A5054407653- Bacteriophages and microbial interactions
- Computational Drug Discovery Methods
- Protein Structure and Dynamics
- Viral Infections and Vectors
- vaccines and immunoinformatics approaches
- Viral Infections and Outbreaks Research
- SARS-CoV-2 and COVID-19 Research
- Reproductive tract infections research
- Protein purification and stability
- Bacterial Genetics and Biotechnology
- Bacillus and Francisella bacterial research
- Advanced Fluorescence Microscopy Techniques
- Mosquito-borne diseases and control
- Yersinia bacterium, plague, ectoparasites research
- Hepatitis B Virus Studies
- Monoclonal and Polyclonal Antibodies Research
- Lipid Membrane Structure and Behavior
- Optical Imaging and Spectroscopy Techniques
- Spectroscopy Techniques in Biomedical and Chemical Research
- RNA Interference and Gene Delivery
- Vibrio bacteria research studies
- Microbial Natural Products and Biosynthesis
- Radioactive contamination and transfer
- Microbial Metabolism and Applications
- Bacterial Infections and Vaccines
Lawrence Livermore National Security
2024
Lawrence Livermore National Laboratory
2010-2024
The COVID-19 pandemic underscored the promise of monoclonal antibody-based prophylactic and therapeutic drugs
Alchemical free energy perturbation (FEP) is a rigorous and powerful technique to calculate the difference between distinct chemical systems. Here we report our implementation of automated large-scale FEP calculations, using Amber software package, facilitate antibody design evaluation. In combination with Hamiltonian replica exchange, simulations aim predict effect mutations on both binding affinity structural stability. Importantly, incorporate multiple strategies faithfully estimate...
A rapid response is necessary to contain emergent biological outbreaks before they can become pandemics. The novel coronavirus (SARS-CoV-2) that causes COVID-19 was first reported in December of 2019 Wuhan, China and reached most corners the globe less than two months. In just over a year since initial infections, infected almost 100 million people worldwide. Although similar SARS-CoV MERS-CoV, SARS-CoV-2 has resisted treatments are effective against other coronaviruses. Crystal structures...
Rift Valley fever virus (RVFV) is a highly pathogenic mosquito-borne capable of causing hepatitis, encephalitis, blindness, hemorrhagic syndrome, and death in humans livestock. Upon aerosol infection with RVFV, the brain major site viral replication tissue damage, yet pathogenesis this organ has been understudied. Here, we investigated immune response RVFV infected mice. In to infection, microglia initiated robust transcriptional upregulation antiviral genes, as well increased levels...
The respiratory virus responsible for coronavirus disease 2019 (COVID-19), severe acute syndrome 2 (SARS-CoV-2), has affected nearly every aspect of life worldwide, claiming the lives over 3.9 million people globally, at time this publication. Neutralizing humanized nanobody (VHH)-based antibodies (VHH-huFc) represent a promising therapeutic intervention strategy to address current SARS-CoV-2 pandemic and provide powerful toolkit future outbreaks. Using synthetic, high-diversity VHH...
Nanolipoprotein particles (NLPs) represent a unique nanometer-sized scaffold for supporting membrane proteins (MP). Characterization of their dynamic shape and association with MP in solution remains challenge. Here, we present rapid method analysis by fluorescence correlation spectroscopy (FCS) to characterize bacteriorhodopsin (bR), protein capable forming NLP complex. By selectively labeling individual components NLPs during cell-free synthesis, FCS enabled us measure specific diffusion...
Fluorescence correlation spectroscopy (FCS) is an important technique for studying biochemical interactions dynamically that may be used in vitro and cell-based studies. It generally claimed FCS only at nM concentrations. We show this general consensus incorrect the limitation to concentrations not fundamental but due detector limits as well laser fluctuations. With a high count rate system applying fluctuation corrections, we demonstrate measurements up 38 μM with same signal-to-noise lower...
Recombinant expression of toxic proteins remains a challenging problem. One potential method to shield toxicity and thus improve these is encapsulate them within protein compartments sequester away from their targets. Many bacteria naturally produce so-called bacterial microcompartments (BMCs) in which enzymes comprising biosynthetic pathway are encapsulated proteinaeous shell, part thought the cells reaction intermediates. As proof-of-concept, we attempted toxic, lysis E (E) bacteriophage...
