Electrostatic Interactions and Binding Orientation of HIV-1 Matrix Studied by Neutron Reflectivity

AbstractThe N-terminal matrix (MA) domain of the HIV-1 Gag protein is responsible for binding to the plasma membrane of host cells during viral assembly. The putative membrane-binding interface of MA was previously mapped by means of mutagenesis and analysis of its trimeric crystal structure. However, the orientation of MA on membranes has not been directly determined by experimental measurements. We present neutron reflectivity measurements that resolve the one-dimensional scattering length density profile of MA bound to a biomimetic of the native viral membrane. A molecular refinement procedure was developed using atomic structures of MA to determine the orientation of the protein on the membrane. The orientation defines a lipid-binding interface consistent with previous mutagenesis results. The MA protein maintains this orientation without the presence of a myristate group, driven only by electrostatic interactions. Furthermore, MA is found to penetrate the membrane headgroup region peripherally such that only the side chains of specific Lys and Arg residues interact with the surface. The results suggest that electrostatic interactions are sufficient to favorably orient MA on viral membrane mimics. The spatial determination of the membrane-bound protein demonstrates the ability of neutron reflectivity to discern orientation and penetration under physiologically relevant conditions

Characterization of an Extensive Interface on Vitronectin for Binding to Plasminogen Activator Inhibitor-1: Adoption of Structure in an Intrinsically Disordered Region

Copyright © 2019 American Chemical Society. Small-angle neutron scattering (SANS) measurements were pursued to study human vitronectin, a protein found in tissues and the circulation that regulates cell adhesion/migration and proteolytic cascades that govern hemostasis and pericellular proteolysis. Many of these functions occur via interactions with its binding partner, plasminogen activator inhibitor-1 (PAI-1), the chief inhibitor of proteases that lyse and activate plasminogen. We focused on a region of vitronectin that remains uncharacterized from previous X-ray scattering, nuclear magnetic resonance, and computational modeling approaches and which we propose is involved in binding to PAI-1. This region, which bridges the N-terminal somatomedin B (SMB) domain with a large central β-propeller domain of vitronectin, appears unstructured and has characteristics of an intrinsically disordered domain (IDD). The effect of osmolytes was evaluated using circular dichroism and SANS to explore the potential of the IDD to undergo a disorder-to-order transition. The results suggest that the IDD favors a more ordered structure under osmotic pressure; SANS shows a smaller radius of gyration (Rg) and a more compact fold of the IDD upon addition of osmolytes. To test whether PAI-1 binding is also coupled to folding within the IDD structure, a set of SANS experiments with contrast variation were performed on the complex of PAI-1 with a vitronectin fragment corresponding to the N-terminal 130 amino acids (denoted the SMB-IDD because it contains the SMB domain and IDD in linear sequence). Analysis of the SANS data using the Ensemble Optimization Method confirms that the SMB-IDD adopts a more compact configuration when bound to PAI-1. Calculated structures for the PAI-1:SMB-IDD complex suggest that the IDD provides an interaction surface outside of the primary PAI-1-binding site located within the SMB domain; this binding is proposed to lead to the assembly of higher-order structures of vitronectin and PAI-1 commonly found in tissues

The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome

The Human Microbiome Project (HMP) [1],[2] is a concept that was long in the making. After the Human Genome Project, interest grew in sequencing the “other genome" of microbes carried in and on the human body [3],[4]. Microbial ecologists, realizing that >99% of environmental microbes could not be easily cultured, developed approaches to study microorganisms in situ [5], primarily by sequencing the 16S ribosomal RNA gene (16S) as a phylogenetic and taxonomic marker to identify members of microbial communities [6]. The need to develop corresponding new methods for culture-independent studies [7],[8] in turn precipitated a sea change in the study of microbes and human health, inspiring the new term “metagenomics" [9] both to describe a technological approach—sequencing and analysis of the genes from whole communities rather than from individual genomes—and to emphasize that microbes function within communities rather than as individual species. This shift from a focus on individual organisms to microbial interactions [10] culminated in a National Academy of Science report [11], which outlined challenges and promises for metagenomics as a way of understanding the foundational role of microbial communities both in the environment and in human health.National Institutes of Health (U.S.) (grant U54HG004969)National Institutes of Health (U.S.) (grant U54HG004973)National Institutes of Health (U.S.) (grant U54AI084844)National Institutes of Health (U.S.) (grant U01HG004866)National Institutes of Health (U.S.) (grant R01HG005969)National Institutes of Health (U.S.) (grant R01HG004872)United States. Army Research Office (grant W911NF-11-1-0473)National Science Foundation (U.S.) (NSF DBI-1053486)Howard Hughes Medical Institute (Early Career Scientist

