Wheezing, coughing that doesn’t stop, a pale and sweaty face: clinically, severe asthma attacks look very similar from patient to patient. But biologically, not all severe asthma is the same — and a team of scientists has, for the first time, identified the key difference in people, a finding that has important implications for treatment.
In a paper published today in Cell Reports, a group of scientists led by immunologists and pulmonologists at the University of Pittsburgh, in collaboration with Stanford University, used advanced tools of immunology, molecular biology and unbiased computational and bioinformatic approaches to characterize immune profiles of patients with severe asthma. These findings invite a new appreciation for the complexity of disease mechanisms and can lead to improved treatments.
“We started this study to better understand immune mediators of inflammation in asthma,” said lead author Matthew Camiolo, M.D., Ph.D., clinical instructor of medicine at Pitt. “We found that despite being grouped broadly as ‘clinically severe,’ these asthma patients actually had very different and distinct immune profiles.”
Asthma is a debilitating condition that affects millions of people each year. According to the Centers for Disease Control and Prevention, 25 million Americans, or 1 in 13 people suffer from asthma. And while current standards of treatment — inhaled immunosuppressive corticosteroids, such as beclomethasone and budesonide — are effective in most patients, clinical markers that can help identify those who are likely to be resistant to treatment are lacking.
For patients who do not respond to standard corticosteroid treatment or respond to it poorly, there is no ‘one size fits all’ approach to treat severe disease. Because of that, while severe asthma accounts for 5 to 10 percent of all asthma cases, it consumes 50 percent of associated health care costs, amounting to $28 billion annually.
“Although breakthroughs in asthma therapy have greatly improved our ability to treat patients, many people still continue with disease that greatly diminishes their quality of life,” said co-senior author Sally Wenzel, M.D., director of Pitt’s Asthma and Environmental Lung Health Institute, and chair of Pitt Public Health’s Department of Environmental and Occupational Health.
To characterize immune cells within the airways of severe asthma patients, the researchers, in collaboration with Kari Nadeau, M.D., Ph.D., director of the Sean N Parker Center for Allergy & Asthma Research at Stanford University School of Medicine, used mass cytometry, RNA-sequencing and machine learning, and established a novel algorithm that links immune cells to cellular pathways potentially related to disease pathogenesis.
The research team found that lung aspirates from one group of patients were enriched with T cells polarized to fight infections, while the other group had a much lower level of T cells. At the same time, the second group had an increased number of innate immune cells expressing an inflammatory molecule IL-4 — a cytokine known to be elevated in asthma.
“We have identified two clusters of severe asthma patients with very similar biomarkers but with strikingly distinct immune profiles and associated biological pathways,” said senior author Anuradha Ray, Ph.D., professor of medicine and immunology at Pitt. “These findings identify new targets for therapy, which are distinct in the two subgroups of severe asthma patients who otherwise would be indistinguishable based on biomarker profiles.”
“We believe that the cell types expressing IL-4 in the airways of one of the groups have not been previously identified in humans in any setting,” Ray added.
Researchers are optimistic that these findings will enhance precision medicine approaches to treating severe asthma patients.
“These important findings are the result of a successful team effort among physician-scientists and basic scientists across institutions that has established a new frontier in asthma research,” said Ray. “We hope the new knowledge gained will be used to develop new therapeutics to treat severe asthma patients and also allow improved stratification of patients for better efficacy of existing therapies.”

