A5054780745- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- Genomics and Chromatin Dynamics
- Enzyme Structure and Function
- Insect and Arachnid Ecology and Behavior
- Fungal and yeast genetics research
- RNA Research and Splicing
- DNA Repair Mechanisms
- Mass Spectrometry Techniques and Applications
- Bacterial Genetics and Biotechnology
- Metabolomics and Mass Spectrometry Studies
- Reproductive biology and impacts on aquatic species
- Invertebrate Immune Response Mechanisms
- Protein purification and stability
- Advanced Fluorescence Microscopy Techniques
- Microbial Metabolic Engineering and Bioproduction
- History of Medicine Studies
- Monoclonal and Polyclonal Antibodies Research
- Animal Genetics and Reproduction
- Porphyrin Metabolism and Disorders
- Folate and B Vitamins Research
- Plant Reproductive Biology
- Marine and fisheries research
- Gene Regulatory Network Analysis
- Copper Interconnects and Reliability
University of Washington
2014-2025
Fred Hutch Cancer Center
2014-2021
Seattle University
2019
Scripps Research Institute
2011-2014
University of Minnesota
2005
An inherent strength of hydrogen/deuterium exchange coupled to mass spectrometry (HDX-MS) is its ability detect the presence multiple conformational states a protein, which often manifest as multimodal isotopic envelopes. However, statistical considerations for accurate analysis spectra have yet be established. Here we outline an unrestrained binomial distribution fitting approach with corresponding tests accurately and, when possible, deconvolute distributions that contain subpopulations....
Transcription activation domains (ADs) are inherently disordered proteins that often target multiple coactivator complexes, but the specificity of these interactions is not understood. Efficient transcription by yeast Gcn4 requires its tandem ADs and four activator-binding (ABDs) on target, Mediator subunit Med15. Multiple ABDs a common feature complexes. We find large Gcn4-Med15 complex heterogeneous contains nearly all possible AD-ABD interactions. forms via dynamic fuzzy protein-protein...
Significance How transcription activators recognize their coactivator targets is a longstanding question and important for understanding activator specificity synergy. Most are not obviously related in sequence, but they common set of coactivators, raising the whether these interactions sequence-specific. We show that yeast factor Gcn4 central activation domain works via short sequence-specific motif can be optimized to generate powerful synthetic activators. Like many natural activators,...
The acidic activation domain (AD) of yeast transcription factor Gal4 plays a dual role in repression and through binding to Gal80 repressor Mediator subunit Med15. function arises from two hydrophobic regions within the 40-residue AD. We show by NMR that each AD region binds Med15 using "fuzzy" protein interface. Remarkably, comparison chemical shift perturbations shows Gcn4, intrinsically disordered ADs different sequence, interact nearly identically with finding sequence use an identical...
ABSTRACT We present pyHXExpress, a customizable codebase for automated high-throughput multimodal analysis of all spectra generated from HDX-MS experiments. The workflow was validated against synthetic test dataset to the fitting algorithms and confirm statistical outputs. further establish framework determination multimodality throughout protein system by rigorous evaluation fits across peptide spectra. demonstrate this approach using entire datasets detect multimodality, conformational...
Escherichia coli dihydrofolate reductase (DHFR) provides a paradigm for the integrated study of role protein dynamics in enzyme function. Previous studies backbone and side chain have yielded unprecedented insights into mechanism by which DHFR progresses through structural changes that occur during its catalytic cycle. Here we report comprehensive χ1 rotamer populations aromatic γ-methyl containing residues complexes cycle, based on NMR measurement 3JCγCO 3JCγN coupling constants. We...
Protein evolution is driven by the sum of different physiochemical and genetic processes that usually results in strong purifying selection to maintain biochemical functions. However, proteins are part systems under arms race dynamics often evolve at unparalleled rates can produce atypical properties. In marine mollusk abalone, lysin vitelline envelope receptor for (VERL) a pair rapidly coevolving essential species-specific interactions between sperm egg. Despite extensive characterization...
Dihydrofolate reductase (DHFR) is a well-studied drug target and paradigm for understanding enzyme catalysis. Preparation of pure DHFR samples, in defined ligand-bound states, prerequisite vitro studies discovery efforts. We use NMR spectroscopy to monitor ligand content human Escherichia coli (ecDHFR), which bind different co-purifying ligands during expression bacteria. An alternate purification strategy yields highly complexes, containing only the desired ligands, quantities required...
The three-dimensional structures of the dihydrofolate reductase enzymes from Escherichia coli (ecDHFR or ecE) and Homo sapiens (hDHFR hE) are very similar, despite a rather low level sequence identity. Whereas active site loops ecDHFR undergo major conformational rearrangements during progression through reaction cycle, hDHFR remains fixed in closed loop conformation all its catalytic intermediates. To elucidate structural dynamic differences between human E. enzymes, we conducted...
Sexual selection can explain the rapid evolution of fertilization proteins, yet sperm proteins evolve rapidly even if not directly involved in fertilization. In marine mollusk abalone, secrete enormous quantities two evolving lysin and sp18, that are stored at nearly molar concentrations. We demonstrate this extraordinary packaging is achieved by associating into Fuzzy Interacting Transient Zwitterion (FITZ) complexes upon binding intrinsically disordered FITZ Anionic Partner (FITZAP). form...
SUMMARY The acidic activation domain (AD) of yeast transcription factor Gal4 plays a dual role in both repression and through sequence-dependent binding to Gal80 repressor sequence-independent Mediator subunit Med15. function arises from two hydrophobic regions within the 40-residue AD. We show by NMR that each AD region binds Med15 using “fuzzy” protein interface. Remarkably, comparison chemical shift perturbations shows Gcn4, ADs different sequence, interact nearly identically with...
Abstract Protein evolution is driven by the sum of different physiochemical and genetic processes that usually results in strong purifying selection to maintain biochemical functions. However, proteins are part systems under arms race dynamics often evolve at unparalleled rates can produce atypical properties. In marine mollusk abalone, lysin VERL a pair rapidly coevolving essential for species-specific interactions between sperm egg. Despite extensive characterization lysin, including...
SUMMARY Transcription activation domains (ADs) are inherently disordered proteins that often target multiple coactivator complexes, but the specificity of these interactions is not understood. Efficient by yeast Gcn4 requires tandem ADs and four activator-binding (ABDs) on its target, Mediator subunit Med15. Multiple ABDs a common feature complexes. We find large Gcn4-Med15 complex heterogeneous, containing nearly all possible AD-ABD interactions. This forms using dynamic fuzzy...
Abstract BRCA1/BARD1 is a tumor suppressor E3 ubiquitin (Ub) ligase with roles in DNA damage repair and transcriptional regulation. RING domains interact nucleosomes to facilitate mono-ubiquitylation of distinct residues on the C-terminal tail histone H2A. These enzymatic constitute small fraction heterodimer, raising possibility functional chromatin interactions involving other regions such as BARD1 that bind containing signal H2A K15-Ub H4 K20me0, or portions expansive intrinsically...
Abstract Sexual selection can explain rapid evolution of fertilization proteins, yet sperm proteins evolve rapidly even if they are not directly involved in fertilization. Here we demonstrate that FITZAP, an intrinsically disordered protein the marine mollusk abalone, exploits differences intracellular and oceanic ionic environments to package lysin at extraordinary concentrations inside by forming Fuzzy Interacting Transient Zwitterion (FITZ) complexes. FITZAP binds same interface as its...