Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries.

Most membrane proteins are modified by covalent addition of complex sugars through N- and O-glycosylation. Unlike proteins, glycans do not typically adopt specific secondary structures and remain very mobile, shielding potentially large fractions of protein surface. High glycan conformational freedom hinders complete structural elucidation of glycoproteins. Computer simulations may be used to model glycosylated proteins but require hundreds of thousands of computing hours on supercomputers, thus limiting routine use. Here, we describe GlycoSHIELD, a reductionist method that can be implemented on personal computers to graft realistic ensembles of glycan conformers onto static protein structures in minutes. Using molecular dynamics simulation, small-angle X-ray scattering, cryoelectron microscopy, and mass spectrometry, we show that this open-access toolkit provides enhanced models of glycoprotein structures. Focusing on N-cadherin, human coronavirus spike proteins, and gamma-aminobutyric acid receptors, we show that GlycoSHIELD can shed light on the impact of glycans on the conformation and activity of complex glycoproteins.

Reexpansion of charged nanoparticle assemblies in concentrated electrolytes.

Electrostatic forces in solutions are highly relevant to a variety of fields, ranging from electrochemical energy storage to biology. However, their manifestation in concentrated electrolytes is not fully understood, as exemplified by counterintuitive observations of colloidal stability and long-ranged repulsions in molten salts. Highly charged biomolecules, such as DNA, respond sensitively to ions in dilute solutions. Here, we use non-base-pairing DNA-coated nanoparticles (DNA-NP) to analyze electrostatic interactions in concentrated salt solutions. Despite their negative charge, these conjugates form colloidal crystals in solutions of sufficient divalent cation concentration. We utilize small-angle X-ray scattering (SAXS) to study such DNA-NP assemblies across the full accessible concentration ranges of aqueous CaCl2, MgCl2, and SrCl2 solutions. SAXS shows that the crystallinity and phases of the assembled structures vary with cation type. For all tested salts, the aggregates contract with added ions at low salinities and then begin expanding above a cation-dependent threshold salt concentration. Wide-angle X-ray scattering (WAXS) reveals enhanced positional correlations between ions in the solution at high salt concentrations. Complementary molecular dynamics simulations show that these ion-ion interactions reduce the favorability of dense ion configurations within the DNA brushes below that of the bulk solution. Measurements in solutions with lowered permittivity demonstrate a simultaneous increase in ion coupling and decrease in the concentration at which aggregate expansion begins, thus confirming the connection between these phenomena. Our work demonstrates that interactions between charged objects continue to evolve considerably into the high-concentration regime, where classical theories project electrostatics to be of negligible consequence.

Atomic resolution structure of full-length human insulin fibrils.

Patients with type 1 diabetes mellitus who are dependent on an external supply of insulin develop insulin-derived amyloidosis at the sites of insulin injection. A major component of these plaques is identified as full-length insulin consisting of the two chains A and B. While there have been several reports that characterize insulin misfolding and the biophysical properties of the fibrils, atomic-level information on the insulin fibril architecture remains elusive. We present here an atomic resolution structure of a monomorphic insulin amyloid fibril that has been determined using magic angle spinning solid-state NMR spectroscopy. The structure of the insulin monomer yields a U-shaped fold in which the two chains A and B are arranged in parallel to each other and are oriented perpendicular to the fibril axis. Each chain contains two ß-strands. We identify two hydrophobic clusters that together with the three preserved disulfide bridges define the amyloid core structure. The surface of the monomeric amyloid unit cell is hydrophobic implicating a potential dimerization and oligomerization interface for the assembly of several protofilaments in the mature fibril. The structure provides a starting point for the development of drugs that bind to the fibril surface and disrupt secondary nucleation as well as for other therapeutic approaches to attenuate insulin aggregation.

Structural and biochemical basis for regiospecificity of the flavonoid glycosyltransferase UGT95A1.

