Featured Research

from universities, journals, and other organizations

Key Mechanisms For Affinity Between Transient Binding Proteins

Date:
July 2, 2008
Source:
Institute for Research in Biomedicine (IRB Barcelona)
Summary:
Researchers 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.

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.

Related Articles


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.

"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.

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.


Story Source:

The above story is based on materials provided by Institute for Research in Biomedicine (IRB Barcelona). Note: Materials may be edited for content and length.


Journal Reference:

  1. Amelie Stein and Patrick Aloy. Contextual specificity in peptide-mediated protein interaction. PLoS One, July 1, 2008 DOI: 10.1371/journal.pone.0002524

Cite This Page:

Institute for Research in Biomedicine (IRB Barcelona). "Key Mechanisms For Affinity Between Transient Binding Proteins." ScienceDaily. ScienceDaily, 2 July 2008. <www.sciencedaily.com/releases/2008/07/080702094601.htm>.
Institute for Research in Biomedicine (IRB Barcelona). (2008, July 2). Key Mechanisms For Affinity Between Transient Binding Proteins. ScienceDaily. Retrieved January 24, 2015 from www.sciencedaily.com/releases/2008/07/080702094601.htm
Institute for Research in Biomedicine (IRB Barcelona). "Key Mechanisms For Affinity Between Transient Binding Proteins." ScienceDaily. www.sciencedaily.com/releases/2008/07/080702094601.htm (accessed January 24, 2015).

Share This


More From ScienceDaily



More Plants & Animals News

Saturday, January 24, 2015

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Florida Might Legalize Black Bear Hunting

Florida Might Legalize Black Bear Hunting

Newsy (Jan. 24, 2015) A string of black bear attacks has Florida officials considering lifting the ban on hunting the animals to control their population. Video provided by Newsy
Powered by NewsLook.com
Ebola Killing Large Portion Of Ape Population

Ebola Killing Large Portion Of Ape Population

Newsy (Jan. 23, 2015) Experts estimate Ebola has wiped out one-third of the world&apos;s gorillas and chimpanzees. Video provided by Newsy
Powered by NewsLook.com
Controversy Shrouds Captive Killer Whale in Miami

Controversy Shrouds Captive Killer Whale in Miami

Reuters - Light News Video Online (Jan. 23, 2015) Activists hope the National Oceanic and Atmospheric Agency (NOAA) will label killer whales endangered, allowing lawyers to sue a Miami aquarium to release an orca into the wild after 44 years. Jillian Kitchener reports. Video provided by Reuters
Powered by NewsLook.com
‘Healthy’ Foods That Surprisingly Pack on Pounds

‘Healthy’ Foods That Surprisingly Pack on Pounds

Buzz60 (Jan. 23, 2015) Some &apos;healthy&apos; foods are actually fattening. Fitness and nutrition expert John Basedow (@JohnBasedow) shines a light on the sneaky foods like nuts, seeds, granola, trail mix, avocados, guacamole, olive oil, peanut butter, fruit juices and salads that are good for you...but not so much for your waistline. Video provided by Buzz60
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:

Strange & Offbeat Stories


Plants & Animals

Earth & Climate

Fossils & Ruins

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins