MBIB News

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.

Statistician Paul Williams, a staff scientist in the Molecular Biophysics and Integrated Bioimaging (MBIB) Division, specializes in investigating the instances where genetics and environment are most closely intertwined. His work focuses on a phenomenon called “quantile-dependent expressivity,” which describes the relationship between the genes that predispose people to certain traits that can be amplified by behavior and environmental factors.

In a study appearing in Nature Plants, researchers from UC Davis, UC Berkeley, and Berkeley Lab report the discovery and characterization of a previously undescribed lineage of form I rubisco – one that the researchers suspect diverged from form I rubisco prior to the evolution of cyanobacteria. The novel lineage, called form I’ rubisco, gives researchers new insights into the structural evolution of form I rubisco, potentially providing clues as to how this enzyme changed the planet.

The work was led by Patrick Shih, a UC Davis assistant professor and the director of Plant Biosystems Design at the Joint BioEnergy Institute (JBEI), and Doug Banda, a postdoctoral scholar in his lab.

Biochemist Jennifer Doudna, a professor at UC Berkeley and faculty scientist in the Molecular Biophysics and Integrated Bioimaging Division, has been awarded the 2020 Nobel Prize in Chemistry for “the development of a method for genome editing.” She shares the Nobel Prize with co-discoverer Emmanuelle Charpentier, who currently serves as the scientific and managing director of the Max Planck Unit for the Science of Pathogens in Berlin. In 2012, Doudna and Charpentier’s research team detailed the underlying mechanisms of the CRISPR-Cas9 system – a component of the bacterial immune system that defends against invading viruses – and explained how it can be programmed to cut DNA at a target sequence.

A team of scientists led by David Baker at the University of Washington developed a method to design artificial proteins to serve as a framework for viral antigens. Their study was published recently in the journal eLife. Berkeley Lab scientists collected data at the Advanced Light Source to visualize the atomic structure and determine the dynamics of the designed scaffolds.