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A Computational Framework for Designing Disordered Proteins at Large Scale
The vast majority of proteins in our bodies contain regions that are in a constant state of wiggling, shape-shifting every few nanoseconds to completely change how they look. Information on how these proteins work is critical to understanding health and disease and to developing drugs for cancer, neurodegeneration, and myriad other conditions. However, it has been challenging for scientists to pin down precisely how these regions function, and how they go awry in disease.
Researchers at Washington University School of Medicine in St. Louis and at Syracuse University have now built a tool that can design such “disordered” proteins (intrinsically disordered protein regions; IDRs) and untangle their functionality. The team suggests the innovation has the potential to accelerate scientific exploration of a vast and underexplored area of biology.
Alex Holehouse, PhD, an associate professor in the WashU Medicine Department of Biochemistry and Molecular Physics, is research co-lead and co-corresponding author of the team’s published paper in Nature, titled “Rational design of disordered proteins for sequence–function investigation,” in which they explained, “Our work uses rational sequence design as a powerful method for exploring function in IDRs and provides a versatile tool for designing functional disordered proteins.”
An important way scientists study proteins is to design synthetic equivalents of the molecules that they can then test in various ways. Until now, advances in such protein design have applied almost entirely to “folded” proteins—or their folded parts—that have a defined three-dimensional shape.
Yet 70% of human proteins also contain what’s known as intrinsically disordered protein regions (IDRs) that don’t have a stable 3D structure. “IDRs exist as a dynamic collection of rapidly interconverting and structurally distinct conformations,” the team explained. These regions can play critical roles in a variety of different cellular processes and human diseases. Researchers’ ability to predict how they will behave, or to design synthetic versions to study their function, has been limited. “Despite their importance, systematically testing the relationship between IDR sequence and molecular function remains challenging,” the authors further wrote. “While rational design of folded proteins has seen substantial recent progress, our ability to design IDRs remains more limited.”
Holehouse said, “The way people would typically try to study and design stable, folded proteins doesn’t really work very well for disordered proteins.” He and colleague Ryan Emenecker, PhD, a faculty instructor in the same department and lead developer and co-corresponding author on the study, have been working on an alternative way to tackle this challenge for almost five years.
Holehouse, Emenecker and their collaborators, including co-corresponding author Shahar Sukenik, PhD, a faculty member in the Department of Chemistry at Syracuse University, have now reported on development of the protein-design system, which they called GOOSE (an acronym derived in an appropriately disordered way from Generate disOrdered prOtiens Specifying propErties).
Loaded with a large library of the sequences for protein building blocks that are associated with specific cell functions, GOOSE produces blueprints for custom-built disordered proteins that are then created in genetically engineered cells. Scientists can remove or add building blocks as desired and test what effect they have on the activities of a cell. “GOOSE enables rapid design of de novo synthetic IDRs and variants of provided sequences, facilitating broad exploration of sequence space,” they commented. “GOOSE can design IDRs by sequence properties (such as amino acid composition, charge, hydrophobicity and charge patterning), conformational properties, chemically specific intermolecular interactions or any arbitrary design constraint (such as specific three-dimensional conformational ensembles).”
Emenecker stated, “The ability to design disordered proteins at a large scale with our platform now allows us to learn how their component sequences affect the cell, and it gives us a lens through which we can learn how naturally occurring changes in these proteins might drive diseases like cancer.”
The technique has potential for driving medical advancements. Holehouse, who is a research member of Siteman Cancer Center, based at Barnes-Jewish Hospital and WashU Medicine, is seeking to optimize therapeutics that rely upon disordered proteins. Holehouse and Emenecker have received a grant to improve CAR T cells, an anti-cancer therapy in which immune cells are genetically modified to attack tumor cells.
A key protein on the surface of CAR T cells contains a disordered region that guides the cell’s attack response. Until now, scientific efforts to improve its performance in destroying cancer cells have been conducted largely by trial and error.
“With our technique, we can design better versions of these disordered regions to do the signaling in different ways,” said Holehouse. “The hope is we won’t be limited by the types of constraints that are currently hurting the efficacy of CAR T therapies. That’s a very concrete place where these tools can move medicine forward.”
Among various applications, one of GOOSE’s first tests was to generate synthetic proteins that could help cells respond to changes in external stressors—in this case, drought. “We were able to very quickly design 2,300 different proteins that would respond to drought conditions in yeast,” said Emenecker, who commented that many of these synthetic proteins proved GOOSE’s utility by working as intended, helping the cells’ recovery after drying out. Even more promising, many of them performed much better than the yeast’s natural proteins.
