A5066230952- Advanced Electron Microscopy Techniques and Applications
- Enzyme Structure and Function
- Protein Structure and Dynamics
- Advanced X-ray Imaging Techniques
- Electron and X-Ray Spectroscopy Techniques
- Nicotinic Acetylcholine Receptors Study
- RNA and protein synthesis mechanisms
- X-ray Diffraction in Crystallography
- Receptor Mechanisms and Signaling
- Spectroscopy and Quantum Chemical Studies
- Ion channel regulation and function
- Pancreatic function and diabetes
- RNA modifications and cancer
- Cancer, Hypoxia, and Metabolism
- Amino Acid Enzymes and Metabolism
- Crystallization and Solubility Studies
- Photosynthetic Processes and Mechanisms
- Computational Drug Discovery Methods
- Photoreceptor and optogenetics research
- Mass Spectrometry Techniques and Applications
- Nanopore and Nanochannel Transport Studies
- Electrostatics and Colloid Interactions
- X-ray Spectroscopy and Fluorescence Analysis
- Advanced Fluorescence Microscopy Techniques
- Image Processing Techniques and Applications
SLAC National Accelerator Laboratory
2016-2024
Stanford University
2016-2024
Linac Coherent Light Source
2020-2024
Stanford Medicine
2016-2024
Palo Alto University
2018-2023
Menlo School
2023
Stanford Synchrotron Radiation Lightsource
2017-2021
University of Nebraska–Lincoln
2021
Lawrence Berkeley National Laboratory
2021
Los Alamos National Laboratory
2021
Abstract Inorganic–organic hybrid materials represent a large share of newly reported structures, owing to their simple synthetic routes and customizable properties 1 . This proliferation has led characterization bottleneck: many are obligate microcrystals with low symmetry severe radiation sensitivity, interfering the standard techniques single-crystal X-ray diffraction 2,3 electron microdiffraction 4–11 Here we demonstrate small-molecule serial femtosecond crystallography (smSFX) for...
Significance We describe the X-ray structures of same pentameric ligand-gated ion channel (pLGIC) in both its liganded or ligand-free conformations. This provides molecular basis for understanding opening and closing (gating mechanism) these key players fast transmission chemical signals at synapses. As described with classical allosteric proteins, tertiary changes subunits are linked together through quaternary constraint by a marked reorganization interfaces between associated binding...
Recently discovered bacterial homologues of eukaryotic pentameric ligand-gated ion channels, such as the Gloeobacter violaceus receptor (GLIC), are increasingly used structural and functional models signal transduction in nervous system. Here we present a one-microsecond-long molecular dynamics simulation GLIC channel pH stimulated gating mechanism. The crystal structure obtained at acidic an open-channel form is equilibrated membrane environment then instantly set to neutral pH. shows...
Small Angle X-ray Scattering (SAXS) techniques are becoming more and useful for structural biologists biochemists, thanks to better access dedicated synchrotron beamlines, detectors the relative easiness of sample preparation. The ability compute theoretical SAXS profile a given model, compare this with measured scattering intensity, yields crucial informations about macromolecule under study and/or its complexes in solution. An important contribution profile, besides itself solvent-excluded...
Pentameric ligand-gated ion channels control synaptic neurotransmission by converting chemical signals into electrical signals. Agonist binding leads to rapid signal transduction via an allosteric mechanism, where global protein conformational changes open a pore across the nerve cell membrane. We use all-atom molecular dynamics with swarm-based string method solve for minimum free-energy gating pathways of proton-activated bacterial GLIC channel. describe stable wetted/open and...
Cytochrome c oxidase (CcO) is an essential enzyme in mitochondrial and bacterial respiration. It catalyzes the four-electron reduction of molecular oxygen to water harnesses chemical energy translocate four protons across biological membranes. The turnover CcO reaction involves oxidative phase, which reduced (R) oxidized metastable O
The COVID-19 pandemic has resulted in 198 million reported infections and more than 4 deaths as of July 2021 (covid19.who.int). Research to identify effective therapies for includes: (1) designing a vaccine future protection; (2) de novo drug discovery; (3) identifying existing drugs repurpose them immediate treatments. To assist repurposing design, we determine two apo structures severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease at ambient temperature by serial...
New synthetic hybrid materials and their increasing complexity have placed growing demands on crystal growth for single-crystal X-ray diffraction analysis. Unfortunately, not all chemical systems are conducive to the isolation of single crystals traditional characterization. Here, small-molecule serial femtosecond crystallography (smSFX) at atomic resolution (0.833 Å) is employed characterize microcrystalline silver n-alkanethiolates with various alkyl chain lengths free electron laser...
Enzymes populate ensembles of structures necessary for catalysis that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography at an x-ray free electron laser observe in a designed mutant isocyanide hydratase (ICH) enzyme enhances sampling important minor conformations. The active site exists mixture conformations, and formation the thioimidate intermediate selects catalytically competent substates. influence cysteine ionization on ICH ensemble...
Proteins and other biomolecules form dynamic macromolecular machines that are tightly orchestrated to move, bind, perform chemistry. Cryo-electron microscopy (cryo-EM) can access the intrinsic heterogeneity of these complexes is therefore a key tool for understanding mechanism function. However, 3D reconstruction resulting imaging data presents challenging computational problem, especially without any starting information, setting termed ab initio reconstruction. Here, we introduce method,...
The number of structures in the Protein Data Bank has grown rapidly recent years. Nonetheless, comparing a specific system often proves challenging due to variant nomenclature, origins from different species, presence various ligands, and missing atoms or chains. To address these issues, we have developed PDBCleanV2, Python package that enables users create consistent datasets structures, simplifying comparison among structures. This library generates individual files for each molecule...
X-ray crystallography reconstruction, which transforms discrete diffraction patterns into three-dimensional molecular structures, relies critically on accurate Bragg peak finding for structure determination. As free electron laser (XFEL) facilities advance toward MHz data rates (1 million images per second), traditional algorithms that require manual parameter tuning or exhaustive grid searches across multiple experiments become increasingly impractical. While deep learning approaches offer...
The SARS-CoV-2 main protease of (Mpro) is an important target for related drug repurposing and development studies. Here, we describe the steps structural characterization Mpro, starting from plasmid preparation protein purification. We detail crystallization using sitting drop, microbatch (under oil) approach. Finally, cover data collection structure determination serial femtosecond crystallography. For complete details on use execution this protocol, please refer to Durdagi et al. (2021).
Abstract Multimeric protein assemblies are abundant in nature. Streptavidin is an attractive that provides a paradigm system to investigate the intra- and intermolecular interactions of multimeric complexes. Also, it offers versatile tool for biotechnological applications. Here, we present two apo-streptavidin structures, first one ambient temperature Serial Femtosecond X-ray crystal (Apo-SFX) structure at 1.7 Å resolution second cryogenic (Apo-Cryo) 1.1 resolution. These structures mostly...