A5024391721- Lipid Membrane Structure and Behavior
- Ion channel regulation and function
- Protein Structure and Dynamics
- Mitochondrial Function and Pathology
- Scientific Measurement and Uncertainty Evaluation
- RNA and protein synthesis mechanisms
- ATP Synthase and ATPases Research
- Photosynthetic Processes and Mechanisms
- Ion Transport and Channel Regulation
- Cellular transport and secretion
- Electrochemical Analysis and Applications
- Neuroscience and Neuropharmacology Research
- Amino Acid Enzymes and Metabolism
- Cardiac electrophysiology and arrhythmias
- Nanopore and Nanochannel Transport Studies
- DNA and Nucleic Acid Chemistry
- Force Microscopy Techniques and Applications
- Bacteriophages and microbial interactions
- Mass Spectrometry Techniques and Applications
- Pancreatic function and diabetes
- Gene Regulatory Network Analysis
- Physics and Engineering Research Articles
- Advanced Measurement and Metrology Techniques
- Influenza Virus Research Studies
- Metabolism and Genetic Disorders
University of California, San Francisco
2016-2025
University of California San Francisco Medical Center
2025
Universidad Católica de Santa Fe
2022-2024
Madonna University
2022
University of San Francisco
2021
University of Pittsburgh
1995-2014
Carnegie Mellon University
2013
Howard Hughes Medical Institute
2003-2006
Babson College
2006
Stanford University
2006
ABSTRACT At this time, about 3,000 different viruses are recognized, but metagenomic studies suggest that these a small fraction of the exist in nature. We have explored viral diversity by deep sequencing nucleic acids obtained from virion populations enriched raw sewage. identified 234 known viruses, including 17 infect humans. Plant, insect, and algal as well bacteriophages were also present. These represented 26 taxonomic families included with single-stranded DNA (ssDNA), double-stranded...
The design of functional membrane proteins from first principles represents a grand challenge in chemistry and structural biology. Here, we report the membrane-spanning, four-helical bundle that transports first-row transition metal ions Zn 2+ Co , but not Ca across membranes. conduction path was designed to contain two di-metal binding sites bind with negative cooperativity. X-ray crystallography solid-state solution nuclear magnetic resonance indicate overall helical is formed tightly...
Intracellular organelles have characteristic pH ranges that are set and maintained by a balance between ion pumps, leaks, internal ionic equilibria. Previously, thermodynamic study Rybak et al. (Rybak, S., F. Lanni, R. Murphy. 1997. Biophys. J. 73:674–687) identified the key elements involved in regulation; however, recent experiments show cellular compartments not equilibrium. We present here nonequilibrium model of lumenal acidification based on interplay pumps channels, physical...
A precise pH gradient between organelles of the regulated secretory pathway is required for sorting and processing prohormones. We studied regulation in live endocrine cells by targeting biotin-based indicators to cellular expressing avidin-chimera proteins. In AtT-20 cells, we found that steady-state decreased from endoplasmic reticulum (ER) (pH<sub>ER</sub> = 7.4 ± 0.2, mean S.D.) Golgi (pH<sub>G</sub> 6.2 0.4) mature granules (MSGs) (pH<sub>MSG</sub>= 5.5 0.4). MSGs active...
Lysosomes must maintain an acidic luminal pH to activate hydrolytic enzymes and degrade internalized macromolecules. Acidification requires the vacuolar-type H+-ATPase pump protons into lumen a counterion flux neutralize membrane potential created by proton accumulation. Early experiments suggested that was chloride, more recently pathway consistent with ClC-7 Cl–/H+ antiporter identified. However, reports steady-state is unaffected in knockout mice raise questions regarding identity of...
The weighted ensemble (WE) path sampling approach orchestrates an of parallel calculations with intermittent communication to enhance the rare events, such as molecular associations or conformational changes in proteins peptides. Trajectories are replicated and pruned a way that focuses computational effort on underexplored regions configuration space while maintaining rigorous kinetics. To enable simulation events at any scale (e.g., atomistic, cellular), we have developed open-source,...
Significance Lipid scramblases play critical roles in diverse biological events, from cellular apoptosis to coagulation of the blood. The transmembrane protein 16 (TMEM16) family membrane proteins consists both ion channels and scramblases, but little is known about how these conduct ions or lipids across bilayer. Here, we present computational results on a fungal TMEM16 member that provide insight into deform facilitate lipid permeation. We identified specific residues surface are...
In eukaryotes, P-type adenosine triphosphatases (ATPases) generate the plasma membrane potential and drive secondary transport systems; however, despite their importance, regulation remains poorly understood. We monitored at single-molecule level activity of prototypic proton-pumping ATPase Arabidopsis thaliana isoform 2 (AHA2). Our measurements, combined with a physical nonequilibrium model vesicle acidification, revealed that pumping is stochastically interrupted by long-lived (~100...
The innately heterodimeric K 2P filter permits two C-type gating mechanisms, pinching and dilation, to operate in one channel.
Lysosomes are important sites for macromolecular degradation, defined by an acidic lumenal pH of ∼4.5. To better understand lysosomal pH, we designed a novel, genetically encoded, fluorescent protein (FP)-based biosensor called Fluorescence Indicator REporting in (FIRE-pHLy). This was targeted to lysosomes with lysosomal-associated membrane 1 (LAMP1) and reported between 3.5 6.0 monomeric teal (mTFP1), bright cyan pH-sensitive FP variant pKa 4.3. Ratiometric quantification enabled...
Lipids in biological membranes are thought to be functionally organized, but few experimental tools can probe nanoscale membrane structure. Using brominated lipids as contrast probes for cryo-EM and a model ESCRT-III membrane-remodeling system composed of human CHMP1B IST1, we observed leaflet-level protein-localized structural lipid patterns within highly constricted thinned nanotubes. These nanotubes differed markedly from protein-free, flat bilayers leaflet thickness, diffusion rates...
The F-ATPase of the bacterium Propionigenium modestum is driven by an electrochemical sodium gradient between cell interior and its environment. Here we present a mechanochemical model for transduction transmembrane sodium-motive force into rotary torque. same mechanism likely to operate in other F-ATPases, including proton-driven F-ATPases Escherichia coli.
Electrostatic forces are one of the primary determinants molecular interactions. They help guide folding proteins, increase binding protein to another and facilitate protein-DNA protein-ligand binding. A popular method for computing electrostatic properties biological systems is numerically solve Poisson-Boltzmann (PB) equation, there several easy-to-use software packages available that PB equation soluble proteins. Here we present a freely program, called APBSmem, carrying out these...
Many pathogenic bacteria utilise sialic acids as an energy source or use them external coating to evade immune detection. As such, that colonise sialylated environments deploy specific transporters mediate import of scavenged acids. Here, we report a substrate-bound 1.95 Å resolution structure and subsequent characterisation SiaT, acid transporter from Proteus mirabilis. SiaT is secondary active the sodium solute symporter (SSS) family, which Na