2-fold Axis Research Articles

Structural studies of the nucleus-like assembly of jumbo bacteriophage 201φ2-1.

The jumbo phages encode proteins that assemble to form a nucleus-like compartment in infected cells. Here we report the cryo-EM structure and biochemistry characterization of gp105, a protein that is encoded by the jumbo phage 201φ2-1 and is involved in the formation of the nucleus-like compartment in phage 201φ2-1 infected Pseudomonas chlororaphis. We found that, although most gp105 molecules are in the monomeric state in solution, a small portion of gp105 assemble to form large sheet-like assemblies and small cube-like particles. Reconstruction of the cube-like particles showed that the particle consists of six flat head-to-tail tetramers arranged into an octahedral cube. The four molecules at the contact interface of two head-to-tail tetramers are 2-fold symmetry-related and constitute a concave tetramer. Further reconstructions without applying symmetry showed that molecules in the particles around the distal ends of a 3-fold axis are highly dynamic and have the tendency to open up the assembly. Local classifications and refinements of the concave tetramers in the cube-like particle resulted in a map of the concave tetramer at a resolution of 4.09 Å. Structural analysis of the concave tetramer indicates that the N and C terminal fragments of gp105 are important for mediating the intermolecular interactions, which was further confirmed by mutagenesis studies. Biochemistry assays showed that, in solution, the cube-like particles of gp105 are liable to either disassemble to form the monomers or recruit more molecules to form the high molecular weight lattice-like assembly. We also found that monomeric gp105s can self-assemble to form large sheet-like assemblies in vitro, and the assembly of gp105 in vitro is a reversible dynamic process and temperature-dependent. Taken together, our results revealed the dynamic assembly of gp105, which helps to understand the development and function of the nucleus-like compartment assembled by phage-encoded proteins.

Antiviral Mechanisms of N-Phenyl Benzamides on Coxsackie Virus A9.

Enteroviruses are one of the most abundant groups of viruses infecting humans, and yet there are no approved antivirals against them. To find effective antiviral compounds against enterovirus B group viruses, an in-house chemical library was screened. The most effective compounds against Coxsackieviruses B3 (CVB3) and A9 (CVA9) were CL212 and CL213, two N-phenyl benzamides. Both compounds were more effective against CVA9 and CL213 gave a better EC50 value of 1 µM with high a specificity index of 140. Both drugs were most effective when incubated directly with viruses suggesting that they mainly bound to the virions. A real-time uncoating assay showed that the compounds stabilized the virions and radioactive sucrose gradient as well as TEM confirmed that the viruses stayed intact. A docking assay, taking into account larger areas around the 2-and 3-fold axes of CVA9 and CVB3, suggested that the hydrophobic pocket gives the strongest binding to CVA9 but revealed another binding site around the 3-fold axis which could contribute to the binding of the compounds. Together, our data support a direct antiviral mechanism against the virus capsid and suggest that the compounds bind to the hydrophobic pocket and 3-fold axis area resulting in the stabilization of the virion.

Evaluating the phonon-phason coupling strength of an Al-Ni-Co decagonal quasicrystal

Recently, a novel method was proposed to probe the phonon-phason coupling effect in quasicrystals, and it was applied to an Al-Pd-Mn icosahedral quasicrystal. In this study, the method was applied to an Al-Ni-Co decagonal quasicrystal with a periodic layered structure of a two-dimensional quasicrystal. We applied elastic phonon strain along a 2-fold (aperiodic) axis in the quasicrystal plane at high temperatures with active phasons. Then, the phason strain was induced to the quasicrystal, which was demonstrated by the phason momentum (G ⊥) dependences of the powder X-ray diffraction peak widths. In contrast, when we applied phonon strain along the 10-fold periodic axis, no appreciable phason strain was observed to be induced. These results present clear evidence on the presence of phonon-phason coupling in a decagonal quasicrystal. The shape and width of the powder X-ray diffraction peaks were calculated based on the generalized elasticity of quasicrystals. The absolute value of the phonon-phason coupling constant was evaluated by quantitatively comparing the calculated results with the measured diffraction peaks.

