saxs

Urease from Canavalia ensiformis seeds was the first enzyme ever to be crystallized, in 1926. These proteins, found in plants, bacteria and fungi, present different biological properties including catalytic hydrolysis of urea, and also enzyme-independent activities, such as induction of exocytosis, pro-inflammatory effects, neurotoxicity, antifungal and insecticidal properties. Urease is toxic to insects and fungi per se but part of this toxicity relies on an internal peptide (~11 kDa), which is released upon digestion of the protein by insect enzymes...

Myotilin is a component of the sarcomere where it plays an important role in organisation and maintenance of Z-disk integrity. This involves direct binding to F-actin and filamin C, a function mediated by its Ig domain pair. While the structures of these two individual domains are known, information about their relative orientation and flexibility remains limited. We set on to characterise the Ig domain pair of myotilin with emphasis on its molecular structure, dynamics and phylogeny. First, sequence conservation analysis of myotilin shed light on the molecular basis of myotilinopathies and revealed several motifs in Ig domains found also in I-band proteins...

Thermal-induced conformational changes and protein-protein interactions of bovine serum albumin (BSA) in aqueous solution are assessed by small angle X-ray scattering (SAXS) at two pH values (7.4 and 9.0) and two ionic strengths (0.1 and 0.5). We demonstrate that Guinier analysis in two ranges of the modulus of the scattering vector allows protein melting and aggregation to be monitored simultaneously, thus providing insights into the mechanism of thermal-induced BSA aggregation. Results of the analysis suggest that at room temperature monomeric and dimeric BSA fractions are present in solution...

Multi-domain proteins play critical roles in fine-tuning essential processes in cellular signaling and gene regulation. Typically, multiple globular domains that are connected by flexible linkers undergo dynamic re-arrangements upon binding to protein, DNA or RNA ligands. RNA binding proteins (RBPs) represent an important class of multi-domain proteins, which regulate gene expression by recognizing linear or structured RNA sequence motifs. Here, we employ segmental perdeuteration of the three RNA recognition motif (RRM) domains in the RBP TIA-1 using Sortase A-mediated protein ligation...

Bicontinous microemulsions (BμE) generally consist of nanodomains formed by surfactant in a mixture of water and oil at nearly equal proportions and are potential candidates for the solubilization and purification of membrane proteins. Here we present the first time report of nanoscopic dynamics of surfactant monolayers within BμEs formed by the anionic surfactant sodium dodecyl sulfate (SDS) measured on the nanosecond to picosecond time scale using quasielastic neutron scattering (QENS). BμEs investigated herein consisted of middle phases isolated from Winsor-III microemulsion systems that were formed by mixing aqueous and oil solutions under optimal conditions...

Microbial enhanced coalbed methane (ME-CBM) recovery is critically examined as a viable technology for natural gas recovery from coalbed methane (CBM) reservoirs. Since the majority of gas-in-place (GIP) is stored as an adsorbed phase in fine pores of coal matrix, the nano-pore structure directly influences gas storage and transport properties. Only limited studies have quantified the alteration of the nano-pore structure due to ME-CBM treatment. This study examines the evolution of the pore structure using a combination of small angle X-ray scattering (SAXS), low-pressure N2 and CO2 adsorption (LPGA) and high-pressure methane adsorption methods...

Silica-loaded poly(glycerol monomethacrylate)-poly(2-hydroxypropyl methacrylate) diblock copolymer vesicles are prepared in the form of concentrated aqueous dispersions via polymerization-induced self-assembly (PISA). As the concentration of silica nanoparticles present during the PISA synthesis is increased up to 35% w/w, higher degrees of encapsulation of this component within the vesicles can be achieved. After centrifugal purification to remove excess non-encapsulated silica nanoparticles, SAXS, DCP, and TGA analysis indicates encapsulation of up to hundreds of silica nanoparticles per vesicle...

Enteroviruses use a type I IRES structure to facilitate protein synthesis and promote genome replication. Type I IRES elements require auxiliary host proteins to organize RNA structure for 40S ribosomal subunit assembly. Heterogeneous nuclear ribonucleoprotein A1 stimulates Enterovirus 71 (EV71) translation in part through specific interactions with its stem loop II (SLII) IRES domain. Here, we determined a conjoined NMR-SAXS structure of the EV71 SLII domain and a mutant that significantly attenuates viral replication by abrogating hnRNP A1 interactions...

Most proteins are not static structures, but many of them are found in a dynamic state, exchanging conformations on various time scales as a key aspect of their biological function. An entire spectrum of structural disorder exists in proteins and obtaining a satisfactory quantitative description of these states remains a challenge. Single-molecule fluorescence spectroscopy techniques are uniquely suited for this task, by measuring conformations without ensemble averaging and kinetics without interference from asynchronous processes...

Macrolide antibiotics are a prominent group of emerging contaminants frequently found in wastewater effluents and wastewater-impacted aquatic environments. In this work, a novel analytical method for simultaneous determination of parent macrolide antibiotics (azithromycin, erythromycin, clarithromycin and roxithromycin), along with their synthesis intermediates, byproducts, metabolites and transformation products in wastewater and surface water was developed and validated. Samples were enriched using solid-phase extraction on Oasis HLB cartridges and analyzed by reversed-phase liquid chromatography coupled to electrospray ionization tandem mass spectrometry...

