MBIB News

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.

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.

Scientists have determined the structure of a unique enzyme, produced by a species of methane-eating bacteria, that converts the greenhouse gas into methanol – a highly versatile liquid fuel and industrial product ingredient.

Their new study, published in the Journal of the American Chemical Society, is the first to report the structure of the enzyme, called soluble methane monooxygenase (sMMO), at room temperature in both its reduced and oxidized forms. This detailed structural information will help researchers design efficient catalysts for industrial methane to methanol conversion processes.

The Andreas Acrivos Award for Professional Progress in Chemical Engineering is endowed by the AIChE Foundation in the name of fluid-dynamics pioneer Andreas Acrivos of the City College of New York. The prize recognizes outstanding progress in chemical engineering by a member of AIChE in their early career. The recipient of the 2020 Professional Progress Award is David Schaffer, a faculty scientist in Molecular Biophysics and Integrated Bioimaging (MBIB), as well as a professor of chemical and biomolecular engineering at UC Berkeley, where he also directs the California Institute for Quantitative Biosciences. Schaffer was recognized for implementing molecular and cellular engineering strategies to overcome challenges in the development of gene and cell therapies. In particular, he developed the concept of applying directed evolution to engineer targeted and efficient viral gene therapy vectors, which led to novel adeno-associated viral vectors being used in multiple human clinical trials. In addition, he has developed new technologies to investigate and control stem cell fate decisions. Read more from AIChE.

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.