This work directly contributes to Holehouse, Emenecker and Sukenik’s ongoing work as part of a larger National Science Foundation initiative to engineer more environmentally resilient crops.
“More broadly, this opens the possibility of being able to make new sensors that are sensitive to things outside what natural sequences would be attuned to, like toxins or cell damage,” Emenecker said. “It has the potential to be very valuable.” In their paper the team concluded, “Taken together, our work highlights how GOOSE can be used to gain insights into IDR sequence–function relationships.”
The post A Computational Framework for Designing Disordered Proteins at Large Scale appeared first on GEN – Genetic Engineering and Biotechnology News.
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Capricor CEO won’t rule out legal action against FDA after negative adcomm
Capricor CEO won’t rule out legal action against FDA after negative adcomm
After an FDA advisory committee voted 9-3 on Wednesday against recommending Capricor Therapeutics’ Duchenne muscular dystrophy cardiomyopathy drug for approval, stakeholders allege an “ulterior motive” and “biased intentions.” Read More
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Ketamine Triggers Sex-Specific Brain Recovery Responses
During ketamine anesthesia the brain’s nerve cells fall silent, and as consciousness returns, they begin to reconnect. A study in mice by researchers at the Institute of Science and Technology Austria (ISTA) and colleagues at Allen Institute for Brain Science in Seattle, has now for the first time shown that immune cells in the brain play a critical role in this process, and indicates that there are differences between female and male brains.
Senior and corresponding author Sandra Siegert, PhD, at ISTA, reported on their findings in Science Advances, in a paper titled “Corticosterone-linked microglial activity underpins sexually dimorphic neuroplasticity after ketamine anesthesia,” in which they concluded “Our study uncovers significant sex-specific differences in neuronal adaptation during recovery from ketamine anesthesia, driven by microglia.”
Recovery from anesthesia is critical for resuming normal physiological and neuronal functions, but the mechanisms involved remain elusive, the authors wrote. “Ketamine distinguishes itself from other anesthetics by its unique pharmacological properties as an N-methyl D-aspartate (NMDA) receptor antagonist, which preferentially targets GABAergic inhibitory interneurons.”
And unlike many other anesthetics, ketamine does more than induce unconsciousness. It alters how we perceive pain and form memories. It dampens communication between neurons—the very network that must later resume normal function as the patient awakens. Exactly how this recovery process unfolds—and whether male and female brains differ in this regard—has been unclear. “… ketamine anesthesia induces mild anxiety behavior phenotypes, interestingly, only in females,” the team continued, “suggesting inherent sex differences in anesthesia recovery with neuronal consequences that extend beyond the immediate sex-dependent metabolic processing described for low-dose ketamine.”
Working with mice, Siegert, together with Alessandro Venturino, PhD, and their colleagues at ISTA, and researchers at the Allen Institute, now offer the first answers to some of these questions. Microglia are specialized immune cells that constantly scan the brain and, when needed, trigger anti‑inflammatory responses. They also monitor neurons and their connections, thus helping to maintain optimal brain function. “Ketamine, across different dosages, affects microglia, which are embedded within the neuronal network,” the team explained. “Locally, microglia influence the synaptic machinery and neuronal firing properties by responding to environmental changes.”
As early as 2017, Siegert’s group at ISTA noticed that male and female mice respond differently to ketamine anesthesia, and more precisely, their microglia do.
For the newly reported study, using a cranial window—a surgically implanted opening that allows microscopic access to the living brain—Venturino analyzed how microglia and neurons behave while mice recover from ketamine anesthesia. Both cell types were labeled with fluorescent markers to glow under the microscope.
The researchers observed microglia processes in their dynamic action towards neurons. Surprisingly, as female mice recovered from anesthesia, microglia began forming prolonged contacts with neurons, coinciding with the onset of synaptic remodeling and plasticity. Notably, this phenomenon was not observable in male mice.
Furthermore, in mice lacking microglia, no such synaptic remodeling occurred, indicating that microglia are critical mediators of this recovery-associated plasticity. “What was fascinating,” Venturino explains, “was that we observed this plasticity—the brain’s ability to change, adapt, and in this case recover—only in females.”
Despite many other projects—or perhaps because of them—the researchers kept returning to their initial observation. “I’ve always believed that women have greater brain plasticity,” Siegert said with a smile. “Alessandro and I just couldn’t let it go—we wanted to know why.”
Further experiments revealed that this plasticity depends on corticosterone, one of the major stress hormones. “During recovery from anesthesia, corticosterone levels rise,” Venturino explained. “In female mice, this specifically activates the stress‑response gene Fkbp5 in microglia. The gene encodes the protein FKBP51, which helps the cell manage stress signals—and apparently prompts microglia to interact with neurons.”
