Tag Archives: capsid

New approach neutralizes influenza with modified bacteria predator membranes

A team of German researchers has developed a new way to deal with seasonal and avian influenza viruses. Their approach involves wrapping the pathogens in chemically-modified bacteriophage capsids, rendering them unable to infect human cells.

Electron micrograph of coliphages (a type of bacteriophage) attached to a bacterial cell. Image credits: Dr Graham Beards via Wikimedia.

The team hopes their work will help usher in new treatment options against such viruses. The method was tested in the lab with very encouraging results and is currently under investigation for possible applications against the coronavirus.

Viral straightjacket

“Pre-clinical trials show that we are able to render harmless both seasonal influenza viruses and avian flu viruses with our chemically modified phage shell,” explained Professor Dr. Christian Hackenberger, Head of the Department Chemical Biology at the Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) and Leibniz Humboldt Professor for Chemical Biology at HU Berlin. “It is a major success that offers entirely new perspectives for the development of innovative antiviral drugs.”

Current antiviral treatments only attack the influenza virus after it has infected our cells, the team reports, which is certainly useful — but preventing infection in the first place would be much more desirable and effective.

The trials — which used infected human lung tissue samples — showed that perfectly fitting a phage capsid onto these viruses can be used to neutralize their ability to infect lung cells. The capsid was specially developed by the team for this job, and works by binding itself to all the (hemagglutinin) proteins the virus can use to gain access through the membranes of human cells. During the infection process, these proteins bind to sugar molecules sprinkled through the membrane of lung tissue cells to allow entry. The core mechanism of this process, however, relies on the virus creating multiple bonds with a cell, rather than a single one.

Their quest to develop an inhibitor for these proteins started six years ago. The plan was to make such an inhibitor functionally resemble the membrane of a human lung cell. The team’s quest led them to the Q-beta phage, a harmless species of bacteriophage that lives in our intestines and usually preys on E.coli. The team removed and attached ligands (binders) to its casing — sugar molecules in this case — to act as bait binding sites for the virus’ proteins

“Our multivalent scaffold molecule is not infectious, and comprises 180 identical proteins that are spaced out exactly as the trivalent receptors of the hemagglutinin on the surface of the virus,” explained Dr. Daniel Lauster, a former Ph.D. student in the Group of Molecular Biophysics (HU) and now a postdoc at Freie Universität Berlin. “It therefore has the ideal starting conditions to deceive the influenza virus — or, to be more precise, to attach to it with a perfect spatial fit. In other words, we use a phage virus to disable the influenza virus!”

When samples of tissue infected with flu viruses were treated with the phage capsid, the influenza viruses were practically unable to reproduce. High-resolution cryo-electron microscopy and standard cryo-electron microscopy revealed that the modified capsids completely cover the viruses.

While definitely encouraging, the findings call for more preclinical studies to assess the method’s viability and safety for human use. We don’t yet know, for example, if the capsids themselves would elicit an immune response in mammals, and if such a response would enhance or impair their effect. And, of course, it has yet to be proven that the inhibitor is also effective in humans.

For now, the team is content to know that their approach has great potential and that it is “the first achievement of its kind in multivalency research,” according to Professor Hackenberger. The approach, he adds, is biodegradable, non-toxic, doesn’t cause an immune response in cell cultures, and is, at least in principle, applicable to other viruses and possibly even bacteria. The team is currently focusing on adapting it to the SARS-CoV-2 virus.

The paper “Phage capsid nanoparticles with defined ligand arrangement block influenza virus entry” has been published in the journal Nature Nanotechnology.

The capsid, in blue, protects the virus after it enters a cell and shuttles it to the nucleus, where it completes the process of infection. Credit: Juan Perilla.

Massive simulation of the HIV ‘shell’ reveals new vulnerabilities that we might exploit to eliminate the virus

We are now learning new details about how the HIV infects cells thanks to a massive simulation of the viral capsid. The capsid is a protein cage that protects the viral genome and delivers it to infected cells.

The capsid, in blue, protects the virus after it enters a cell and shuttles it to the nucleus, where it completes the process of infection. Credit: Juan Perilla.

The capsid, in blue, protects the virus after it enters a cell and shuttles it to the nucleus, where it completes the process of infection. Credit: Juan Perilla.

To get an idea of the sheer complexity of this project, the team led by Juan Perilla and Klaus Schulten, both at the University of Illinois, performed a 64-million-atom simulation of how the virus senses its environment and completes the infective cycle. Even so, we’re still scratching the surface. It took them two years to simulate just 1.2 microseconds in the life of the HIV capsid.

 

Viruses come in all shapes and sizes. Some are simple protein shells filled with RNA or DNA while others are surrounded by a membrane which rivals cells in complexity. HIV is one of these really complex viruses which is surrounded by a membrane and filled with viral and cellular molecules. HIV’s viral genome is comprised of two strands of RNA packaged inside a cone-shaped capsid.