Glycosylation is a predominant strategy plants employ to fine-tune the properties of small molecule metabolites to affect their bioactivity, transport, and storage. It is also important in biotechnology and medicine as many glycosides are utilized in human health. Small molecule glycosylation is largely carried out by family 1 glycosyltransferases. Here, we report a structural and biochemical investigation of UGT95A1, a family 1 GT enzyme from Pilosella officinarum that exhibits a strong, unusual regiospecificity for the 3'-O position of flavonoid acceptor substrate luteolin. We obtained an apo crystal structure to help drive the analyses of a series of binding site mutants, revealing that while most residues are tolerant to mutations, key residues M145 and D464 are important for overall glycosylation activity. Interestingly, E347 is crucial for maintaining the strong preference for 3'-O glycosylation, while R462 can be mutated to increase regioselectivity. The structural determinants of regioselectivity were further confirmed in homologous enzymes. Our study also suggests that the enzyme contains large, highly dynamic, disordered regions. We showed that while most disordered regions of the protein have little to no implication in catalysis, the disordered regions conserved among investigated homologues are important to both the overall efficiency and regiospecificity of the enzyme. This report represents a comprehensive in-depth analysis of a family 1 GT enzyme with a unique substrate regiospecificity and may provide a basis for enzyme functional prediction and engineering.

ASCC1 structures and bioinformatics reveal a novel helix-clasp-helix RNA-binding motif linked to a two-histidine phosphodiesterase.

Activating signal co-integrator complex 1 (ASCC1) acts with ASCC-ALKBH3 complex in alkylation damage responses. ASCC1 uniquely combines two evolutionarily ancient domains: nucleotide-binding K-Homology (KH) (associated with regulating splicing, transcriptional, and translation) and two-histidine phosphodiesterase (PDE; associated with hydrolysis of cyclic nucleotide phosphate bonds). Germline mutations link loss of ASCC1 function to spinal muscular atrophy with congenital bone fractures 2 (SMABF2). Herein analysis of The Cancer Genome Atlas (TCGA) suggests ASCC1 RNA overexpression in certain tumors correlates with poor survival, Signatures 29 and 3 mutations, and genetic instability markers. We determined crystal structures of Alvinella pompejana (Ap) ASCC1 and Human (Hs) PDE domain revealing high-resolution details and features conserved over 500 million years of evolution. Extending our understanding of the KH domain Gly-X-X-Gly sequence motif, we define a novel structural Helix-Clasp-Helix (HCH) nucleotide binding motif and show ASCC1 sequence-specific binding to CGCG-containing RNA. The V-shaped PDE nucleotide binding channel has two His-Φ-Ser/Thr-Φ (HXT) motifs (Φ being hydrophobic) positioned to initiate cyclic phosphate bond hydrolysis. A conserved atypical active-site histidine torsion angle implies a novel PDE substrate. Flexible active site loop and arginine-rich domain linker appear regulatory. Small-angle X-ray scattering (SAXS) revealed aligned KH-PDE RNA binding sites with limited flexibility in solution. Quantitative evolutionary bioinformatic analyses of disease and cancer-associated mutations support implied functional roles for RNA binding, phosphodiesterase activity, and regulation. Collective results inform ASCC1's roles in transactivation and alkylation damage responses, its targeting by structure-based inhibitors, and how ASCC1 mutations may impact inherited disease and cancer.

Strategy for modeling higher-order G-quadruplex structures recalcitrant to NMR determination.

Guanine-rich nucleic acids can form intramolecularly folded four-stranded structures known as G-quadruplexes (G4s). Traditionally, G4 research has focused on short, highly modified DNA or RNA sequences that form well-defined homogeneous compact structures. However, the existence of longer sequences with multiple G4 repeats, from proto-oncogene promoters to telomeres, suggests the potential for more complex higher-order structures with multiple G4 units that might offer selective drug-targeting sites for therapeutic development. These larger structures present significant challenges for structural characterization by traditional high-resolution methods like multi-dimensional NMR and X-ray crystallography due to their molecular complexity. To address this current challenge, we have developed an integrated structural biology (ISB) platform, combining experimental and computational methods to determine self-consistent molecular models of higher-order G4s (xG4s). Here we outline our ISB method using two recent examples from our lab, an extended c-Myc promoter and long human telomere G4 repeats, that highlights the utility and generality of our approach to characterizing biologically relevant xG4s.

Possibility of two-dimensional ordering of cryptochrome 4a from European robin.