A sex ed teacher talks about how young people can try to keep themselves safe from sexual assault and be allies to others.I was making lunch when my 17-year-old son sat down at the kitchen table. “Hey Mom, is this real?” he asked, and showed me an Instagram post that read: “97% of young women have experienced sexual harassment. If you are surprised, then you’re probably not listening.”I asked to take a closer look and he handed me his phone. The statistic wasn’t completely accurate but it was close. It was pulled from a British study that found that among women aged 18 to 24, 86 percent had been harassed in public spaces, 3 percent didn’t recall ever having experienced sexually harassing behavior, and 11 percent chose not to answer the question. There was more to the post; when I swiped left, it demanded: “Boys do better.”“What do I do with that?,” my son asked. “What does that mean?”It was a good question.Posts like the one my son showed me have been all over social media since the death of Sarah Everard, the young British woman who was kidnapped and killed several weeks ago (a police officer has been charged).As a high school sex educator, working both in person and remotely as a national consultant, I talk to young people all over the country. The posts they see include statistics about sexual harassment, sexual assault and rape that my students describe as “devastating” and “terrifying.”When I asked some of my students and other teens I know about the statement “Boys do better,” several boys said they felt “attacked” or “hopeless” because it feels as if they are being accused of perpetrating crimes they haven’t committed. Many say they consider themselves a “good guy” and want to help, but don’t know how.According to another survey, this one done in the United States, 87 percent of 18- to 25-year-old women reported having experienced sexual harassment. The report found that 76 percent of respondents (72 percent male, 80 percent female) had never had a conversation about how not to harass, or express other forms of misogyny. The National Violence Resource Center concluded that one in four girls and one in six boys is sexually abused by the age of 18. We also know that boys experience sexual abuse not only at the hands of men, but in some cases, girls and women. And a large number of those who experience sexual assault are gay, lesbian, bisexual or transgender.So, yes, sexual violence is a significant problem. Chalina Morgan-Lopez, 17, from Raleigh, N.C., who told me she had been repeatedly harassed and grabbed at school, said: “It made me feel powerless and like an object. I felt uncomfortable and unsafe in my classes with my harassers.”When I teach, there are certain questions about sexual assault that teenagers always ask. They want to know, “How do I keep myself safe?” “How can I be a supportive friend and ally?” They also want to know, “What’s the deal with drunk sex?” Here are some answers to those questions.Promote respectSpeak up about objectifying and dehumanizing language, whether in the media or in school hallways. During Donald Trump’s presidential campaign in 2016, he dismissed his vulgar comments about grabbing women as “locker room banter.” The incident heightened awareness of the way that talking about women as sex objects normalizes sexual harassment and may contribute to sexual assault.Amanda Ehrenhalt, a 16-year-old who lives in Philadelphia and plays field hockey and track and field, said, “Locker room talk isn’t made up. It’s for real. As an athlete who is around other athletes, I hear it all of the time.” If you hear someone talking about sex in a demeaning way, you might say, “Hey, let’s keep it respectful,” or “What do you mean by that?”Take care of yourselfAs you go through adolescence, it’s important to understand consent. Your body and sexuality belong to you. Just because you say yes to one form of sexual activity, doesn’t mean you’ve said yes to another. You and your partner have to agree about what you’re doing together and whether to take things to a new level. You also have the right to change your mind at any time and choose not to move on or even to stop the activity altogether.If you choose to be sexual with someone else, know how to manage what’s going on. You can say “No,” “This is making me uncomfortable,” or “Let’s go back to what we were doing before.” If you don’t feel you can say something directly, you can make up an excuse: “I forgot that I’m supposed to be home early — I have to go.” If the person you are with continues to try and persuade you or is just not listening, you can say, “If you continue you will be assaulting/raping me.”We all deserve to be treated with dignity and enjoy our romantic and sexual relationships with others. If you are sexually active, you have to ask the person you’re with to make sure your interactions are welcome, and keep on asking. It can be as simple as, “you good?” or “this OK?” Pressuring, manipulating, pushing or talking someone into saying yes to sexual activity is not a “yes” or consent. It is coercion and potentially illegal.Remember that federal law recognizes that someone who is incapacitated by alcohol or drugs is legally incapable of giving consent. Each state has its own laws, as well.Put