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Molecular Biomechanics - Projects

Force Distribution Analysis with Gromacs.

Force distribution analysis (FDA) is a method to detect stress propagation in proteins, reminiscent of finite element analysis used to engineer macroscopic structures. The method is based on molecular dynamics simulations during which we directly calculate forces between each atom pair in a system. The most recent version of FDA is now implemented in Gromacs-4.0.5.

The FDA code can be downloaded at the FDA-google-code website.


Force distribution through biomolecules 

 We apply the newly developed force distribution analysis (FDA) to understand protein regulation and function by revealing how force propagates through mechanical networks in proteins. Internal forces imposed by molecular interactions or external stress govern conformational transitions and enzymatic reactions. Elucidating the underlying mechanism of how force acting at a specific site of the protein triggers the protein's function at another distant site remains a major task in biology. We have successfully applied FDA to explain the mechanical robustness of immunoglobulins and silk. We are also applying this approach to allostery to reveal the allosteric network within proteins and protein/DNA systems responsible for signal propagation upon perturbation.

 
Elasticity of disordered proteins

Intrinsically disordered proteins are emerging as crucial building blocks in many if not all biological systems and materials. Their structural heterogeneity and complexity, however, poses a challenge to both experimental and theoretical approaches.

We are investigating how nature designed various intrinsically disordered springs in insect muscle, in nucleopores and elsewhere. We also quantified the effect of covalent glycosylation of an unfolded protein, as it occurs in the endoplasmatic reticulum prior to folding, on its elasticity and folding behavior.

 


Mechanics of biomaterials.

 Living species produce protein-based bio-materials such as silk, muscle or amyloid with exceptional mechanical properties, far from being achieved by any synthetic fibers to date. The determinants crucial for the mechanical resilience and robustness lie ultimately in the nano-scale arrangement of the molecular protein domains and the resulting nano-mechanics, the subject of our studies. Determining the biomolecular nano-templates of protein elastic material will ultimately allow the design new biomimetic polymer architectures.
 


Mechano(bio)chemistry.
Chemical and enzymatic reactions can be guided by mechanical stress. While single molecule force spectroscopy is an emerging technique to study biochemistry under external forces, theoretical knowledge to rationalize or predict the force dependency of reactions rates is limited to simple models. We are examining the effect of force on the electronic and molecular structures and energies during chemical reactions, among others disulfide bond reduction, including quantum and dynamical effects.
 



Proteins under shear flow.

Shear flow, as it occurs for example in blood vessel, is an alternative way of subjecting proteins to forces for signalling propagation nature is making use of. We are investigating how the multiple domains of the von Willebrand factor, a blood clotting factor, react to the tensile forces present in the protein under high shear conditions, and how the resulting force sensing mechanisms balance haemostasis, and thereby thrombosis and bleeding disorders.


 
page last modified: 22.12.2011,15:37



Group Leader

Dr. Frauke Gräter
Email:
Phone: +49 (0)6221 - 533 - 267
Fax: +49 (0)6221 - 533 - 298