Tyler O'Neal, Staff Editor HEALTH

Max Planck's MD simulations of SARS-CoV-2 spike protein reveal potential new vaccine targets

The new model captures glycan molecules whose motions shield much of the spike from immune defenses

A new, detailed model of the surface of the SARS-CoV-2 spike protein reveals previously unknown vulnerabilities that could inform the development of vaccines. Mateusz Sikora of the Max Planck Institute of Biophysics in Frankfurt, Germany, and colleagues present these findings in the open-access journal PLOS Computational Biology.

SARS-CoV-2 is the virus responsible for the COVID-19 pandemic. A key feature of SARS-CoV-2 is its spike protein, which extends from its surface and enables it to target and infect human cells. Extensive research has resulted in detailed static models of the spike protein, but these models do not capture the flexibility of the spike protein itself nor the movements of protective glycans--chains of sugar molecules--that coat it. In this visualization of antibody target sites, the SARS-CoV-2 spike protein is tethered to the viral membrane with a slender stalk. Patches of intense purple color at the surface of spike indicate potential target sites for antibodies that are not protected by the glycans --chains of sugar molecules--shown in green. These binding sites and their accessibility were identified with molecular dynamics simulations that capture the complete structure of the spike protein and its motions in a realistic environment. CREDIT Mateusz Sikora, Sören von Bülow, Florian E. C. Blanc, Michael Gecht, Roberto Covino and Gerhard Hummer

To support vaccine development, Sikora and colleagues aimed to identify novel potential target sites on the surface of the spike protein. To do so, they developed molecular dynamics simulations that capture the complete structure of the spike protein and its motions in a realistic environment.

These simulations show that glycans on the spike protein act as a dynamic shield that helps the virus evade the human immune system. Similar to car windshield wipers, the glycans cover nearly the entire spike surface by flopping back and forth, even though their coverage is minimal at any given instant.

By combining the dynamic spike protein simulations with bioinformatic analysis, the researchers identified spots on the surface of the spike proteins that are least protected by the glycan shields. Some of the detected sites have been identified in previous research, but some are novel. The vulnerability of many of these novel sites was confirmed by other research groups in subsequent lab experiments.

"We are in a phase of the pandemic driven by the emergence of new variants of SARS-CoV-2, with mutations concentrated in particular in the spike protein," Sikora says. "Our approach can support the design of vaccines and therapeutic antibodies, especially when established methods struggle."

The method developed for this study could also be applied to identify potential vulnerabilities of other viral proteins.

Chinese method for spin-to-charge conversion achieves 95% overall qubit readout fidelity

Tyler O'Neal, Staff Editor HEALTH

The team led by Professor DU Jiangfeng and Professor WANG Ya from the Chinese Academy of Sciences (CAS) Key Laboratory of Microscale Magnetic Resonance of the University of Science and Technology of China put forward an innovative spin-to-charge conversion method to achieve high-fidelity readout of qubits, stepping closer towards fault-tolerant quantum supercomputing.

Fault-tolerant quantum supercomputing requires the accumulated logic gate error and the spin readout fidelity to exceed the fault-tolerant threshold. DU's team has resolved the first requirement in the nitrogen-vacancy (NV) center system previously and this work targeted at the high-fidelity readout of qubits.

Qubit state, such as spin state, is fragile: a common readout approach may cause the flip between the 0 and 1 states for even a few photons resulting in a reading error. The readout fidelity of the traditional resonance fluorescence method is strictly limited by such property. Since the spin state is difficult to measure, researchers blazed a trail to replace it with an easy-to-readout and measurable property: the charge state.

They first compared the optical readout lifetime of the charge state and spin state, finding that the charge state is more stable than the spin state by five orders of magnitude. Experiment results showed that the average non-demolition charge readout fidelity reached 99.96%. a) Energy levels used to achieve SCC. b) A schematic diagram of SCC readout. c) The excitation spectrum of the nitrogen-vacancy (NV) center used here at cryogenic temperature of 8?K. d) Spin-flip process induces the photoluminescence (PL) decay. CREDIT ZHANG Qi et al.

