Seminars and Events

Past Events

Category Other
Date and Time 2014-09-02 14:00 - 15:00
Venue Seminar RoomD2F
Speaker Alexander Mikhailov
Affiliation Fritz-Haber-Institut der Max-Planck-Gesellschaft, Germany
Title Simple elastic models of protein machines
Poster click here to download(PDF)
Host Tatsuo Shibata
abstract Protein machines, acting as enzymes, ion pumps, or molecular motors, and performing operations with different biomolecules, such as DNA or other proteins, play a fundamental role in biological cells. Once developed, their synthetic analogs may provide the basis for a new generation of nanotechnology. In this talk, some of the results of recent research in this field, undertaken in my group in Berlin, will be presented.
While chemical structures and equilibrium conformations of protein machines are known, full direct modeling of their molecular dynamics encounters serious difficulties. Even when supercomputers are employed, the dynamics of a single molecule cannot be followed for more than a microsecond, whereas one operation cycle of a molecular machine typically takes tens of milliseconds. Elastic-network models, proposed almost two decades ago, provide a reduced description which has turned out to be highly efficient and, at the same time, very simple. They are broadly used in the normal-mode analysis of experimental protein data and are furthermore applied to understand sensitivity of proteins with respect to local perturbations. A review of the applications, with the foreword by the Nobel prize laureate M. Karplus, can be found in the book [1].
The novel aspect in our research is that we have started to use nonlinear elastic models for dynamical simulations of molecular motors and other protein machines [2-5]. We have moreover begun to design synthetic machines based on such modeling principles [6,7].
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