Cryptochrome (Cry) in some species could act as a quantum senser to detect the inclination angle of geomagnetic field, the function of which attributes the magnetic sensitivity of spins of unpaired electrons in radical pair (RP) in CRY generated by blue light irradiation. However, the effect of blue light on the structure and molecular behavior of Cry has not been well investigated. We conducted the size exclusion chromatography (SEC) and small-angle X-ray scattering (SAXS) analyses to inspect the molecular structure and behavior of cryptochrome 4a (ErCry4a) from European robin, a representative magnetosensory animal. The results indicated that ErCry4a could form flat-shape oligomers. Moreover, blue light irradiation induced the contraction of the ErCry4a molecule at the monomer scale and simultaneously accelerated the two-dimensional oligomerization of ErCry4a. This oligomerization may enhance the regularity of the two-dimensional arrangement of ErCry4a molecules, providing a positive effect for detecting the inclination angle.

Direct Synthesis of CuPd Icosahedra Supercrystals Studied by In Situ X-Ray Scattering.

Nanocrystal self-assembly into supercrystals provides a versatile platform for creating novel materials and devices with tailored properties. While common self-assembly strategies imply the use of purified nanoparticles after synthesis, conversion of chemical precursors directly into nanocrystals and then supercrystals in simple procedures has been rarely reported. Here, the nucleation and growth of CuPd icosahedra and their consecutive assembly into large closed-packed face-centered cubic (fcc) supercrystals are studied. To this end, the study simultaneously and in situ measures X-ray total scattering with pair distribution function analysis (TS-PDF) and small-angle X-ray scattering (SAXS). It is found that the supercrystals' formation is preceded by an intermediate dense phase of nanocrystals displaying short-range order (SRO). It is further shown that the organization of oleic acid/oleylamine surfactants into lamellar structures likely drives the emergence of the SRO phase and later of the supercrystals by reducing the volume accessible to particle diffusion. The supercrystals' formation as well as their disassembly are triggered by temperature. The study demonstrates that ordering of solvent molecules can be crucial in the direct synthesis of supercrystals. The study also provides a general approach to investigate novel preparation routes of supercrystals in situ and across several length scales via X-ray scattering.

Cyclodextrin-Induced Suppression of PEG Crystallization from the Melt in a PEG-Peptide Conjugate.

The influence of alpha-cyclodextrin (αCD) on PEG crystallization is examined for a peptide-PEG conjugate, YYKLVFF-PEG3k comprising an amyloid peptide YYKLVFF linked to PEG with molar mass 3 kg mol-1. Remarkably, differential scanning calorimetry (DSC) and simultaneous synchrotron small-angle/wide-angle X-ray scattering (SAXS/WAXS) show that crystallization of PEG is suppressed by αCD, provided that the cyclodextrin content is sufficient. A hexagonal mesophase is formed instead. The αCD threading reduces the conformational flexibility of PEG, and hence suppresses crystallization. These results show that addition of cyclodextrins can be used to tune the crystallization of peptide-polymer conjugates and potentially other polymer/biomolecular hybrids.

Developing an in situ LED irradiation system for small-angle X-ray scattering at B21, Diamond Light Source.

Beamline B21 at the Diamond Light Source synchrotron in the UK is a small-angle X-ray scattering (SAXS) beamline that specializes in high-throughput measurements via automated sample delivery systems. A system has been developed whereby a sample can be illuminated by a focused beam of light coincident with the X-ray beam. The system is compatible with the highly automated sample delivery system at the beamline and allows a beamline user to select a light source from a broad range of wavelengths across the UV and visible spectrum and to control the timing and duration of the light pulse with respect to the X-ray exposure of the SAXS measurement. The intensity of the light source has been characterized across the wavelength range enabling experiments where a quantitative measure of dose is important. Finally, the utility of the system is demonstrated via measurement of several light-responsive samples.

The Role of Alkalis in Orchestrating Uranyl-Peroxide Reactivity Leading to Direct Air Capture of Carbon Dioxide.

Spectator ions have known and emerging roles in aqueous metal-cation chemistry, respectively directing solubility, speciation, and reactivity. Here, we isolate and structurally characterize the last two metastable members of the alkali uranyl triperoxide series, the Rb+ and Cs+ salts (Cs-U1 and Rb-U1). We document their rapid solution polymerization via small-angle X-ray scattering, which is compared to the more stable Li+, Na+ and K+ analogues. To understand the role of the alkalis, we also quantify alkali-hydroxide promoted peroxide deprotonation and decomposition, which generally exhibits increasing reactivity with increasing alkali size. Cs-U1, the most unstable of the uranyl triperoxide monomers, undergoes ambient direct air capture of CO2 in the solid-state, converting to Cs4[UVIO2(CO3)3], evidenced by single-crystal X-ray diffraction, transmission electron microscopy, and Raman spectroscopy. We have attempted to benchmark the evolution of Cs-U1 to uranyl tricarbonate, which involves a transient, unstable hygroscopic solid that contains predominantly pentavalent uranium, quantified by X-ray photoelectron spectroscopy. Powder X-ray diffraction suggests this intermediate state contains a hydrous derivative of CsUVO3, where the parent phase has been computationally predicted, but not yet synthesized.

In vitro and in vivo investigation of Argiope bruennichi spider silk-based novel biomaterial for medical use.

As a natural and biocompatible material with high strength and flexibility, spider silk is frequently used in biomedical studies. In this study, the availability of Argiope bruennichi spider silk as a surgical suture material was investigated. The effects of spider silk-based and commercial sutures, with and without Aloe vera coating, on wound healing were evaluated by a rat dorsal skin flap model, postoperatively (7th and 14th days). Biochemical, hematological, histological, immunohistochemical, small angle x-ray scattering (SAXS) analyses and mechanical tests were performed. A. bruennichi silk did not show any cytotoxic effect on the L929 cell line according to MTT and LDH assays, in vitro. The silk materials did not cause any allergic reaction, infection, or systemic effect in rats according to hematological and biochemical analyses. A. bruennichi spider silk group showed a similar healing response to commercial sutures. SAXS analysis showed that the 14th-day applications of A. bruennichi spider silk and A. vera coated commercial suture groups have comparable structural results with control group. In conclusion, A. bruennichi spider silk is biocompatible in line with the parameters examined and shows a healing response similar to the commercial sutures commonly used in the skin.

Eutectic Resolves Lysolipid Paradox in Thermoresponsive Liposomes.

A better molecular understanding of the temperature-triggered drug release from lysolipid-based thermosensitive liposomes (LTSLs) is needed to overcome the recent setbacks in developing this important drug delivery system. Enhanced drug release was previously rationalized in terms of detergent-like effects of the lysolipid monostearyl lysophosphatidylcholine (MSPC), stabilizing local membrane defects upon LTSL lipid melting. This is highly surprising and here referred to as the 'lysolipid paradox,' because detergents usually induce the opposite effect─they cause leakage upon freezing, not melting. Here, we aim at better answers to (i) why lysolipid does not compromise drug retention upon storage of LTSLs in the gel phase, (ii) how lysolipids can enhance drug release from LTSLs upon lipid melting, and (iii) why LTSLs typically anneal after some time so that not all drug gets released. To this end, we studied the phase transitions of mixtures of dipalmitoylphosphatidylcholine (DPPC) and MSPC by a combination of differential scanning and pressure perturbation calorimetry and identified the phase structures with small- and wide-angle X-ray scattering (SAXS and WAXS). The key result is that LTSLs, which contain the standard amount of 10 mol % MSPC, are at a eutectic point when they release their cargo upon melting at about 41 °C. The eutectic present below 41 °C consists of a MSPC-depleted gel phase as well as small domains of a hydrocarbon chain interdigitated gel phase containing some 30 mol % MSPC. In these interdigitated domains, the lysolipid is stored safely without compromising membrane integrity. At the eutectic temperature, both the MSPC-depleted bilayer and interdigitated MSPC-rich domains melt at once to fluid bilayers, respectively. Intact, fluid membranes tolerate much less MSPC than interdigitated domains─where the latter have melted, the high local MSPC content causes transient pores. These pores allow for fast drug release. However, these pores disappear, and the membrane seals again as the MSPC distributes more evenly over the membrane so that its local concentration decreases below the pore-stabilizing threshold. We provide a pseudobinary phase diagram of the DPPC-MSPC system and structural and volumetric data for the interdigitated phase.

