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Argonne Contribute 1,000th Structure to Protein Data Bank
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Argonne Contribute 1,000th Structure to Protein Data Bank

Argonne Contribute 1,000th Structure to Protein Data Bank
News

Argonne Contribute 1,000th Structure to Protein Data Bank

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Researchers at the Structural Biology Center (SBC) at the U.S. Department of Energy's Argonne National Laboratory have contributed their 1,000th structure to the Protein Data Bank

The data bank houses the molecular structures of all proteins characterized so far and makes them available to researchers worldwide to study.

This structure - and its 999 predecessors determined with data obtained at Argonne's SBC - provides important pieces to the puzzle of understanding human and environmental health by imaging the molecules that control and regulate it.

The 1,000th deposit is a three-dimensional structure of thrombospondin-1 that provides insight into how cells sense and communicate information about their health and how that information triggers cell responses ranging from raising defenses to fight disease and other perceived threats to cell death.

Thrombospondins are a family of extracellular glycoproteins that regulate cellular behavior during tissue genesis and repair such as wound healing.

These functions are mediated by its interaction with a proteins and proteoglycans in the extracellular environment and at the cell surface.

The research was published in Structure (2006 Jan. 14 (1): 33-42), and is a collaboration between the Dana Farber Cancer Institute of Harvard Medical School and Argonne's SBC.

"SBC has been a pioneer of protein structure determination at the APS and worldwide," said Argonne's Associate Laboratory Director for Scientific User Facilities Murray Gibson. "This is a marvelous achievement."

Some of the structures have revealed how proteins are synthesized inside the cell (ribosome), how we see light (rhodopsin), how cells communicate (integrin) and how cells differentiate (gene regulatory factors).

Other findings have shed insight into origins of diseases including cancer, diabetes, osteoporosis, and infections by human pathogens causing staph, anthrax and other infectious diseases.

Among the characterized proteins are 280 related to human disease - including cancer, the deadly anthrax bacterium and the common cold virus - 150 from human pathogens and 210 more with biotechnological applications that will contribute to increased productivity, new biomedical tests and applications.

"This is the first time any center has produced so many structures," said Argonne's Director of the SBC Andrzej Joachimiak.

"When you consider it took six years (starting in 1972) to deposit the first 37 structures into the Protein Data Bank, you see how technology has advanced for SBC users to have deposited 1,000 structures in six years."

"One of the challenges facing structural biologists and indeed much of biology has been the slow pace, often measured in months or years, of determining the structures of biomolecules that are important for advances in energy, health and the environment," said Ari Patrinos, DOE associate director of science for biological and environmental research.

"This achievement represents an important step to narrow the gap between the current pace of gene discovery and the ability of scientists to have access to new information on the functions of those genes," Patrinos said.

"This Department of Energy-funded user facility continues to find ways for scientists to further speed the process of protein structure determination."

Joachimiak credits the high productivity, quality and efficiency to the powerful X-rays beams at the APS and advances in technology, automation and software.

"They allow us to deliver the greatest detail to scientists, and to do it quickly and efficiently," he said.

"It is also a reflection of the quality of the scientific team that Joachimiak has assembled," said Argonne Biosciences Director Lee Makowski.

"These scientists are available around the clock to help visiting scientists from all over the world to collect data from their protein crystals."

"We are committed," said Joachimiak, "to modernize the facility and expand its capabilities to maintain its leadership in structural biology for the community."

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