simply, getting someone drunk so they will have sex with you could land you with a criminal charge or in jail.And, if you are the one who is assaulted, no matter what choices you make, what you are wearing or consuming, it is not your fault.Step in to help othersThere are several ways to be a supportive friend or an ally to someone who has experienced sexual harassment or assault. They include raising awareness, speaking up when you see or hear suspicious, risky or dangerous behavior and being compassionate to survivors.Ramis Banuri, 19, of Salt Lake City, Utah, said he speaks up whenever he can, and tries to get others to do the same. “People don’t necessarily want to intervene because there’s this notion that it’s not your business and they don’t want to embarrass themselves if they misread a situation, he said. “I tell them ‘would you rather be embarrassed for a moment about a small situation that nobody will really remember, or be sorry because you were right and could have prevented someone from getting hurt?’”Bystander intervention is a strategy for preventing harassment and assault from happening or continuing. The goal is to disrupt what feels like a loaded moment before things can escalate. Every situation is different and there is no single way to intervene, but here are some guidelines from the Green Dot program, a widely used bystander intervention training system, which encourages people to act using what are called the Three Ds.Direct intervention is straightforward. If someone uses sexist language or makes someone uncomfortable with sexual comments or jokes, you could say, “Hey, that’s making people uncomfortable — that’s harassment. Stop.” Or “You’ve had way too much to drink. You’re in no shape to even think about hooking up — let’s get you home.”You can also interrupt a risky dynamic with a distraction. If someone is making another person uncomfortable with their attention, you could say, “Hey, the guys are looking for you downstairs. Let’s go see what’s up.”In other situations, you may delegate to someone else who has more training, authority or social leverage and may be more effective at intervening.If you see someone you don’t know well acting inappropriately, tell the people they came with and encourage them to intervene. If you witness a couple fighting and it seems to be getting physical, find a trusted adult or authority figure, or call the police.If you or a friend are harassed or assaulted, the National Sexual Assault Hotline can provide information and guidance.Ms. Morgan-Lopez took steps to be proactive: “I began by forming a small group of students at my school who were also passionate about targeting this issue, and we connected with local organizations who offered us trainings in sexual assault.”Mr. Banuri also had training through a peer-led sex education program. He said what inspires him is knowing that “I am doing the right thing — that reaffirms my values: community, connection, family and friendship. That’s affirming and strong — helping people stay safe.”Shafia Zaloom is the author of “Sex, Teens and Everything in Between.”

Violent blows or jolts to the head can cause traumatic brain injury (TBI), and there are currently about five million people in the U.S. living with some form of chronic impairment after suffering a TBI. Even in a mild form, TBI can lead to lifelong nerve cell deterioration associated with a wide array of neuropsychiatric conditions. Tragically, there are no medicines to protect nerve cells after injury. Behind aging and genetics, TBI is the third leading cause of Alzheimer’s disease (AD), yet the link between these two conditions is not understood.
In a new study, published online today in Cell, researchers have discovered a new way to prevent brain nerve cells from deteriorating after injury, which also revealed a potential mechanistic link between TBI and AD. Their discovery also yielded a new blood biomarker of nerve cell degeneration after injury, which is significant because there is an urgent need for mechanism-based blood biomarkers that can diagnose TBI and stage its severity.
Prior to this study, it had been previously reported that a small protein in nerve cells, called tau, was modified by a chemical process called acetylation in the post-mortem brains of AD patients. But how this modification came about, as well as its role in the disease process, was not understood.
“Normally, tau functions in nerve cells to maintain the appropriate structure of the axon, which is the nerve cell extension required for nerve cells to communicate with one another,” said Andrew A. Pieper, MD, PhD, senior author on the study, Harrington Discovery Institute (HDI) Investigator and Director of the HDI Neurotherapeutics Center at University Hospitals (UH), Morley-Mather Chair in Neuropsychiatry at UH, Director of the Translational Therapeutics Core of the Cleveland Alzheimer’s Disease Research Center, and VA Geriatric Research, Educational and Clinical Care (GRECC) Investigator. “Given the relationship between AD and TBI, we wondered whether elevated acetylated-tau (ac-tau) might also occur in TBI, and if so, then whether this could provide an experimental platform to study its potential role in nerve cell deterioration.”
