SLAC National Accelerator Laboratory
Showing 1-50 of 75 Results
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Soichi Wakatsuki
Professor of Photon Science and of Structural Biology
Current Research and Scholarly InterestsUbiquitin signaling: structure, function, and therapeutics
Ubiquitin is a small protein modifier that is ubiquitously produced in the cells and takes part in the regulation of a wide range of cellular activities such as gene transcription and protein turnover. The key to the diversity of the ubiquitin roles in cells is that it is capable of interacting with other cellular proteins either as a single molecule or as different types of chains. Ubiquitin chains are produced through polymerization of ubiquitin molecules via any of their seven internal lysine residues or the N-terminal methionine residue. Covalent interaction of ubiquitin with other proteins is known as ubiquitination which is carried out through an enzymatic cascade composed of the ubiquitin-activating (E1), ubiquitin-conjugating (E2), and ubiquitin ligase (E3) enzymes. The ubiquitin signals are decoded by the ubiquitin-binding domains (UBDs). These domains often specifically recognize and non-covalently bind to the different ubiquitin species, resulting in distinct signaling outcomes.
We apply a combination of the structural (including protein crystallography, small angle x-ray scattering, cryo-electron microscopy (Cryo-EM) etc.), biocomputational and biochemical techniques to study the ubiquitylation and deubiquitination processes, and recognition of the ubiquitin chains by the proteins harboring ubiquitin-binding domains. Current research interests including SARS-COV2 proteases and their interactions with polyubiquitin chains and ubiquitin pathways in host cell responses, with an ultimate goal of providing strategies for effective therapeutics with reduced levels of side effects.
Protein self-assembly processes and applications.
The Surface layers (S-layers) are crystalline protein coats surrounding microbial cells. S-layer proteins (SLPs) regulate their extracellular, self-assembly by crystallizing when exposed to an environmental trigger. We have demonstrated that the Caulobacter crescentus SLP readily crystallizes into sheets both in vivo and in vitro via a calcium-triggered multistep assembly pathway. Observing crystallization using a time course of Cryo-EM imaging has revealed a crystalline intermediate wherein N-terminal nucleation domains exhibit motional dynamics with respect to rigid lattice-forming crystallization domains. Rate enhancement of protein crystallization by a discrete nucleation domain may enable engineering of kinetically controllable self-assembling 2D macromolecular nanomaterials. In particular, this is inspiring designing robust novel platform for nano-scale protein scaffolds for structure-based drug design and nano-bioreactor design for the carbon-cycling enzyme pathway enzymes. Current research focuses on development of nano-scaffolds for high throughput in vitro assays and structure determination of small and flexible proteins and their interaction partners using Cryo-EM, and applying them to cancer and anti-viral therapeutics.
Multiscale imaging and technology developments.
Multimodal, multiscale imaging modalities will be developed and integrated to understand how molecular level events of key enzymes and protein network are connected to cellular and multi-cellular functions through intra-cellular organization and interactions of the key machineries in the cell. Larger scale organization of these proteins will be studied by solution X-ray scattering and Cryo-EM. Their spatio-temporal arrangements in the cell organelles, membranes, and cytosol will be further studied by X-ray fluorescence imaging and correlated with cryoEM and super-resolution optical microscopy. We apply these multiscale integrative imaging approaches to biomedical, and environmental and bioenergy research questions with Stanford, DOE national labs, and other domestic and international collaborators. -
William Weis
William M. Hume Professor in the School of Medicine, Professor of Structural Biology, of Molecular and Cellular Physiology and of Photon Science
On Partial Leave from 01/01/2022 To 08/31/2022Current Research and Scholarly InterestsOur laboratory studies molecular interactions that underlie the establishment and maintenance of cell and tissue structure. Our principal areas of interest are the architecture and dynamics of intercellular adhesion junctions, signaling pathways that govern cell fate determination, and determinants of cell polarity. Our overall approach is to reconstitute macromolecular assemblies with purified components in order to analyze them using biochemical, biophysical and structural methods.
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Paul B. Welander
Staff Scientist, SLAC National Accelerator Laboratory
BioPaul Welander is a Staff Scientist in the Technology Innovation Directorate at SLAC National Accelerator Laboratory, and Department Head for Q-NEXT, a DOE-funded quantum information science research center led jointly by Argonne National Laboratory and SLAC. Paul’s research interests concern materials for quantum devices, from the study of materials-induced decoherence mechanisms in superconducting quantum bits, to the development of materials platforms that enable novel quantum technologies. He’s a researcher in both the Detector Microfabrication Facility and Nano-X, two new state-of-the-art cleanrooms at SLAC geared toward superconductor quantum device fabrication and rapid nano-prototyping, respectively. His expertise includes molecular beam epitaxy of metal-oxide heterostructures, superconducting device fabrication, and an array of materials characterization techniques including x-ray diffraction and scanning probe microscopy. Paul received his Ph.D. in physics from the University of Illinois at Urbana-Champaign, and holds Bachelor’s degrees from both Caltech and Occidental College. Prior to joining SLAC in 2012, he spent five years as a member of the technical staff at MIT Lincoln Laboratory.
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Baraa Werghi
Postdoctoral Scholar, Photon Science, SLAC
BioBaraa Werghi is currently a post-doctoral research fellow focusing on uniform and well-defined heterogenous catalysts design and synthesis for various catalytic application. She earned her Ph.D. in Chemical science from King Abdullah University of Science and Technology (KAUST) in 2018 under the supervisor of Professor Jean Marie Basset, where she focused on the development of aluminum-based supports using the organometallic chemistry tools and its use for the immobilization of various transition metals for various catalytic reactions (alkane/olefin metathesis and hydrogen generation reactions) along with a deep mechanical understanding of all the steps involved. Before joining KAUST, she received her M.S. degree in Chemical Engineering from the University of Rennes I (France) and her B.S. in Industrial chemistry from National Institute of Applied Sciences and Technologies (INSAT),(Tunisia).
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Gregory R. White
Information Systems Spec, SLAC National Accelerator Laboratory
Current Role at StanfordGregory White presently holds the position of Senior Advisor in Computer Science to the Associate Laboratory Director for Accelerators at SLAC National Accelerator Laboratory. He also has a continuing role as engineering-physicist in the Accelerator Directorate.