Capsid structure of a fungal dsRNA megabirnavirus reveals its previously unidentified surface architecture.

Rosellinia necatrix megabirnavirus 1-W779 (RnMBV1) is a non-enveloped icosahedral double-stranded (ds)RNA virus that infects the ascomycete fungus Rosellinia necatrix, a causative agent that induces a lethal plant disease white root rot. Herein, we have first resolved the atomic structure of the RnMBV1 capsid at 3.2 Å resolution using cryo-electron microscopy (cryo-EM) single-particle analysis. Compared with other non-enveloped icosahedral dsRNA viruses, the RnMBV1 capsid protein structure exhibits an extra-long C-terminal arm and a surface protrusion domain. In addition, the previously unrecognized crown proteins are identified in a symmetry-expanded cryo-EM model and are present over the 3-fold axes. These exclusive structural features of the RnMBV1 capsid could have been acquired for playing essential roles in transmission and/or particle assembly of the megabirnaviruses. Our findings, therefore, will reinforce the understanding of how the structural and molecular machineries of the megabirnaviruses influence the virulence of the disease-related ascomycete fungus.

Slow Magnetic Relaxation of Linear Trinuclear M(II)–Gd(III)–M(II) Complexes with D3 Point Group Symmetry (M(II) = Zn(II) and Mg(II))

Trinuclear M(II)-Gd(III)-M(II) complexes 1 (M = Zn), 2 (M = Mg), and the magnetically dilute sample 1′ were synthesized and the slow magnetization relaxation originating from Gd(III) ions was investigated in detail. These complexes are crystallographically isostructural and belong to D3 point group symmetry, with M-Gd-M arrayed on the crystallographic 3-fold axis. From the angular-resolved magnetization of a single crystal of 1, an easy-axis-type magnetic anisotropy of Gd(III) with an anisotropy parameter D of −0.21(3) K were revealed. All the complexes underwent slow relaxation under the application of an external magnetic field. The temperature dependence of the relaxation rate τ–1 differed considerably between 1′ and 1, 2 such that: for 1′,τ–1∝ T1.1 over the entire temperature range, whereas for 1 and 2, τ–1 ∝ T1.56 and τ–1 ∝ T1.49 above 3 K, respectively. The discrepancy can be attributed to the presence of competing multiple relaxation processes, such as direct and Raman processes, and at dilution, the direct process becomes faster, leading to its predominance in 1′. For 1 and 2, the larger power number (∼1.5) was attributed to the significantly greater contribution from the Raman process, which may be originated from intramolecular atomic vibrations.

Solid-state NMR spectroscopy uncovers internal dynamics of antiviral compounds.

In this study we analyzed the internal dynamics of antiviral compounds such as amantadine and rimantadine and the model compound hexamethylbenzene (HMB) using solid-state 2H NMR spectroscopy. Amantadine and rimantadine have been successfully used to treat influenza and dyskinesia, and their antiviral activity can be characterized using structural and dynamical information from solid-state 2H NMR relaxation. The relaxation data collected for a range of temperatures can be fit using analytical models for the internal dynamics of these compounds to yield physical parameters such as activation energies and diffusion constants that quantify the different modes of motion. Here, we performed quadrupolar-echo and relaxation experiments on powdered samples of deuterated amantadine, rimantadine, and HMB for temperatures between −150⁰C and 60⁰C. HMB displayed two rotational modes about its internal symmetry axes with vastly different timescales. Quadrupolar-echo spectra showed that rimantadine exhibits methyl rotation about its 3-fold axis with no rotation about the C-C axis linked to the cage, while amantadine undergoes slow rotation about the cage axis. The order parameters calculated from the residual quadrupolar couplings for all three compounds were large (>0.8), indicating restricted off-axial dynamics. Spin-lattice (T1Z) and quadrupolar-order relaxation times (T1Q) were calculated for different orientations within the polycrystalline samples. The temperature and angular dependences of these relaxation times were fit using three models: anisotropic rotational diffusion [1,2], axial diffusion, and discrete jumps, among which the anisotropic rotational diffusion model displayed universal applicability. Application of NMR relaxometry to these drugs within the membrane channel will further enable us to understand their activity and the effect of the lipid environment on their structural dynamics.

