Featured Research

from universities, journals, and other organizations

MIT Finds Most Complex Protein Knot Ever Seen

Date:
September 26, 2006
Source:
Massachusetts Institute of Technology
Summary:
An MIT team has discovered the most complicated knot ever seen in a protein, and they believe it may be linked to the protein's function as a rescue agent for proteins marked for destruction.

MIT researchers recently found that human ubiquitin hydrolase, shown here, has the most complicated knot ever observed in a protein. The simplified diagram, inset, shows the knot in the protein, which crosses itself five times.
Credit: Image courtesy of Peter Virnau

An MIT team has discovered the most complicated knot ever seen in a protein, and they believe it may be linked to the protein's function as a rescue agent for proteins marked for destruction.

"In proteins, the three-dimensional structure is very important to the function, and this is just one example," said Peter Virnau, a postdoctoral fellow in physics and an author of a paper on the work that appears in the Sept. 15 issue of the Public Library of Science, Computational Biology.

Knots are rare in proteins - less than 1 percent of all proteins have any knots, and most are fairly simple. The researchers analyzed 32,853 proteins, using a computational technique never before applied to proteins at this scale.

Of those that had knots, all were enzymes. Most had a simple three-crossing, or trefoil knot, a few had four crossings, and the most complicated, a five-crossing knot, was initially found in only one protein - ubiquitin hydrolase.

That complex knot may hold some protective value for ubiquitin hydrolase, whose function is to rescue other proteins from being destroyed - a dangerous job.

When a protein in a cell needs to be destroyed, it gets labeled with another protein called ubiquitin. "It's a death mark for the protein," said Leonid Mirny, an author of the paper and an associate professor in the MIT-Harvard Division of Health Sciences and Technology.

Once the "death mark" is applied, proteins are shuttled to a cell structure called a proteasome, which pulls the protein in and chops it into pieces. However, if ubiquitin hydrolase intervenes and removes the ubiquitin, the protein is saved.

The complicated knot found in ubiquitin hydrolase may prevent it from getting sucked into the proteasome as it works, Mirny said. The researchers hypothesize that proteins with complex knots can't be pulled into the proteasome as easily, and the knots may make it harder for the protein to unfold, which is necessary for degradation.

The same knot is found in ubiquitin hydrolase in humans and in yeast, supporting the theory that there is a connection between the knot and the protein's function. This also seems to suggest that the knot has been "highly preserved throughout evolution," Virnau said.

Until now, scientists have not paid much attention to knots in proteins, but the MIT researchers hope their work will ignite further interest in the subject. "We just hope this will become a part of the routine crystallographers and NMR spectroscopists do when they solve a structure," Mirny said.

Virnau is working on a computer program and a web server, soon to be publicly available, that can analyze the structure of any protein to see if it has knots, which he believes could be helpful to researchers in structural genomics. (Structural genomics aims to determine the structure of all proteins produced by a given organism.)

Since their initial screening, the researchers have discovered five-crossing knots in two other proteins - a brain protein whose overexpression and mutations are linked with cancer and Parkinson's disease, and a protein involved in the HIV replication cycle.

They have also found examples of proteins that are closely related and structurally similar except for the presence or absence of a knot. Two versions of the enzyme transcarbamylase, from humans and certain bacteria, catalyze different reactions, depending on whether or not there is a knot. The researchers speculate that somewhere along the evolutionary line, the sequence that allowed a protein to form the knot was added or deleted.

The third author on the paper is Mehran Kardar, an MIT physics professor. The research was funded by the National Science Foundation and the German Research Foundation.


Story Source:

The above story is based on materials provided by Massachusetts Institute of Technology. Note: Materials may be edited for content and length.


Cite This Page:

Massachusetts Institute of Technology. "MIT Finds Most Complex Protein Knot Ever Seen." ScienceDaily. ScienceDaily, 26 September 2006. <www.sciencedaily.com/releases/2006/09/060925143301.htm>.
Massachusetts Institute of Technology. (2006, September 26). MIT Finds Most Complex Protein Knot Ever Seen. ScienceDaily. Retrieved August 1, 2014 from www.sciencedaily.com/releases/2006/09/060925143301.htm
Massachusetts Institute of Technology. "MIT Finds Most Complex Protein Knot Ever Seen." ScienceDaily. www.sciencedaily.com/releases/2006/09/060925143301.htm (accessed August 1, 2014).

Share This




More Matter & Energy News

Friday, August 1, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Britain Testing Driverless Cars on Roadways

Britain Testing Driverless Cars on Roadways

AP (July 30, 2014) — British officials said on Wednesday that driverless cars will be tested on roads in as many as three cities in a trial program set to begin in January. Officials said the tests will last up to three years. (July 30) Video provided by AP
Powered by NewsLook.com
7 Ways to Use Toothpaste: Howdini Hacks

7 Ways to Use Toothpaste: Howdini Hacks

Howdini (July 30, 2014) — Fresh breath and clean teeth are great, but have you ever thought, "my toothpaste could be doing more". Well, it can! Lots of things! Howdini has 7 new uses for this household staple. Video provided by Howdini
Powered by NewsLook.com
Smoked: 2015 Ducati Diavel Vs 2014 Chevy Corvette Stingray Drag Race

Smoked: 2015 Ducati Diavel Vs 2014 Chevy Corvette Stingray Drag Race

Cycle World (July 30, 2014) — The Bonnier Motorcycle Group presents Smoked; a three part video series. In this episode the 2015 Ducati Diavel takes on the 2014 Chevy Corvette Stingray Video provided by Cycle World
Powered by NewsLook.com
Amid Drought, UCLA Sees Only Water

Amid Drought, UCLA Sees Only Water

AP (July 30, 2014) — A ruptured 93-year-old water main left the UCLA campus awash in 8 million gallons of water in the middle of California's worst drought in decades. (July 30) Video provided by AP
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:
from the past week

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