Research discovery: Near-complete set of templates for protein complexes exists today

Jun 08, 2012

(Phys.org) -- Visualize trying to finish a jigsaw puzzle where each individual piece keeps changing shape. If that sounds like an impossible task, imagine the vexing job scientists have faced in computer modeling of interactions between tens of thousands of proteins that are fundamental to biology.

“Proteins are not rigid bodies — they change shape, and they’re flexible — so often you’d want to match two structures that do not match,” said Ilya Vakser, professor of bioinformatics and molecular biosciences and director of the Center for Bioinformatics at the University of Kansas. “A reliable solution to this problem has been a holy grail of computational structural biology.”

For years, scientists have depended on computer modeling to characterize proteins as physical objects. Such accurate computer modeling is based on “template” structures of proteins determined by X-ray crystallography and nuclear magnetic resonance.

Until now, it was believed that many years of work were required before a practically useful set of templates is available to model protein-protein complexes. But Vakser and his colleague Petras Kundrotas at KU, along with their collaborators at Université Paris-Sud, France, and University of California San Diego have discovered that an almost-whole set exists already, a breakthrough that has far-reaching implications for structural , and could pave the way for new drugs and therapies to treat a host of diseases.

Their paper, “Templates are available to model nearly all complexes of structurally characterized proteins,” is published in the Early Edition issue of Proceedings of the National Academies of Sciences.

An improved grasp of protein would be key to developing drugs and therapies that change behavior to benefit human health, according to Vakser.

“You can think of the world of proteins as a crowded environment where a lot of individual molecules float around and bump into each other,” he said. “If it’s a random interaction, nothing happens — they walk away. But if it has physiological importance, then they might stick to each other and change shape or transfer an electron.”

The ability to influence these protein-protein interactions could mean new treatments for common killers like cancer and coronary heart disease, as well as a host of other ailments.

“This gives us a greater ability to model these interactions and to find ways to cure diseases,” Vakser said. “Lots of diseases are caused by abnormalities of protein-protein interactions, or interactions that are undesirable. But to modulate them through drugs, we need to know how it all happens.”

Best of all, the KU researcher said that new approaches to affect protein-protein interactions could be developed quickly.

“It wouldn’t be decades,” said Vakser. “As opposed to studies that would have importance many years from now, to drug design this has immediate application.”

Explore further: Scientists find key to te first cell differentiation in mammals

Related Stories

New protein structure model to inhibit cancer

Jul 29, 2011

Researchers at the University of Hertfordshire have developed a new structural model of a protein, which makes it possible to develop more effective drugs to target diseases such as cancer, heart disease and influenza.

Cell survival protein research reveals surprise structure

Oct 14, 2011

Researchers from the Walter and Eliza Hall Institute have found a structural surprise in a type of protein that encourages cell survival, raising interesting questions about how the proteins function to influence ...

Protein discovery could lead to new HIV drugs

Jan 27, 2012

(Medical Xpress) -- A team of researchers at the Johns Hopkins Bloomberg School of Public Health recently discovered a new protein that enables HIV to destroy human cells. The finding provides scientists with ...

Predicting how proteins will partner

Mar 28, 2012

Growing up with a father who taught at Cornell University, and surrounded by friends whose parents were also on Cornell faculty, Amy Keating had little doubt that she would follow the same path.

Untangling a protein's influences

Jan 06, 2012

Most proteins have multiple moving parts that rearrange into different conformations to execute particular functions. Such changes may be induced by molecules in the immediate environment, including water ...

Recommended for you

Research helps identify memory molecules

18 hours ago

A newly discovered method of identifying the creation of proteins in the body could lead to new insights into how learning and memories are impaired in Alzheimer's disease.

Computer simulations visualize ion flux

19 hours ago

Ion channels are involved in many physiological and pathophysiological processes throughout the human body. A young team of researchers led by pharmacologist Anna Stary-Weinzinger from the Department of Pharmacology ...

Neutron diffraction sheds light on photosynthesis

19 hours ago

Scientists from ILL and CEA-Grenoble have improved our understanding of the way plants evolved to take advantage of sunlight. Using cold neutron diffraction, they analysed the structure of thylakoid lipids found in plant ...

DNA may have had humble beginnings as nutrient carrier

Sep 01, 2014

New research intriguingly suggests that DNA, the genetic information carrier for humans and other complex life, might have had a rather humbler origin. In some microbes, a study shows, DNA pulls double duty ...

Central biobank for drug research

Sep 01, 2014

For the development of new drugs it is crucial to work with stem cells, as these allow scientists to study the effects of new active pharmaceutical ingredients. But it has always been difficult to derive ...

User comments : 1

Adjust slider to filter visible comments by rank

Display comments: newest first

Moebius
5 / 5 (1) Jun 08, 2012
This article is completely uninformative.