Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Protein analysis: Less is more

28.03.2018

CONAN to the rescue! The new software-package for molecular dynamic simulations compresses 3D data to contact maps and helps to analyze protein structures. The tool developed at HITS CONAN (CONtact ANalysis) has now been presented in the latest issue of „Biophysical Journal“.

Proteins constantly move and change their conformation. Molecular dynamics typically answers the question of what the possible conformations of proteins are. Proteins, however, have a highly complicated and crowded structure, and understanding the changes in their behavior is a challenging task due to the high number of coordinates to monitor.


CONAN transforms the 3D structure of the protein ubiquitin into a 2D contact map. Left: Structure of ubiquitin, colored by residue index. Right: Inter-residue distance map computed by CONAN.

Image: Csaba Daday, HITS

Digesting the large amount of molecular data often involves creative 3D visualization, but even with considerable effort, important details can be missed. This led to a dual problem; not only was data visualization a challenge, but scientists also ran the risk of overlooking aspects of their own results.

A novel tool called CONAN (CONtact ANalysis), developed from the “Molecular Biomechanics” at HITS, can alleviate these issues through compressing this 3D data into simpler 2D images capturing the key interactions, named contact maps.

Contact maps measure inter-residue distances, thereby compressing 3D structures into 2D images. This often facilitates data interpretation and makes important changes easier to spot. These contact maps have usually only been used to study single protein structures as a single snapshot, but in fact they can easily be obtained for many structures, resulting in a contact map movie.

This analysis somehow extends the saying "a figure is worth more than 1000 words" into the dynamic regime, since it creates a multitude of possible contact-map snapshots out of one simulation, identifying conformational subpopulations and transitions.

Until now, contact maps-based analysis methods have been widely used only as understanding single structures, such as those in the protein data base (PDB). Even when the methods were generalized for dynamic simulations, the implementations were often various “ad hoc” analysis scripts, since there wasn’t a standardized tool.

This meant that the measured quantities and definitions were inconsistent and results weren’t directly comparable. The new tool “CONAN” however is a standardized, easy-to-use package that allows several different types of analyses, for example including principal component analysis and cluster analysis.

The tool developed by the HITS researchers Csaba Daday and Frauke Gräter of the Molecular Biomechanics group as well as former group member Davide Mercadante therefore fills a gap and offers a comprehensive, user-friendly program requiring no programming experience that can help scientists performing molecular dynamics calculations understand and present their data.

Hopefully, this will lead to a more widespread use of these measures, and a more uniform set of definitions. The tool is open access and free of use. The team at HITS also constantly optimizes the software and is open to feedback from the community.

CONAN is freely available at: https://github.com/HITS-MBM/conan/tree/master/docs
Examples and illustrations can be found on our blog: https://contactmaps.blogspot.de/ and our YouTube channel: https://www.youtube.com/channel/UCEjgMtcojYuucVLI2PPv7oA

Article in "Biophysical Journal":
CONAN: A Tool to Decode Dynamical Information from Molecular Interaction Maps. Davide Mercadante, Frauke Gräter, Csaba Daday. Biophysical Journal,
Volume 114, Issue 6, p1267–1273, 27 March 2018. DOI: https://doi.org/10.1016/j.bpj.2018.01.033
http://www.cell.com/biophysj/fulltext/S0006-3495(18)30193-0

Scientific Contact:

Prof. Dr. Frauke Gräter
Group Leader „Molecular Biomechanics“
HITS - Heidelberg Institute for Theoretical Studies
E-mail: frauke.graeter@h-its.org

Dr. Csaba Daday
Group Member „Molecular Biomechanics“
HITS - Heidelberg Institute for Theoretical Studies
E-mail: Csaba.Daday@h-its.org

About HITS

The Heidelberg Institute for Theoretical Studies (HITS) was established in 2010 by the physicist and SAP co-founder Klaus Tschira (1940-2015) and the Klaus Tschira Foundation as a private, non-profit research institute. HITS conducts basic research in the natural sciences, mathematics and computer science, with a focus on the processing, structuring, and analyzing of large amounts of complex data and the development of computational methods and software. The research fields range from molecular biology to astrophysics. The shareholders of HITS are the HITS Stiftung, which is a subsidiary of the Klaus Tschira Foundation, Heidelberg University and the Karlsruhe Institute of Technology (KIT). HITS also cooperates with other universities and research institutes and with industrial partners. The base funding of HITS is provided by the HITS Stiftung with funds received from the Klaus Tschira Foundation. The primary external funding agencies are the Federal Ministry of Education and Research (BMBF), the German Research Foundation (DFG), and the European Union.

