Now scientists report that they have found a way to penetrate the mystery. They have worked out every step in the molecular dance that enables one such transporter to do its job.
The new findings, reported in the Proceedings of the National Academy of Sciences, will help scientists figure out how other transporters work. The work also offers new insights into multi-drug-resistant (MDR) cancers, some of which use these transporters to export cancer-killing drugs. (Watch a video about the research that includes an animation of the transport protein in action.)
The transporter in the study, MsbA, belongs to an ancient family of proteins that carry large molecules across membranes. It is the bacterial version of a transporter in human cells (called p-glycoprotein) that helps pump drugs out of the cell, said Emad Tajkhorshid, a University of Illinois professor of biochemistry and of pharmacology who led the research. P-glycoprotein is overexpressed in some cancer cells, helping the cells eject drugs meant to kill them.
“There is a lot of research going on in pharmaceutical companies trying to find an inhibitor of p-glycoprotein,” Tajkhorshid said. “If we can understand the transport cycle, we have a much larger repertoire of structures for rational drug design.”
Research on large, membrane-bound proteins like MsbA has always been problematic because they are not easy to crystallize (a common technique for determining a protein’s three-dimensional shape) and each crystal structure reflects only one of the many conformations these shape-shifting proteins undergo, Tajkhorshid said.
“If you want to design a drug for a protein usually you look at the structure and see how you can design a molecule that binds to a particular conformation,” he said. Knowing all the different conformations a protein adopts will offer more targets for drug design, he said.
Before this study, researchers had to guess at the changes that occurred between the transporter’s inward-facing (open to the cell interior) and outward-facing (open to the cell exterior) states, the only two known conformations. Rather than guessing, Tajkhorshid and his co-author, postdoctoral researcher Mahmoud Moradi, took a more painstaking, but ultimately more fruitful, approach. They used molecular dynamics simulations to look at many potential pathways leading from one conformation to the other, simulating individual steps in the transport cycle in atomic-level detail. Then they measured the energetics of each step to discover which steps required the least work, and thus were most likely to occur.
“The main thing that was new here was trying many pathways and using what we call non-equilibrium work – how much work it takes to walk that path – to judge the quality of the pathway,” Tajkhorshid said.
Their simulations included every atom in the protein, the adjoining membrane and the surrounding water molecules – about 250,000 atoms in all, the researchers said.
“It took us many months to search as many possible paths as we could imagine connecting the two end states,” Tajkhorshid said. “And when we did that we slowly realized that we could discover much better pathways” than those that had been proposed before. The result was what the researchers call a “minimum work path” leading from one known protein configuration to the other.
The research indicates that MsbA has components in its interior that are locked together as long as the transporter remains open to the cell’s interior. A series of random undulations gradually lead this middle section to twist, unlocking those components and allowing other changes that eventually open the protein to the outside of the cell.
“We call it a doorknob mechanism,” Tajkhorshid said. “It’s locked, so you have to twist it first before you open it.”
The new approach will aid other studies of complex protein transporters whose behavior has baffled researchers, Tajkhorshid said.
“This is the first time that we are characterizing a very complex structural transition at atomic-level resolution for a large protein,” he said.
Tajkhorshid is an affiliate of the Beckman Institute for Advanced Science and Technology at the U. of I.
The National Institutes of Health (grants U54-GM087519, R01-GM086749 and P41-GM104601) supported this research.
Diana Yates | University of Illinois
Novel mechanisms of action discovered for the skin cancer medication Imiquimod
21.10.2016 | Technische Universität München
Second research flight into zero gravity
21.10.2016 | Universität Zürich
Researchers from the Institute for Quantum Computing (IQC) at the University of Waterloo led the development of a new extensible wiring technique capable of controlling superconducting quantum bits, representing a significant step towards to the realization of a scalable quantum computer.
"The quantum socket is a wiring method that uses three-dimensional wires based on spring-loaded pins to address individual qubits," said Jeremy Béjanin, a PhD...
In a paper in Scientific Reports, a research team at Worcester Polytechnic Institute describes a novel light-activated phenomenon that could become the basis for applications as diverse as microscopic robotic grippers and more efficient solar cells.
A research team at Worcester Polytechnic Institute (WPI) has developed a revolutionary, light-activated semiconductor nanocomposite material that can be used...
By forcefully embedding two silicon atoms in a diamond matrix, Sandia researchers have demonstrated for the first time on a single chip all the components needed to create a quantum bridge to link quantum computers together.
"People have already built small quantum computers," says Sandia researcher Ryan Camacho. "Maybe the first useful one won't be a single giant quantum computer...
COMPAMED has become the leading international marketplace for suppliers of medical manufacturing. The trade fair, which takes place every November and is co-located to MEDICA in Dusseldorf, has been steadily growing over the past years and shows that medical technology remains a rapidly growing market.
In 2016, the joint pavilion by the IVAM Microtechnology Network, the Product Market “High-tech for Medical Devices”, will be located in Hall 8a again and will...
'Ferroelectric' materials can switch between different states of electrical polarization in response to an external electric field. This flexibility means they show promise for many applications, for example in electronic devices and computer memory. Current ferroelectric materials are highly valued for their thermal and chemical stability and rapid electro-mechanical responses, but creating a material that is scalable down to the tiny sizes needed for technologies like silicon-based semiconductors (Si-based CMOS) has proven challenging.
Now, Hiroshi Funakubo and co-workers at the Tokyo Institute of Technology, in collaboration with researchers across Japan, have conducted experiments to...
14.10.2016 | Event News
14.10.2016 | Event News
12.10.2016 | Event News
21.10.2016 | Health and Medicine
21.10.2016 | Information Technology
21.10.2016 | Materials Sciences