Dr. Pieper’s lab discovered that ac-tau increased rapidly in multiple forms of TBI in mice and rats, and persisted chronically when nerve cell degeneration was untreated. They also showed that the increased ac-tau in human AD brain was further exacerbated when the AD patient also had a prior history of TBI.
“Our research showed that after ac-tau rises, a specific structure at the junction of the nerve cell body and its axon, called the axon initial segment, breaks down,” explained Min-Kyoo Shin, PhD, co-first author of the study. “As a result, tau is no longer appropriately sequestered in axons. This leads to axonal degeneration, followed by neurologic impairment.”
The team tested therapeutic interventions after TBI at each of the three nodal points in the new signaling pathway that they identified as leading to increased nerve cell ac-tau after injury. Using known medicines or experimental drugs, they saw that all three points provided effective therapeutic opportunity.

Almost all bacteria rely on the same emergency valves — protein channels that pop open under pressure, releasing a deluge of cell contents. It is a last-ditch effort, a failsafe that prevents bacteria from exploding and dying when stretched to the limit. If we understood how those protein channels worked, antibiotic drugs could be designed to open them on demand, draining a bacterium of its nutrients by exploiting a floodgate common to many species.
But these channels are tricky to operate in the lab. And how precisely they open and close, passing through a sub-conducting state and ending in a desensitized state under the influence of mechanical forces, remains poorly understood. Now, new research from the laboratory of Rockefeller’s Thomas Walz introduces a novel method to activate and visualize these channels, making it possible to explain their function. The findings shed light on key membrane proteins in bacteria, and the same method can be used to improve our understanding of similar channels in humans.
“We were actually able to see the entire cycle of the protein channel passing through a series of functional stages,” Walz says.
Walz has long focused upon MscS, a protein embedded in bacterial membranes that opens in response to mechanical force. MscS proteins exist in a closed state while resting in a thick membrane. Scientists once suspected that, when fluid build-up causes the cell to swell and puts tension on the membrane, it stretches so thin that its proteins protrude. Thrust into an unfamiliar environment, the protein channels snap open, releasing the contents of the cell and relieving pressure until the membrane returns to its original thickness and its channels slam shut.
But when Yixiao Zhang, a postdoctoral associate in the Walz group, tested this theory over five years ago, reconstituting MscS proteins into small custom-designed membrane patches, he discovered that it was impossible to prise the channel open by thinning membranes within the natural range. “We realized that membrane thinning is not how these channels open,” Walz says.
These custom patches, called nanodiscs, allow researchers to study proteins in an essentially native membrane environment and to visualize them with cryo-electron microscopy. Walz and Zhang resolved to push the limits of nanodisc technology, removing membrane lipids with ?-cyclodextrin, a chemical used to excise cholesterol from cell cultures. This induced tension in the membrane, and Walz and his team could observe with cryo-electron microscopy as the channel reacted accordingly — eventually snapping closed for good, a phenomenon known as desensitization.
What they observed matched computer simulations, and a new model for the function of MscS emerged. When fluid builds up inside the cell, they found, lipids are called in from all corners to help ease tension throughout the membrane. If the situation becomes dire, even lipids associated with the MscS channels flee. Without lipids keeping them closed, the channels have the legroom to pop open.
“We could see that, when you expose the membranes to ?-cyclodextrin, the channels open and then close again,” Walz says.
Walz and Zhang’s new method of manipulating nanodiscs with ?-cyclodextrin will allow researchers studying dozens of similar mechanosensitive protein channels to, at long last, test their hypotheses in the lab. Many such proteins play key roles in humans, from hearing and sense of touch to the regulation of blood pressure. Of more immediate interest, however, is the prospect of exploiting protein channels that many different bacteria rely upon to survive. Novel drug targets are a particular necessity, given the rise of dangerous antibiotic resistant bacteria such as MRSA.
