Change institution
Advanced Nano and Microtechnologies Advanced Materials Structural Biology Gen. and Prot. of Plant Systems Molecular Medicine Brain and Mind Research Molecular Vet. Medicine

Supramolecular chemistry of cucurbiturils and bambusurils

Free energy calculations based on potential of mean force methods to reproduce results from experimental NMR studies

The main aim of the project is an efective implemenattion of methods for free energy calculation. Free energy is the one of the most importatnt state quantity for biochemical processes description. Multidimensional reaction coordinate driving of system is one part of a project. Driving means, we are able to influenece system in desired way to explore interesting areas of phase space in sense of possible biochemical processes and state change. Current used software packages (AMBER) are able to run molecular simulations in parallel thus implementation of mentioned methods has to be parallelized as well. One of the entire part of the project is testing and case study on selected biochemical systems. At present pseudorotaxane complexe was selected for a study.
 

free_energy_pseudorotaxane

Figure 1: Two possible states of pseudorotaxane molecule. Fully interlocked state, and partially interlocked state have different energy. Energy levels of these two states can be switched when change of environmental pH occurs.
 

free_energy_graph2  free_energy_graph1

Figure 2: Resultant graph of free energy profile of pseudorotaxane complex. For unprotonated case of system (0q), preferable state is at distance 0A (full interlocation). In protonated case of system (2p), preferable state is at distance 7.5A (partial interlocation).

More CEITEC News ...
Dr. Ondrej Hovorka: Models of magnetic nanoparticles for biomedical applications

29. ledna 2018 9:46

Dr. Ondrej Hovorka: Models of magnetic nanoparticles for biomedical…

LECTURE: Dr. Ondrej Hovorka: Models of magnetic nanoparticles for biomedical applications

Advanced Materials and Nanotechnology Seminar Series 2018: Dr Andriy Marko

25. ledna 2018 18:21

Advanced Materials and Nanotechnology Seminar Series 2018: Dr Andriy…

WHEN: 30. 01. 2018 WHERE: CEITEC BUT, Purkynova 123, large meeting room SPEAKER: Dr Andriy Marko TALK: Advances in PELDOR…