Synthesis, structural, spectroscopic and magnetic studies of tetranuclear Ni(II) and Co(II) clusters based on cyclobutyl and cyclopentyl-substituted analogues of zoledronic acid

Three discrete tetranuclear coordination compounds with formulae (H3O)+[M4(HL)3(H2O)6]–·xH2O where M = Ni(II), HL = HcbtZol3– (1a), M = Ni(II)/Co(II), HL = HcptZol3– (2a/2b) and x = 13.8, 16.8 or 10.5 for 1a, 2a and 2b, respectively, (H4cbtZol = 1-hydroxy-2-[1-(1H-imidazol-1-yl)cyclobutyl]ethylidene-1,1-diphosphonic acid, H4cptZol = 1-hydroxy-2-[1-(1H-imidazol-1-yl)cyclopentyl]ethylidene-1,1-diphosphonic acid) were hydrothermally prepared and characterized by single crystal X-ray diffraction, IR, UV-Vis-NIR, thermal analysis and magnetic studies. All the compounds crystallize in the trigonal R3¯ space group and show a propeller-shaped {M1IIM2II3O6} cores with M cations arranged into trigonal pyramid, in which the M1 ion is located in the apex while three peripheral M2 ions occupy the vertices of a triangle base. Both M1 and M2 are six-coordinate with M1 coordination octahedron slightly contracted along the 3-fold axis towards trigonal antiprism and peripheral M2 octahedrons slightly rotated towards trigonal prism. Discrete [M4(HL)3(H2O)6]– coordination units are assembled by O–H···O interactions involving hydroxyl O atom and coordinated water molecules as proton donors. Multiple lattice water molecules additionally stabilize the crystal structure through O–H···O interactions.All the compounds reveal thermal stability up to ca. 90 °C above which lattice water starts to be released. The architecture of [M4(HL)3(H2O)6]– cores remains intact up to ca. 130–140 °C.Qualitative analysis of potential paths of magnetic interactions in tetranuclear cores suggests ferromagnetic exchange with antiferromagnetic admixture.

Mapping of foot-and-mouth disease virus antigenic sites recognized by single-domain antibodies reveals different 146S particle specific sites and particle flexibility.

Vaccination with intact (146S) foot-and-mouth disease virus (FMDV) particles is used to control FMD. However, 146S particles easily dissociate into stable pentameric 12S particles which are less immunogenic. We earlier isolated several single-domain antibody fragments (VHHs) that specifically bind either 146S or 12S particles. These particle-specific VHHs are excellent tools for vaccine quality control. In this study we mapped the antigenic sites recognized by these VHHs by competition ELISAs, virus neutralization, and trypsin sensitivity of epitopes. We included two previously described monoclonal antibodies (mAbs) that are either 12S specific (mAb 13A6) or 146S specific (mAb 9). Although both are 12S specific, the VHH M3F and mAb 13A6 were found to bind independent antigenic sites. M3F recognized a non-neutralizing and trypsin insensitive site whereas mAb 13A6 recognized the trypsin sensitive VP2 N-terminus. The Asia1 146S-specific site was trypsin sensitive, neutralizing and also recognized by the VHH M8F, suggesting it involves the VP1 GH-loop. The type A 146S-specific VHHs recognized two independent antigenic sites that are both also neutralizing but trypsin insensitive. The major site was further mapped by cross-linking mass spectrometry (XL-MS) of two broadly strain reactive 146S-specific VHHs complexed to FMDV. The epitopes were located close to the 2-fold and 3-fold symmetry axes of the icosahedral virus 3D structure, mainly on VP2 and VP3, overlapping the earlier identified mAb 9 site. Since the epitopes were located on a single 12S pentamer, the 146S specificity cannot be explained by the epitope being split due to 12S pentamer dissociation. In an earlier study the cryo-EM structure of the 146S-specific VHH M170 complexed to type O FMDV was resolved. The 146S specificity was reported to be caused by an altered conformation of this epitope in 12S and 146S particles. This mechanism probably also explains the 146S-specific binding by the two type A VHHs mapped by XL-MS since their epitopes overlapped with the epitope recognized by M170. Surprisingly, residues internal in the 146S quaternary structure were also cross-linked to VHH. This probably reflects particle flexibility in solution. Molecular studies of virus-antibody interactions help to further optimize vaccines and improve their quality control.

