Biosciences Area

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.

Cataloging Nature’s Hidden Arsenal: Viruses that Infect Bacteria

Viruses that infect bacteria, or phages, are continually evolving ways to target and exploit their specific hosts. Their bacterial hosts, in turn, are continually evolving means to evade the phages. These perpetual battles for survival yield incredibly diverse molecular arsenals that researchers are itching to study, yet doing so can be tedious and labor-intensive.

A team led by Berkeley Lab scientists has developed an efficient and inexpensive new method to gain insight into these defensive strategies. They reported in PLOS Biology that a combination of three recently developed techniques can reveal which bacterial receptors phages exploit to infect the cell, as well as what cellular mechanisms the bacteria use to respond to a phage infection.

This Anti-COVID Mask Breaks the Mold

In the early days of the pandemic, amidst all the uncertainty, one thing was for sure: N95 masks – the personal protective respiratory devices that filter out viruses, bacteria, and wildfire smoke – were in short supply. So when materials scientists Jeff Urban and Peter Hosemann heard that a local HMO needed advice on N95 alternatives, they immediately knew what to do: Make a better mask.   

Urban and Hosemann were responding to a Berkeley Lab-wide call for research ideas in support of fighting COVID-19, which ultimately led to their receiving DOE support through the National Virtual Biotechnology Laboratory (NVBL), a consortium of DOE National laboratories with core capabilities relevant to the threats posed by COVID-19, and funded under the Coronavirus Aid, Relief, and Economic Security (CARES) Act.

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.

Was this page useful?

Send
like not like
Follow us: