A5079328278- Protein Structure and Dynamics
- Enzyme Structure and Function
- Advanced biosensing and bioanalysis techniques
- RNA Interference and Gene Delivery
- Advanced Electron Microscopy Techniques and Applications
- Bacteriophages and microbial interactions
- Cardiomyopathy and Myosin Studies
- RNA and protein synthesis mechanisms
- Cardiovascular Effects of Exercise
- Genetic Neurodegenerative Diseases
- Muscle Physiology and Disorders
- Plasmonic and Surface Plasmon Research
- Hemoglobin structure and function
- Molecular spectroscopy and chirality
- Electron and X-Ray Spectroscopy Techniques
- Fungal and yeast genetics research
- Immunotherapy and Immune Responses
- Stochastic processes and statistical mechanics
- Nanofabrication and Lithography Techniques
- Advanced Biosensing Techniques and Applications
- T-cell and B-cell Immunology
- Physics of Superconductivity and Magnetism
- Machine Learning in Bioinformatics
- Amino Acid Enzymes and Metabolism
- Nuclear Structure and Function
University of California, San Francisco
2018-2024
Johns Hopkins University
2009-2024
Nautilus (United States)
2022
Stanford University
2014-2016
Cardiomyopathies due to mutations in human β-cardiac myosin are a significant cause of heart failure, sudden death, and arrhythmia. To understand the underlying molecular basis changes contractile system's force production such search for potential drugs that restore generation, an vitro assay is necessary evaluate cardiac myosin's ensemble using purified proteins. Here, we characterize α- isoforms those myosins carrying left ventricular non-compaction (M531R) dilated cardiomyopathy (S532P)...
The application of hydrostatic pressure generally leads to protein unfolding, implying, in accordance with Le Chatelier's principle, that the unfolded state has a smaller molar volume than folded state. However, origin change upon ΔVu, yet be determined. We have examined systematically effects size and sequence on value ΔVu using as model system series deletion variants ankyrin repeat domain Notch receptor. results provide strong evidence support notion major contributing factor proteins is...
Significance It has been proposed that the spatial arrangement of ligands plays a key role in regulating downstream intracellular signals. Because methodological limitations precise ligand patterning, however, relationship between configuration clusters and signaling dynamics remains poorly understood. By developing DNA-based molecular “pegboard” for we demonstrated nanometer significant roles modulating signal transduction T cells. Ligand clustering not only affects triggering sensitivity...
Abstract DNA origami, a method for constructing nanoscale objects, relies on long single strand of to act as the ‘scaffold’ template assembly numerous short oligonucleotide ‘staples’. The ability generate custom scaffold sequences can greatly benefit origami design processes. Custom provide better control overall size final object and low-level structural details, such locations specific base pairs within an object. Filamentous bacteriophages related phagemids work well sources DNA. However,...
We describe design principles for accurate folding of three-dimensional DNA origami. To evaluate rules, we reduced the problem strand routing to known shortest-path finding in a weighted graph. score candidate routes used thermodynamic model that accounts enthalpic and entropic contributions initial binding, hybridization, loop closure. encoded analyzed new previously reported heuristics. Using emerging from this analysis, redesigned fabricated multiple shapes compared their accuracy using...
In biomolecules, bifurcated H-bonds typically involve the interaction of two donor protons with lone pairs oxygen. Here, we present direct NMR evidence for a H-bonding arrangement involving nitrogen as acceptor atom. Specifically, H-bond network comprises Nδ1 atom histidine and both backbone N-H side-chain Oγ-H threonine within conserved TXXH motif ankyrin repeat (AR) proteins. Identification partners is achieved via solution scalar coupling (HBC) H/D isotope shift experiments. Quantitative...
Abstract Polymerase Chain Reaction (PCR) requires thermal cycling to melt DNA and proceed through the subsequent cycles of synthesis needed for exponential amplification. Previously, we engineered a superhelicase, with enhanced processivity speed, replace this traditional PCR melting step enzymatic unwinding while retaining desired characteristics, such as multi-kb amplicon size applicability cloning gene editing outcome assessment. This isothermal amplification method is named SHARP...
A collection of programs is presented to analyze the thermodynamics folding linear repeat proteins using a 1D Ising model determine intrinsic and interfacial coupling free energies. Expressions for transitions are generated series constructs with different numbers globally fitted these constructs. These designed parameters capped homopolymeric consensus as well heteropolymeric that contain point substitutions, providing rigorous framework analysis effects mutation on directional (i.e., N-...
SUMMARY T cell receptor clustering plays a key role in triggering activation, but the relationship between spatial configuration of clusters and elicitation downstream intracellular signals remains poorly understood. We developed DNA-origami-based system that is easily adaptable to other cellular systems enables rich interrogation responses variety spatially defined inputs. Using chimeric antigen (CAR) model with relevance cancer therapy, we studied signaling dynamics at single resolution....
ABSTRACT Single-molecule proteomic studies are critically important for understanding the molecular origins of cellular phenotypes. However, no currently available technology can achieve both single-molecule sensitivity and high dynamic range required to comprehensively analyze complex mixtures proteins in biological samples. One approach across a wide would be create protein array that arranges billions single molecules with regular spacing on patterned surface. creating such has remained...
Abstract Correct reconstruction of macromolecular structure by cryo-electron microscopy relies on accurate determination the orientation single-particle images. For small (<100 kDa) DNA-binding proteins, obtaining particle images with sufficiently asymmetric features to correctly guide alignment is challenging. DNA nanotechnology was conceived as a potential tool for building host nanostructures prescribe locations and orientations docked proteins. We used origami construct molecular...
We describe design principles for accurate folding of three-dimensional DNA origami. To evaluate rules, we reduced the problem strand routing to known shortest-path finding in a weighted graph. score candidate routes used thermodynamic model that accounts enthalpic and entropic contributions initial binding, hybridization, loop closure. encoded analyzed new previously reported heuristics. Using emerging from this analysis, redesigned fabricated multiple shapes compared their accuracy using...
Abstract DNA origami, a method for constructing nanoscale objects, relies on long single strand of to act as the “scaffold” template assembly numerous short oligonucleotide “staples”. The ability generate custom scaffold sequences can greatly benefit origami design processes. Custom provide better control overall size final object and low-level structural details, such locations specific base pairs within an object. Filamentous bacteriophages related phagemids work well sources DNA. However,...
Abstract Cryo-EM samples prepared using the traditional methods often suffer from too few particles, poor particle distribution, or strongly biased orientation, damage air-water interface. Here we report that functionalization of graphene oxide (GO) coated grids with amino groups concentrates on grid improved distribution and orientation. By introducing a PEG spacer, particles are kept away both GO surface interface, protecting them potential denaturation.
Abstract A collection of programs is presented to analyze the thermodynamics folding linear repeat proteins using a 1D Ising model determine intrinsic and interfacial coupling free energies. Expressions for transitions are generated series constructs with different numbers globally fitted these constructs. These designed parameters capped homopolymeric consensus as well heteropolymeric that contain point substitutions, providing rigorous framework analysis effects mutation on directional...