The HIV capsid is made from a single type of protein called the capsid protein, also known as CA or p24. The capsid folds to form two domains connected by a flexible linker given the protein enormous flexibility enabling it to fold in numerous possible configurations. Hundreds of identical proteins link up to form the HIV capsid. The larger domain associates with other copies of the protein to form rings of six, and slightly less often, rings of five. The smaller domain then links these rings together to form the larger structure.

It’s this inherent complexity and flexibility of the HIV virus that has always proven challenging to researchers. Building on a method called ‘computational microscopy’ pioneered by professor Schulten, the team was able to not only peer into the structure of the HIV capsid but also learned how it responds to its biological environment. Sadly, Schulten passed away in October 2016 before this paper was published in Nature Communications. 

This is a crocheted depiction of the protein structures that make up the HIV capsid. The identical proteins are arrayed in a series of pentamers, seen here in green, and hexamers, in orange, that together give the capsid its conical shape. A pore lies at the center of each grouping of proteins. Credit: Jodi Hadden, Beckman Institute

This is a crocheted depiction of the protein structures that make up the HIV capsid. The identical proteins are arrayed in a series of pentamers, seen here in green, and hexamers, in orange, that together give the capsid its conical shape. A pore lies at the center of each grouping of proteins. Credit: Jodi Hadden, Beckman Institute

The simulation was run on the Titan supercomputer operated by the Department of Energy, with help from a second supercomputer called Blue Water housed at the University of Illinois’s National Center for Supercomputing Applications.

 

According to the new study, there are likely several properties that enhance the capsid’s ability to better navigate its environment and, eventually, find its way into a cell’s nucleus. For instance, different parts of the capsid oscillate at different frequencies, which likely serves to communicate information from one part of the capsid to another. Each capsid ring has a tiny pore at its center and the study showed ions flow into and out of these pores. Negative ions accumulate on the positively charged surface of the capsid, while positive ions adhere to the outside, which carries a negative charge. This may be an exciting valuable insight to scientists toiling to find a way to destroy the virus.

“If you can break this electrostatic balance that the capsid is trying to keep together, you may be able to force it to burst prematurely,” Perilla said.

That’s not all. The positively charged interior of the pores could facilitate the influx of DNA building blocks called nucleotides, which carry a negative charge and are small enough to pass through the tiny pores. The nucleotides are essential so the virus can use them to convert its own RNA into DNA. What’s more, stress seems to propagate through the capsid in patterns and some regions are more susceptible to bursting. These are all quite a few new vulnerabilities that we’ve learned and could use them to our advantage in the fight against HIV.

Self assembling nano material brings us tangibly close to water-powered cars

Indiana University scientists have built a highly efficient bio-material that can serve as a catalyst for hydrogen production. This material takes us halfway towards the long sought-after “holy grail” of splitting water to make hydrogen and oxygen for fueling cheap and efficient cars that run on water.

Artist’s rendering of P22-Hyd, the new biomaterial created by encapsulating a hydrogen-producing enzyme within a virus shell.
Image via sciencedaily

The team started with an enzyme called hydrogenase that can extract pure hydrogen gas out of water. The substance broke down easily however, so they strengthened it by placing it inside the capsid (the protein shell) of a bacterial virus. The new material is now 150 times as efficient than the unaltered enzyme.

“Essentially, we’ve taken a virus’s ability to self-assemble myriad genetic building blocks and incorporated a very fragile and sensitive enzyme with the remarkable property of taking in protons and spitting out hydrogen gas,” said lead author Trevor Douglas, the Earl Blough Professor of Chemistry in the IU Bloomington College of Arts and Sciences’ Department of Chemistry.

“The end result is a virus-like particle that behaves the same as a highly sophisticated material that catalyzes the production of hydrogen.”

The hydrogenase was produced using genetic material harvested from the common bacteria Escherichia coli, namely the genes hyaA and hyaB. The enzyme was then inserted inside the protective capsid of a virus known as bacteriophage P22,using methods previously developed by IU scientists.

The resulting biomaterial, called “P22-Hyd,” is much more efficient and durable than the enzyme alone, and is obtained through fermentation process at room temperature. P22-Hyd is dirt cheap (fermentation is free) and more environmentally friendly than materials currently used for fuel cells. The authors compare it to platinum, the most commonly used hydrogen catalyst today.

“This material is comparable to platinum, except it’s truly renewable,” Douglas said.

“You don’t need to mine it; you can create it at room temperature on a massive scale using fermentation technology; it’s biodegradable. It’s a very green process to make a very high-end sustainable material.”

As a bonus, P22-Hyd both breaks the chemical bonds of water to create hydrogen and also works in reverse to recombine hydrogen and oxygen to generate power.

“The reaction runs both ways — it can be used either as a hydrogen production catalyst or as a fuel cell catalyst,” he added.

Out of three naturally ocuring forms of hydrogenase, the team chose to use nickel-iron (NiFe)-hydrogenase — the others being di-iron (FeFe)- and iron-only (Fe-only)-hydrogenase. This form was preferred due to its ability to easily integrate into biomaterials and tolerate exposure to oxygen.

