Covalent Labeling Automated Data Analysis Platform for High Throughput in R (coADAPTr): A Proteome-Wide Data Analysis Platform for Covalent Labeling Experiments.

Covalent labeling methods coupled to mass spectrometry have emerged in recent years for studying the higher order structure of proteins. Quantifying the extent of modification of proteins in multiple states (i.e.

The utilization of the search engine, Bolt, to decrease search time and increase peptide identifications in hydroxyl radical protein footprinting-based workflows.

Hydroxyl radical protein footprinting (HRPF) utilizes hydroxyl radicals to covalently modify solvent exposed regions of proteins. When coupled with mass spectrometry, HRPF can provide insightful information on protein structural changes including inside cells. However, the complex mixture of proteins and modifications makes identification a complicated task.

Laser-free Hydroxyl Radical Protein Footprinting to Perform Higher Order Structural Analysis of Proteins.

Hydroxyl Radical Protein Footprinting (HRPF) is an emerging and promising higher order structural analysis technique that provides information on changes in protein structure, protein-protein interactions, or protein-ligand interactions. HRPF utilizes hydroxyl radicals (OH) to irreversibly label a protein's solvent accessible surface. The inherent complexity, cost, and hazardous nature of performing HRPF have substantially limited broad-based adoption in biopharma.

Characterizing Cellular Proteins with In-cell Fast Photochemical Oxidation of Proteins.

Fast photochemical oxidation of proteins (FPOP) is a hydroxyl radical protein footprinting method used to characterize protein structure and interactions. FPOP uses a 248 nm excimer laser to photolyze hydrogen peroxide producing hydroxyl radicals. These radicals oxidatively modify solvent exposed side chains of 19 of the 20 amino acids.

Insights on the Conformational Ensemble of Cyt C Reveal a Compact State during Peroxidase Activity.

Cytochrome c (cyt c) is known for its role in the electron transport chain but transitions to a peroxidase-active state upon exposure to oxidative species. The peroxidase activity ultimately results in the release of cyt c into the cytosol for the engagement of apoptosis. The accumulation of oxidative modifications that accompany the onset of the peroxidase function are well-characterized.

Rosetta Protein Structure Prediction from Hydroxyl Radical Protein Footprinting Mass Spectrometry Data.

In recent years mass spectrometry-based covalent labeling techniques such as hydroxyl radical footprinting (HRF) have emerged as valuable structural biology techniques, yielding information on protein tertiary structure. These data, however, are not sufficient to predict protein structure unambiguously, as they provide information only on the relative solvent exposure of certain residues. Despite some recent advances, no software currently exists that can utilize covalent labeling mass spectrometry data to predict protein tertiary structure.

Modifications generated by fast photochemical oxidation of proteins reflect the native conformations of proteins.

Hydroxyl radical footprinting (HRF) is a nonspecific protein footprinting method that has been increasingly used in recent years to analyze protein structure. The method oxidatively modifies solvent accessible sites in proteins, which changes upon alterations in the protein, such as ligand binding or a change in conformation. For HRF to provide accurate structural information, the method must probe the native structure of proteins.

Analyzing the structure of macromolecules in their native cellular environment using hydroxyl radical footprinting.

Hydroxyl radical footprinting (HRF) has been successfully used to study the structure of both nucleic acids and proteins. The method utilizes hydroxyl radicals to oxidize solvent accessible sites in macromolecules. In recent years, the method has shown some utility for live cell analysis.

Design, synthesis, and immunologic evaluation of vaccine adjuvant conjugates based on QS-21 and tucaresol.

Immunoadjuvants are used to potentiate the activity of modern subunit vaccines that are based on molecular antigens. An emerging approach involves the combination of multiple adjuvants in a single formulation to achieve optimal vaccine efficacy. Herein, to investigate such potential synergies, we synthesized novel adjuvant conjugates based on the saponin natural product QS-21 and the aldehyde tucaresol via chemoselective acylation of an amine at the terminus of the acyl chain domain in QS saponin variants.

Optical phase locking of two infrared continuous wave lasers separated by 100 THz.

We report on phase locking of two continuous wave IR laser sources separated by 100 THz emitting around 1029 and 1544 nm, respectively. Our approach uses three independent harmonic generation processes of the IR laser frequencies in periodically poled MgO:LiNbO3 crystals to generate second and third harmonics of those two IR sources. The beat note between the two independent green radiations generated around 515 nm is used to phase lock one IR laser to the other, with tunable radio frequency offset.