MscS and the related bacterial protein channel MscL are “extremely interesting drug targets,” Walz says. “Almost every bacterium has one of these proteins. Because these channels are so widely distributed, a drug that targets MscS or MscL could become a broad-spectrum antibiotic.”
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A study done in rooms where COVID-19 patients were isolated shows that the virus’s RNA — part of the genetic material inside a virus — can persist up to a month in dust.
The study did not evaluate whether dust can transmit the virus to humans. It could, however, offer another option for monitoring COVID-19 outbreaks in specific buildings, including nursing homes, offices or schools.
Karen Dannemiller, senior author of the study, has experience studying dust and its relationship to potential hazards like mold and microbes.
“When the pandemic started, we really wanted to find a way that we could help contribute knowledge that might help mitigate this crisis,” said Dannemiller, assistant professor of civil, environmental and geodetic engineering and environmental health sciences at The Ohio State University.
“And we’ve spent so much time studying dust and flooring that we knew how to test it.”
The study, published today (April 13, 2021) in the journal mSystems, found some of the genetic material at the heart of the virus persists in dust, even though it is likely that the envelope around the virus may break down over time in dust. The envelope — the crown-like spiked sphere that contains the virus’s material — plays an important role in the virus’s transmission to humans.

Researchers have identified molecular signatures of the aging process in mice, publishing their results today in the open-access eLife journal.
Their analyses provide one of the most comprehensive characterisations of the molecular signatures of aging across diverse types of cells from different tissues in a mammal, and will aid future studies on aging and related topics.
Aging leads to the decline of major organs and is the main risk factor for many diseases, including cancer, cardiovascular and neurodegenerative diseases. While previous studies have highlighted different hallmarks of the aging process, the underlying molecular and cellular mechanisms remain unclear.
To gain a better understanding of these mechanisms, the Tabula Muris Consortium created the single-cell transcriptomic dataset, called Tabula Muris Senis (TMS). The TMS contains over 300,000 annotated cells from 23 tissues and organs of male and female mice. “These cells were collected from mice of diverse ages, making the data a tremendous opportunity to study the genetic basis of aging across different tissues and cell types,” says first author Martin Jinye Zhang, Postdoctoral Researcher in the Department of Epidemiology, Harvard University, Boston, US.
The original TMS study mainly explored the cell-centric effects of aging, aiming to characterise changes in the composition of cell types within different tissues. In the current gene-centric study, Zhang and colleagues focused on changes in gene expression that occur during the aging process across different cell types.
Using the TMS data, they identified aging-dependent genes in 76 cell types from 23 tissues. They then characterised the aging behaviours of these genes that were both shared among all cell types (‘globally’) and specific to different tissue cells.
“We found that the cell-centric and gene-centric perspectives of the previous and current studies are complementary, as gene expression can change within the same cell type during aging, even if the composition of cells in the tissue does not vary over time,” explains co-senior author Angela Oliveira Pisco, Associate Director of Bioinformatics at the Chan Zuckerberg Biohub, San Francisco, US. “The identification of many shared aging genes suggests that there is a coordinated global aging behaviour in mice.”
The team then used this coordinated activity to develop a single-cell aging score based on the global aging genes. This new high-resolution aging score revealed that different tissue-cell types in the same animal can have a different aging status, shedding light on the diverse aging process across different types of cells.
“Taken together, our results provide a characterisation of aging genes across a wide range of tissue-cell types in the mouse,” concludes senior author James Zou, Assistant Professor of Biomedical Data Science at Stanford University, Stanford, US, and a Chan Zuckerberg Biohub Investigator. “In addition to providing new biological insights on the aging process, this work serves as a comprehensive reference for researchers working in related fields.”
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A gene therapy protects eye cells in mice with a rare disorder that causes vision loss, especially when used in combination with other gene therapies, shows a study published today in eLife.