Then the team adopted near-infrared (NIR) light (1064 nm) to induce the ionization of the excited spin state, transforming the spin state 0 and 1 to the "electrically neutral" and "negatively charged" charge states respectively. This process converted the spin readout to the charge readout.

The results indicated that the error of the traditional resonance fluorescence method reached 20.1%, while the error of this new method can be suppressed to 4.6%.

The article was published in an academic journal.

This new method is compatible with traditional methods, provisioning a spin readout fidelity exceeding the fault-tolerant threshold in real applications. Thanks to the less damage of NIR light to biological tissues and other samples, this method will also effectively improve the detection efficiency of quantum sensors.

University of Copenhagen's new supercomputer model sows doubt about the composition of 70 percent of our universe

Tyler O'Neal, Staff Editor HEALTH

Researchers the world over have long believed that 70 percent of the universe is composed of dark energy, a substance that makes it possible for the universe to expand at an ever-increasing rate. But in a new study, University of Copenhagen researchers 

Until now, researchers have believed that dark energy accounted for nearly 70 percent of the ever-accelerating, expanding universe.

For many years, this mechanism has been associated with the so-called cosmological constant, developed by Einstein in 1917, that refers to an unknown repellant cosmic power.

But because the cosmological constant--known as dark energy--cannot be measured directly, numerous researchers, including Einstein, have doubted its existence--without being able to suggest a viable alternative. 

Until now. In a new study by researchers at the University of Copenhagen, a model was tested that replaces dark energy with dark matter in the form of magnetic forces.

"If what we discovered is accurate, it would upend our belief that what we thought made up 70 percent of the universe does not actually exist. We have removed dark energy from the equation and added in a few more properties for dark matter. This appears to have the same effect upon the universe's expansion as dark energy," explains Steen Harle Hansen, an associate professor at the Niels Bohr Institute's DARK Cosmology Centre.

Photo: Getty Images

The universe expands no differently without dark energy

The usual understanding of how the universe's energy is distributed is that it consists of five percent normal matter, 25 percent dark matter, and 70 percent dark energy.

In the UCPH researchers' new model, the 25 percent share of dark matter is accorded special qualities that make the 70 percent of dark energy redundant.

"We don't know much about the dark matter other than that it is a heavy and slow particle. But then we wondered--what if the dark matter had some quality that was analogous to magnetism in it? We know that as normal particles move around, they create magnetism. And, magnets attract or repel other magnets--so what if that's what's going on in the universe? That this constant expansion of dark matter is occurring thanks to some sort of magnetic force?" asks Steen Hansen.

Supercomputer model tests dark matter with a type of magnetic energy

Hansen's question served as the foundation for the new supercomputer model, where researchers included everything that they know about the universe--including gravity, the speed of the universe's expansion, and X, the unknown force that expands the universe.

"We developed a model that worked from the assumption that dark matter particles have a type of magnetic force and investigated what effect this force would have on the universe. It turns out that it would have exactly the same effect on the speed of the university's expansion as we know from dark energy," explains Steen Hansen. In 1572, the Danish physicist Tycho Brahe discovered this supernova called Stella Nova. By measuring the distance from this supernova and other novas, researchers later on concluded, that the universe is expanding constantly and with accellerating speed. Photo: NASA/CXC/SAO

However, there remains much about this mechanism that has yet to be understood by the researchers.

And it all needs to be checked in better models that take more factors into consideration. As Hansen puts it: "Honestly, our discovery may just be a coincidence. But if it isn't, it is truly incredible. It would change our understanding of the universe's composition and why it is expanding. As far as our current knowledge, our ideas about the dark matter with a type of magnetic force and the idea about dark energy are equally wild. Only more detailed observations will determine which of these models is the more realistic. So, it will be incredibly exciting to retest our result."