The diffraction limit is a fundamental property of light that has long prevented optical microscopes from bringing into focus anything smaller than half the wavelength of visible light (~200 nanometers), which is at least an order of magnitude larger than the tiny protein machines that keep cells, and us, running. A team of researchers co-led scientists in Berkeley Lab’s Molecular Foundry and Columbia University’s school of engineering developed a new class of crystalline material that, when used as a microscopic probe, overcomes the diffraction limit without heavy computation or a super-resolution microscope. The amazing new material, called avalanching nanoparticles (ANPs), will advance high-resolution, real-time bio-imaging of a cell’s organelles and proteins, as well as the development of ultrasensitive optical sensors and neuromorphic computing that mimics the neural structure of the human brain, among other applications. The work was reported in a cover article in the journal Nature.
Scientists Map Coronavirus Protein Linked to Immune Evasion, Disease Severity
A team of UC Berkeley and Berkeley Lab researchers used X-ray crystallography performed at the Advanced Light Source (ALS) to determine the atomic structure of ORF8, a protein secreted by the SARS-CoV-2 virus that is thought to help the pathogen evade and dampen response from human immune cells.
Unique X-Ray Microscope Reveals Dazzling 3D Cell Images
A team based at Berkeley Lab’s Advanced Light Source is making waves with its new approach for whole-cell visualization, using the world’s first soft X-ray tomography (SXT) microscope built for biological and biomedical research. In its latest study, published in Science Advances, the team used its platform to reveal never-before-seen details about insulin secretion in pancreatic cells taken from rats. This work was done in collaboration with a consortium of researchers dedicated to whole-cell modeling, called the Pancreatic β-Cell Consortium.
New Refinement Technique Promises Greater Protein Structure Accuracy
X-ray free-electron lasers (XFELs) came into use in 2010 for protein crystallography, allowing scientists to study fully hydrated specimens at room temperature without radiation damage. Researchers have developed many new experimental and computational techniques to optimize the technology and draw the most accurate picture of proteins from crystals. Now scientists in the Molecular Biophysics and Integrated Bioimaging (MBIB) Division have developed a new program, diffBragg, which can process every pixel collected from an XFEL for a protein structure independently. In a recent IUCrJ paper, the team led by MBIB Senior Scientist Nicholas Sauter proposed a new processing framework for more accurate determination of protein structures.
Get a Move On: Protein Translates Chemistry into Motion
The protein CheY plays a role in relaying sensory signals from chemoreceptors to the rotary motor at the base of the tail-like appendage, or flagellum, that protrudes from the cell body of certain bacteria and eukaryotic cells. It has been studied as a model for dissecting the mechanism of allostery—the process by which the binding of biological macromolecules (mainly proteins) at one location regulates activity at another, often distant, functional site. When it is transiently phosphorylated in response to chemotactic cues, CheY’s binding affinity for a flagellar motor switch protein called FliM is enhanced. CheY binding to FliM changes the direction of flagellar rotation from counterclockwise to clockwise.
Using X-ray footprinting with mass spectroscopy (XFMS), a team led by Shahid Khan, a senior scientist with the Molecular Biology Consortium, established that CheY changes shape when it tethers to the motor, and further parsed the contribution of phosphorylation to this shape change. The results of the XFMS experiments validated atomistic molecular dynamics (MD) predictions of the architecture of the allosteric communication network, marking the first time that XFMS has been used to validate protein dynamics simulations at single-residue resolution sampled over the complete protein.
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