Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

The pathway into the cell

17.02.2012
MATHEON mathematicians are helping to unravel molecular processes

“Imagine an inflated balloon attached to a pump, but much, much smaller. By pinching off the neck of the balloon with a noose, it is detached from the pump and is able to move about freely.” The description is an approximation of one of the molecular processes looked at by mathematician Dr. Frank Noe as part of MATHEON’S ‘A19, Modelling and Optimisation of Functional Molecules’ project. Specifically, the molecular structure and mechanism of dynamin.


In the case of dynamin, the precise mechanism of action can be visualised in individual steps
Noe

Dynamin is a protein and the ‘noose’ which detaches the balloon from the pump. The vesicle (the scientific name for the balloon) has to be detached to allow it to perform its role as a vesicle for transporting messenger substances and nutrients into the cell. Substances which need to be transported into the cell first accumulate in a vesicle formed by invagination from the surface of the cell. The dynamin molecule then attaches to the neck of the vesicle and forms a spiral around it. It then severs the neck of the vesicle. The vesicle is now free to transport nutrients into the cell.

Whilst scientists have long known about the process, the molecular details of how dynamin works were until now unknown. A group of researchers at the Max Delbrück Center for Molecular Medicine (MDC) in Berlin has now managed to obtain snapshots of the detailed molecular structure and, with the help of mathematical research carried out by Frank Noe and his team at MATHEON, been able to breathe life into these static structures.

“Without mathematical methods, it would not have been possible to simulate the processes which occur when the neck of the vesicle is severed,” explains the mathematician.

Simulating this molecular process is extremely difficult. “A simulation encompasses 250,000 particles and each iteration of the calculation takes around 1 second, even on a mainframe. To directly simulate this process, we would have to perform millions of iterations. That would take decades – scission within the cell takes just milliseconds.” With the help of mathematical methods developed at MATHEON, it was possible to divide the scission process up into many smaller, more manageable simulations.

In the case of dynamin, this allowed the precise mechanism of action to be visualised in individual steps. It turns out that the molecule operates via a specific pathway. “We were able to identify three primary states of the molecule,” explains the mathematician, describing the process as follows, “Initially, dynamin molecules attach to the neck of the vesicle individually, before linking up to form between one and a half and two tight turns around the neck of the vesicle. This structure then expands like a spring and rotates in on itself. The result is that the semi-fluid material making up the neck of the vesicle is more or less ripped apart. “

Understanding this process is important for medical science, as it represents a point of attack for fighting poisons and disease. “Many neurotoxins, for example, act at this point, thereby blocking nerve function,” explains Frank Noe. Degenerative neurological diseases such as Parkinson’s also affect the uptake of vesicles by nerve cells. “If we can obtain a better understanding of the mechanism of dynamin, we may be able to find new approaches to early diagnosis or treatments,” says Dr. Noe.

Collaboration between doctors, structural biologists and mathematicians in this area is set to continue. “The mathematical research being carried out within the MATHEON project will continue to make an important contribution to producing further useful insights,” explains Frank Noe.

The study has been published in the journal ‘Nature’, issue 477, page 556. Further information on the study can be found at
http://www.nature.com/nature/journal/v477/n7366/full/nature10369.html
and
www.biocomputing-berlin.de/biocomputing/en/projects/matheon_project_
a19_modelling_and_optimization_of_functional_molecules
Frank Noe will also be happy to provide you with further information and can be contacted by telephone on 030 838 75354 or by email at noe@math.fu-berlin.de

Rudolf Kellermann | idw
Further information:
http://www.matheon.de/
http://numerik.mi.fu-berlin.de/Forschung/Noe/index.php

More articles from Life Sciences:

nachricht Surprisingly many peculiar long introns found in brain genes
10.07.2020 | Moscow Institute of Physics and Technology

nachricht Did nerve cells evolve to talk to microbes?
10.07.2020 | Christian-Albrechts-Universität zu Kiel

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: The spin state story: Observation of the quantum spin liquid state in novel material

New insight into the spin behavior in an exotic state of matter puts us closer to next-generation spintronic devices

Aside from the deep understanding of the natural world that quantum physics theory offers, scientists worldwide are working tirelessly to bring forth a...

Im Focus: Excitation of robust materials

Kiel physics team observed extremely fast electronic changes in real time in a special material class

In physics, they are currently the subject of intensive research; in electronics, they could enable completely new functions. So-called topological materials...

Im Focus: Electrons in the fast lane

Solar cells based on perovskite compounds could soon make electricity generation from sunlight even more efficient and cheaper. The laboratory efficiency of these perovskite solar cells already exceeds that of the well-known silicon solar cells. An international team led by Stefan Weber from the Max Planck Institute for Polymer Research (MPI-P) in Mainz has found microscopic structures in perovskite crystals that can guide the charge transport in the solar cell. Clever alignment of these "electron highways" could make perovskite solar cells even more powerful.

Solar cells convert sunlight into electricity. During this process, the electrons of the material inside the cell absorb the energy of the light....

Im Focus: The lightest electromagnetic shielding material in the world

Empa researchers have succeeded in applying aerogels to microelectronics: Aerogels based on cellulose nanofibers can effectively shield electromagnetic radiation over a wide frequency range – and they are unrivalled in terms of weight.

Electric motors and electronic devices generate electromagnetic fields that sometimes have to be shielded in order not to affect neighboring electronic...

Im Focus: Gentle wall contact – the right scenario for a fusion power plant

Quasi-continuous power exhaust developed as a wall-friendly method on ASDEX Upgrade

A promising operating mode for the plasma of a future power plant has been developed at the ASDEX Upgrade fusion device at Max Planck Institute for Plasma...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

Contact Tracing Apps against COVID-19: German National Academy Leopoldina hosts international virtual panel discussion

07.07.2020 | Event News

International conference QuApps shows status quo of quantum technology

02.07.2020 | Event News

Dresden Nexus Conference 2020: Same Time, Virtual Format, Registration Opened

19.05.2020 | Event News

 
Latest News

Looking at linkers helps to join the dots

10.07.2020 | Materials Sciences

Surprisingly many peculiar long introns found in brain genes

10.07.2020 | Life Sciences

Goodbye Absorbers: High-Precision Laser Welding of Plastics

10.07.2020 | Materials Sciences

VideoLinks
Science & Research
Overview of more VideoLinks >>>