The findings suggest that this therapy, whether used alone or in combination with other gene therapies that boost eye health, may offer a new approach to preserving vision in people with retinitis pigmentosa or other conditions that cause vision loss.
Retinitis pigmentosa is a slowly progressive disease, which begins with the loss of night vision due to genetic lesions that affect rod photoreceptors — cells in the eyes that sense light when it is low. These photoreceptors die because of their intrinsic genetic defects. This then impacts cone photoreceptors, the eye cells that detect light during the day, which leads to the eventual loss of daylight vision. One theory about why cones die concerns the loss of nutrient supply, especially glucose.
Scientists have developed a few targeted gene therapies to help individuals with certain mutations that affect the photoreceptors, but no treatments are currently available that would be effective for a broad set of families with the disease. “A gene therapy that would preserve photoreceptors in people with retinitis pigmentosa regardless of their specific genetic mutation would help many more patients,” says lead author Yunlu Xue, Postdoctoral Fellow at senior author Constance Cepko’s lab, Harvard Medical School, Boston, US.
To find a widely effective gene therapy for the disease, Xue and colleagues screened 20 potential therapies in mouse models with the same genetic deficits as humans with retinitis pigmentosa. The team chose the therapies based on the effects they have on sugar metabolism.
Their experiments showed that using a virus carrier to deliver a gene called Txnip was the most effective approach in treating the condition across three different mouse models. A version of Txnip called C247S worked especially well, as it helped the cone photoreceptors switch to using alternative energy sources and improved mitochondria health in the cells.
The team then showed that giving the mice gene therapies that reduced oxidative stress and inflammation, along with Txnip gene therapy, provided additional protection for the cells. Further studies are now needed to confirm whether this approach would help preserve vision in people with retinitis pigmentosa.
“The immediate next step is to test Txnip for safety in animals beyond mice, before moving on to a clinical trial in humans,” explains senior author and Howard Hughes Institute Investigator Constance Cepko, the Bullard Professor of Genetics and Neuroscience at Harvard Medical School. “If it ultimately proves safe in people, then we would hope to see it become an effective approach for treating those with retinitis pigmentosa and other forms of progressive vision loss, such as age-related macular degeneration.”
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A new study published in Elementa by researchers at the University of California, Santa Cruz and NOAA examines traditional aspects of seafood sustainability alongside greenhouse gas emissions to better understand the “carbon footprint” of U.S. tuna fisheries.
Fisheries in the United States are among the best managed in the world, thanks to ongoing efforts to fish selectively, end overfishing, and rebuild fish stocks. But climate change could bring dramatic changes in the marine environment that threaten seafood productivity and sustainability. That’s one reason why researchers set out to broaden the conversation about sustainability in seafood by comparing the carbon emissions of different tuna fishing practices.
The paper also puts those emissions in context relative to other sources of protein, like tofu, chicken, pork, or beef. In particular, the study examined how the carbon footprint of tuna was affected by how far from shore fishing fleets operated, or what type of fishing gear they used.
“This can be an opportunity to look at fisheries from different angles, all of which may be important,” said Brandi McKuin, the study’s lead author and a postdoctoral researcher in environmental studies at UC Santa Cruz.
Comparing Carbon Footprints
Generally speaking, less selective tuna fishing gear — like purse seine nets that scoop up many tuna all at once — are more likely to accidentally catch other species during the fishing process. That’s called bycatch, and it’s a conservation concern that often factors into seafood sustainability assessments.

In a series of experiments that began with amoebas — single-celled organisms that extend podlike appendages to move around — Johns Hopkins Medicine scientists say they have identified a genetic pathway that could be activated to help sweep out mucus from the lungs of people with chronic obstructive pulmonary disease a widespread lung ailment.
“Physician-scientists and fundamental biologists worked together to understand a problem at the root of a major human illness, and the problem, as often happens, relates to the core biology of cells,” says Doug Robinson, Ph.D., professor of cell biology, pharmacology and molecular sciences, medicine (pulmonary division), oncology, and chemical and biomedical engineering at the Johns Hopkins University School of Medicine.