Characterization of mRNA Lipid Nanoparticles by Electron Density Mapping Reconstruction: X-ray Scattering with Density from Solution Scattering (DENSS) Algorithm.

PURPOSE: This study aimed to test the feasibility of using Small Angle X-ray Scattering (SAXS) coupled with Density from Solution Scattering (DENSS) algorithm to characterize the internal architecture of messenger RNA-containing lipid nanoparticles (mRNA-LNPs). METHODS: The DENSS algorithm was employed to construct a three-dimensional model of average individual mRNA-LNP. The reconstructed models were cross validated with cryogenic transmission electron microscopy (cryo-TEM), and dynamic light scattering (DLS) to assess size, morphology, and internal structure. RESULTS: Cryo-TEM and DLS complemented SAXS, revealed a core-shell mRNA-LNP structure with electron-rich mRNA-rich region at the core, surrounded by lipids. The reconstructed model, utilizing the DENSS algorithm, effectively distinguishes mRNA and lipids via electron density mapping. Notably, DENSS accurately models the morphology of the mRNA-LNPs as an ellipsoidal shape with a "bleb" architecture or a two-compartment structure with contrasting electron densities, corresponding to mRNA-filled and empty lipid compartments, respectively. Finally, subtle changes in the LNP structure after three freeze-thaw cycles were detected by SAXS, demonstrating an increase in radius of gyration (Rg) associated with mRNA leakage. CONCLUSION: Analyzing SAXS profiles based on DENSS algorithm to yield a reconstructed electron density based three-dimensional model can be a useful physicochemical characterization method in the toolbox to study mRNA-LNPs and facilitate their development.

One-pot synthesis of alginate-antimicrobial peptide nanogel.

Nanosized alginate-based particles (NAPs) were obtained in a one-pot solvent-free synthesis procedure, achieving the design of a biocompatible nanocarrier for the encapsulation of IbM6 antimicrobial peptide (IbM6). IbM6 is integrated in the nascent nanosized hydrogel self-assembly guided by electrostatic interactions and by weak interactions, typical of soft matter. The formation of the nanogel is a dynamic and complex process, which presents an interesting temporal evolution. In this work, we optimized the synthesis conditions of IbM6-NAPs based on small-angle X-ray scattering (SAXS) measurements and evaluated its time evolution over several weeks by sensing the IbM6 environment in IbM6-NAPs from photochemical experiments. Fluorescence deactivation experiments revealed that the accessibility of different quenchers to the IbM6 peptide embedded in NAPs is dependent on the aging time of the alginate network. Lifetimes measurements indicate that the deactivation paths of the excited state of the IbM6 in the nanoaggregates are reduced when compared with those exhibited by the peptide in aqueous solution, and are also dependent on the aging time of the nanosized alginate network. Finally, the entrapment of IbM6 in NAPs hinders the degradation of the peptide by trypsin, increasing its antimicrobial activity against Escherichia coli K-12 in simulated operation conditions.

A systematic study of solvation structure of asymmetric lithium salts in water.

Aqueous electrolytes are promising in large-scale energy storage applications due to intrinsic low toxicity, non-flammability, high ion conductivity, and low cost. However, pure water's narrow electrochemical stability window (ESW) limits the energy density of aqueous rechargeable batteries. Water-in-salt electrolytes (WiSE) proposal has expanded the ESW to over 3 V by changing electrolyte solvation structure. The limited solubility and WIS electrolyte crystallization have been persistent concerns for imide-based lithium salts. Asymmetric lithium salts compensate for the above flaws. However, studying the solvation structure of asymmetric salt aqueous electrolytes is rare. Here, we applied small-angle x-ray scattering (SAXS) and Raman spectroscope to reveal the solvation structure of imide-based asymmetric lithium salts. The SAXS spectra show the blue shifts of the lowerqpeak with decreased intensity as the increasing of concentration, indicating a decrease in the average distance between solvated anions. Significantly, an exponential decrease in the d-spacing as a function of concentration was observed. In addition, we also applied the Raman spectroscopy technique to study the evolutions of solvent-separated ion pairs (SSIPs), contacted ion pairs (CIPs), and aggregate ions (AGGs) in the solvation structure of asymmetric salt solutions.

