Molecular modeling suggests structural consequences of an early protein mutation that promoted viral transmission.
RIKEN researchers discovered that an early mutation (D614G) in the SARS-CoV-2 virus may have contributed to its rapid spread by altering the spike protein’s shape, improving the virus’s ability to adapt to human hosts. The finding could help inform the development of next-generation vaccines and antiviral drugs.
The rapid spread of COVID-19 may have been partly due to changes in the structure of the SARS-CoV-2 virus wrought by an early mutation in its genome, a detailed analysis by RIKEN researchers suggests. The finding could help inform the development of next-generation vaccines and antiviral drugs.
Yuji Sugita of the RIKEN Center for Computational Science (R-CCS) and Hisham Dokainish, who was at R-CCS at the time of the study, investigated the effect of mutations on viral structure. They did this by simulating the atomic positions of molecules found in different forms of the virus’s important spike protein—a tool coronaviruses use to bind and enter human cells.
They found that the substitution of a single amino acid altered this protein’s shape, helping SARS-CoV-2 to adapt to human hosts. This finding demonstrates how even tiny mutations—swapping a single amino acid in this case—can greatly affect protein dynamics.
To understand why the mutation proved so advantageous to the virus, the pair ran detailed simulations of the protein’s structure and stability. Their analysis—done using the RIKEN Fugaku supercomputer, one of the fastest in the world—revealed how the mutation (known as D614G) breaks an ionic bond with a second subunit of the Spike protein. It also changes the shape of a nearby loop structure, which alters the orientation of the entire protein, locking it into a form that makes it easier for the virus to enter cells (Fig. 1).
“A single and local change in an interaction within the molecule caused by a single mutation could affect the global structure of the spike protein,” explains Sugita, who is additionally affiliated with the RIKEN Center for Biosystems Dynamics Research. The resulting mutant proved better at replicating and transmitting between human hosts, and the D614Glineage quickly outcompeted its ancestral lineages and spread across the globe. It remains a fixture of every dominant variant that has followed.
Sugita’s team is now performing similar investigations of adaptive viral mutations that arose later in the course of the pandemic, including those found in the Omicron variant.
“Information obtained from our molecular dynamics simulations should help increase the opportunities for us to find effective drugs and other medicines,” he says.

News
A potential milestone in cancer therapy
Researchers from the University of Bern, Inselspital, University Hospital Bern, and the University of Connecticut have made a significant breakthrough in the fight against cancer. They identified a previously unknown weak point of prostate [...]
Cardiovascular Crystal Ball: New Tool Predicts Future Heart Disease Risk
Faculty members at the UM School of Medicine have created a cutting-edge tool that enables the early identification and assessment of risks in vulnerable patients. Heart disease, being the leading cause of death globally, [...]
Scientists analyze a single atom with X-rays for the first time
In the most powerful X-ray facilities in the world, scientists can analyze samples so small they contain only 10,000 atoms. Smaller sizes have proved exceedingly difficult to achieve, but a multi-institutional team has scaled [...]
AI Demonstrates Superior Performance in Predicting Breast Cancer
AI algorithms outperformed traditional clinical risk models in a large-scale study, predicting five-year breast cancer risk more accurately. These models use mammograms as the single data source, offering potential advantages in individualizing patient care [...]
Stanford Medicine Reveals: Tiny DNA Circles Defying Genetic Laws Drive Cancer Formation
Tiny circles of DNA harbor cancer-associated oncogenes and immunomodulatory genes promoting cancer development. They arise during the transformation from pre-cancer to cancer, say Stanford Medicine-led team. Tiny circles of DNA that defy the accepted laws of [...]
Death to Blood Cancer Cells: New Drug Combination Could Revive the Power of Leading Treatment
Future clinical trials will be conducted to investigate whether the combination of chloroquine and venetoclax can prevent disease recurrence. Although new drugs have been developed to induce cancer cell death in individuals with acute [...]
Illuminating Science: X-Rays Visualize How One of Nature’s Strongest Bonds Breaks
Scientists have deciphered how an activated catalyst breaks down the strong carbon-hydrogen bonds in potent greenhouse gas methane, according to a study published in Science. Using advanced X-ray technology and quantum-chemical calculations, they tracked the [...]
Using magnetic nanoparticles as a rapid test for sepsis
Qun Ren, an Empa researcher, and her team are currently developing a diagnostic procedure that can rapidly detect life-threatening blood poisoning caused by staphylococcus bacteria. Staphylococcal sepsis is fatal in up to 40% of [...]
Team develops nanoparticles to deliver brain cancer treatment
University of Queensland researchers have developed a nanoparticle to take a chemotherapy drug into fast growing, aggressive brain tumors. Research team lead Dr. Taskeen Janjua from UQ's School of Pharmacy said the new silica [...]
Tumor Avatars – A New Approach to Personalized Cancer Treatment
A team from the University of Geneva (UNIGE) has devised a novel method for customizing treatments by testing them on artificial tumors. Determining the optimal treatment for colon cancer can be challenging as each [...]
STING Like a Bee: MIT’s Revolutionary Approach to Cancer Immunotherapy
A cancer vaccine combining checkpoint blockade therapy and a STING-activating drug eliminates tumors and prevents recurrence in mice. MIT researchers have engineered a therapeutic cancer vaccine that targets the STING pathway, vital for immune response [...]
AI Battles Superbugs: Helps Find New Antibiotic Drug To Combat Drug-Resistant Infections
The machine-learning algorithm identified a compound that kills Acinetobacter baumannii, a bacterium that lurks in many hospital settings. Using an artificial intelligence algorithm, researchers at MIT and McMaster University have identified a new antibiotic that can kill a [...]
Cancer and AI – Can ChatGPT Be Trusted?
A study published in the Journal of The National Cancer Institute Cancer Spectrum delved into the increasing use of chatbots and artificial intelligence (AI) in providing cancer-related information. The researchers discovered that these digital resources accurately [...]
Breathing New Life: Oxygen Therapy Improves Heart Function in Long COVID Patients
A small trial has found that hyperbaric oxygen therapy (HBOT) may help restore proper heart function in patients with post-COVID syndrome, with participants in the HBOT group experiencing a significant increase in global longitudinal [...]
Wireless Brain-Spine Interface: A Leap Towards Reversing Paralysis
Summary: In a pioneering study, researchers designed a wireless brain-spine interface enabling a paralyzed man to walk naturally again. The ‘digital bridge’ comprises two electronic implants — one on the brain and another on the [...]
New study reveals a gel that promises to wipe out brain cancer for good
An anti-cancer gel promises to wipe out glioblastoma permanently, a feat that's never been accomplished by any drug or surgery. So what makes this gel so special? Scientists at Johns Hopkins University (JHU) have [...]