Navigation Links
Opening the data bank -- scientists try to match new protein structures
Date:11/7/2011

Imagine playing Go Fish with 3,000 cards.

Scientists at Rochester Institute of Technology and Dowling College are engaged in a similar game with higher stakes. Instead of cards, they are matching the protein to the job it performs in the human body. Their research could lead to drugs that target proteins and switch on or off specific functions associated with various diseases.

The three-year study is funded by a $417,000 grant from the National Institutes of Health's National Institute of General Medical Sciences and furthers research started in 2006 by Paul Craig, professor in the Department of Chemistry at RIT, and Herbert Bernstein, professor in the Department of Mathematics and Computer Science at Dowling College, in Long Island, N.Y.

Proteins are like nanomachines in the human body that carry out their missionssuch as digesting fats and sugars in muscles, or carrying oxygenand then rapidly degrade. Likewise, rogue proteins can do terrible things. A misshaped protein is like a hastily folded roadmap shoved into a glove compartment, leading to detours down roads of disease. Creutzfeldt-Jakob Disease, or mad cow disease, for instance, results from proteins misfolded into infectious prions.

Students from both universities work with Craig and Bernstein to identify the biological functions of each protein based on the shape or fold of its enzymes. Approximately 75,000 compounds in the Research Collaboratory for Structural Biology Protein Data Banka repository of biological structures of proteins, nucleic acids and complex assemblieshave already been assigned functions. The RIT-Dowling team will investigate the structural coordinates of the remaining 3,000 proteins in the bank.

They will compare proteins from the bank with a library of 400 protein motifs associated with known functions from the Catalytic Site Atlas database, focusing on amino acids and their spatial relationships that dictate a protein's specific mission in the human body. The team will verify and statistically rate the matches using three-dimensional modeling and recommend two or three candidates as possible functions for each protein. The project uses existing active-site templates and new templates created by RIT students.

"We are concentrating on similarities between the active sitesthe places where proteins interact with other molecules," Craig says. "Using active sites allows for much faster processing than finding structural similarity between the entire backbone of two proteins."

Craig is a biochemist who uses computers to address biological questions; Bernstein is a computer scientist who applies algorithms and database design to biological problems. They hope to produce two papers annually throughout the duration of the project.

"We want to be part of the conversation," Craig says.

"We collaborate on problems in molecular graphics and bioinformatics," Bernstein adds. "Our students actively contribute to our research and present their work at scientific meetings. The Internet allows us to function as a coherent group despite the distance between our campuses."


'/>"/>

Contact: Susan Gawlowicz
smguns@rit.edu
585-475-5061
Rochester Institute of Technology
Source:Eurekalert

Related medicine news :

1. New scarless surgery takes out tumors through natural skull opening
2. Heart valve replacement without opening the chest gives new option for non-operable patients
3. Deaths from drug overdose decline 35 percent after the opening of supervised injection site
4. Overdose deaths down 35 percent after opening of Vancouvers supervised injection site: UBC-BC-CfE study
5. Vein-Opening Treatment for MS Stirs Controversy
6. Scientists develop designer protein, opening new door in cancer research
7. Bling My Sling LL Announces Website Launch - A fashionable arm sling manufacturer, announce the opening of their new website bling-my-sling.com
8. Grand Opening of GreenProductsandGifts.com Online Store Offering Eco Friendly Gifts that are Proudly Made in the USA
9. Experts honored at EAU opening ceremony
10. Dreambikes Announces Grand Opening Event
11. Azia Medical Spa in Birmingham, AL to Host Two Day Grand Opening Event March 25 and March 26, 2010.
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:7/24/2017)... ... 2017 , ... Peruvian Ayahuasca retreat, East West Lodge, announced ... and divided between two full-time university students enrolled in U.S. or Canadian accredited ... apply for the scholarship, students are asked to submit an essay between 750 ...
(Date:7/24/2017)... ... ... The International Essential Tremor Foundation (IETF) will host a free educational forum in ... take place on Saturday, Aug. 26 at the Embassy Suites by Hilton Cleveland Rockside ... a.m. to 12 p.m., with check-in beginning at 8 a.m. The event is sponsored ...
(Date:7/24/2017)... ... , ... Every year, thousands of dedicated Higher Education and K12 professionals flock ... coupled with a dynamic theme like Camp Canvas; this year, they’ve managed to take ... , To extend their partnership with Canvas beyond the LMS integration, Modo Labs secured ...
(Date:7/24/2017)... CA (PRWEB) , ... July 24, 2017 , ... ... financial organizations, today announced it has partnered with WALLIX to expand its ... Publication 800-171 . , There are a number of ways to address the authentication ...
(Date:7/24/2017)... ... July 24, 2017 , ... The Topricin Companies, formerly Topical ... Topricin’s revolutionary, natural, after-burn skin care product, Topricin After Burn Cream. ... term skin conditions, including cancer. In the short term, overexposure to sun, ...
Breaking Medicine News(10 mins):
(Date:7/24/2017)... -- Diplomat Pharmacy, Inc. (NYSE: DPLO ) announced ... operating results on Monday, August 7, 2017 after market ... p.m. ET. Shareholders ... of the conference call by dialing 877-201-0168 or 647-788-4901 ... 15 minutes prior to the call. A live webcast ...
(Date:7/21/2017)... EDMONTON, Alberta , July 21, 2017  IBM ... of Alberta in Edmonton, Canada ... journal, Schizophrenia 1 , demonstrating that AI and ... with 74% accuracy. This retrospective analysis also showed ... in schizophrenia patients with significant correlation, based on ...
(Date:7/21/2017)... SPRING, Md. and RESEARCH TRIANGLE ... United Therapeutics Corporation (NASDAQ: UTHR ) announced ... financial results before the market opens on Thursday, July ... Therapeutics will host a teleconference on Thursday, July 27, ... accessible by dialing 1-877-351-5881, with international callers dialing 1-970-315-0533.  ...
Breaking Medicine Technology: