PhD position

Stellenangebot vom 1. August 2018

Topic: Investigating mechanical deformation and force-dependent pathways in proteins using molecular dynamics simulations

Supervisors: Ana Vila Verde and Reinhard Lipowsky
Start of position: as soon as possible
Duration: 36 months
Location: Theory and Bio-Systems Department, Max Planck Institute of Colloids and Interfaces, Wissenschaftspark Golm, Am Mühlenberg 1, 14476 Potsdam, Germany

Proteins in vivo are often under significant mechanical stress, which affects their conformation and conformational fluctuations. These changes will affect the proteins’ ability to carry out their function, e.g., the enzymatic turnover rate or the stability of a multi-protein complex.  At present, however, the molecular mechanisms by which force is transmitted within or between proteins are not understood.  Such knowledge is critical to understand how the response of proteins  to mechanical force depends on the intensity, the direction or the application point of the force.  In this project, we will address this general problem by using atomistic molecular dynamics simulations to investigate the effect of mechanical forces on two categories of proteins: enzymes such as lysozymes, and complexes of three proteins such as trimeric coiled coils, see Figure 1. The project will involve learning advanced simulation techniques to enhance sampling of configuration space.

Figure 1: Trimeric coiled coil.

Figure 1: Trimeric coiled coil.

The simulation studies will be pursued in close collaboration with the experimental group of Kerstin Blank at our Max Planck Institute, where atomic force microscopy and single molecule fluorescence experiments will be carried out on the same proteins with the same focus on force-dependent pathways.

Required background: Strong background in chemical physics, physical chemistry and/or statistical physics.  Prior experience with molecular dynamics or Monte Carlo simulation techniques will be useful.   

Contact: Interested candidates should send a CV and copies of their undergraduate transcripts to Dr. Ana Vila Verde (ana.vilaverde@mpikg.mpg.de)

 
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