SARS-CoV2 Nsp1 is a metal-dependent DNA and RNA endonuclease.

Over recent years, we have been living under a pandemic, caused by the rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV2). One of the major virulence factors of Coronaviruses is the Non-structural protein 1 (Nsp1), known to suppress the host cells protein translation machinery, allowing the virus to produce its own proteins, propagate and invade new cells. To unveil the molecular mechanisms of SARS-CoV2 Nsp1, we have addressed its biochemical and biophysical properties in the presence of calcium, magnesium and manganese. Our findings indicate that the protein in solution is a monomer and binds to both manganese and calcium, with high affinity. Surprisingly, our results show that SARS-CoV2 Nsp1 alone displays metal-dependent endonucleolytic activity towards both RNA and DNA, regardless of the presence of host ribosome. These results show Nsp1 as new nuclease within the coronavirus family. Furthermore, the Nsp1 double variant R124A/K125A presents no nuclease activity for RNA, although it retains activity for DNA, suggesting distinct binding sites for DNA and RNA. Thus, we present for the first time, evidence that the activities of Nsp1 are modulated by the presence of different metals, which are proposed to play an important role during viral infection. This research contributes significantly to our understanding of the mechanisms of action of Coronaviruses.

Small-Angle X-Ray Scattering for Macromolecular Complexes.

Small angle X-ray scattering (SAXS) is a versatile technique that can provide unique insights in the solution structure of macromolecules and their complexes, covering the size range from small peptides to complete viral assemblies. Technological and conceptual advances in the last two decades have tremendously improved the accessibility of the technique and transformed it into an indispensable tool for structural biology. In this chapter we introduce and discuss several approaches to collecting SAXS data on macromolecular complexes, including several approaches to online chromatography. We include practical advice on experimental design and point out common pitfalls of the technique.

Thermodynamic and Structural Study of Budesonide-Exogenous Lung Surfactant System.

The clinical benefits of using exogenous pulmonary surfactant (EPS) as a carrier of budesonide (BUD), a non-halogenated corticosteroid with a broad anti-inflammatory effect, have been established. Using various experimental techniques (differential scanning calorimetry DSC, small- and wide- angle X-ray scattering SAXS/WAXS, small- angle neutron scattering SANS, fluorescence spectroscopy, dynamic light scattering DLS, and zeta potential), we investigated the effect of BUD on the thermodynamics and structure of the clinically used EPS, Curosurf®. We show that BUD facilitates the Curosurf® phase transition from the gel to the fluid state, resulting in a decrease in the temperature of the main phase transition (Tm) and enthalpy (ΔH). The morphology of the Curosurf® dispersion is maintained for BUD < 10 wt% of the Curosurf® mass; BUD slightly increases the repeat distance d of the fluid lamellar phase in multilamellar vesicles (MLVs) resulting from the thickening of the lipid bilayer. The bilayer thickening (~0.23 nm) was derived from SANS data. The presence of ~2 mmol/L of Ca2+ maintains the effect and structure of the MLVs. The changes in the lateral pressure of the Curosurf® bilayer revealed that the intercalated BUD between the acyl chains of the surfactant's lipid molecules resides deeper in the hydrophobic region when its content exceeds ~6 wt%. Our studies support the concept of a combined therapy utilising budesonide-enriched Curosurf®.

Drosophila Protein Z4 Possesses ZAD Dimerization Domain.

The transcription factor Z4 (putzig) is one of the key proteins that determine the chromatin structure in Drosophila. Z4 is found at the boundaries of bands on polytene chromosomes, and the bands are currently thought to correlate with chromatin domains. Z4 is a component of a protein complex that additionally includes Chromator and BEAF-32, and a conserved domain is necessary to occur at the N end of Z4 to ensure its interaction with the two proteins. In this study, a zinc finger-associated domain (ZAD) domain was identified in Z4. The capability of dimerization was confirmed for the domain by biochemical methods. A dimer model of the domain was obtained using AlphaFold2, and the model structure was confirmed using small-angle X-ray scattering (SAXS). The dimer structure shows a fold typical of ZAD domains.