Optical study of oriented double-Se8-ring clusters and luminescent Se2− anions in LTA at extremely high selenium loading density

Recently, LTA-Se(1–8) samples with 1–8 Se atoms per cavity (simplified unit cell, large cavity + sodalite cage) obtained via adsorption at the temperature of ∼450 °C were reported. It was shown that single Se8 or single Se12 ring are formed in the large LTA cavities, Se8/Se12 ring concentration ratio decreasing with an increase in the Se loading density. Contrary, in the present work, using Se vapour adsorption at ∼550 °C, we succeeded in encapsulation of ∼17 Se atoms per cavity (LTA-Se(17)) with a significant increase in the Se8/Se12 concentration ratio manifesting double Se8-ring cluster formation in the most of the LTA large cavities, which is a step towards cluster crystal fabrication. According to our polarization/orientation Raman spectroscopic study of LTA-Se(17) single crystals, the orientations of the Se8 and Se12 appeared to be similar to those in previously investigated LTA-Se(1–8). Importantly, luminescent Se2− anions, oriented along the LTA 4-fold axes and located in the sodalite cages, are detected via Raman polarization/orientation dependencies of LTA-Se(17). Bright Se2− light emission with a maximum at ∼1.56 eV and vibronic structure is observed in the 1.3–1.8 eV spectral range. We show that the anions experience a compression in LTA which is slightly relaxing with a decrease in temperature producing an anomalous Raman band downshift. The compression of Se2− in LTA is weaker/stronger than that in sodalite/cancrinite, luminescence band photon energy depending on its strength. High concentration of regularly arranged Se2− in LTA suggests considering LTA-Se(17) as an important novel light-emitting material.

Evidence that the liquid structure affects the nucleation of the primary metastable L12-Al3Zr in additive manufacturing

The strategy aiming at promoting the precipitation of the primary metastable L12-Al3X phase is the most widely used to refine grain size in Al alloys designed for additive manufacturing. It is generally admitted that Al grains nucleate onto the primary L12-Al3X precipitates by epitaxy resulting in a cube-cube orientation relationship. Here we report TEM observations showing clusters of precipitates of this primary L12-Al3X phase. Using Automated Crystallographic Orientation Mapping in the TEM, we show that such clusters consist of various orientations. Analysis of those clusters reveals that some orientations share common 5-fold rotational symmetry axes suggesting that they have nucleated from an icosahedral template. We conclude that Icosahedral Short Range Order (ISRO) in the liquid can play a role in the nucleation of the primary metastable L12-Al3Zr phase through the ISRO-mediated nucleation mechanism.

Structural Analysis of the Complex of Human Transthyretin with 3',5'-Dichlorophenylanthranilic Acid at 1.5 Å Resolution.

Human transthyretin (hTTR) can form amyloid deposits that accumulate in nerves and organs, disrupting cellular function. Molecules such as tafamidis that bind to and stabilize the TTR tetramer can reduce such amyloid formation. Here, we studied the interaction of VCP-6 (2-((3,5-dichlorophenyl)amino)benzoic acid) with hTTR. VCP-6 binds to hTTR with 5 times the affinity of the cognate ligand, thyroxine (T4). The structure of the hTTR:VCP-6 complex was determined by X-ray crystallography at 1.52 Å resolution. VCP-6 binds deeper in the binding channel than T4 with the 3',5'-dichlorophenyl ring binding in the 'forward' mode towards the channel centre. The dichlorophenyl ring lies along the 2-fold axis coincident with the channel centre, while the 2-carboxylatephenylamine ring of VCP-6 is symmetrically displaced from the 2-fold axis, allowing the 2-carboxylate group to form a tight intermolecular hydrogen bond with Nζ of Lys15 and an intramolecular hydrogen bond with the amine of VCP-6, stabilizing its conformation and explaining the greater affinity of VCP-6 compared to T4. This arrangement maintains optimal halogen bonding interactions in the binding sites, via chlorine atoms rather than iodine of the thyroid hormone, thereby explaining why the dichloro substitution pattern is a stronger binder than either the diiodo or dibromo analogues.

The Y430F mutant of Salmonella d-ornithine/d-lysine decarboxylase has altered stereospecificity and a putrescine allosteric activation site

Tyrosine-430 of d-ornithine/d-lysine decarboxylase (DOKDC) is located in the active site, and was suggested to be responsible for the D-stereospecificity of the enzyme. We have prepared the Y430F mutant form of Salmonella enterica serovar typhimurium DOKDC and evaluated its catalytic activity with D- and l-lysine and ornithine. The kinetic results show that the Y430F mutant has measurable decarboxylase activity with both D- and l-lysine and ornithine, which wild type DOKDC does not. Spectroscopic experiments show that these amino acids bind to form external aldimine complexes with the pyridoxal-5′-phosphate with λmax = 425 nm. In addition, we have obtained crystal structures of Y430F DOKDC bound to HEPES, putrescine, d-ornithine, d-lysine, and d-arginine. The d-amino acids bind in the crystals to form equilibrium mixtures of gem-diamine and external aldimine complexes. Furthermore, the crystal structures reveal an unexpected allosteric product activator site for putrescine located on the 2-fold axis between the two active sites. Putrescine binds by donating hydrogen bonds from the ammonium groups to Asp-361 and Gln-358 in the specificity helix of both chains. Addition of 0.1–1 mM putrescine eliminates the lag in steady state kinetics and abolishes the sigmoid kinetics. The catalytic loop was modeled with AlphaFold2, and the model shows that Glu-181 can form additional hydrogen bonds with the bound putrescine, likely stabilizing the catalytic closed conformation.

The rhombic hexecontahedron boron carbide microcrystals – crystal structure analysis

One way of boron carbide superhard particles formation is a liquid-phase reaction of M-carborane at high pressure and high temperature. Surprisingly, we found that the particles synthesized in this reaction exhibited the rhombic hexecontahedron morphology with twelve faces formed by five vertices stars (“spikey”). Electron microscopy and X-ray diffraction was applied to the study of the crystal structure of these spectacular particles with twelve 5-fold axis. Results unambiguously demonstrate no quasi-crystalline symptoms and point to the multiple cycling twinning. The decrease of the surface energy during spikey formation at high pressure and high temperature explains the specific shape of the particles.

Simplified Purification of Glycoprotein-Modified Ferritin Nanoparticles for Vaccine Development.

Ferritin-based, self-assembling protein nanoparticle vaccines are being developed against a range of viral pathogens, including SARS-CoV-2, influenza, HIV-1, and Epstein-Barr virus. However, purification of these nanoparticles is often laborious and requires customization for each potential nanoparticle vaccine. We propose that the simple insertion of a polyhistidine tag into exposed flexible loops on the ferritin surface (His-Fer) can mitigate the need for complex purifications and enable facile metal-chelate-based purification, thereby allowing for optimization of early stage vaccine candidates. Using sequence homology and computational modeling, we identify four sites that can accommodate insertion of a polyhistidine tag and demonstrate purification of both hemagglutinin-modified and SARS-CoV-2 spike-modified ferritins, highlighting the generality of the approach. A site at the 4-fold axis of symmetry enables optimal purification of both protein nanoparticles. We demonstrate improved purification through modulating the polyhistidine length and optimizing both the metal cation and the resin type. Finally, we show that purified His-Fer proteins remain multimeric and elicit robust immune responses similar to those of their wild-type counterparts. Collectively, this work provides a simplified purification scheme for ferritin-based vaccines.

Crystallographic studies of fac- and mer-isomers of Cu[1,4,7,10,13,16-hexaazacyclooctadecane]2+. Influence of counterion and crystallization solvent on crystal structure and dynamic Jahn-Teller effects. Computational studies of structures, energetics, and mechanism of mer-fac isomerization

The syntheses and crystal structures of mer- and fac-isomers of [Cu(18N6)]2+(X−)2 are reported (18 N6 = 1,4,7,10,13,16-hexaazacyclooctadecane; X− = BF4−, ClO4−, NO3−) and compared to a previously reported example (X− = Cl−). Solution structures of the [Cu(18N6)]2+ dication in MeNO2 or MeOH are shown by FT-IR to be almost exclusively mer, and simple evaporation of these solutions or crystallization using Et2O co-solvent also afford the solid mer-salts. However, using C6H6 or CCl4 as crystallization co-solvents afforded the corresponding fac-isomers of the BF4− and ClO4− salts, in which the anions and the symmetrical solvent occupy locations on the crystallographic 3-fold axis. Similar treatment of the less symmetrical NO3− salts affords the mer-isomer without inclusion of C6H6. The solid-state structures of the mer-isomers each exhibit the anticipated tetragonal Jahn-Teller distortions, with two longer Cu-N bonds. In contrast the fac-isomers all show internally identical Cu-N distances, due to a dynamic exchange between Jahn-Teller distorted structures in the crystal. Density Functional Theory (DFT) is used to provide rationalizations of these observations and to elucidate an energetically feasible mechanistic pathway for the facile interconversion of mer and fac isomers in solution.

Raman and optical absorption spectra of oriented Se8 and Se12 rings formed in zeolites: Dependence on the Se loading density

We encapsulated selenium (Se) into AFI and LTA zeolites via Se vapour adsorption at ∼450 °C and studied Raman and optical absorption spectra (RS and OAS, respectively) of zeolite single crystals with incorporated Se. At high Se loading density (D), Se8 rings are formed in the AFI channels along with Se chains. The rings are oriented by their 4-fold axis parallel to channels. Se8 is also formed in the LTA large cavities with its 4-fold axis oriented parallel to the 4-fold axis of LTA at any D up to ∼8 Se atoms per cavity (at/c). However, at D > 0.5 at/c, nearly unexplored Se12 rings oriented by their 3-fold axis parallel to the LTA 3-fold axis are formed along with Se8 in neighboring cavities. We discriminate between Se8 and Se12 rings via 1) RS frequencies; 2) RS and OAS band intensities vs. D; 3) RS band intensities vs. excitation wavelength and light polarization configuration. With an increase in D, the number of Se12 rings grows faster than that of Se8. We extract OAS of Se8 and Se12 from the experimental AFI-Se and LTA-Se OAS and show that the 3.0–3.3 eV absorption of Se12 is enhanced compared to that of Se8. This absorption is responsible for the observed resonant Raman effect of Se12 at the 514.5 nm wavelength excitation. Both LTA-confined Se8 and Se12 display rather high thermal stability.

3,4-Dicaffeoylquinic Acid from the Medicinal Plant Ilex kaushue Disrupts the Interaction Between the Five-Fold Axis of Enterovirus A-71 and the Heparan Sulfate Receptor

While infections by enterovirus A71 (EV-A71) are generally self-limiting, they can occasionally lead to serious neurological complications and death. No licensed therapies against EV-A71 currently exist. Using anti-virus-induced cytopathic effect assays, 3,4-dicaffeoylquinic acid (3,4-DCQA) from Ilex kaushue extracts was found to exert significant anti-EV-A71 activity, with a broad inhibitory spectrum against different EV-A71 genotypes. Time-of-drug-addition assays revealed that 3,4-DCQA affects the initial phase (entry step) of EV-A71 infection by directly targeting viral particles and disrupting viral attachment to host cells. Using resistant virus selection experiments, we found that 3,4-DCQA targets the glutamic acid residue at position 98 (E98) and the proline residue at position 246 (P246) in the 5-fold axis located within the VP1 structural protein. Recombinant viruses harboring the two mutations were resistant to 3,4-DCQA-elicited inhibition of virus attachment and penetration into human rhabdomyosarcoma (RD) cells. Finally, we showed that 3,4-DCQA specifically inhibited the attachment of EV-A71 to the host receptor heparan sulfate (HS), but not to the scavenger receptor class B member 2 (SCARB2) and P-selectin glycoprotein ligand-1 (PSGL1). Molecular docking analysis confirmed that 3,4-DCQA targets the 5-fold axis to form a stable structure with the E98 and P246 residues through noncovalent and van der Waals interactions. The targeting of E98 and P246 by 3,4-DCQA was found to be specific; accordingly, HS binding of viruses carrying the K242A or K244A mutations in the 5-fold axis was successfully inhibited by 3,4-DCQA.The clinical utility of 3,4-DCQA in the prevention or treatment of EV-A71 infections warrants further scrutiny. IMPORTANCE The canyon region and the 5-fold axis of the EV-A71 viral particle located within the VP1 protein mediate the interaction of the virus with host surface receptors. The three most extensively investigated cellular receptors for EV-A71 include SCARB2, PSGL1, and cell surface heparan sulfate. In the current study, a RD cell-based anti-cytopathic effect assay was used to investigate the potential broad spectrum inhibitory activity of 3,4-DCQA against different EV-A71 strains. Mechanistically, we demonstrate that 3,4-DCQA disrupts the interaction between the 5-fold axis of EV-A71 and its heparan sulfate receptor; however, no effect was seen on the SCARB2 or PSGL1 receptors. Taken together, our findings show that this natural product may pave the way to novel anti-EV-A71 therapeutic strategies.

