A5056402447- Advanced biosensing and bioanalysis techniques
- Bacteriophages and microbial interactions
- Protein Structure and Dynamics
- RNA Interference and Gene Delivery
- Advanced Fluorescence Microscopy Techniques
- Modular Robots and Swarm Intelligence
- Enzyme Structure and Function
- Photoreceptor and optogenetics research
- RNA and protein synthesis mechanisms
- Nanofabrication and Lithography Techniques
- Advanced Electron Microscopy Techniques and Applications
- DNA and Nucleic Acid Chemistry
- Cell Image Analysis Techniques
- Monoclonal and Polyclonal Antibodies Research
- Orbital Angular Momentum in Optics
- Fibroblast Growth Factor Research
- Yersinia bacterium, plague, ectoparasites research
- Diatoms and Algae Research
- Bacterial Genetics and Biotechnology
- Biosensors and Analytical Detection
- Supramolecular Self-Assembly in Materials
- Photosynthetic Processes and Mechanisms
- Vector-borne infectious diseases
- Tissue Engineering and Regenerative Medicine
- DNA and Biological Computing
University of Washington
2021-2024
Institute of Science and Technology Austria
2024
Technical University of Munich
2014-2019
Center for Integrated Protein Science Munich
2011-2018
Institute for Advanced Study
2016-2017
Schott (Germany)
2014-2017
Abstract DNA has become a prime material for assembling complex three‐dimensional objects that promise utility in various areas of application. However, achieving user‐defined goals with been hampered by the difficulty to prepare them at arbitrary concentrations and solution conditions. Here, we describe method solves this problem. The is based on poly(ethylene glycol)‐induced depletion species high molecular weight. We demonstrate our applicable wide spectrum shapes it achieves excellent...
In nature, proteins that switch between two conformations in response to environmental stimuli structurally transduce biochemical information a manner analogous how transistors control flow computing devices. Designing with distinct but fully structured is challenge for protein design as it requires sculpting an energy landscape minima. Here we describe the of “hinge” populate one designed state absence ligand and second presence ligand. X-ray crystallography, electron microscopy, double...
Allosteric modulation of protein function, wherein the binding an effector to a triggers conformational changes at distant functional sites, plays central part in control metabolism and cell signalling1–3. There has been considerable interest designing allosteric systems, both gain insight into mechanisms underlying such 'action distance' create synthetic proteins whose functions can be regulated by effectors4–7. However, emulating subtle distributed across many residues, characteristic...
Protein-folded DNA nanostructures A wide variety of have been assembled by folding long single strands with short staples. However, such structures typically need annealing at elevated temperatures in order to form. To accommodate the formation living cells, Praetorius and Dietz developed an approach which custom protein staples based on transcription activator–like effector proteins fold double-stranded templates (see Perspective Douglas). The folded into user-defined geometric shapes scale...
DNA origami nano-objects are usually designed around generic single-stranded "scaffolds". Many properties of the target object determined by details those scaffold sequences. Here, we enable designers to fully specify structure not only in terms desired 3D shape but also sequences used. To this end, built design tools construct de novo based on strand diagrams, and developed scalable production methods for creating design-specific strands with user-defined We used 17 custom scaffolds having...
Understanding the mechanism of protein folding requires a detailed knowledge structural properties barriers separating unfolded from native conformations. The S-peptide ribonuclease S forms its α-helical structure only upon binding to folded S-protein. We characterized transition state for this binding-induced reaction at high resolution by determining effect site-specific backbone thioxylation and side-chain modifications on kinetics thermodynamics reaction, which allows us monitor...
Scaffolded DNA origami enables the fabrication of a variety complex nanostructures that promise utility in diverse fields application, ranging from biosensing over advanced therapeutics to metamaterials. The broad applicability as material beyond level proof-of-concept studies critically depends, among other factors, on availability large amounts pure single-stranded scaffold DNA. Here, we present method for efficient production M13 bacteriophage-derived genomic using high-cell-density...
