Speeding up drug discovery with rapid 3-D mapping of proteins

May 30, 2012
Using their new rapid technique, Choe's team generated the structure of a hIMP known as TMEM14A, shown here in multiple three-dimensional conformations. Credit: Courtesy of the Salk Institute for Biological Studies

A new method for rapidly solving the three-dimensional structures of a special group of proteins, known as integral membrane proteins, may speed drug discovery by providing scientists with precise targets for new therapies, according to a paper published May 20 in Nature Methods.

The technique, developed by scientists at the Salk Institute for Biological Studies, provides a shortcut for determining the structure of human integral (hIMPs), molecules found on the surface of cells that serve as the targets for about half of all current drugs.

Knowing the exact three-dimensional shape of hIMPs allows drug developers to understand the precise by which current drugs work and to develop that target the proteins.

"Our cells contain around 8,000 of these proteins, but structural biologists have known the three-dimensional structure of only 30 hIMPs reported by the entire field over many years," says Senyon Choe, a professor in Salk's Laboratory and lead author on the paper. "We solved six more in a matter of months using this new technique. The very limited information on the shape of human membrane proteins hampers structure-driven drug design, but our method should help address this by dramatically increasing the library of known hIMP structures."

Integral membrane proteins are attached to the membrane surrounding each cell, serving as gateways for absorbing nutrients, hormones and drugs, removing waste products, and allowing cells to communicate with their environment. Many diseases, including Alzheimer's, and cancer have been linked to malfunctioning hIMPs, and many drugs, ranging from aspirin to schizophrenia medications, target these proteins.

Most of the existing drugs were discovered through brute force methods that required screening thousands of potential molecules in laboratory studies to determine if they had a . Given a blueprint of the 3D structure of a hIMP involved in a specific disease, however, drug developers could focus only on molecules that are most likely to interact with the target hIMP, saving time and expense.

In the past, it was extremely difficult to solve the structure of hIMPs, due to the difficulty of harvesting them from cells and the difficulty of labeling the amino acids that compose the proteins, a key step in determining their three-dimensional configuration.

"One problem was that hIMPs serve many functions in a cell, so if you tried to engineer cells with many copies of the proteins on their membrane, they would die before you could harvest the hIMPs," says Christian Klammt, a postdoctoral researcher in Choe's lab and a first author on the paper.

To get around this, the scientists created an outside-the-cell environment, called cell-free expression system, to synthesize the proteins. They used a plexiglass chamber that contained all the biochemical elements necessary to manufacture hIMPs as if they were inside the cell. This system provided the researchers with enough of the proteins to conduct structural analysis.

The cell-free method also allowed them to easily add labeled amino acids into the biochemical stew, which were then incorporated into the proteins. These amino acids gave off telltale structural clues when analyzed with nuclear magnetic resonance spectroscopy, a method for using the magnetic properties of atoms to determine a molecule's physical and chemical properties.

"It was very difficult and inefficient to introduce labeled amino acids selectively into the protein produced in live cells," says Innokentiy Maslennikov, a Salk staff scientist and co-first author on the paper. "With a cell-free system, we can precisely control what are available for protein production, giving us isotope-labeled hIMPs in large quantities. Using a proprietary labeling strategy we devised a means to minimize the number of samples to prepare."

Prior methods might take up to a year to determine a single protein structure, but using their new method, the Salk scientists determined the structure of six hIMPs within just 18 months. They have already identified 38 more hIMPs that are suitable for analysis with their technique, and expect it will be used to solve the structure for many more.

Paul Slesinger, an associate professor in Salk's Clayton Foundation Laboratories for Peptide Biology, contributed to the research, as did scientists at the Joint Center for Biosciences in Korea, ETH Zurich in Switzerland and the University of California San Francisco.

Other authors on the paper were Monika Bayrhuber, Cédric Eichmann, Navratna Vajpai, Ellis Jeremy Chua Chiu, Katherine Blain, Luis Esquivies, June Hyun Jung Kwon, Bartosz Balana, Ursula Pieper, Andrej Sali, Witek Kwiatkowski and Roland Riek.

Explore further: Scientists create renewable fossil fuel alternative using bacteria

Related Stories

A new tool to reveal structure of proteins

Mar 19, 2012

A new method to reveal the structure of proteins could help researchers understand biological molecules – both those involved in causing disease and those performing critical functions in healthy cells.

The future of drug development

Sep 03, 2010

John Engen, associate professor of chemistry and chemical biology at the Northeastern University, is at the forefront of research that will advance drug discovery and development by making it easier to analyze ...

Similarities cause protein misfolding

May 31, 2011

A large number of illnesses stem from misfolded proteins, molecules composed of amino acids. Researchers at the University of Zurich have now studied protein misfolding using a special spectroscopic technique. ...

Recommended for you

A new synthetic amino acid for an emerging class of drugs

Aug 31, 2014

Swiss scientists have developed a new amino acid that can be used to modify the 3-D structure of therapeutic peptides. Insertion of the amino acid into bioactive peptides enhanced their binding affinity up to 40-fold. Peptides ...

Protein glue shows potential for use with biomaterials

Aug 28, 2014

Researchers at the University of Milan in Italy have shown that a synthetic protein called AGMA1 has the potential to promote the adhesion of brain cells in a laboratory setting. This could prove helpful ...

User comments : 0