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Category: chemistry – Page 3

A vision of chromosome organization

The DNA of eukaryotic organisms is packaged by histone proteins into chromatin. The structural organization of chromatin is tied to its function. Loosely packed, more transcriptionally active regions of chromatin are known as euchromatin, whereas highly condensed, less transcriptionally active regions are known as heterochromatin.

Despite advances in the study of chromatin structure over the past 100 years, a biochemical understanding of how basic structural motifs beget higher-order chromatin organization remains lacking.

In a new Science study, researchers present an approach that enables imaging and analysis of the structure of chromatin condensates in situ, which moves the field much closer toward defining the structural chromatin motifs that underpin its nuclear functions.

Learn more in a new Science Perspective.

Cryogenic electron tomography of condensed chromatin enables multiscale analysis of its structure.

Kaite Zhang and Vijay Ramani Authors Info & Affiliations

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Non-opioid analgesic binding sites on glycine transporter 2

Glycine is a major inhibitory neurotransmitter that reduces nerve activity, helping to regulate pain signals, motor control and sensory processing. Glycine transporter 2 (GlyT2) is a key regulator of glycinergic neurotransmission because it removes glycine from the synaptic clefts. When GlyT2 is inhibited, glycine reuptake is reduced, allowing synaptic glycine levels to rise and enhance inhibitory signaling. Because of its ability to modulate glycinergic transmission, GlyT2 is an attractive therapeutic target for neuropathic pain. It is particularly attractive because it suggests new means of non-opioid pain management.

In a new study published in PNAS, researchers reported high-resolution cryo-EM structures of GlyT2 in three major conformational states. These structures illuminate the transporter’s molecular mechanisms and provide critical insights into how analgesic compounds are recognized.

The researchers identified a previously unknown third sodium-binding site (Na3) on GlyT2. Whereas other neurotransmitter transporters use two Na ⁺ ions and one Cl ⁻ ion, the additional binding site demonstrates that GlyT2 uses three Na ⁺ ions and one Cl ⁻ ion to transport glycine per cycle. This additional sodium ion supplies the extra energetic drive required for glycine transport and offers new understanding of Na ⁺ /Cl ⁻-coupled substrate binding and conformational changes, supporting GlyT2’s specialized physiological function.

The researchers also uncovered a distinctive allosteric binding pocket that accommodates lipid-based inhibitors such as oleoyl-D-lysine, a derivative of the endogenous lipid N-arachidonyl glycine. Structural and biochemical analyzes revealed features that determine the inhibitory potency of this class of lipid molecules, providing a foundation for rational design of improved lipid-based GlyT2 analgesics.

Additionally, the researchers resolved structures of GlyT2 bound to several small-molecule inhibitors, including ALX1393, opiranserin, and ORG25543. These structures reveal distinct competitive and allosteric inhibition mechanisms and identify key residues responsible for selectivity between GlyT1 and GlyT2.

Shortest light pulse ever created captures ultrafast electron dynamics

Electrons determine everything: how chemical reactions unfold, how materials conduct electricity, how biological molecules transfer energy, and how quantum technologies operate. But electron dynamics happens on attosecond timescales—far too fast for conventional measurement tools.

Researchers have now generated a 19.2-attosecond soft X-ray pulse, which effectively creates a camera capable of capturing these elusive dynamics in real time with unprecedented detail, enabling the observation of processes never observed before. Dr. Fernando Ardana-Lamas, Dr. Seth L. Cousin, Juliette Lignieres, and ICREA Prof. Jens Biegert, at ICFO, has published this new record in Ultrafast Science. At just 19.2 attoseconds long, it is the shortest and brightest soft X-ray pulse ever produced, giving rise to the fastest “camera” in existence.

Flashes of light in the soft X-ray spectral range provide fingerprinting identification, allowing scientists to track how electrons reorganize around specific atoms during reactions or phase transitions. Generating an isolated pulse this short, required innovations in high-harmonic generation, advanced laser engineering, and attosecond metrology. Together, these developments allow researchers to observe electron dynamics, which define material properties, at their natural timescales.

Molecular basis of DNA cross-linking by bacteria

The relevance of the gut microbiome, the community of microorganisms living in the digestive tract, to human health is a topic of intense interest. However, among the numerous benevolent bacteria living in the gut, there are some species that are harmful to humans.

For example, certain strains of Escherichia coli produce the genotoxin colibactin, which causes DNA damage and is linked with colon cancer. However, the colibactin molecule is complex and unstable, which has made it challenging to elucidate its chemical structure and the mechanism by which it damages DNA. In the culmination of years of research from multiple laboratories, researchers in a new Science study reveal the structure of the active form of colibactin bound to DNA.

