An international research consortium has, with significant involvement of Luxembourg Centre for Systems Biomedicine (LCSB) scientists including FNR ATTRACT Fellow Prof Ines Thiele, developed the first computer model to include 3D in the representation of human metabolic processes. The results have just been published in the journal ‘Nature Biotechnology’.
The importance of scientific computer models continues to increase. They make the existing knowledge tangible and thereby help scientists to accurately formulate and work on targeted problems in research. To create such models, researchers analyse all the publications and databases they can find on a topic and feed this information into their model.
Human metabolism research is one example, as FNR ATTRACT Fellow Prof Ines Thiele, Head of the Molecular Systems Physiology group at the LCSB of the University of Luxembourg and one of the driving forces behind the new computer-based tool by the name of Recon3D, says:
“For the predecessor of Recon3D, Recon 2, a large team of research groups in different fields aggregated an enormous volume of data on the genome, chemical metabolic activities and physiological properties of the human organism.”
This data basis has now been considerably expanded yet again for Recon3D, Thiele reports. In order to make Recon3D, the researchers integrated the three-dimensional structures of over 4,000 metabolic products (also known as metabolites) into an existing computer model, along with nearly 13,000 proteins. They also added an enormous volume of genetic and chemical information to the model on which the simulation runs.
Computer model of human metabolic processes
What is unique about the new computer model is the integrated three-dimensional structural data of proteins and metabolites. Dr Ronan Fleming, head of the LCSB Systems Biochemistry group which was responsible for integrating the structural data of the metabolites into Recon3D, says “so far, we have been able to say of a given metabolic reaction that substance A and B turn into substances C and D. Now, we know precisely which atoms each substance consists of, how the atoms are arranged in the starting materials and where those very same atoms can be found again in the products of the chemical reaction.”
“Recon3D now allows us to study metabolic processes that run differently, for example, in Parkinson’s patients than in healthy people, much better and with more accuracy,” Thiele sums up the possibilities that the new computer model offers.
An expanded computer model available to all researchers
Dr Andreas Dräger from the Center for Bioinformatics at the University of Tübingen (ZBIT) has put it into a standardised format so that other researchers can use the model for their scientific questions.
Thanks to the three-dimensional structures of the metabolites and proteins in Recon3D, it is now possible to follow, at atomic resolution, how a genetic mutation could affect the development of certain diseases.
The researchers’ results on Recon3D appear in the journal Nature Biotechnology (doi:10.1038/nbt.4072).
Recon3D is available at vmh.live, Virtual Metabolic Human database.