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Study Finds ‘Missing Link’ in the Evolutionary History of Carbon-Fixing Protein Rubisco

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.

Crystallization Screen Created by Berkeley Lab Biosciences Scientists Reaches the Market

Crystals obtained using the Berkeley Screen conditions and the resulting protein structureX-ray crystallography has been the most successful technique used to solve macromolecular structures, contributing several thousand new entries to the Protein Data Bank (PDB) every year. The protein crystal is the critical starting point for X-ray data collection, and consequently, its properties are correlated with the quality of the data and the level of detail that can be extracted for a macromolecular structure. However, proteins require solutions of specific composition to form crystals for structure determination studies. These specifications are usually determined from exposing the protein to several different solutions in a crystallization screen.

A team of researchers in the Molecular Biophysics and Integrated Bioimaging (MBIB) Division led by Paul Adams and Jose Henrique Pereira have developed a new crystal screen, the Berkeley Screen, with 96 conditions proven to be highly effective at producing crystals for structural determination. The Berkeley Screen is now available to the wider crystallography community commercially.

Designing Protein Cavities from Curved Beta Sheets

Curved beta sheets are important for the architecture of protein cavities, such as enzyme active sites and ligand-binding pockets. Beginning by analyzing classic protein formations and running folding simulations, University of Washington (UW) researchers under the leadership of David Baker designed six protein folds inspired by naturally occurring protein superfamilies. A research report published in the January 13 issue of Science describes how a multi-institutional team of scientists compared the predicted models to physical structures of these designed proteins.

Three Is Not a Crowd: Designed Metalloprotein Trimer Provides Stable Platform for Further Development

4iww_300University of Washington (UW) researchers have designed a novel protein with properties that could lead to the generation of new photoactive proteins. This three-fold symmetric, self-assembling protein homotrimer contains a highly stable noncanonical amino acid. Noncanonical amino acids are not found among the 20 encoded amino acids in the body and can contain modifications to allow for new functionality. In this case, this amino acid contains a bipyridine group that chelates metal, thereby introducing new photochemical properties into the protein interface, and nucleating the formation of the homotrimer.

An article published last month in PNAS describes this work from a team of scientists led by David Baker at UW, which included Jose Henrique Pereira, Banumathi Sankaran, and Peter Zwart of the Molecular Biophysics & Integrated Bioimaging Division (MBIB). The MBIB scientists developed the crystal screen that was used to crystallize the novel protein and performed X-ray crystallography on Beamline 8.2.1 in the Berkeley Center for Structural Biology at the Advanced Light Source. Their X-ray crystallographic analysis of the homotrimer showed that the design process had near-atomic-level accuracy, demonstrating that computational protein design together with the utilization of noncanonical amino acids could be used to generate novel protein functions. These methods could be used to develop new therapeutics, biomaterials, and metalloproteins with useful optical or photochemical properties.

Bioscientists Validate Novel Protein Design Program

Over the course of billions of years, nature has evolved particular molecular structures that form the basis of life, such as those found in nucleic acids and proteins. Using the natural form as a springboard, University of Washington researchers have designed protein homo-oligomers, or identical interacting subunits, which can contain interchangeable hydrogen bonding modules for building different structures or functions. The team of researchers, led by David Baker at the University of Washington, included Jose Henrique Pereira, Banumathi Sankaran, and Peter Zwart of the Molecular Biophysics & Integrated Bioimaging Division (MBIB).

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