Weitere Informationen:

https://www.h-its.org/scientific-news/protein-analysis-less-is-more/ HITS Press release
http://www.cell.com/biophysj/fulltext/S0006-3495(18)30193-0 Article in "Biophysical JOurnal"
example video: Ubiquitin unfolding and evolution of contact map

Dr. Peter Saueressig | idw - Informationsdienst Wissenschaft

More articles from Life Sciences:

nachricht Structure of a mitochondrial ATP synthase
19.11.2019 | Science For Life Laboratory

nachricht Mantis shrimp vs. disco clams: Colorful sea creatures do more than dazzle
19.11.2019 | University of Colorado at Boulder

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Atoms don't like jumping rope

Nanooptical traps are a promising building block for quantum technologies. Austrian and German scientists have now removed an important obstacle to their practical use. They were able to show that a special form of mechanical vibration heats trapped particles in a very short time and knocks them out of the trap.

By controlling individual atoms, quantum properties can be investigated and made usable for technological applications. For about ten years, physicists have...

Im Focus: Images from NJIT's big bear solar observatory peel away layers of a stellar mystery

An international team of scientists, including three researchers from New Jersey Institute of Technology (NJIT), has shed new light on one of the central mysteries of solar physics: how energy from the Sun is transferred to the star's upper atmosphere, heating it to 1 million degrees Fahrenheit and higher in some regions, temperatures that are vastly hotter than the Sun's surface.

With new images from NJIT's Big Bear Solar Observatory (BBSO), the researchers have revealed in groundbreaking, granular detail what appears to be a likely...

Im Focus: New opportunities in additive manufacturing presented

Fraunhofer IFAM Dresden demonstrates manufacturing of copper components

The Fraunhofer Institute for Manufacturing Technology and Advanced Materials IFAM in Dresden has succeeded in using Selective Electron Beam Melting (SEBM) to...

Im Focus: New Pitt research finds carbon nanotubes show a love/hate relationship with water

Carbon nanotubes (CNTs) are valuable for a wide variety of applications. Made of graphene sheets rolled into tubes 10,000 times smaller than a human hair, CNTs have an exceptional strength-to-mass ratio and excellent thermal and electrical properties. These features make them ideal for a range of applications, including supercapacitors, interconnects, adhesives, particle trapping and structural color.

New research reveals even more potential for CNTs: as a coating, they can both repel and hold water in place, a useful property for applications like printing,...

Im Focus: Magnets for the second dimension

If you've ever tried to put several really strong, small cube magnets right next to each other on a magnetic board, you'll know that you just can't do it. What happens is that the magnets always arrange themselves in a column sticking out vertically from the magnetic board. Moreover, it's almost impossible to join several rows of these magnets together to form a flat surface. That's because magnets are dipolar. Equal poles repel each other, with the north pole of one magnet always attaching itself to the south pole of another and vice versa. This explains why they form a column with all the magnets aligned the same way.

Now, scientists at ETH Zurich have managed to create magnetic building blocks in the shape of cubes that - for the first time ever - can be joined together to...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

First International Conference on Agrophotovoltaics in August 2020

15.11.2019 | Event News

Laser Symposium on Electromobility in Aachen: trends for the mobility revolution

15.11.2019 | Event News

High entropy alloys for hot turbines and tireless metal-forming presses

05.11.2019 | Event News

 
Latest News

Structure of a mitochondrial ATP synthase

19.11.2019 | Life Sciences

The measurements of the expansion of the universe don't add up

19.11.2019 | Physics and Astronomy

Ayahuasca compound changes brainwaves to vivid 'waking-dream' state

19.11.2019 | Health and Medicine

VideoLinks
Science & Research
Overview of more VideoLinks >>>