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:4/29/2016)... Ferry, New York (PRWEB) , ... April 30, 2016 , ... ... the Dobbs Ferry campus. The following programs will be expanding due to high ... Management (HRM). The expansion will begin this summer. , School of ...
(Date:4/29/2016)... MA (PRWEB) , ... April 29, 2016 , ... ... the Two Ten Footwear Foundation, the national charitable foundation serving the footwear industry, ... With 8,000 volunteers representing more than 130 companies across 23 states during the ...
(Date:4/29/2016)... , ... April 29, 2016 , ... ... Spiritual Awakening , announces the addition Onnit brand Alpha BRAIN and New Mood ... of Onnit brain and mood optimization products to the store is just one ...
(Date:4/29/2016)... Georgia (PRWEB) , ... April 29, 2016 , ... On ... rural hospitals across the Southeast, celebrated the signature of Gov. Nathan Deal on SB ... Rep. Geoff Duncan (R - Cumming), offers a 70% tax credit to individuals and ...
(Date:4/29/2016)... CA (PRWEB) , ... April 29, 2016 , ... ... advocating optimistic healthcare awareness and author of best seller "LOVE, MEDICINE and MIRACLES") ... Radio Monday, May 2, 2016 and podcasted thereafter . Dr. Bernie Siegel, ...
Breaking Medicine News(10 mins):
(Date:4/28/2016)... 2016 Treato , the ... announced today that it has been named a Cool ... in Life Sciences, 2016, Stephen Davies , ... focuses on life-science- oriented analytics, algorithms and smart machine ... doctors, confirm medication ingestion, and analyze unstructured information.   ...
(Date:4/28/2016)... Calif. , April 28, 2016 /PRNewswire/ ... Validation Lifecycle Management Solutions (VLMS) today announced ... and services for sufferers of chronic kidney ... System to manage their corporate validation process. ... seeking a software solution to manage their ...
(Date:4/27/2016)... 2016   ... sur le trimestre, soutenu par une croissance de ... Croissance de +16% des ventes aux hôpitaux et ... Technologies (Euronext : MKEA, FR0010609263 ; OTCQX : MKEAY), inventeur de ... son chiffre d,affaires pour le premier trimestre clos ...
Breaking Medicine Technology: