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Biochemistry

Unlocking Nature’s Secrets: The Amazing Defenses of CRISPR Systems

Newly discovered weapons of bacterial self-defense take different approaches to achieving the same goal: preventing a virus from spreading through the bacterial population.

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The collective work of our labs is revealing just how effective — and different — these CARF effectors are,” says Luciano Marraffini. As researchers at Rockefeller’s Laboratory of Bacteriology and MSKCC’s Structural Biology Laboratory continue to study key immune components of some CRISPR systems, they’ve made a groundbreaking discovery: the newest CARF effector, dubbed Cat1, takes an unusually complex molecular approach to achieving its goal.

Unlike other defense mechanisms that rely on genetic scissors or molecular fumigation, Cat1 depletes a metabolite essential for cellular function, leaving viral invaders without fuel. This unique strategy was unveiled in a recent publication in Science, where the scientists announced their findings on the newly discovered protein.

CRISPR systems are mechanisms in the adaptive immune systems of bacteria and other single-cell organisms that offer protection against viruses, called phages. The six types of CRISPR systems work roughly the same way: A CRISPR RNA identifies foreign genetic code, which triggers a cas enzyme to mediate an immune response, often snipping off the invader material.

But research indicates that CRISPR systems deploy a wide variety of defensive strategies beyond genetic scissors. Marraffini’s lab has led the way on much of this research, particularly in studying CARF effectors – proteins activated upon phage infection of a bacterium.

CARF effector immunity is believed to work by creating an inhospitable environment for viral replication. For example, the Cam1 CARF effector causes membrane depolarization of an infected cell, while Cad1 triggers a sort of molecular fumigation, flooding an infected cell with toxic molecules.

For the current study, the researchers used Foldseek, a powerful structural homology search tool, to find Cat1. They discovered that Cat1 is alerted to the presence of a virus by the binding of secondary messenger molecules called cyclic tetra-adenylate, or cA4, which stimulate the enzyme to cleave an essential metabolite in the cell called NAD+.

Once a sufficient amount of NAD+ is cleaved, the cell enters a growth-arrest state. With cellular function on pause, the phage can no longer propagate and spread to the rest of the bacterial population. In this way, Cat1 is similar to Cam1 and Cad1 in that they all provide population-level bacterial immunity.

However, while its immune strategy may be similar to these other CARF effectors, its form is not, as detailed structural analysis using cryo-EM revealed. The Cat1 protein has a surprisingly complex structure in which Cat1 dimers are glued by cA4 signal molecule, forming long filaments upon viral infection, and trap the NAD+ metabolites within sticky molecular pockets.

Also unusual is the fact that Cat1 often seems to work alone. Normally in type III CRISPR systems, you have two activities that contribute to the immunity effect. However, most of the bacteria that encode Cat1 seem to primarily rely on Cat1 for their immunity effect.

The collective work of our labs is revealing just how effective — and different — these CARF effectors are,” says Marraffini. “The range of their molecular activities is quite amazing.”

Biochemistry

Shape-Shifting Catalysts: Revolutionizing Green Chemistry with a Single Atom

A team in Milan has developed a first-of-its-kind single-atom catalyst that acts like a molecular switch, enabling cleaner, more adaptable chemical reactions. Stable, recyclable, and eco-friendly, it marks a major step toward programmable sustainable chemistry.

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The scientific community has witnessed a groundbreaking development in sustainable chemistry with the creation of a shape-shifting single-atom catalyst at the Politecnico di Milano. This innovative material has demonstrated the capability to selectively adapt its chemical activity, paving the way for more efficient and programmable industrial processes.

Published in the Journal of the American Chemical Society, one of the world’s most esteemed scientific journals in chemistry, this study marks a significant breakthrough in the field of single-atom catalysts. For the first time, scientists have successfully designed a material that can change its catalytic function depending on the chemical environment, much like a ‘molecular switch.’ This allows complex reactions to be performed more cleanly and efficiently, using less energy than conventional processes.

The research focuses on a palladium-based catalyst in atomic form encapsulated in a specially designed organic structure. This unique setup enables the material to ‘switch’ between two essential reactions in organic chemistry – bioreaction and carbon-carbon coupling – simply by varying the reaction conditions. The team has successfully demonstrated this phenomenon, showcasing the potential for more intelligent, selective, and sustainable chemical transformations.

Lead researcher Gianvito Vilé, lecturer at the Politecnico di Milano’s ‘Giulio Natta’ Department of Chemistry, Materials and Chemical Engineering, emphasizes the significance of their discovery: “We have created a system that can modulate catalytic reactivity in a controlled manner, paving the way for more intelligent, selective, and sustainable chemical transformations.”

The new catalyst stands out not only for its reaction flexibility but also for its stability, recyclability, and reduced environmental impact. ‘Green’ analyses conducted by the team reveal a substantial decrease in waste and hazardous reagents, making it an exemplary model for sustainable chemistry.

