Scientists Report Cryo-EM Structure of a Human Platelet Integrin Molecule

By Jason Socrates Bardi

Two researchers at The Scripps Research Institute (TSRI) recently published the first detailed three-dimensional model for the human platelet integrin alphaIIbbeta3—a signaling molecule that is important for activating platelets, which leads to the healthy formation of blood clots in response to a cut as well as clots that obstruct blood flow to healthy tissue.

The structure, which was obtained through electron cryo-microscopy (cryo-EM), image analysis, and molecular modeling, will appear in this week's issue of the journal Proceedings of the National Academy of the Sciences and reveals new structural details of this important molecule.

These results will be relevant for the design of new drugs to treat health conditions in which the formation of blood clots is undesirable, such as during myocardial infarctions (heart attacks) and strokes. Medical techniques like balloon angioplasty and intracoronary stent implantation are designed to clear blocked arteries but can also cause the formation of thrombi. In fact, several recent clinical trials have demonstrated that alphaIIbbeta3 inhibitors have benefit in the medical treatment not only for heart attacks but also during angioplasty and stent placement.

The Structure Revealed

Picture an integrin as a large button on an overcoat. Most of it sits exposed on the outside of the coat, but it is connected by threads that extend to the inside of the material.

Actually, the integrin is something of a scientific marvel because it transduces signals over a distance of nearly 200 Ångstroms, whereas most signaling molecules work over a distance of 10 to 15 Ångstroms. Integrins are made up of two separate polypeptide chains (called the alpha and beta chains) that come in a variety of forms. Recent crystallographic studies by the Arnaout group at Harvard revealed that the large extracellular portion of the molecule, the "button," has 12 distinct folding "domains."

"Integrins have a large and very complicated structure," says Mark Yeager, M.D., Ph.D., who published this latest integrin structure with his postdoctoral fellow Brian Adair, Ph.D. "They are a broad class of signaling molecules that affect diverse biological processes such as development, angiogenesis, wound healing, neoplastic transformation, and thrombosis."

The integrin alphaIIbbeta3 is particularly important in the process that leads to thrombosis because it is one of the key signaling molecules on platelets, the disk-shaped cells that are involved in blood clotting. There are typically 40,000 to 80,000 on the surface of any given platelet, spanning the platelet membranes, where they are involved in signal transduction—detecting specific molecules (ligands) outside the cell and communicating that detection to the inside, or vice-versa. The ligands are proteins attached to other cells, in the extracellular matrix, or that freely circulate in the bloodstream.

When these ligand molecules bind to the extracellular integrin subunits, they induce "outside-in" signaling in which a three-dimensional conformational change at one end of the integrin is propagated through the membrane to the other end of the integrin. Thus, the binding event on one side of the cell is "transduced" through the cellular membrane. Proteins inside cells can also bind to the cytoplasmic "threads" of the integrins and alter the extracellular affinity for ligands, a process termed "inside-out" signaling.

According to the model that Adair and Yeager now propose, the alphaIIbbeta3 integrins have multiple conformations and undergo dramatic shape changes depending on whether the molecule is in the high- or low-affinity state. The "threads" that transmit the signal through the membrane are folded as a coiled-coil of alpha-helices.

When the platelet is activated, the integrin is in a "high-affinity" form, extending far out on the outside of the cell and exposing its binding site to potential ligands. One of the ligands that binds to the high-affinity conformation is fibrinogen, a circulating blood protein that can bind integrins at both ends. Fibrinogen is present in large amounts in the blood, and when platelets are active, the high-affinity integrins bind to fibrinogen proteins, which in turn bind more integrins at their other end, and this leads to the formation of massive clots of platelets.

"We hypothesize that the switch between the high- and low-affinity states for the integrin involves flexing at hinge-like connections between certain domains in the extracellular subunits so that the molecule collapses into a tighter overall structure," says Yeager. "It is a very dramatic event."

A Suspect Jackknife

Though scientists have known for many years that integrins are important in many physiological processes, detailed structural information on these molecules has been elusive.

The size of the integrins, and the fact that they span the membrane confounded structural studies of the proteins. In fact, the only way to solve the structure was to chop off the membrane-spanning regions and solve the individual parts separately by x-ray crystallography.

But until recently, there were no high-resolution structures even of these extracellular domains. Then the Arnaout group published the crystal structure of the domains in the journal Science about a year ago.

However, this structure showed that the ligand-binding head region was bent back, like a jackknife, to the point where it was almost touching the region of the protein that would connect the transmembrane "threads".

"The crystal structure provided a lot of new insight," says Adair, "But it does not seem that this 'jackknife' form is the major conformation for the intact molecule."

How the Technique of Electron Microscopy Works

The first electron microscope was built by Ernst Ruska in 1933, for which he received the Nobel Prize in 1986 at age 80. Electron microscopes use magnetic lenses to bend a beam of electrons to image tiny objects, similar to the bending of light by glass lenses in a light microscope. EM looks at a range of magnifications, from no more than an ordinary light microscope that magnifies up to 60 times to those that magnify up to 1,000,000 times.

TSRI is one of the few centers in the world with an integrated program in electron microscopy of biological complexes and macromolecular machines. The Center for Integrated Molecular Biosciences is directed by Ron Milligan. Two other Scripps scientists, Bridget Carragher and Clint Potter, were recently awarded an NIH Research Resource Grant to develop automated molecular microscopy. Adair and Yeager used the Philips/FEI microscopes at CimBIO to collect their data.

Cryo-EM, which is the technique used in the current study, requires that samples be spread in a thin film and then frozen on a copper meshwork grid. The freezing process occurs in a few milliseconds at about a million degrees a second. In this way the frozen water is in a glass-like vitreous state, which is an excellent environment to preserve biological molecules in near-physiological conditions—a significant advantage over x-ray crystallography, where the proteins are often crystallized in pieces and in exotic buffers.

Adair and Yeager purified the integrin molecules from human platelets in mild detergent solutions that mimic the oily environment of the platelet membrane.

The computational challenge was to sort out thousands of different views of the integrin molecules and combine them to derive a 3-D map. The map revealed the overall shape and size of the entire integrin, including the large extracellular domain, the small cytoplasmic domains and the transmembrane coiled-coil.

Adair and Yeager then used the EM structure as a "molecular envelope"—like a mold, into which the 12 domains derived by x-ray crystallography could be docked. By this combined approach a detailed description of the structure and action of complicated molecular machines such as integrins can be derived.

The article, "Three-dimensional model of the human platelet integrin alphaIIbbeta3 based on electron cryomicroscopy and x-ray crystallography" is authored by Brian D. Adair and Mark Yeager and appears in the October 29, 2002 edition of the journal Proceedings of the National Academy of Sciences.

This work was supported by the National Institutes of Health, the National Heart, Lung, and Blood Institute, and a postdoctoral fellowship from the California affiliate of the American Heart Association (to Adair). During the course of this work, Yeager was an Established Investigator of the American Heart Association and is now the recipient of a Clinical Scientist Award in Translational Research from the Burroughs Wellcome Fund.


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Brian Adair (left) and Mark Yeager are publishing an integrin structure in the journal Proceedings of the National Academy of the Sciences. Photo by Jason S. Bardi.



























Surface-shaded 3D density map of the alphaIIbbeta3 heterodimer at 20 Ångstroms resolution determined by electron cryomicroscopy and computer image analysis. The large ectodomain (blue, violet and orange) and small cytoplasmic domain (red) are connected by a rod of density (yellow) that are interpreted as two parallel transmembrane alpha-helices. A 30 Ångstrom thick box indicates the putative position of the membrane bilayer.