Design of a gold clustering site in an engineered apo-ferritin cage

Water-soluble and biocompatible protein-protected gold nanoclusters (Au NCs) hold great promise for numerous applications. However, design and precise regulation of their structure at an atomic level remain challenging. Herein, we have engineered and constructed a gold clustering site at the 4-fold symmetric axis channel of the apo-ferritin cage. Using a series of X-ray crystal structures, we evaluated the stepwise accumulation process of Au ions into the cage and the formation of a multinuclear Au cluster in our designed cavity. We also disclosed the role of key residues in the metal accumulation process. X-ray crystal structures in combination with quantum chemical (QC) calculation revealed a unique Au clustering site with up to 12 Au atoms positions in the cavity. Moreover, the structure of the gold nanocluster was precisely tuned by the dosage of the Au precursor. As the gold concentration increases, the number of Au atoms position at the clustering site increases from 8 to 12, and a structural rearrangement was observed at a higher Au concentration. Furthermore, the binding affinity order of the four Au binding sites on apo-ferritin was unveiled with a stepwise increase of Au precursor concentration.

Artificial Protein Cage with Unusual Geometry and Regularly Embedded Gold Nanoparticles.

Artificial protein cages have great potential in a number of areas including cargo capture and delivery and as artificial vaccines. Here, we investigate an artificial protein cage whose assembly is triggered by gold nanoparticles. Using biochemical and biophysical methods we were able to determine both the mechanical properties and the gross compositional features of the cage which, combined with mathematical models and biophysical data, allowed the structure of the cage to be predicted. The accuracy of the overall geometrical prediction was confirmed by the cryo-EM structure determined to sub-5 Å resolution. This showed the cage to be nonregular but similar to a dodecahedron, being constructed from 12 11-membered rings. Surprisingly, the structure revealed that the cage also contained a single, small gold nanoparticle at each 3-fold axis meaning that each cage acts as a synthetic framework for regular arrangement of 20 gold nanoparticles in a three-dimensional lattice.

A Cysteine Variant at an Allosteric Site Alters MIF Dynamics and Biological Function in Homo- and Heterotrimeric Assemblies.

Macrophage migration inhibitory factor (MIF) is an inflammatory protein with various non-overlapping functions. It is not only conserved in mammals, but it is found in parasites, fish, and plants. Human MIF is a homotrimer with an enzymatic cavity between two subunits with Pro1 as a catalytic base, activates the receptors CD74, CXCR2, and CXCR4, has functional interactions in the cytosol, and is reported to be a nuclease. There is a solvent channel down its 3-fold axis with a recently identified gating residue as an allosteric site important for regulating, to different extents, the enzymatic activity and CD74 binding and signaling. In this study we explore the consequence of converting the allosteric residue Tyr99 to cysteine (Y99C) and characterize its crystallographic structure, NMR dynamics, stability, CD74 function, and enzymatic activity. In addition to the homotrimeric variant, we develop strategies for expressing and purifying a heterotrimeric variant consisting of mixed wild type and Y99C for characterization of the allosteric site to provide more insight.