Significance As the scope of macromolecular structure determination by cryo-electron microscopy (cryo-EM) is expanding rapidly, it becoming increasingly clear that many biological complexes are too fragile to withstand harsh conditions involved in making cryo-EM samples. We describe an original approach protect proteins from harmful forces during sample preparation enclosing them inside a three-dimensional support we designed using DNA origami techniques. By binding transcription cofactor...
Asymmetric multiprotein complexes that undergo subunit exchange play central roles in biology but present a challenge for design because the components must not only contain interfaces enable reversible association also be stable and well behaved isolation. We use implicit negative to generate β sheet–mediated heterodimers can assembled into wide variety of complexes. The designs are stable, folded, soluble isolation rapidly assemble upon mixing, crystal structures close computational...
Abstract DNA has become a prime material for assembling complex three‐dimensional objects that promise utility in various areas of application. However, achieving user‐defined goals with been hampered by the difficulty to prepare them at arbitrary concentrations and solution conditions. Here, we describe method solves this problem. The is based on poly(ethylene glycol)‐induced depletion species high molecular weight. We demonstrate our applicable wide spectrum shapes it achieves excellent...
Pore-forming toxins (PFT) are virulence factors that transform from soluble to membrane-bound states. The Yersinia YaxAB system represents a family of binary α-PFTs with orthologues in human, insect, and plant pathogens, unknown structures. was shown be cytotoxic likely involved pathogenesis, though the molecular basis for its two-component lytic mechanism remains elusive. Here, we present crystal structures YaxA YaxB, together cryo-electron microscopy map complex. Our reveal pore...
One key goal of DNA nanotechnology is the bottom-up construction macroscopic crystalline materials. Beyond applications in fields such as photonics or plasmonics, DNA-based crystal matrices could possibly facilitate diffraction-based structural analysis guest molecules. Seeman and co-workers reported 2009 first designed based on a 38 kDa triangle that was composed seven chains. The lattice stabilized, unprecedentedly, by Watson-Crick base pairing. However, 3D crystallization larger objects...
The bacteriophage M13 has found frequent applications in nanobiotechnology due to its chemically and genetically tunable protein surface ability self-assemble into colloidal membranes. Additionally, single-stranded (ss) genome is commonly used as scaffold for DNA origami. Despite the manifold uses of M13, upstream production methods phage ssDNA are underexamined with respect future industrial usage. Here, high-cell-density Escherichia coli host organism was studied medium composition,...
Growth factors and cytokines signal by binding to the extracellular domains of their receptors drive association transphosphorylation receptor intracellular tyrosine kinase domains, initiating downstream signaling cascades. To enable systematic exploration how valency geometry affects outcomes, we designed cyclic homo-oligomers with up 8 subunits using repeat protein building blocks that can be modularly extended. By incorporating a de novo fibroblast growth-factor (FGFR) module into these...
Protein design has focused primarily on the of ground states, ensuring they are sufficiently low energy to be highly populated. Designing kinetics and dynamics a system requires, in addition, excited states that traversed transitions from one low-lying state another. This is challenging task as such must strained poorly populated, but not so populated at all, because protein methods have generally creating near-ideal structures. Here we describe general approach for designing systems which...
Allosteric modulation of protein function, wherein the binding an effector to a triggers conformational changes at distant functional sites, plays central role in control metabolism and cell signaling 1–3 . There has been considerable interest designing allosteric systems, both gain insight into mechanisms underlying such “action distance” create synthetic proteins whose functions can be regulated by effectors 4–7 However, emulating subtle distributed across many residues, characteristic...
Abstract Proteins that switch between two structural states as a function of environmental stimuli are widespread in nature. These proteins structurally transduce biochemical information manner analogous to how transistors control flow computing devices. Engineering challenges ranging from biological devices molecular motors require such two-state switches, but designing these is an unsolved problem it requires sculpting energy landscape with low-energy distinct conformations can be...
Abstract Asymmetric multi-protein complexes that undergo subunit exchange play central roles in biology, but present a challenge for protein design. The individual components must contain interfaces enabling reversible addition to and dissociation from the complex, be stable well behaved isolation. Here we employ set of implicit negative design principles generate beta sheet mediated heterodimers which enable generation wide variety structurally defined asymmetric assemblies. Crystal...