Development of a minimal saponin vaccine adjuvant based on QS-21.

Adjuvants are materials added to vaccines to enhance the immunological response to an antigen. QS-21 is a natural product adjuvant under investigation in numerous vaccine clinical trials, but its use is constrained by scarcity, toxicity, instability and an enigmatic molecular mechanism of action. Herein we describe the development of a minimal QS-21 analogue that decouples adjuvant activity from toxicity and provides a powerful platform for mechanistic investigations.

Arsenic in groundwater and its influence on exposure risks through traditionally cooked rice in Prey Vêng Province, Cambodia.

Arsenic (As) contamination of communal tubewells in Prey Vêng, Cambodia, has been observed since 2000. Many of these wells exceed the WHO As in drinking water standard of 10 μg/L by a factor of 100. The aim of this study was to assess how cooking water source impacts dietary As intake in a rural community in Prey Vêng.

Synthesis and preclinical evaluation of QS-21 variants leading to simplified vaccine adjuvants and mechanistic probes.

QS-21 is a potent immunostimulatory saponin that is currently under clinical investigation as an adjuvant in various vaccines to treat infectious diseases, cancers, and cognitive disorders. Herein, we report the design, synthesis, and preclinical evaluation of simplified QS-21 congeners to define key structural features that are critical for adjuvant activity. Truncation of the linear tetrasaccharide domain revealed that a trisaccharide variant is equipotent to QS-21, while the corresponding disaccharide and monosaccharide congeners are more toxic and less potent, respectively.

Gata3 regulates trophoblast development downstream of Tead4 and in parallel to Cdx2.

The mouse blastocyst and stem cells derived from its tissue lineages provide a unique genetic system for examining the establishment and loss of pluripotency. The transcription factor Cdx2 plays a central role by repressing pluripotency genes, such as Oct4, and promoting extraembryonic trophoblast fate at the blastocyst stage. However, genetic evidence has suggested that Cdx2 does not work alone in the trophoblast lineage.

Nod1 and Nod2 direct autophagy by recruiting ATG16L1 to the plasma membrane at the site of bacterial entry.

Autophagy is emerging as a crucial defense mechanism against bacteria, but the host intracellular sensors responsible for inducing autophagy in response to bacterial infection remain unknown. Here we demonstrated that the intracellular sensors Nod1 and Nod2 are critical for the autophagic response to invasive bacteria. By a mechanism independent of the adaptor RIP2 and transcription factor NF-kappaB, Nod1 and Nod2 recruited the autophagy protein ATG16L1 to the plasma membrane at the bacterial entry site.

The germline stem cells of Drosophila melanogaster partition DNA non-randomly.

The Immortal Strand Hypothesis proposes that asymmetrically dividing stem cells cosegregate chromatids to retain ancestral DNA templates. Using both pulse-chase and label retention assays, we show that non-random partitioning of DNA occurs in germline stem cells (GSCs) in the Drosophila ovary as these divide asymmetrically to generate a new GSC and a differentiating cystoblast. This process is disrupted when GSCs are forced to differentiate through the overexpression of Bag of Marbles, a factor that impels the terminal differentiation of cystoblasts.

How accurate and statistically robust are catalytic site predictions based on closeness centrality?

Background: We examine the accuracy of enzyme catalytic residue predictions from a network representation of protein structure. In this model, amino acid alpha-carbons specify vertices within a graph and edges connect vertices that are proximal in structure. Closeness centrality, which has shown promise in previous investigations, is used to identify important positions within the network.

Elucidating the Conformational Dependence of Calculated pKa Values.

The variability within calculated protein residue pKa values calculated using Poisson-Boltzmann continuum theory with respect to small conformational fluctuations is investigated. As a general rule, sites buried in the protein core have the largest pKa fluctuations but the least amount of conformational variability; conversely, sites on the protein surface generally have large conformational fluctuations but very small pKa fluctuations. These results occur because of the heterogeneous or uniform nature of the electrostatic microenvironments at the protein core or surface, respectively.

Clinical characteristics and risk factors for Vibrio cholerae infection in children.

Surveillance was conducted during February and March 1991 in the pediatric emergency department of Cayetano Heredia Hospital, Lima, Peru, to contrast the characteristics of children with epidemic cholera with those of children with noncholera-associated diarrhea. Among 626 patients 14 years of age or younger, Vibrio cholerae O1 was isolated from stool specimens of 310 patients (49%), more commonly from children older than 24 months of age (66%; p < 0.0001) than from younger children.