Nanolipoprotein particles (NLPs) are nanometer-scale discoidal that feature a phospholipid bilayer confined within an apolipoprotein "scaffold," which useful for solubilizing hydrophobic molecules such as drugs and membrane proteins. NLPs synthesized either by mixing the purified with phospholipids other cofactors or cell-free protein synthesis followed self-assembly of nanoparticles in reaction mixture. Either method can be problematic regarding production homogeneous monodispersed...
Francisella tularensis is classified as a Class A bioterrorism agent by the U.S. government due to its high virulence and ease with which it can be spread an aerosol. It facultative intracellular pathogen causative of tularemia. Ciprofloxacin (Cipro) broad spectrum antibiotic effective against Gram-positive Gram-negative bacteria. Increased Cipro resistance in pathogenic microbes serious concern when considering options for medical treatment bacterial infections. Identification genes loci...
In vivo delivery of large RNA molecules has significant implications for novel gene therapy, biologics delivery, and vaccine applications. We have developed cationic nanolipoprotein particles (NLPs) to enhance the complexation self-amplifying mRNAs (replicons) in vivo. NLPs are high-density lipoprotein (HDL) mimetics, comprised a discoidal lipid bilayer stabilized by apolipoproteins that readily functionalized provide versatile platform. Herein, we systematically screened NLP assembly with...
Yersinia pestis enters host cells and evades defenses, in part, through interactions between proteins membranes. One such interaction is the type III secretion system, which uses a highly conserved ordered complex for outer membrane effector protein translocation called injectisome. The portion of injectisome that interacts directly with cell membranes referred to as translocon. translocon believed form pore allowing molecules enter cells. To facilitate mechanistic studies translocon, we...
Structure-based Deep Fusion models were recently shown to outperform several physics- and machine learning-based protein-ligand binding affinity prediction methods. As part of a multi-institutional COVID-19 pandemic response, over 500 million small molecules computationally screened against four protein structures from the novel coronavirus (SARS-CoV-2), which causes COVID-19. Three enhancements made in order evaluate more than 5 billion docked poses on SARS-CoV-2 targets. First, concept was...
Rift Valley fever phlebovirus (RVFV) is a highly pathogenic mosquito-borne virus with bioweapon potential due to its ability be spread by aerosol transmission. Neurological symptoms are among the worst outcomes of infection, and understanding pathogenesis mechanisms within brain limited. RVFV classified as an overlap select agent CDC USDA; therefore, experiments involving fully virulent strains tightly regulated. Here, we present two methods for inactivation live samples derived from mouse...
ABSTRACT Lytic proteins encoded by bacterial genomes have been implicated in cell wall biosynthesis and recycling. The Bacillus cereus E33L ampD gene encodes a putative N -acetylmuramoyl- l -alanine amidase. This gene, expressed vitro , produced very stable, highly active lytic protein. Very low concentrations rapidly efficiently lyse vegetative anthracis cells.
Abstract Chlamydia trachomatis is the most prevalent bacterial sexually transmitted pathogen worldwide. Since chlamydial infection largely asymptomatic with potential for serious complications, a preventative vaccine likely viable long-term answer to this public health threat. Cell-free protein synthesis (CFPS) utilizes cellular manufacturing machinery decoupled from requirement maintaining viability, offering flexible, rapid, and de-centralized production of recombinant antigens. Here, we...
is the most prevalent bacterial sexually transmitted pathogen in humans worldwide. Since chlamydial infection largely asymptomatic with potential for serious complications, a preventative vaccine likely viable long-term answer to this public health threat. Cell-free protein synthesis (CFPS) utilizes cellular manufacturing machinery decoupled from requirement maintaining viability, offering flexible, rapid, and decentralized production of recombinant antigens.
Abstract Rift Valley fever virus (RVFV) is a highly pathogenic mosquito-borne capable of causing hepatitis, encephalitis, blindness, hemorrhagic syndrome, and death in humans livestock. Upon aerosol infection with RVFV, the brain major site viral replication tissue damage, yet pathogenesis this organ has been understudied. Here, we investigated immune response RVFV infected mice. In to infection, microglia initiate robust transcriptional upregulation antiviral genes, as well increased levels...
Structure-based Deep Fusion models were recently shown to outperform several physics- and machine learning-based protein-ligand binding affinity prediction methods. As part of a multi-institutional COVID-19 pandemic response, over 500 million small molecules computationally screened against four protein structures from the novel coronavirus (SARS-CoV-2), which causes COVID-19. Three enhancements made in order evaluate more than 5 billion docked poses on SARS-CoV-2 targets. First, concept was...