Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Scientists reveal the key mechanisms for affinity between transient binding proteins

02.07.2008
Most of the functions performed by a cell are the result of interactions between proteins, which recognise their binding partner by affinity features localized on the protein surface.

There are many kinds of interactions; however, the most complicated to study from the perspective of structural biology are those which are transient. This type of interaction is brief and occurs through a large section of the protein surface- the globular domain -, and a very small section of the surface of another proteins, the so-called lineal motif or peptide.

The difficulty lies in the fact that these relations are of short duration and there are few crystallized peptide structures. Researchers at the Institute for Research in Biomedicine (IRB Barcelona) have performed the first computational analysis of transient interactions between proteins in order to reveal what determines their recognition as ideal partners and have unveiled part of the molecular mechanisms involved in the specificity of this binding. The results of this study have been published in the scientific journal PLoS One.

“Knowing what determines protein-protein binding may have implications, for example, in the design of new drugs”, explains Patrick Aloy, ICREA research professor at IRB Barcelona, “however, we currently know very little about this type of binding”. These kinds of interactions occur mainly between proteins involved in signalling pathways and regulatory networks, and they serve to translate and transmit extracellular signals to the cell nucleus.

... more about:
»Protein »Transient »lineal »motif
The context is relevant
In Patrick Aloy’s Structural Biology Laboratory they have detected all interactions possible between the globular domain and peptide by exploring the 45,000 3D protein structures currently available on the international database PDB (Protein Data Base), and establishing rules from them. “One of the conclusions from the study is that what determines that two proteins recognise each other as binding partners falls outside the lineal contact motif, in what is called the context”, explains Aloy.

The contextual residues are amino acids that are found in nearby regions of the lineal motif but do not form part of it. “The binding strength between two proteins is determined by contacts found in the lineal motif but it is the contextual residues that hold information about the most suitable proteins, thereby preventing undesirable binding between similar proteins”, explains Amelie Stein, a pre-doctoral student with Aloy’s lab and first author of the article.

The analysis performed by the researchers has also revealed that in certain conditions non native interactions may occur, that is to say, interactions with other proteins that are not optimum. “This is what we refer to as complementary partners, other interaction proteins that can compensate for the lack of the ideal protein”, explains Stein. According to the researchers, these non-optimum interactions allow the establishment of emergency circuits that increase the strength of cellular networks. Specifically, one line of research derived from the study by Aloy and Stein focuses on the identification of proteins unable to establish safety circuits and therefore with a good chance of becoming future therapeutic targets.

Sonia Armengou | alfa
Further information:
http://www.irbbarcelona.org
http://www.irbbarcelona.org/index.php/en/news/irb-news/scientific/scientists-reveal-the-key-mechanisms-for-affinity-between-transient-b

Further reports about: Protein Transient lineal motif

More articles from Life Sciences:

nachricht The secret sulfate code that lets the bad Tau in
16.07.2018 | American Society for Biochemistry and Molecular Biology

nachricht Colorectal cancer risk factors decrypted
16.07.2018 | Max-Planck-Institut für Stoffwechselforschung

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: First evidence on the source of extragalactic particles

For the first time ever, scientists have determined the cosmic origin of highest-energy neutrinos. A research group led by IceCube scientist Elisa Resconi, spokesperson of the Collaborative Research Center SFB1258 at the Technical University of Munich (TUM), provides an important piece of evidence that the particles detected by the IceCube neutrino telescope at the South Pole originate from a galaxy four billion light-years away from Earth.

To rule out other origins with certainty, the team led by neutrino physicist Elisa Resconi from the Technical University of Munich and multi-wavelength...

Im Focus: Magnetic vortices: Two independent magnetic skyrmion phases discovered in a single material

For the first time a team of researchers have discovered two different phases of magnetic skyrmions in a single material. Physicists of the Technical Universities of Munich and Dresden and the University of Cologne can now better study and understand the properties of these magnetic structures, which are important for both basic research and applications.

Whirlpools are an everyday experience in a bath tub: When the water is drained a circular vortex is formed. Typically, such whirls are rather stable. Similar...

Im Focus: Breaking the bond: To take part or not?

Physicists working with Roland Wester at the University of Innsbruck have investigated if and how chemical reactions can be influenced by targeted vibrational excitation of the reactants. They were able to demonstrate that excitation with a laser beam does not affect the efficiency of a chemical exchange reaction and that the excited molecular group acts only as a spectator in the reaction.

A frequently used reaction in organic chemistry is nucleophilic substitution. It plays, for example, an important role in in the synthesis of new chemical...

Im Focus: New 2D Spectroscopy Methods

Optical spectroscopy allows investigating the energy structure and dynamic properties of complex quantum systems. Researchers from the University of Würzburg present two new approaches of coherent two-dimensional spectroscopy.

"Put an excitation into the system and observe how it evolves." According to physicist Professor Tobias Brixner, this is the credo of optical spectroscopy....

Im Focus: Chemical reactions in the light of ultrashort X-ray pulses from free-electron lasers

Ultra-short, high-intensity X-ray flashes open the door to the foundations of chemical reactions. Free-electron lasers generate these kinds of pulses, but there is a catch: the pulses vary in duration and energy. An international research team has now presented a solution: Using a ring of 16 detectors and a circularly polarized laser beam, they can determine both factors with attosecond accuracy.

Free-electron lasers (FELs) generate extremely short and intense X-ray flashes. Researchers can use these flashes to resolve structures with diameters on the...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

Leading experts in Diabetes, Metabolism and Biomedical Engineering discuss Precision Medicine

13.07.2018 | Event News

Conference on Laser Polishing – LaP: Fine Tuning for Surfaces

12.07.2018 | Event News

11th European Wood-based Panel Symposium 2018: Meeting point for the wood-based materials industry

03.07.2018 | Event News

 
Latest News

Nano-kirigami: 'Paper-cut' provides model for 3D intelligent nanofabrication

16.07.2018 | Physics and Astronomy

New players, standardization and digitalization for more rail freight transport

16.07.2018 | Transportation and Logistics

Researchers discover natural product that could lead to new class of commercial herbicide

16.07.2018 | Agricultural and Forestry Science

VideoLinks
Science & Research
Overview of more VideoLinks >>>