A new low molecular weight hydrogelator with a saccharide (lactobionic) polar head linked by azide-alkyne click chemistry was prepared in three steps. It was obtained in high purity without chromatography, by phase separation and ultrafiltration of the aqueous gel. Gelation was not obtained reproducibly by conventional heating-cooling cycles and instead was obtained by shearing the aqueous solutions, from 2 wt% to 0.25 wt%. This method of preparation favored the formation of a quite unusual network of interconnected large but thin 2D-sheets (7nm-thick) formed by the association side-by-side of long and aligned 7nm diameter wormlike micelles...

Taking advantage of the aqueous biphasic behavior of polyethylene glycol (PEG)/salts, recent experiments have demonstrated self-assembly and crystallization of PEG-grafted gold nanoparticles (PEG-AuNPs) into tunable two-dimensional (2D) supercrystals by adjusting salt concentration (for instance, K2CO3). In those studies, combined experimental evidence and theoretical analysis have pointed out the possibility that similar strategies can lead to three-dimensional (3D) formation of ordered nanoparticle precipitates...

The Escherichia coli Complex II homolog quinol:fumarate reductase (QFR, FrdABCD) catalyzes the interconversion of fumarate and succinate at a covalently attached FAD within the FrdA subunit. The SdhE assembly factor enhances covalent flavinylation of Complex II homologs, but the mechanisms underlying the covalent attachment of FAD remain to be fully elucidated. Here, we explored the mechanisms of covalent flavinylation of the E. coli QFR FrdA subunit. Using a ΔsdhE E. coli strain, we show that the requirement for the assembly factor depends on the cellular redox environment...

Antibacterial resistance has become a serious crisis for world health over the last few decades, so that new therapeutic approaches are strongly needed to face the threat of resistant infections. Transcription factor decoys (TFD) are a promising new class of antimicrobial oligonucleotides with proven in vivo activity when combined with a bolaamphiphilic cationic molecule, 12-bis-THA. These two molecular species form stable nanoplexes which, however, present very scarce colloidal stability in physiological media, which poses the challenge of drug formulation and delivery...

Twenty-seven new species of the genus Neoxyphinus are described, all from Brazil, raising the total number of species of the genus to 48. The new species with the respective geographic distribution and known sexes are: N. capiranga sp. nov. (♂♀) from Amazonas, Pará, Mato Grosso and Rondônia; N. caprichoso sp. nov. (♂♀) and N. garantido sp. nov. (♂♀) from Amazonas and Pará; N. crasto sp. nov. (♂♀) from Bahia and Sergipe; N. murici sp. nov. (♂♀) from Alagoas and Sergipe; N. meurei sp. nov...

In this work we investigate the salt-induced cluster formation of monodisperse, spherical gold nanoparticles possessing negative surface charge. Time dependent dynamic light scattering was used to determine the critical coagulation concentration and to study the kinetics of cluster growth. Cryo-TEM as well as small angle X-ray scattering allowed to obtain insights into the cluster morphology at various salt concentrations. The time dependent cluster growth was monitored by stopped-flow small angle X-ray scattering experiments and UV-Visible extinction measurements simultaneously...

A heterogeneous distribution of crosslinker in micro-hydrogels (microgels) results in a non-uniform polymer density inside the particles. Identifying the morphology of the hydrogel backbone enables a bottom-up approach towards the structural and rheological properties of microgel systems. On a local level we use a Flory-Rehner inspired model that focuses on highly swollen networks, characterized by a Poisson's ratio of 1/4. Our ab initio calculations take account for the nonuniform distribution of crosslinker species during the synthesis of poly(N-isopropylacylamide) (PNIPAM) microgels, yet the method is also applicable to other microgel architectures...

A detailed data analysis utilizing the string-of-beads model was performed on experimental small-angle X-ray scattering (SAXS) curves in a targeted structural study of three, very important, industrial polysaccharides. The results demonstrate the quality of performance for this model on three polymers with quite different thermal structural behavior. Furthermore, they show the advantages of the model used by way of excellent fits in the ranges where the classic approach to the small-angle scattering data interpretation fails and an additional 3D visualization of the model's molecular conformations and anticipated polysaccharide supramolecular structure...

Background: Cardiovascular disease (CVD) is an increasing cause of morbidity among persons living with HIV (PLWH). We projected cumulative CVD risk in PLWH in care compared to the US general population and persons HIV-uninfected, but at high risk for HIV. Methods: We used a mathematical model to project cumulative CVD incidence. We simulated a male and female cohort for each of three populations: 1) US general population; 2) HIV-uninfected, at high risk for HIV; and 3) PLWH...

Background: Current guidelines recommend genotype resistance testing at diagnosis to guide initial selection of antiretroviral therapy (ART). Many standard resistance genotypes exclude testing for resistance to integrase inhibitors ("IR-testing"), although this class of drugs is a component of most recommended first-line regimens. Methods: We compared the 96-week clinical outcomes and cost-effectiveness of two strategies: no IR-testing vs. IR-testing performed at HIV diagnosis...