The authors further noted, “Mechanistically, we found that female microglia selectively up-regulated the cochaperone Fkbp5/FK506-binding protein 51 (FKBP51), which is a key intermediary in the corticosteroid-induced stress response … Our findings underscore that microglia serve as a relevant interface between the endocrine stress response and the brain -immune cell system.”
To confirm this link, the team removed the adrenal glands—the endocrine organs that produce corticosterone. Without them, the close contact between microglia and neurons during recovery disappeared. “These results clearly show that corticosterone triggers this reaction in female mice,” said Venturino.
Siegert added, “They also remind us that stress is not always harmful—stress hormones are essential for certain processes in the brain.” In their paper the investigators commented, “The selective hypothalamic activation and elevated blood plasma corticosterone levels during the recovery phase in females shape the microglia-neuron interactions, highlighting a link between the endocrine and the brain-immune axes.”
Why this process differs between female and male mice remains uncertain; it is still unclear whether the male brain uses a similar mechanism, just delayed, or has another strategy. “Microglia enable rapid adaptation, and these cells in females are likely more sensitive to specific stress signals,” Siegert noted.
From an evolutionary viewpoint, she speculates, females may have faced greater demands for social, emotional, and multitasking adaptability—for example, in childcare, food gathering, or coordinating group activities. The female brain, therefore, had to adapt and respond more swiftly. “That’s a good thing,” Siegert added “But if this plasticity becomes too frequent or too intense, it can increase the risk of depression. We also know that psychiatric disorders are more prevalent in women than in men.”
Siegert further pointed out that during the literature review, her team found very few studies in which ketamine had been tested in females. “There were only a handful of anecdotal studies showing that women experience nausea and sickness more often after ketamine anesthesia,” she stated. Given that ketamine is also used as an antidepressant, understanding how its mechanisms differ between the sexes is all the more important. “It’s astonishing how readily people assume that men and women respond to drugs in the same way—when clearly they do not,” Siegert stressed.
Research like this is a step in the right direction: it highlights that medications can act differently in women and men and serves as a call to consider sex‑specific differences in future studies. “Our findings contribute to a growing body of evidence recognizing sex-specific differences in brain function and immune responses, the latter of which is already well known for increased susceptibility to infection and autoimmune diseases,” the team pointed out. “Our results identified a link between microglia-specific Fkbp5 expression and ketamine action, warranting a reevaluation of assumptions that ketamine is a general anesthetic and fully reversible across sexes.”
Insights into the microglia response to ketamine have since inspired Siegert and Venturino to co‑found Syntropic Medical, a start‑up in ISTA’s XISTA ecosystem exploring how 60 Hz flickering light can soften such neural networks in the brain.
The post Ketamine Triggers Sex-Specific Brain Recovery Responses appeared first on GEN – Genetic Engineering and Biotechnology News.
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STAT+: Trump administration revises rebate pilot for 340B drug discount program, angering hospitals
The Trump administration has revised the terms of a pilot effort that allows some drugmakers to offer rebates to certain hospitals and clinics for purchased medicines, a controversial move that may transform a key tenet of a federal drug discount program.
The anticipated pilot for the 340B Drug Pricing Program, which is slated to go into effect on Jan. 1, 2027, will allow pharmaceutical companies to provide “timely” rebates, rather than offering upfront discounts. The program targets specific drugs and pharmaceutical companies that are involved in the first two rounds of the Medicare Drug Price Negotiation Program.
“This revised pilot helps modernize program oversight by improving visibility into 340B transactions while helping preserve the program’s long-term sustainability for the patients and communities it was created to serve,” said Tom Engels, who heads the Health Resources and Services Administration, the government agency that oversees the program, in a statement.
The Trump administration has revised the terms of a pilot effort that allows some drugmakers to offer rebates to certain hospitals and clinics for purchased medicines, a controversial move that may transform a key tenet of a federal drug discount program.
The anticipated pilot for the 340B Drug Pricing Program, which is slated to go into effect on Jan. 1, 2027, will allow pharmaceutical companies to provide “timely” rebates, rather than offering upfront discounts. The program targets specific drugs and pharmaceutical companies that are involved in the first two rounds of the Medicare Drug Price Negotiation Program.
“This revised pilot helps modernize program oversight by improving visibility into 340B transactions while helping preserve the program’s long-term sustainability for the patients and communities it was created to serve,” said Tom Engels, who heads the Health Resources and Services Administration, the government agency that oversees the program, in a statement.
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