Stanford ChEM-H

Showing 111-120 of 126 Results

  • Aaron F. Straight

    Aaron F. Straight

    Professor of Biochemistry and, by courtesy, of Chemical and Systems Biology

    Current Research and Scholarly InterestsWe study the biology of chromosomes. Our research is focused on understanding how chromosomal domains are specialized for unique functions in chromosome segregation, cell division and cell differentiation. We are particularly interested in the genetic and epigenetic processes that govern vertebrate centromere function, in the organization of the genome in the eukaryotic nucleus and in the roles of RNAs in the regulation of chromosome structure.

  • James Swartz

    James Swartz

    James H. Clark Professor in the School of Engineering and Professor of Chemical Engineering and of Bioengineering

    BioUsing and Understanding Cell-Free Biology

    Swartz Lab General Research Focus:

    The current and projected research in the Swartz lab balances basic research in microbial metabolism, protein expression, and protein folding with a strong emphasis on compelling applications. The power and versatility of cell-free methods coupled with careful evaluation and engineering of these new systems enables a whole new range of applications and scientific investigation. Fundamental research on: the mechanisms and kinetics of ribosomal function, fundamental bioenergetics, basic mechanisms of protein folding, functional genomics, and metabolic pathway analysis is motivated by a variety of near- and medium term applications spanning medicine, energy, and environmental needs.

    Swartz Lab Application Focus:

    In the medical area , current research addresses the need for patient-specific vaccines to treat cancer. Particularly for lymphomas, there is a strong need to be able to make a new cancer vaccine for each patient. Current technologies are not practical for this demanding task, but cell-free approaches are rapid and inexpensive. We have already demonstrated feasibility in mouse tumor challenge studies and are now expanding the range of applications and working to improve the relevant technologies. Experience with these vaccines has also suggested a new and exciting format for making inexpensive and very potent vaccines for general use.

    To address pressing needs for a new and cleaner energy source, we are working towards an organism that can efficiently capture solar energy and convert it into hydrogen. The first task is to develop an oxygen tolerant hydrogenase using cell-free technology to express libraries of mutated enzymes that can be rapidly screened for improved function. Even though these are very complex enzymes, we have produced active hydrogenases with our cell-free methods. We are now perfecting the screening methods for rapid and accurate identification of improved enzymes. After these new enzymes are identified, the project will progress toward metabolic engineering and bioreactor design research to achieve the scales and economies required.

    To address environmental needs, we are developing an improved water filters using an amazing membrane protein, Aquaporin Z. It has the ability to reject all other chemicals and ions except water. We have efficiently expressed the protein into lipid bilayer vesicles and are now working to cast these membranes on porous supports to complete the development of a new and powerful water purification technology. The same lessons will be applied toward the development of a new class of biosensors that brings high sensitivity and selectivity.

  • Sindy Tang

    Sindy Tang

    Associate Professor of Mechanical Engineering, Senior Fellow at the Woods Institute for the Environment and Professor, by courtesy, of Radiology (Precision Health and Integrated Diagnostics)

    Current Research and Scholarly InterestsThe long-term goal of Dr. Tang's research program is to harness mass transport in microfluidic systems to accelerate precision medicine and material design for a future with better health and environmental sustainability.

    Current research areas include: (I) Physics of droplets in microfluidic systems, (II) Interfacial mass transport and self-assembly, and (III) Applications in food allergy, single-cell wound repair, and the bottom-up construction of synthetic cell and tissues in close collaboration with clinicians and biochemists at the Stanford School of Medicine, UCSF, and University of Michigan.

    For details see

  • Alice Ting

    Alice Ting

    Professor of Genetics, of Biology and, by courtesy, of Chemistry

    Current Research and Scholarly InterestsWe develop chemogenetic and optogenetic technologies for probing and manipulating protein networks, cellular RNA, and the function of mitochondria and the mammalian brain. Our technologies draw from enzyme engineering, directed evolution, chemical biology, organic synthesis, high-resolution microscopy, genetics, and computational analysis.

  • Soichi Wakatsuki

    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.

  • Robert Waymouth

    Robert Waymouth

    Robert Eckles Swain Professor in Chemistry and Professor, by courtesy, of Chemical Engineering

    BioRobert Eckles Swain Professor in Chemistry Robert Waymouth investigates new catalytic strategies to create useful new molecules, including bioactive polymers, synthetic fuels, and sustainable plastics. In one such breakthrough, Professor Waymouth and Professor Wender developed a new class of gene delivery agents.

    Born in 1960 in Warner Robins, Georgia, Robert Waymouth studied chemistry and mathematics at Washington and Lee University in Lexington, Virginia (B.S. and B.A., respectively, both summa cum laude, 1982). He developed an interest in synthetic and mechanistic organometallic chemistry during his doctoral studies in chemistry at the California Institute of Technology under Professor R.H. Grubbs (Ph.D., 1987). His postdoctoral research with Professor Piero Pino at the Institut fur Polymere, ETH Zurich, Switzerland, focused on catalytic hydrogenation with chiral metallocene catalysts. He joined the Stanford University faculty as assistant professor in 1988, becoming full professor in 1997 and in 2000 the Robert Eckles Swain Professor of Chemistry.

    Today, the Waymouth Group applies mechanistic principles to develop new concepts in catalysis, with particular focus on the development of organometallic and organic catalysts for the synthesis of complex macromolecular architectures. In organometallic catalysis, the group devised a highly selective alcohol oxidation catalyst that selectively oxidizes unprotected polyols and carbohydrates to alpha-hyroxyketones. In collaboration with Dr. James Hedrick of IBM, we have developed a platform of highly active organic catalysts and continuous flow reactors that provide access to polymer architectures that are difficult to access by conventional approaches.

    The Waymouth group has devised selective organocatalytic strategies for the synthesis of functional degradable polymers and oligomers that function as "molecular transporters" to deliver genes, drugs and probes into cells and live animals. These advances led to the joint discovery with the Wender group of a general, safe, and remarkably effective concept for RNA delivery based on a new class of synthetic cationic materials, Charge-Altering Releasable Transporters (CARTs). This technology has been shown to be effective for mRNA based cancer vaccines.

  • William Weis

    William Weis

    William M. Hume Professor in the School of Medicine, Professor of Structural Biology, of Molecular and Cellular Physiology and of Photon Science

    Current 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.

  • Paul Wender

    Paul Wender

    Francis W. Bergstrom Professor of Chemistry and Professor, by courtesy, of Chemical and Systems Biology
    On Leave from 10/01/2020 To 12/31/2020

    Current Research and Scholarly InterestsMolecular imaging, therapeutics, drug delivery, drug mode of action, synthesis