Chronic obstructive pulmonary disease (COPD) is the fourth leading cause of death in the U.S., affecting more the 15 million adults, according to the U.S. Centers for Disease Control and Prevention. The disease causes the lungs to fill up with mucus and phlegm, and people with COPD experience chronic cough, wheezing and difficulty breathing. Cigarette smoking is the main cause in as many as three-quarters of COPD cases, and there is no cure or effective treatment available despite decades of research.
In a report on their new work, published Feb. 25 in the Journal of Cell Science, the researchers say they took a new approach to understanding the biology of the disorder by focusing on an organism with a much simpler biological structure than human cells to identify genes that might protect against the damaging chemicals in cigarette smoke.
Robinson and his collaborator, Ramana Sidhaye, M.D., also a professor of medicine in the Division of Pulmonology at Johns Hopkins, with their former lab member Corrine Kliment, M.D., Ph.D., counted on the knowledge that as species evolved, genetic pathways were frequently retained across the animal kingdom.
Enter the soil-dwelling amoeba Dictyostelium discoideum, which has long been studied to understand cell movement and communication. The scientists pumped lab-grade cigarette smoke through a tube and bubbled it into the liquid nutrients bathing the amoeba. Then, the scientists used engineered amoeba to identify genes that could provide protection against the smoke.

Researchers from North Carolina State University have found a way to fine-tune the molecular assembly line that creates antibiotics via engineered biosynthesis. The work could allow scientists to improve existing antibiotics as well as design new drug candidates quickly and efficiently.
Bacteria — such as E. coli — harness biosynthesis to create molecules that are difficult to make artificially.
“We already use bacteria to make a number of drugs for us,” says Edward Kalkreuter, former graduate student at NC State and lead author of a paper describing the research. “But we also want to make alterations to these compounds; for example, there’s a lot of drug resistance to erythromycin. Being able to make molecules with similar activity but improved efficacy against resistance is the general goal.”
Picture an automobile assembly line: each stop along the line features a robot that chooses a particular piece of the car and adds it to the whole. Now substitute erythromycin for the car, and an acyltransferase (AT) — an enzyme — as the robot at the stations along the assembly line. Each AT “robot” will select a chemical block, or extender unit, to add to the molecule. At each station the AT robot has 430 amino acids, or residues, which help it select which extender unit to add.
“Different types of extender units impact the activity of the molecule,” says Gavin Williams, professor of chemistry, LORD Corporation Distinguished Scholar at NC State and corresponding author of the research. “Identifying the residues that affect extender unit selection is one way to create molecules with the activity we want.”
The team used molecular dynamic simulations to examine AT residues and identified 10 residues that significantly affect extender unit selection. They then performed mass spectrometry and in vitro testing on AT enzymes that had these residues changed in order to confirm their activity had also changed. The results supported the computer simulation’s predictions.
“These simulations predict what parts of the enzyme we can change by showing how the enzyme moves over time,” says Kalkreuter. “Generally, people look at static, nonmoving structures of enzymes. That makes it hard to predict what they do, because enzymes aren’t static in nature. Prior to this work, very few residues were thought or known to affect extender unit selection.”
Williams adds that manipulating residues allows for much greater precision in reprogramming the biosynthetic assembly line.
“Previously, researchers who wanted to change an antibiotic’s structure would simply swap out the entire AT enzyme,” Williams says. “That’s the equivalent of removing an entire robot from the assembly line. By focusing on the residues, we’re merely replacing the fingers on that arm — like reprogramming a workstation rather than removing it. It allows for much greater precision.
“Using these computational simulations to figure out which residues to replace is another tool in the toolbox for researchers who use bacteria to biosynthesize drugs.”
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Materials provided by North Carolina State University. Original written by Tracey Peake. Note: Content may be edited for style and length.