Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Using computational biology for the annotation of proteins

26.11.2012
Research carried out at Universidad Carlos III of Madrid (UC3M) in collaboration with the Centro Nacional de Investigaciones Oncológicas (CNIO – Spanish National Cancer Research Center) employed computational techniques to improve the characterization of proteins.
The system they developed has allowed them to predict, for example, the relationship between two human proteins and telomeres, which led to their possible implication in cellular aging and the development of cancer; this awaits experimental verification.

Proteins are molecules that are formed by chains of amino acids and they play a fundamental role in all of life, given that they contain the coded information in genes; they, therefore, carry out numerous functions in an organism: immunological (antibodies), structural (they constitute the majority of cellular material), bioregulating (they form part of enzymes) and a long list of etceteras. In short, they regulate thousands of process that take place within all organisms, including inside the human organism, and they frequently do so by means of relationships they establish with other cells.

“Analyzing and using this network of interactions is a very interesting task due to the large number of associations that exist and to the multiple forms in which one protein can influence the function of others,” explains Professor Beatriz García, of UC3M’s Computer Science department. “In such a complex biological scenario, determining the functional associations through experiments is very costly, so we have tried to apply computational tools to predict these functions and so orient experimentation,” she points out.

Thus, the idea is to use techniques from the field of Artificial Intelligence, specifically from the area of Machine Learning, to obtain useful results for Biology, as part of an emerging interdisciplinary field known as Biocomputing or Computational Biology. In this context, this line of research goes further in the annotation of the function of proteins, that is, in the determination of which protein or which group of proteins performs which task within an organism.

In short, these scientists have dealt with two specific problems: the prediction of functional associations between pairs of proteins in the bacteria Escherichia coli and the extension of biological pathways in humans. In addition, they offer conclusions regarding the interpretation of those predictions, which may help explain the function of the cellular processes that were studied.

“In particular,” states Beatriz García, “the predictions obtained regarding two human proteins stand out (E3 SUMO-protein ligase y E3 ubiquitin-protein ligase DTX1); these were previously related to the controlled degradation of certain proteins, and we can now propose a new function related to the stabilization of telomeres and, therefore, their possible implication in cellular aging and the development of cancer, which will require experimental verification”.

For this study, part of which was recently published in the journal PLoS ONE, the researcher has received the award for the best doctoral dissertation in her field (Experimental Sciences and Technology) from the Real Academia de Doctores de España (Spanish Royal Academy of Doctors).

The implications that this work holds for the scientific community are already being felt. In fact, the results of the first problem that the project analyzes have already been integrated into the predictions server EcID (E.coli Interaction Database) and they offer a reliability value for the predictions that improves the system’s performance when finding functional associations among the proteins that appear in this database.

Moreover, the second biological problem dealt with in the study opens a new area of research in Biocomputing, by extending already existing pathways. “The procedure it presents complements the only previously existing publication in the field, extending the pathways with many more proteins and exploring a greater surface of the network of interactions,” comments the researcher.

In addition, it could be applied to many more problems of functional annotation in Biology and other fields in which there is relevant information with multiple relationships. In any case, much work remains to be done in the area of Biocomputation. “There are still so many unresolved biological problems that need computational solutions,” assures Beatriz García, who highlights the relevance of this field, which is growing with the advances in new technologies; yet many computational challenges remain, such as the analysis of the new generation of sequencing. “This is an area that needs more trained professionals who can integrate Biology and Computer Science, in order to improve our knowledge of our organism at the molecular level and, finally, to facilitate the treatment of diseases,” she concludes.

Ana María Herrera | alfa
Further information:
http://www.uc3m.es/portal/page/portal/actualidad_cientifica/noticias/biology

More articles from Life Sciences:

nachricht Multi-institutional collaboration uncovers how molecular machines assemble
02.12.2016 | Salk Institute

nachricht Fertilized egg cells trigger and monitor loss of sperm’s epigenetic memory
02.12.2016 | IMBA - Institut für Molekulare Biotechnologie der Österreichischen Akademie der Wissenschaften GmbH

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Novel silicon etching technique crafts 3-D gradient refractive index micro-optics

A multi-institutional research collaboration has created a novel approach for fabricating three-dimensional micro-optics through the shape-defined formation of porous silicon (PSi), with broad impacts in integrated optoelectronics, imaging, and photovoltaics.

Working with colleagues at Stanford and The Dow Chemical Company, researchers at the University of Illinois at Urbana-Champaign fabricated 3-D birefringent...

Im Focus: Quantum Particles Form Droplets

In experiments with magnetic atoms conducted at extremely low temperatures, scientists have demonstrated a unique phase of matter: The atoms form a new type of quantum liquid or quantum droplet state. These so called quantum droplets may preserve their form in absence of external confinement because of quantum effects. The joint team of experimental physicists from Innsbruck and theoretical physicists from Hannover report on their findings in the journal Physical Review X.

“Our Quantum droplets are in the gas phase but they still drop like a rock,” explains experimental physicist Francesca Ferlaino when talking about the...

Im Focus: MADMAX: Max Planck Institute for Physics takes up axion research

The Max Planck Institute for Physics (MPP) is opening up a new research field. A workshop from November 21 - 22, 2016 will mark the start of activities for an innovative axion experiment. Axions are still only purely hypothetical particles. Their detection could solve two fundamental problems in particle physics: What dark matter consists of and why it has not yet been possible to directly observe a CP violation for the strong interaction.

The “MADMAX” project is the MPP’s commitment to axion research. Axions are so far only a theoretical prediction and are difficult to detect: on the one hand,...

Im Focus: Molecules change shape when wet

Broadband rotational spectroscopy unravels structural reshaping of isolated molecules in the gas phase to accommodate water

In two recent publications in the Journal of Chemical Physics and in the Journal of Physical Chemistry Letters, researchers around Melanie Schnell from the Max...

Im Focus: Fraunhofer ISE Develops Highly Compact, High Frequency DC/DC Converter for Aviation

The efficiency of power electronic systems is not solely dependent on electrical efficiency but also on weight, for example, in mobile systems. When the weight of relevant components and devices in airplanes, for instance, is reduced, fuel savings can be achieved and correspondingly greenhouse gas emissions decreased. New materials and components based on gallium nitride (GaN) can help to reduce weight and increase the efficiency. With these new materials, power electronic switches can be operated at higher switching frequency, resulting in higher power density and lower material costs.

Researchers at the Fraunhofer Institute for Solar Energy Systems ISE together with partners have investigated how these materials can be used to make power...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

ICTM Conference 2017: Production technology for turbomachine manufacturing of the future

16.11.2016 | Event News

Innovation Day Laser Technology – Laser Additive Manufacturing

01.11.2016 | Event News

#IC2S2: When Social Science meets Computer Science - GESIS will host the IC2S2 conference 2017

14.10.2016 | Event News

 
Latest News

UTSA study describes new minimally invasive device to treat cancer and other illnesses

02.12.2016 | Medical Engineering

Plasma-zapping process could yield trans fat-free soybean oil product

02.12.2016 | Agricultural and Forestry Science

What do Netflix, Google and planetary systems have in common?

02.12.2016 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>