The findings go a long way toward explaining the mutation signatures associated with colibactin exposure and provide substantial insight into how colibactin contributes to colorectal carcinogenesis.

Learn more in a new Science Perspective.

The structure of the bacterial genotoxin colibactin bound to DNA shows how it might contribute to cancer risk.

Orlando D. Schärer Authors Info & Affiliations

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Microgel-based antioxidant system advances biohybrid brain research

Researchers have unveiled a breakthrough technology that could transform the way scientists build and study lab-grown brain tissue models. The innovation, called Cellular RedOx Spreading Shield (CROSS), delivers long-lasting antioxidant protection to stem cells, enabling the reliable production of high-quality extracellular vesicles (EVs) that strengthen neuron-glia networks.

The study, published in the journal Advanced Functional Materials, was led by University of Illinois Urbana-Champaign chemical and biomolecular engineering professor Hyunjoon Kong and chemistry professor Hee Sun Han, and performed by Ryan Miller, currently a post-doctoral fellow at Georgia Tech.

Jonghwi Lee, in the chemical engineering department at Chung-Ang University in South Korea, and Young Jun Kim at the Korean Institute of Science and Technology–Europe, collaborated on the project.

Observing synapses in action: Images capture real-time neurotransmitter release

It takes just a few milliseconds: A vesicle, only a few nanometers in size and filled with neurotransmitters, approaches a cell membrane, fuses with it, and releases its chemical messengers into the synaptic cleft—making them available to bind to the next nerve cell.

A team led by Professor Christian Rosenmund of Charité—Universitätsmedizin Berlin has captured this critical moment of brain function in microscopic images. They describe their achievement in the journal Nature Communications.

The Psychedelic Scientist

The reality is Deamer and the psychedelics-inspired Damer may very well be right about the origin of life on Earth. They may never win over scientists like Nick Lane, an evolutionary biochemist at University College London, who argues life needed the singular mix of physics and chemistry in hydrothermal ocean vents to originate. As recently as 2024, Lane and chemist Joana C. Xavier of Imperial College London explained in Nature that the wet and dry cycles of hot springs, key to Deamer’s and Damer’s hypothesis, could not lead to “the network of hundreds of reactions that keeps all cells alive.”

However, biologist Jack Szostak, a Nobel laureate, whose lab at the University of Chicago focuses on the origin of life, told me it’s likely that life did begin in volcanically active regions or impact craters on Earth’s surface. “Deep sea hydrothermal vents are not a plausible site for the origin of life,” he said. “Geothermally active areas,” he added, “are attractive because they do provide the environmental fluctuations needed to drive the primordial cell cycle.” Synthetic biologist Kate Adamala, from the University of Minnesota, who builds artificial protocells to probe how life might have first taken shape, agreed. “I’m on Team Dave and Bruce,” she said.

Presented with either criticism or praise of his origin-of-life theory, Damer remained as sanguine as ever. “You’re never going to have a complete understanding of the origin of life on the early Earth, because we just can’t reproduce the exact conditions,” he said. Of course, he believed the hot springs hypothesis would stand the test of time.

Psilocybin shows greater potential than cannabinoids for obsessive-compulsive disorder treatment

In a review of previous studies, McMaster University researchers observe a stronger signal for psilocybin as a treatment for obsessive-compulsive disorder than cannabinoids.

Obsessive-compulsive disorder involves persistent, intrusive thoughts and repetitive mental or physical behaviors, and requires long-term treatment to alleviate symptoms. The ethology of the disorder appears complex, involving multiple biological pathways. Imbalances in central serotonin, dopamine, and glutamate activities are widely thought to play a causative role, placing neurochemistry at the center of many treatment strategies.

First-line treatment includes selective serotonin reuptake inhibitors and cognitive behavioral therapy using exposure and response prevention. Roughly 40–60% of patients remain unresponsive to psychotherapy or pharmacotherapy, alone or combined, placing many people in the category of treatment-resistant OCD.

Electrochemical tuning of Ni-rich cathodes curbs c-collapse, enhancing lithium-ion battery durability

Lithium-ion batteries (LiBs) remain the most widely used rechargeable batteries worldwide, due to their light weight, high energy densities and their short charging times. Energy engineers have been trying to identify new materials and strategies that could help to further boost the energy stored by LiBs, while also extending their lifespan (i.e., the period for which they can be used reliably).

LiBs work by moving charged lithium atoms (i.e., ions) between a positive electrode (i.e., cathode) and a negative electrode (i.e., anode). When lithium ions enter and leave these materials, they can experience significant structural changes.

These changes include the sudden shrinkage of the spacing between the materials’ horizontal layers, which can be experimentally monitored through the crystal’s c-lattice parameter. This phenomenon, referred to as c-collapse, can deform the material, crack the particles and in turn shorten the life of batteries.

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