Structural Biology Planet

The extracellular domain of the A. thaliana ATP receptor DORN1 has been expressed and purified; a protein orthologous to DORN1 from C. sativa has been crystallized and its X-ray diffraction data have been collected.

New crystallization conditions were identified that allowed the structure determination of human cyclooxygenase-2 in complex with rofecoxib (Vioxx) and the structure was subsequently determined to 2.7 Å resolution.

TtuA and TtuB are the sulfur transferase and sulfur carriers for the biosynthesis of 2-thioribothymidine in some bacterial tRNAs. To elucidate their mechanism of interaction, the TtuA–TtuB complex from T. thermophilus was crystallized and a Zn-MAD data set was collected to a resolution of 2.5 Å.

A high-resolution crystal structure of an unknown glycoside hydrolase enzyme from the rumen of B. taurus is presented. Unique dual carbohydrate-binding domains are revealed.

Microgravity was used in an attempt to define the crystal structure of the polyQ repeat of huntingtin alone or bound to MW1, an anti-polyQ Fab. While huntingtin was not crystallized in the experiments, analysis of microgravity-grown and Earth-grown MW1 Fab crystals showed that, on average, microgravity-grown crystals of MW1 Fab showed an increase in size and an improvement in resolution and mosaicity when compared with Earth-grown crystals in one space group, in agreement with data published for other proteins, although the highest overall resolution X-ray data in our experiments were obtained from a crystal grown on Earth.

Crystals of the multicopper oxidase CueO obtained from a perdeuterated sample for neutron diffraction diffracted to 1.8 Å resolution using X-rays and their crystal structure was solved.

We generated a global genetic interaction network for Saccharomyces cerevisiae, constructing more than 23 million double mutants, identifying about 550,000 negative and about 350,000 positive genetic interactions. This comprehensive network maps genetic interactions for essential gene pairs, highlighting essential genes as densely connected hubs. Genetic interaction profiles enabled assembly of a hierarchical model of cell function, including modules corresponding to protein complexes and pathways, biological processes, and cellular compartments. Negative interactions connected functionally related genes, mapped core bioprocesses, and identified pleiotropic genes, whereas positive interactions often mapped general regulatory connections among gene pairs, rather than shared functionality. The global network illustrates how coherent sets of genetic interactions connect protein complex and pathway modules to map a functional wiring diagram of the cell. Authors: Michael Costanzo, Benjamin VanderSluis, Elizabeth N. Koch, Anastasia Baryshnikova, Carles Pons, Guihong Tan, Wen Wang, Matej Usaj, Julia Hanchard, Susan D. Lee, Vicent Pelechano, Erin B. Styles, Maximilian Billmann, Jolanda van Leeuwen, Nydia van Dyk, Zhen-Yuan Lin, Elena Kuzmin, Justin Nelson, Jeff S. Piotrowski, Tharan Srikumar, Sondra Bahr, Yiqun Chen, Raamesh Deshpande, Christoph F. Kurat, Sheena C. Li, Zhijian Li, Mojca Mattiazzi Usaj, Hiroki Okada, Natasha Pascoe, Bryan-Joseph San Luis, Sara Sharifpoor, Emira Shuteriqi, Scott W. Simpkins, Jamie Snider, Harsha Garadi Suresh, Yizhao Tan, Hongwei Zhu, Noel Malod-Dognin, Vuk Janjic, Natasa Przulj, Olga G. Troyanskaya, Igor Stagljar, Tian Xia, Yoshikazu Ohya, Anne-Claude Gingras, Brian Raught, Michael Boutros, Lars M. Steinmetz, Claire L. Moore, Adam P. Rosebrock, Amy A. Caudy, Chad L. Myers, Brenda Andrews, Charles Boone

Crystallography has been fundamental to the development of many fields of science over the last century. However, much of our modern science and technology relies on materials with defects and disorders, and their three-dimensional (3D) atomic structures are not accessible to crystallography. One method capable of addressing this major challenge is atomic electron tomography. By combining advanced electron microscopes and detectors with powerful data analysis and tomographic reconstruction algorithms, it is now possible to determine the 3D atomic structure of crystal defects such as grain boundaries, stacking faults, dislocations, and point defects, as well as to precisely localize the 3D coordinates of individual atoms in materials without assuming crystallinity. Here we review the recent advances and the interdisciplinary science enabled by this methodology. We also outline further research needed for atomic electron tomography to address long-standing unresolved problems in the physical sciences. Authors: Jianwei Miao, Peter Ercius, Simon J. L. Billinge

In vitro, some RNAs can form stable four-stranded structures known as G-quadruplexes. Although RNA G-quadruplexes have been implicated in posttranscriptional gene regulation and diseases, direct evidence for their formation in cells has been lacking. Here, we identified thousands of mammalian RNA regions that can fold into G-quadruplexes in vitro, but in contrast to previous assumptions, these regions were overwhelmingly unfolded in cells. Model RNA G-quadruplexes that were unfolded in eukaryotic cells were folded when ectopically expressed in Escherichia coli; however, they impaired translation and growth, which helps explain why we detected few G-quadruplex–forming regions in bacterial transcriptomes. Our results suggest that eukaryotes have a robust machinery that globally unfolds RNA G-quadruplexes, whereas some bacteria have instead undergone evolutionary depletion of G-quadruplex–forming sequences. Authors: Junjie U. Guo, David P. Bartel