IRAC Full-Scale Flight Testbed Capabilities

Overview: Provide validation of adaptive control law concepts through full scale flight evaluation in a representative avionics architecture. Develop an understanding of aircraft dynamics of current vehicles in damaged and upset conditions Real-world conditions include: a) Turbulence, sensor noise, feedback biases; and b) Coupling between pilot and adaptive system. Simulated damage includes 1) "B" matrix (surface) failures; and 2) "A" matrix failures. Evaluate robustness of control systems to anticipated and unanticipated failures

Observation of Small Cluster Formation in Concentrated Monoclonal Antibody Solutions and Its Implications to Solution Viscosity

AbstractMonoclonal antibodies (mAbs) are a major class of biopharmaceuticals. It is hypothesized that some concentrated mAb solutions exhibit formation of a solution phase consisting of reversibly self-associated aggregates (or reversible clusters), which is speculated to be responsible for their distinct solution properties. Here, we report direct observation of reversible clusters in concentrated solutions of mAbs using neutron spin echo. Specifically, a stable mAb solution is studied across a transition from dispersed monomers in dilute solution to clustered states at more concentrated conditions, where clusters of a preferred size are observed. Once mAb clusters have formed, their size, in contrast to that observed in typical globular protein solutions, is observed to remain nearly constant over a wide range of concentrations. Our results not only conclusively establish a clear relationship between the undesirable high viscosity of some mAb solutions and the formation of reversible clusters with extended open structures, but also directly observe self-assembled mAb protein clusters of preferred small finite size similar to that in micelle formation that dominate the properties of concentrated mAb solutions

Designing a Regional System of Social Indicators to Evaluate Nonpoint Source Water Projects

A collaborative team has developed a system to measure the social outcomes of nonpoint source water projects as indicators of progress towards environmental goals. The system involves a set of core indicators, additional supplemental indicators, and a process for collecting and using the indicators. This process is supported by methodologies and instruments for data collection, analysis, and reporting that are coordinated and supported through detailed written guidance and an on-line data management tool. Its multi-state scope and application offer a unique opportunity to target, measure, and report interim resource management accomplishments consistently at multiple levels

KELT-10b: The First Transiting Exoplanet from the KELT-South Survey -- A Hot Sub-Jupiter Transiting a V = 10.7 Early G-Star

We report the discovery of KELT-10b, the first transiting exoplanet discovered using the KELT-South telescope. KELT-10b is a highly inflated sub-Jupiter mass planet transiting a relatively bright $V = 10.7$ star (TYC 8378-64-1), with T$_{eff}$ = $5948\pm74$ K, $\log{g}$ = $4.319_{-0.030}^{+0.020}$ and [Fe/H] = $0.09_{-0.10}^{+0.11}$, an inferred mass M$_{*}$ = $1.112_{-0.061}^{+0.055}$ M$_{\odot}$ and radius R$_{*}$ = $1.209_{-0.035}^{+0.047}$ R$_{\odot}$. The planet has a radius R$_{P}$ = $1.399_{-0.049}^{+0.069}$ R$_{J}$ and mass M$_{P}$ = $0.679_{-0.038}^{+0.039}$ M$_{J}$. The planet has an eccentricity consistent with zero and a semi-major axis $a$ = $0.05250_{-0.00097}^{+0.00086}$ AU. The best fitting linear ephemeris is $T_{0}$ = 2457066.72045$\pm$0.00027 BJD$_{TDB}$ and P = 4.1662739$\pm$0.0000063 days. This planet joins a group of highly inflated transiting exoplanets with a radius much larger and a mass much less than those of Jupiter. The planet, which boasts deep transits of 1.4%, has a relatively high equilibrium temperature of T$_{eq}$ = $1377_{-23}^{+28}$ K, assuming zero albedo and perfect heat redistribution. KELT-10b receives an estimated insolation of $0.817_{-0.054}^{+0.068}$ $\times$ 10$^9$ erg s$^{-1}$ cm$^{-2}$, which places it far above the insolation threshold above which hot Jupiters exhibit increasing amounts of radius inflation. Evolutionary analysis of the host star suggests that KELT-10b is unlikely to survive beyond the current subgiant phase, due to a concomitant in-spiral of the planet over the next $\sim$1 Gyr. The planet transits a relatively bright star and exhibits the third largest transit depth of all transiting exoplanets with V $<$ 11 in the southern hemisphere, making it a promising candidate for future atmospheric characterization studies.Comment: 20 pages, 13 figures, 7 tables, accepted for publication in MNRA