Featured Research

from universities, journals, and other organizations

Algorithm Predicts Interactions Between Proteins Whose Structures Are Unsolved

Date:
November 13, 2002
Source:
University At Buffalo
Summary:
A promising new algorithm that can predict interactions between proteins whose structures are unsolved has been developed by Jeffrey Skolnick, Ph.D., University at Buffalo Distinguished Professor and director of the Center of Excellence in Bioinformatics.

BUFFALO, N.Y. -- A promising new algorithm that can predict interactions between proteins whose structures are unsolved has been developed by Jeffrey Skolnick, Ph.D., University at Buffalo Distinguished Professor and director of the Center of Excellence in Bioinformatics.

The research is published in today's (Nov. 15, 2002) issue of Proteins.

Called MULTIPROSPECTOR, the new algorithm takes protein interaction prediction to a new level because it works on proteins on which little structural information exists, providing three-dimensional models of the protein-protein complex and identifying the amino acid residues that interact.

According to Skolnick, the new method takes the entire field of structural genomics an important step closer to the ultimate goal of using detailed information about genes and the proteins they encode to design more effective pharmaceuticals.

"The overall goal," he said, "is to develop personalized medicine, which is based on understanding how a drug affects you versus how it affects me."

He noted: "With this paper, we are moving toward an understanding of how the whole system works, what's known as systems biology, which is the key revolution in the post-genomic era," he explained.

According to Skolnick, complexes of interacting proteins provide exciting and novel targets for potential new drugs.

"Right now, very few drugs exist that inhibit protein-protein interactions; most work against single molecules," he said.

But, he noted, the Protein Data Bank, the international "public library" of solved protein structures from which scientists draw data, contains not just isolated molecules, but in many instances solved compounds of two or more proteins interacting.

"Lots of cellular signals are mediated by these protein-protein interactions," he said, "and we want to know exactly who's interacting with whom. Often, the function of one protein can be deduced by studying the proteins with which it interacts."

Skolnick conjectured that perhaps there are millions of these interactions, a seemingly intractable problem.

But, he said, the process is greatly accelerated if you have a computational method that helps pinpoint the sites on the interacting proteins that will help scientists discover their role in biochemical pathways.

"That's what our method aims to do," he explained. "So, using our supercomputer, we can start to see how the path fits together, how this enzyme interacts with that small molecule or functions in a cascade of cellular processes."

The paper describes how MULTIPROSPECTOR was able to correctly predict protein-protein interactions between many thousands of proteins in brewer's yeast, a model organism in structural genomics.

Skolnick and his colleagues took what is known as a threading approach to the problem, in which an amino acid sequence is "threaded" through a library of protein structures that already have been solved.

But they take the threading process a step further. After finding matches for an amino acid sequence, the process goes through a second threading phase for both proteins, but this time a value is assigned for the interfacial energy, the surface energy between the proteins, revealing the stability of the interaction and thus, the likelihood that these are the structures that are interacting.

"We have built a sensitive interfacial potential that appears to often work at assessing interaction stability," said Skolnick.

He explained that predicting interactions between proteins provides scientists with an additional and important tool in reaching the point where genotype (what's happening genetically) can be linked to phenotype (what's happening clinically, i.e. what is the physiological manifestation of specific protein structures in a particular cellular pathway).

The research was conducted while Skolnick was at the Danforth Plant Science Center in St. Louis. The paper is co-authored by Long Lu, Ph.D., and Hui Lu, Ph.D., both of Danforth.


Story Source:

The above story is based on materials provided by University At Buffalo. Note: Materials may be edited for content and length.


Cite This Page:

University At Buffalo. "Algorithm Predicts Interactions Between Proteins Whose Structures Are Unsolved." ScienceDaily. ScienceDaily, 13 November 2002. <www.sciencedaily.com/releases/2002/11/021113071213.htm>.
University At Buffalo. (2002, November 13). Algorithm Predicts Interactions Between Proteins Whose Structures Are Unsolved. ScienceDaily. Retrieved July 31, 2014 from www.sciencedaily.com/releases/2002/11/021113071213.htm
University At Buffalo. "Algorithm Predicts Interactions Between Proteins Whose Structures Are Unsolved." ScienceDaily. www.sciencedaily.com/releases/2002/11/021113071213.htm (accessed July 31, 2014).

Share This




More Matter & Energy News

Thursday, July 31, 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
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
Smartphone Powered Paper Plane Debuts at Airshow

Smartphone Powered Paper Plane Debuts at Airshow

AP (July 30, 2014) Smartphone powered paper airplane that was popular on crowdfunding website KickStarter makes its debut at Wisconsin airshow (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