This study is the result of an international collaboration with esteemed institutions from around the world, including the University of Milan-Bicocca, the University of Ostrava (Czech Republic), the University of Graz (Austria), and Kunsan National University (South Korea). The joint efforts of these researchers have led to a groundbreaking achievement that has far-reaching implications for the field of green chemistry.

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Biochemistry

Scientists Finally Tame the Impossible: A Stable 48-Atom Carbon Ring is Achieved

Researchers have synthesized a stable cyclo[48]carbon, a unique 48-carbon ring that can be studied in solution at room temperature, a feat never achieved before.

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The discovery of a new type of molecular carbon allotrope, known as cyclocarbon, has been a long-standing challenge for chemists. A team of researchers from Oxford University’s Department of Chemistry, led by Dr Yueze Gao and senior author Professor Harry Andersen, have successfully synthesized a stable 48-atom carbon ring in solution at room temperature. This achievement marks a significant breakthrough in the field, as previous attempts to study cyclocarbons were limited to the gas phase or extremely low temperatures (4 to 10 K).

The researchers employed a unique approach by synthesizing a cyclocarbon catenane, where the C48 ring is threaded through three other macrocycles. This design increases the stability of the molecule, preventing access to the sensitive cyclocarbon core. The team developed mild reaction conditions for the unmasking step in the synthesis process, which allowed them to achieve a stable cyclocarbon in solution at 20°C.

The cyclocarbon catenane was characterized using various spectroscopic techniques, including mass spectrometry, NMR, UV-visible, and Raman spectroscopy. The observation of a single intense 13C NMR resonance for all 48 sp1 carbon atoms provides strong evidence for the cyclocarbon catenane structure.

Lead author Dr Yueze Gao stated that achieving stable cyclocarbons in a vial at ambient conditions is a fundamental step, making it easier to study their reactivity and properties under normal laboratory conditions. Senior author Professor Harry Andersen added that this achievement marks the culmination of a long endeavor, with the original grant proposal written in 2016 based on preliminary results from 2012-2015.

The study also involved researchers from the University of Manchester, the University of Bristol, and the Central Laser Facility, Rutherford Appleton Laboratory. This collaborative effort demonstrates the power of interdisciplinary research in advancing our understanding of complex molecular systems.

This achievement has significant implications for future studies on cyclocarbons and their potential applications in various fields. The researchers’ innovative approach to synthesizing stable cyclocarbons at room temperature opens up new possibilities for exploring the properties and reactivity of these intriguing molecules.

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Biochemistry

“Revolutionizing Medicine: A 100x Faster Path to Life-Saving Drugs with Metal Carbenes”

Using a clever combo of iron and radical chemistry, scientists have unlocked a safer, faster way to create carbenes molecular powerhouses key to modern medicine and materials. It s 100x more efficient than previous methods.

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Chemists have made a groundbreaking breakthrough in developing a novel method to generate highly useful chemical building blocks by harnessing metal carbenes. This achievement is expected to revolutionize the synthesis of life-saving drugs and materials development.

Typically used in chemical reactions essential for drug synthesis, carbenes are short-lived, highly reactive carbon atoms. However, creating these carbenes has been a challenging task due to limited methods and hazardous procedures.

Researchers at The Ohio State University have now developed an approach that makes producing metal carbenes much easier and safer. According to David Nagib, co-author of the study and distinguished professor in arts and sciences, “Our goal all along was to determine if we could come up with new methods of accessing carbenes that others hadn’t found before.”

The team’s innovative method uses iron as a metal catalyst and combines it with chlorine-based molecules that easily generate free radicals. This combination works to form the carbene of their choice, including many that had never been made before.

These three-sided molecular fragments, known as cyclopropanes, are vital to the synthesis of medicines and agrichemicals due to their small size and unusual energy. The researchers’ work was inspired by looking for the best ways to create these shape, which is one of the most common found in medicines.

“Our lab is obsessed with trying to get the best methods for making cyclopropanes out there as soon as possible,” said Nagib. “We have the eye on the prize of inventing better tools to make better medicines, and along the way, we’ve solved a huge problem in the carbene world.”

The study was recently published in Science, and the team’s discovery is expected to become extremely impactful. By accessing a new way of creating and classifying carbenes, scientists can simplify and improve the current wasteful, multistep process of producing them.

For consumers, this method suggests that future drugs developed by this technology may be cheaper, more potent, faster-acting, and longer-lasting. The work could prevent shortages of important medicines like antibiotics and antidepressants, as well as drugs that treat heart disease, COVID, and HIV infections, said Nagib.

Additionally, the team would like to ensure that their transformational organic chemistry tool is accessible to both big and small research labs and drug manufacturers around the world. One way to guarantee this is by continuing to improve the current technique, said Nagib.

“Our team at Ohio State came together in the coolest, most collaborative way to develop this tool,” he said. “So we’re going to continue racing to show how many different types of catalysts it could work on and make all kinds of challenging and valuable molecules.”

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