Revealing the Solution Conformation and Hydration Structure of Type I Tropocollagen Using X-ray Scattering and Molecular Dynamics Simulation.

Hydration plays a crucial role in regulating the dispersion behavior of biomolecules in water, particularly in how pH-sensitive hydration water network forms around proteins. This study explores the conformation and hydration structure of Type-I tropocollagen using small- and wide-angle X-ray scattering (SWAXS) and molecular dynamics (MD) simulations. The results reveal that tropocollagen exhibits a significant softening conformation in solution, transitioning from its rod-like structure in tissues to a worm-like conformation, characterized by a reduced radius of gyration of 50 nm and a persistent length of 34 nm.

Decoding the Biomimetic Mineralization of Metal-Organic Frameworks in Water.

This study unveils the "green" metal-organic framework (MOF) structuring mechanism by decoding proton transfer in water during ZIF-8 synthesis. Combining small- to wide-angle X-ray scattering, multiscale simulations, and quantum calculations, we reveal that the ZIF-8 early-stage nucleation and crystallization process in aqueous solution unfolds in three distinct stages. In stage I, imidazole ligands replace water in zinc-water cages, triggering an "acidity flip" that promotes proton transfer.

Structural insights into the regulation, ligand recognition, and oligomerization of bacterial STING.

The cyclic GMP-AMP synthase (cGAS)/stimulator of interferon gene (STING) signaling pathway plays a critical protective role against viral infections. Metazoan STING undergoes multilayers of regulation to ensure specific signal transduction. However, the mechanisms underlying the regulation of bacterial STING remain unclear.

An integrative approach unveils a distal encounter site for rPTPε and phospho-Src complex formation.

The structure determination of protein tyrosine phosphatase (PTP): phospho-protein complexes, which is essential to understand how specificity is achieved at the amino acid level, remains a significant challenge for protein crystallography and cryoEM due to the transient nature of binding interactions. Using rPTPεD1 and phospho-SrcKD as a model system, we have established an integrative workflow to address this problem, by means of which we generate a protein:phospho-protein complex model using predetermined protein structures, SAXS and pTyr-tailored MD simulations. Our model reveals transient protein-protein interactions between rPTPεD1 and phospho-SrcKD and is supported by three independent experimental validations.

Revealing cholesterol effects on PEGylated HSPC liposomes using AF4-MALS and simultaneous small- and wide-angle X-ray scattering.

Liposome development is of great interest owing to increasing requirements for efficient drug carriers. The structural features and thermal stability of such liposomes are crucial in drug transport and delivery. Reported here are the results of the structural characterization of PEGylated liposomes via small- and wide-angle X-ray scattering and an asymmetric flow field-flow fractionation (AF4) system coupled with differential refractive-index detection, multi-angle light scattering (MALS) and dynamic light scattering.

Structures of honeybee-infecting Lake Sinai virus reveal domain functions and capsid assembly with dynamic motions.

Understanding the structural diversity of honeybee-infecting viruses is critical to maintain pollinator health and manage the spread of diseases in ecology and agriculture. We determine cryo-EM structures of T = 4 and T = 3 capsids of virus-like particles (VLPs) of Lake Sinai virus (LSV) 2 and delta-N48 LSV1, belonging to tetraviruses, at resolutions of 2.3-2.

Condition-dependent structural collapse in the intrinsically disordered N-terminal domain of prion protein.

Prion protein is composed of a structure-unsolved N-terminal domain and a globular C-terminal domain. Under limited trypsin digestion, mouse recombinant prion protein can be cleaved into two parts at residue Lys105. Here, we termed these two fragments as the N-domain (sequence 23-105) and the C-domain (sequence 106-230).

Diatom-inspired self-assembly for silica thin sheets of perpendicular nanochannels.

Hypothesis: Multistage silicate self-organization into light-weight, high-strength, hierarchically patterned diatom frustules carries hints for innovative silica-based nanomaterials. With sodium silicate in a biomimetic sol-gel system templated by a tri-surfactant system of hexadecyltrimethylammonium bromide, sodium dodecylsulfate, and poly(oxyethylene-b-oxypropylene-b-oxyethylene) (P123), mesoporous silica nanochannel plates with perpendicular channel orientation are synthesized. The formation process, analogous to that of diatom frustules, is postulated to be directed by an oriented self-assembly of the block copolymer micelles shelled with charged catanionic surfactants upon silication.

Improving immunogenicity of influenza virus H7N9 recombinant hemagglutinin for vaccine development.

Human infections of novel avian influenza A virus (H7N9) emerged in early 2013 and caused about 40% case-fatality through 2017. Therefore, development of influenza H7N9 vaccines is critical for pandemic preparedness. Currently, there are three means of production of commercial influenza vaccines: egg-based, mammalian cell-based, and insect cell-based platforms.

Membrane Charging and Swelling upon Calcium Adsorption as Revealed by Phospholipid Nanodiscs.

Direct binding of calcium ions (Ca) to phospholipid membranes is an unclarified yet critical signaling pathway in diverse Ca-regulated cellular phenomena. Here, high-pressure-liquid-chromatography, small-angle X-ray scattering (SAXS), UV-vis absorption, and differential refractive index detections are integrated to probe Ca-binding to the zwitterionic lipid membranes in nanodiscs. The responses of the membranes upon Ca-binding, in composition and conformation, are quantified through integrated data analysis.

Homology Modeling and Molecular Dynamics Simulation Combined with X-ray Solution Scattering Defining Protein Structures of Thromboxane and Prostacyclin Synthases.

A combination of molecular dynamics (MD) simulations and X-ray scattering (SAXS) has emerged as the approach of choice for studying protein structures and dynamics in solution. This approach has potential applications for membrane proteins that neither are soluble nor form crystals easily. We explore the water-coupled dynamic structures of thromboxane synthase (TXAS) and prostacyclin synthase (PGIS) from scanning HPLC-SAXS measurements combined with MD ensemble analyses.

The intrinsically disordered N-terminal domain of galectin-3 dynamically mediates multisite self-association of the protein through fuzzy interactions.

Galectins are a family of lectins that bind β-galactosides through their conserved carbohydrate recognition domain (CRD) and can induce aggregation with glycoproteins or glycolipids on the cell surface and thereby regulate cell activation, migration, adhesion, and signaling. Galectin-3 has an intrinsically disordered N-terminal domain and a canonical CRD. Unlike the other 14 known galectins in mammalian cells, which have dimeric or tandem-repeated CRDs enabling multivalency for various functions, galectin-3 is monomeric, and its functional multivalency therefore is somewhat of a mystery.

Oligomerization process of Bcl-2 associated X protein revealed from intermediate structures in solution.

Upon apoptotic stress, Bcl-2 associated X (BAX) protein undergoes conformational changes and oligomerizes, leading to the mitochondrial membrane permeabilization and cell death. While structures of the resultant oligomer have been extensively studied, little is known about the intermediates that describe the reaction pathway from the inactive monomers to activated oligomers. Here we characterize the intermediate structures of BAX using combined small-angle X-ray scattering (SAXS) with on-line gel-filtration and electron spin resonance (ESR).

Probing the Acid-Induced Packing Structure Changes of the Molten Globule Domains of a Protein near Equilibrium Unfolding.

Using simultaneously scanning small-angle X-ray scattering (SAXS) and UV-vis absorption with integrated online size exclusion chromatography, supplemental with molecular dynamics simulations, we unveil the long-postulated global structure evolution of a model multidomain protein bovine serum albumin (BSA) during acid-induced unfolding. Our results differentiate three global packing structures of the three molten globule domains of BSA, forming three intermediates I, I, and E along the unfolding pathway. The I-I transition, overlooked in all previous studies, involves mainly coordinated reorientations across interconnected molten globule subdomains, and the transition activates a critical pivot domain opening of the protein for entering into the E form, with an unexpectedly large unfolding free energy change of -9.

Intrinsic coordination for revealing local structural changes in protein folding-unfolding.

With a deformed object of a rigid rod inside, the local dislocations may be tracked relatively easily with respect to the internal rigid rod. We apply this concept on protein folding-unfolding to track the internal structural changes of an unfolded protein in solution. Proposed here is a protein internal coordination based on the major axis X of an ellipsoidal protein and the stable intrinsic transition dipole moment μ of the protein during unfolding.

Formation of hollow silica nanospheres by reverse microemulsion.

Uniform hollow silica nanospheres (HSNs) synthesized with reverse microemulsion have great application potential as nanoreactors because enzymes or nanocatalysts can be easily encapsulated de novo in synthesis. Water-in-oil (w/o) reverse microemulsions comprising the polymeric surfactant polyoxyethylene (5) isooctylphenyl ether (Igepal CA-520), ammonia and water in a continuous oil phase (alkanes) coalesce into size-tunable silica nanoparticles via diffusion aggregation after the introduction of silica precursors. Here, we elucidate in detail the growth mechanism for silica nanoparticles via nucleation of ammonium-catalyzed silica oligomers from tetraethylorthosilicate (TEOS) and nanoporous aminopropyltrimethoxy silane (APTS) in the reverse microemulsion system.

Density and anomalous thermal expansion of deeply cooled water confined in mesoporous silica investigated by synchrotron X-ray diffraction.

A synchrotron X-ray diffraction method was used to measure the average density of water (H2O) confined in mesoporous silica materials MCM-41-S-15 and MCM-41-S-24. The average density versus temperature at atmospheric pressure of deeply cooled water is obtained by monitoring the intensity change of the MCM-41-S Bragg peaks, which is directly related to the scattering length density contrast between the silica matrix and the confined water. Within MCM-41-S-15, the pore size is small enough to prevent the crystallization at least down to 130 K.

Microstructural changes of globules in calcium-silicate-hydrate gels with and without additives determined by small-angle neutron and X-ray scattering.

The microstructure of calcium-silicate-hydrate (C-S-H) gel, a major hydrated phase of Ordinary Portland Cement, with and without polycarboxylic ether (PCE) additives is investigated by combined analyses of small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) data. The results show that these comb-shaped polymers tend to increase the size of the disk-like globules but have little influence on the thickness of the water and calcium silicate layers within the globules. As a result, the fractal packing of the globules becomes more open in the range of a few hundred nanometers, in the sense that the mass fractal dimension diminishes, since the PCE adsorption on the globules increases the repulsive force between and polydispersity of the C-S-H units.

Mesoporous silica SBA-15 sheet with perpendicular nanochannels.

Free-standing thin sheet form of mesoporous silica materials with perpendicular orientation is a much desired materials for its possible applications in catalysis, mask, and separation. A three component amphiphile system of sodium dodecyl sulfate/hexadecyltrimethylammonium bromide/pluronic-123(C(16)TMAB/SDS/P123) was employed to template the condensation of sodium silicates for the formation of SBA(⊥), a thin sheet of SBA-15 with perpendicular nanochannels. SBA(⊥) can be synthesized at SDS/C(16)TMAB=1.

Synthesis of hollow silica spheres with mesostructured shell using cationic-anionic-neutral block copolymer ternary surfactants.

Hollow silica spheres with mesostructured shells (HSSMS) were prepared with a vesicle template of cetyltrimethylammonium bromide-sodium dodecyl sulfate-Pluronic P123 (C(16)TMAB-SDS-EO(20)PO(70)EO(20)) at a SDS/C(16)TMAB ratio of 0.6-0.8 following a fast silicification in dilute silicate solution at pH approximately 5.