For structural biologists who study proteins, predicting their shape offers a key to understanding their function and accelerating treatments for diseases like cancer and COVID-19. The current approaches to accurately mapping that shape have their limitations, but by applying powerful machine learning methods to the large library of protein structures it is now possible to predict a protein’s shape from its gene sequence.
Chasing Their Tails But Getting Somewhere: Reimagining the Shape of Noise Leads to Improved Molecular Models
Elliot Perryman, a computer science and physics major at the University of Tennessee, began working with staff scientist Peter Zwart in the Center for Advanced Mathematics for Energy Research Applications (CAMERA) last fall through the Berkeley Lab Undergraduate Research (BLUR) program. Together they developed an algorithm that will extract better structures from low-quality crystallographic diffraction data.
New Algorithm Sharpens Focus of World’s Most Powerful Microscopes
In recent years, cryo-electron microscopy (cryo-EM) technology has advanced to the point that it can produce structures with atomic-level resolution for many types of molecules. Yet in some situations, even the most sophisticated cryo-EM methods still generate maps with lower resolution and greater uncertainty than required to tease out the details of complex chemical reactions.
In a study published in Nature Methods, a multi-institutional team led by Tom Terwilliger from the New Mexico Consortium and including researchers from Berkeley Lab demonstrates how a new computer algorithm improves the quality of the 3D molecular structure maps generated with cryo-EM.
Paper Summarizes Major Tools, Recent Developments in Phenix
Researchers at Berkeley Lab and their collaborators who work on the Phenix software suite have published a new paper that summarizes how to determine three-dimensional macromolecular structures from three experimental methods: X-ray crystallography, neutron diffraction, and electron cryo-microscopy (cryo-EM). The article appeared in the journal Acta Crystallographica Section D: Structural Biology and is featured on the cover of the October 2019 issue.
BCSB Helps Elucidate Mechanism of Innate Immune Response
The crystallographic study of STING (stimulator of interferon genes), a transmembrane protein that plays a key role in innate immunity, in complex with TBK1 (serine/threonine-protein kinase), an enzyme that regulates the inflammatory response to foreign DNA, is extremely challenging due to weakly diffracting crystals. But thanks to the expertise of Berkeley Center for Structural Biology (BCSB) scientists, researchers from Texas A&M University (TAMU) were able to pinpoint the conserved motif of STING that mediates the recruitment and activation of TBK1. They published their results in Nature.
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