Unaltered NiFe-hydrogenase is highly susceptible to destruction from chemicals in the environment and breaks down at room temperatures — a poor choice for fuel cells. Encapsulation allows it much greater chemical resistance and enables it to catalyze at temperatures exceeding “comfortable,” permitting its use in manufacturing and commercial products such as cars.

“[These shortcomings are] some of the key reasons enzymes haven’t previously lived up to their promise in technology,” Douglas added.

Another is their difficulty to produce.

“No one’s ever had a way to create a large enough amount of this hydrogenase despite its incredible potential for biofuel production. But now we’ve got a method to stabilize and produce high quantities of the material — and enormous increases in efficiency.”

Seung-Wuk Lee, professor of bioengineering at the University of California-Berkeley, whose work has been cited in a U.S. Congressional report on the use of viruses in manufacturing and unaffiliated with the study, applauds the team’s work, saying:

“Douglas’ group has been leading protein- or virus-based nanomaterial development for the last two decades. This is a new pioneering work to produce green and clean fuels to tackle the real-world energy problem that we face today and make an immediate impact in our life in the near future.”

Beyond the new study, Douglas and his colleagues continue to craft P22-Hyd into an ideal ingredient for hydrogen power by investigating ways to activate a catalytic reaction with sunlight, as opposed to introducing elections using laboratory methods.

“Incorporating this material into a solar-powered system is the next step,” Douglas concluded.

Klaus Schulten, professor of physics; and Juan Perilla, postdoc with Theoretical and Computational Biophysics Group at the Beckman Institute with projection of atomic-level detail of the structure of the HIV capsid (outer shell).

Largest supercomputer bio-simulation ever reveals key HIV protective shell structure

Klaus Schulten, professor of physics; and Juan Perilla, postdoc with Theoretical and Computational Biophysics Group at the Beckman Institute with projection of atomic-level detail of the structure of the HIV capsid (outer shell).

Klaus Schulten, professor of physics; and Juan Perilla, postdoc with Theoretical and Computational Biophysics Group at the Beckman Institute with projection of atomic-level detail of the structure of the HIV capsid (outer shell).

One big obstacle scientists face in their efforts to develop effective drugs against HIV is the virus’ capsid – an outer cell membrane-derived envelope and an inner viral protein shell that protects HIV essential proteins and genetic information. Current drugs have a hard time breaching this structure, however this might change. Using a supercomputer that crunched immense amounts of data, scientists have recently reported they have decoded the structure that contains and protects HIV’s genetic material.

“The capsid is critically important for HIV replication, so knowing its structure in detail could lead us to new drugs that can treat or prevent the infection,” said senior author Peijun Zhang, associate professor at the University of Pittsburgh School of Medicine.“This approach has the potential to be a powerful alternative to our current HIV therapies, which work by targeting certain enzymes, but drug resistance is an enormous challenge due to the virus’ high mutation rate.”

The capsid is one tricky fellow though, and accurately describing its structure was no easy task by any means. For one, the shell is comprised of nonuniform combinations of five- and six-subunit protein structures that link together to form an asymmetric shape. To model it, scientists had to piece together each of the 3 to 4 million atoms comprising it, while also  accounting for all of the water molecules and salt ions also present, creating an output of some 64 million atoms.

The  University of Pittsburgh researchers first used electron-scan microscope to see in incredible detail the protein molecules that comprise the capsid, then used an imaging technique to visualize how these molecules connect to each other to form the general shape of the shell. The data was then sent to University of Illinois physicists, who fed the data into computer models they ran on Blue Waters, their new supercomputer at the National Center for Supercomputing Applications capable processing 1 quadrillion operations per second. The data was run through the computer using a process called molecular dynamic flexible fitting, which outputted  the minute details of the capsid’s structure.

 The researchers used the supercomputer Blue Waters to determine the complete HIV capsid structure, a simulation that accounted for the interactions of 64 million atoms.

The researchers used the supercomputer Blue Waters to determine the complete HIV capsid structure, a simulation that accounted for the interactions of 64 million atoms.

The process revealed a three-helix bundle with critical molecular interactions at the seams of the capsid, areas that are necessary for the shell’s assembly and stability, which represent vulnerabilities in the protective coat of the viral genome.

“This is a big structure, one of the biggest structures ever solved,” said University of Illinois physics professor Klaus Schulten. “It was very clear that it would require a huge amount of simulation – the largest simulation ever published. You basically simulate the physical characteristics and behavior of large biological molecules but you also incorporate the data into the simulation so that the model actually drives itself toward agreement with the data.”

If capsid assembly or disassembly is disrupted, viral replication, and consequently transmission, can be stopped. Now armed with this new found information, researchers have opened up a new front in their ongoing war with HIV.

“The capsid is very sensitive to mutation, so if we can disrupt those interfaces, we could interfere with capsid function,” Zhang said. “The capsid has to remain intact to protect the HIV genome and get it into the human cell, but once inside it has to come apart to release its content so that the virus can replicate. Developing drugs that cause capsid dysfunction by preventing its assembly or disassembly might stop the virus from reproducing.”

The findings appeared in Nature.