A5022898221- Ubiquitin and proteasome pathways
- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- Peptidase Inhibition and Analysis
- Chemical Synthesis and Analysis
- Glycosylation and Glycoproteins Research
- Modular Robots and Swarm Intelligence
- Cell Image Analysis Techniques
- Cellular Mechanics and Interactions
- Protein Degradation and Inhibitors
- Alzheimer's disease research and treatments
- Microbial Community Ecology and Physiology
- 14-3-3 protein interactions
- Monoclonal and Polyclonal Antibodies Research
- Genomics and Phylogenetic Studies
- Bacteriophages and microbial interactions
- Epigenetics and DNA Methylation
- Advanced Proteomics Techniques and Applications
- Advanced Electron Microscopy Techniques and Applications
- Cancer, Hypoxia, and Metabolism
- Crystal structures of chemical compounds
- Mass Spectrometry Techniques and Applications
- Blood properties and coagulation
- Genetic Neurodegenerative Diseases
- Proteins in Food Systems
Hubrecht Institute for Developmental Biology and Stem Cell Research
2024
University of Washington
2020-2024
Howard Hughes Medical Institute
2022-2023
Cancer Genomics Centre
2014-2016
The Netherlands Cancer Institute
2011-2016
Abstract The deubiquitinating enzyme BAP1 is an important tumor suppressor that has drawn attention in the clinic since its loss leads to a variety of cancers. activated by ASXL1 deubiquitinate mono-ubiquitinated H2A at K119 Polycomb gene repression, but mechanism this reaction remains poorly defined. Here we show C-terminal extension for deubiquitination auto-recruiting nucleosomes process does not require nucleosome acidic patch. This initial encounter-like complex unproductive and needs...
Relating the macroscopic properties of protein-based materials to their underlying component microstructure is an outstanding challenge. Here, we exploit computational design specify size, flexibility, and valency de novo protein building blocks, as well interaction dynamics between them, investigate how molecular parameters govern viscoelasticity resultant hydrogels. We construct gel systems from pairs symmetric homo-oligomers, each comprising 2, 5, 24, or 120 individual components, that...
Highlights•The RPN13 DEUBAD domain activates UCH-L5 by positioning its CL and ULD domain•The INO80G inhibits blocking ubiquitin binding•The FRF hairpin in the of drives inhibition•DEUBAD domains regulate activity tuning substrate affinitySummaryDeubiquitinating enzymes (DUBs) control vital processes eukaryotes hydrolyzing adducts. Their activities are tightly regulated, but mechanisms remain elusive. In particular, DUB can be either activated or inhibited conserved regulatory proteins...
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...
During DNA damage response, the RING E3 ligase RNF168 ubiquitinates nucleosomal H2A at K13–15. Here we show that ubiquitination reaction is regulated by its substrate. We define a region on domain important for target recognition and identify H2A/H2B dimer as minimal substrate to confer lysine specificity reaction. Importantly, find an active role in dimers nucleosomes enhance E3-mediated discharge of ubiquitin from E2 redirect towards relevant target, process depends intact acidic patch....
Abstract Segments of proteins with high β-strand propensity can self-associate to form amyloid fibrils implicated in many diseases. We describe a general approach bind such segments and β-hairpin conformations using de novo designed scaffolds that contain deep peptide-binding clefts. The designs their cognate peptides vitro nanomolar affinities. crystal structure protein−peptide complex is close the design model, NMR characterization reveals how cleft protected apo state. use binders...
Significance The de novo design of proteins that bind natural target is useful for a variety biomedical and biotechnological applications. We describe strategy to containing an exposed beta edge strand. use the approach binders human transferrin receptor which shuttles back forth across blood–brain barrier. Such could be delivery therapeutics into brain.
Significance Designed protein assemblies have many applications in medicine and technology. A long-standing design paradigm generates through genetic fusion of homo-oligomers via α-helical linkers. Here, we introduce a rigid strategy that finds greater number solutions reduces formation unintended assembly states, method for doubly anchoring target binding domains the resulting could contribute to cryogenic electron microscopy structure determination small proteins.
With the recent success in calculating protein structures from amino acid sequences using artificial intelligence-based algorithms, an important next step is to decipher how dynamics encoded by primary sequence so as better predict function. Such information critical for design, where strategies could then focus not only on that fold into particular perform a given task, but would also include low-lying excited states influence function of designed protein. Herein, we illustrate importance...
Abstract Segments of proteins with β-strand propensity can self associate to form amyloid fibrils associated many diseases. These regions often adopt alternative structures in their folded states, or are intrinsically disordered solution, making it difficult generate binders inhibitors existing strategies. Here we describe a general approach bind such segments and β-hairpin conformations using de novo designed scaffolds that contain deep peptide binding clefts flanked by β-strands hydrogen...
Abstract Protein nanomaterial design is an emerging discipline with applications in medicine and beyond. A longstanding approach uses genetic fusion to join protein homo-oligomer subunits via α-helical linkers form more complex symmetric assemblies, but this method hampered by linker flexibility a dearth of geometric solutions. Here, we describe general computational that performs rigid three-body spacer building blocks generate user-defined architectures, while at the same time...
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...
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...
Relating the macroscopic properties of protein-based materials to their underlying component microstructure is an outstanding challenge. Here, we exploit computational design specify size, flexibility, and valency