structural dynamics is as important. Hence a long-standing challenge in the field of biomolecular simulation has been to extend the spectrum of accessible time scales of protein dynamics at atomic resolution. While the millisecond (ms) time regime is accessible for simulations of small peptides, protein simulations are still restricted to <100 microseconds (µs).

Intriguingly, the extent of the time regime of protein dynamics is not directly related to the size of a protein: While even small peptides (i.e. <10 amino acids) exhibit slow processes in the range of µs, the function of large proteins can depend on very fast dynamics in the ns regime. The current major challenge is to address the µs to ms time regime. In a joint approach we will increase the time scale of Molecular Dynamics (MD) simulations and at the same time extend the time resolution of fluorescence based single molecule Förster resonance energy transfer (smFRET) microscopy to merge in the µs – ms time regime.

A key system will be the heat shock protein 90 (Hsp90), where it is already evident that a thorough understanding requires all timescales of the protein motion from sub-ns to hours. Besides providing a deeper understanding of the functional cycle of HSP90, PDZ domains, and T4 lysozyme, we expect our joint work to be a model project for the understanding of protein state transition networks, and for the interdisciplinary combination between computational and experimental biophysics.

 


Organisers

 

Prof. Dr. Gerhard Stock

Institute of Physics
University of Freiburg

Email:

Prof. Dr. Thorsten Hugel

Institute of Physical Chemistry
University of Freiburg

Email:

Dr. Steffen Wolf

Institute of Physics
University of Freiburg

Email:

Bianca Hermann

Institute of Physical Chemistry
University of Freiburg

Email: