A5070955667- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- Protein Kinase Regulation and GTPase Signaling
- RNA modifications and cancer
- Protein Structure and Dynamics
- Carcinogens and Genotoxicity Assessment
- Cell death mechanisms and regulation
- Enzyme Structure and Function
- Melanoma and MAPK Pathways
- DNA Repair Mechanisms
- Metabolomics and Mass Spectrometry Studies
- Effects and risks of endocrine disrupting chemicals
- Protein Tyrosine Phosphatases
- Cell Adhesion Molecules Research
- CRISPR and Genetic Engineering
- PI3K/AKT/mTOR signaling in cancer
- Receptor Mechanisms and Signaling
- Lipoproteins and Cardiovascular Health
- 14-3-3 protein interactions
- Lipid Membrane Structure and Behavior
- Erythrocyte Function and Pathophysiology
- Radiopharmaceutical Chemistry and Applications
- Infection Control and Ventilation
- Cancer Mechanisms and Therapy
- Educational Robotics and Engineering
QB3
2015-2022
University of California, Berkeley
2015-2022
Howard Hughes Medical Institute
2017-2018
MRC Laboratory of Molecular Biology
2010-2015
Medical Research Council
2014-2015
Tokyo Institute of Technology
2013
Wakayama Prefectural Tanabe High School
1986-2002
Kyoto Prefectural University of Medicine
2001
Nagoya University
1988-1989
Pall Corporation (United States)
1989
The guanine nucleotide exchange factor (GEF) Son of Sevenless (SOS) is a key Ras activator that autoinhibited in the cytosol and activates upon membrane recruitment. Autoinhibition release involves structural rearrangements protein at thus introduces delay between initial recruitment activation. In this study, we designed single-molecule assay to resolve time receptor-mediated initiation GEF activity individual SOS molecules on microarrays Ras-functionalized supported membranes....
U1 snRNP binds to the 5' exon-intron junction of pre-mRNA and thus plays a crucial role at an early stage splicing. We present two crystal structures engineered sub-structures, which together reveal atomic resolution almost complete network protein-protein RNA-protein interactions within snRNP, show how splice site is recognised by snRNP. The zinc-finger U1-C interacts with duplex between 5'-end snRNA. binding RNA stabilized hydrogen bonds electrostatic backbone around but makes no...
Raf kinases are important cancer drug targets. Paradoxically, many B-Raf inhibitors induce the activation of kinases. Cryo-electron microscopy structural analysis a phosphorylated kinase domain dimer in complex with dimeric 14-3-3, at resolution ~3.9 angstroms, shows an asymmetric arrangement which one is canonical "active" conformation. The distal segment C-terminal tail this interacts with, and blocks, active site cognate arrangement. Deletion reduces activity. unexpected quaternary...
Ras proteins are highly conserved signaling molecules that exhibit regulated, nucleotide-dependent switching between active and inactive states. The high conservation of requires mechanistic explanation, especially given the general mutational tolerance proteins. Here, we use deep scanning, biochemical analysis molecular simulations to understand constraints on sequence. exhibits global sensitivity mutation when regulated by a GTPase activating protein nucleotide exchange factor. Removing...
We reconstitute a phosphotyrosine-mediated protein condensation phase transition of the ∼200 residue cytoplasmic tail epidermal growth factor receptor (EGFR) and adaptor protein, Grb2, on membrane surface. The depends phosphorylation EGFR tail, which recruits crosslinking through Grb2-Grb2 binding interface. Grb2 Y160 plays structurally critical role in interaction, or mutation prevents EGFR:Grb2 condensation. By extending reconstitution experiment to include guanine nucleotide exchange...
Introduction Evolution and design of protein complexes are frequently viewed through the lens amino acid mutations at interfaces, but we showed previously that residues distant from interfaces also commonly involved in evolution alternative quaternary structures. We hypothesized these families, difference oligomeric state is due to a change intersubunit geometry. The indirect would act by changing conformation dynamics, similar way which allosteric small molecules introduce functional...
To examine whether micronucleus tests can be incorporated into general toxicology assays, we performed applying the treatment protocols typically used in such assays. In this 13th Collaborative Study of CSGMT, both rats and mice were tested, although majority studies. Fifteen mutagens tested rats, mainly by oral (p.o.) administration. Micronucleus induction was evaluated 2, 3, 4 days, 1, 28 days after beginning peripheral blood, at bone marrow. Of 15 chemicals that induced micronuclei...
RasGRPs are guanine nucleotide exchange factors that specific for Ras or Rap, and important regulators of cellular signaling. Aberrant expression mutation results in disease. An analysis RasGRP1 SNP variants led to the conclusion charge His 212 alters signaling activity plasma membrane recruitment, indicating is a pH sensor balance between inactive active forms RasGRP1. To understand structural basis this effect we compared structure autoinhibited RasGRP1, determined previously, those...
In large ribonucleoprotein machines, such as ribosomes and spliceosomes, RNA functions an assembly scaffold well a critical catalytic component. Protein binding to the can induce structural changes, which in turn modulate subsequent of other components. The spliceosomal U4/U6 di-snRNP contains extensively base paired U4 U6 snRNAs, Snu13, Prp31, Prp3 Prp4, seven Sm LSm proteins. We have studied successive all protein components snRNA duplex during by electrophoretic mobility shift assay...
Macrocyclic peptides are potentially a source of powerful drugs, but their de novo discovery remains challenging. Here we describe the high-affinity (Kd = 10 nM) peptide macrocycle (M21) against human tumor necrosis factor-alpha (hTNFα), key drug target in treatment inflammatory disorders, directly from diverse semi-synthetic phage repertoires. The bicyclic M21 (ACPPCLWQVLC) comprises two loops covalently anchored to 2,4,6-trimethyl-mesitylene core and upon binding induces disassembly...
The core domain of small nuclear ribonucleoprotein (snRNP), comprised a ring seven paralogous proteins bound around single-stranded RNA sequence, functions as the assembly nucleus in maturation U1, U2, U4 and U5 spliceosomal snRNPs. structure human snRNP was initially solved at 3.6 Å resolution by experimental phasing using data with tetartohedral twinning. Molecular replacement from this model followed density modification untwinned recently led to minimal U1 3.3 resolution. With latter...
U1 snRNA is an interesting biological tool for splicing correction and regulation of gene expression. However, has never been chemically synthesized. In this study, the first chemical synthesis U1snRNA its analogues was carried out. Moreover, it found that binding affinity modified with ethylene glycol linkage to snurportin 1 (nuclear import adaptor) as high unmodified RNA.
Son of Sevenless (SOS) is a Ras guanine nucleotide exchange factor (GEF) that plays central role in numerous cellular signaling pathways. Like many other molecules, SOS autoinhibited the cytosol and activates only after recruitment to membrane. The mean activation time individual molecules has recently been measured be ∼60 s, which unexpectedly long seemingly contradictory with timescales, have as fast several seconds. Here, we rectify this discrepancy using first-passage analysis...
Oxidative stress may be an important factor in the development of diabetic complications. Advanced glycation end-products have drown attention as potential sources oxidative diabetes. We investigated protective effects fluvastatin, a 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitor, on DNA damage from reactive oxygen species or advanced vitro, well main fluvastatin metabolites and other inhibitors same enzyme, pravastatin simvastatin. Protective were assessed terms breakage rate...
We investigated the effects of fluvastatin, a 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitor, on reactive oxygen species (ROS) and oxidative DNA damage in vitro, as well main fluvastatin metabolites (M2, M3, M4) other inhibitors same enzyme, pravastatin simvastatin. The hydroxyl radical superoxide anion scavenging activities its were evaluated using an electron spin resonance spectrometer. Fluvastatin showed activity hypoxanthine-xanthine oxidase system strong effect produced from...
ABSTRACT We reconstitute a phosphotyrosine-mediated protein condensation phase transition of the ∼200 residue cytoplasmic tail epidermal growth factor receptor (EGFR) and adaptor protein, Grb2, on membrane surface. The depends phosphorylation EGFR tail, which recruits dimerization provides crosslinking element for with EGFR. Grb2 Y160 plays structurally critical role in dimer formation, or mutation prevents EGFR:Grb2 condensation. By extending reconstitution experiment to include guanine...