Navigation Links
Many needles, many haystacks

Most of what happens in cells is the work of machines that contain dozens of molecules, chiefly proteins. With the completion of human and other genomes, researchers now have a nearly complete "parts list" of such machines; what's lacking now is the manual telling where all the pieces go. A new study by scientists at the European Molecular Biology Laboratory (EMBL) promises to answer this question for some of the smallest and trickiest components in the cellular toolbox. Their work appears in the current issue of the Public Library of Science's on-line journal, PLoS Biology.

A protein consists of a sticky string of amino acids which usually folds up because of attractions between some of its atoms. This creates a bundle called a globular domain whose shape and chemistry determine what other molecules can bind to it.

"If we could look at the chemical 'spelling' of a protein and guess what machines it fits into, we'd know a lot more about what happens in cells," says Rob Russell, head of the Heidelberg lab that carried out the current study. "We've made a lot of progress in predicting how globular domains interact with each other. But sometimes a surface on one globular domain will grab a tiny, string-like region of another protein called a linear motif. Finding such motifs and predicting where they fit in is like looking for needles in haystacks."

Or like looking at a line of automobiles and trying to decide which one a bulky motor fits into ?versus trying to find where a tiny screw goes. Linear motifs are so small that it is hard to tell what features allow them to bind to other molecules. Now Victor Neduva, a PhD student in Russell's group, has developed a method to scan molecules and tease out new linear motifs.

"If two or more different proteins share a binding partner, there is often a common motif," Neduva says. "The hard part is finding a 3-to-8 'letter' pattern in a protein sequence that may be thousands of amino acids long."The method Neduva and his colleagues invented draws on large-scale studies of protein binding in the cells of yeast, flies, worms and humans. Those studies have produced parts lists of molecular machines. And the data holds a wealth of information about linear motifs ?if it can be mined.

The scientists distilled all of this information in a series of steps ?discarding parts of the proteins likely to dock via large surfaces, and zooming in on small regions of the remaining molecules that might hold motifs. Then it was up to the computer to scan the sequences for small patterns. The attempt was successful: in the fly data, for example, 26 sets of proteins seemed to be interacting through linear motifs.

"One challenge was to eliminate red herrings, which crop up everywhere when you look for very small patterns," Russell says. "The fact that nine of these motifs were already known was a sign we were on the right trail; we then did follow-up experiments in collaboration with Luis Serrano's group at EMBL to test some of the others."

One prediction, for example, suggested that a linear motif would bind to the fly protein translin. The scientists verified that this happened, then they made subtle changes in the sequence. When these changes stopped the molecules binding, they knew they had a new linear motif.

Now the lab will expand the method; Russell predicts that hundreds of linear motifs remain to be discovered. This has important implications for the study of genetic diseases. "A lot of work has gone into discovering mutations that affect protein binding," he says. "Because linear motifs are so small, every bit of information is crucial, and any change is likely to be disruptive. But so far, because of their size, these motifs have been below the radar of most methods to tie protein structures to disease."


'"/>

Source:European Molecular Biology Laboratory


Related biology news :

1. Finding Cures For Tropical Diseases: Is Open Source An Answer?
2. Fundamental Finding Yields Insight into Stem Cells, Cancer; Opens Door to Drug Discovery
3. Findings have implications for tracking disease, drugs at the molecular level
4. Finding hidden invaders in a Hawaiian rain forest
5. New Finding May Aid Adult Stem Cell Collection
6. Finding the minds eye
7. Findings advance use of adult stem cells for replacement bone
8. Finding a virus is not all bad news
9. Finding a better way to make biodiesel
10. Finding paves way for better treatment of autoimmune disease
11. Finding the right mix: A biomaterial blend library
Post Your Comments:
*Name:
*Comment:
*Email:


(Date:1/8/2016)... and MANCHESTER, United Kingdom , Jan. ... developer of innovative sensor-based diagnostic products, today announced the closing ... new and existing investors.  Proceeds from the financing will be ... , a hand-held device for detecting early-stage pressure ulcers. ... Ireland after receiving CE Mark approval. The device,s ...
(Date:1/7/2016)... NEW YORK , Jan. 7, 2016 ... as regional markets for biometric technologies and devices, identifying ... application market for various types of biometric devices. Includes ... report to: Identify newer markets and explore the ... of biometric devices. Examine each type of biometric technology, ...
(Date:1/7/2016)... , Jan. 7, 2016  A United States ... the first court in the country to interpret a ... lawsuit to go forward against the photo website Shutterfly ... BRIAN NORBERG vs. SHUTTERFLY, INC.; and ... plaintiff alleges that Shutterfly violates the Illinois Biometric Privacy ...
Breaking Biology News(10 mins):
(Date:2/4/2016)... ... 2016 , ... Shimadzu Scientific Instruments will showcase several new ... poster sessions, and present on the analysis of mycotoxins and medical cannabis at ... 10 at the Georgia World Congress Center in Atlanta, Georgia. , Attendees ...
(Date:2/4/2016)... , Feb. 4, 2016 Beike Biotechnology, the ... medical institutions attended a ceremony in late 2015 to ... cell therapy in 2016. --> ... Translation Platform for Personalized Cell Therapy" was hosted by ... Production Center, both subsidiaries of Beike Biotechnology Co., Ltd. ...
(Date:2/4/2016)... VANCOUVER, British Columbia and MENLO PARK, ... Inc. (OTCQX: DMPI) ("DelMar" and the "Company"), a biopharmaceutical ... therapies, today announced that it will present at the ... on Monday, February 8, 2016 at 10:00 a.m. EST in ... Jeffrey Bacha , DelMar,s president and CEO, will provide an ...
(Date:2/4/2016)... 2016 ContraVir Pharmaceuticals, Inc. (NASDAQ: CTRV ... commercialization of targeted antiviral therapies, announced today that it ... to be held February 8-9, 2016, at the Waldorf ... Growth & Healthcare Conference, taking place in ... James Sapirstein , Chief Executive Officer of ContraVir, ...
Breaking Biology Technology: