Insights into varicella-zoster virus assembly from the B-and C-capsid at near-atomic resolution structures

Varicella-zoster is a highly communicable virus that can be transmitted through the airborne route.About one quarter of people are infected with this virus.Previous studies have described the structure of A-capsid and a blurred reconstruction of the C-capsid with icosahedral symmetry.In this study,we have determined the more precise detailed structures of the varicella-zoster virus(VZV)B-and C-capsid in icosahedral symmetry using a combination of block-based reconstruction and symmetry relaxation strategies.In addition,we are reporting structural details of the portal vertex reconstructions in five-fold symmetry and portal reconstructions in twelve-fold symmetry.The structures unveil the basis for the high thermal stability of the VZV capsid.The conformational flexibility of structural elements of the capsid plays a role in the assembly of the capsid and drives processes critical for the viral life cycle.The results of the study open up new avenues for the development of drugs against a highly prevalent and contagious pathogen.

Effect of semi-continuous water washing on the combustion behaviors of agricultural organic solid waste

Combustion of agricultural organic solid waste(AOSW)was an ideal solution for their resource utilization in view of their massive annual production and great potential for reduction of fossil fuel utilization.However,high alkali and alkaline earth metals(AAEMs)content in the feedstock can arose severe fouling and slagging issues and thus prohibiting its vast utilization.In this study,a semi-continuous water washing method was proposed to preliminarily remove AAEMs from agricultural organic solid waste and its effects on the combustion behaviors of washed solid product were investigated.Results showed that the combustion index S were improved to 2.63×10-6,over 68%of the total ashes were removed from the cotton stalk,and 96.3%,89.0%and 74.7%of K,Na and Mg were effectively removed,respectively.Moreover,the softening temperature of low temperature ash from the washed sample was as high as 1450◦C,538◦C higher than the low temperature ash from the original sample;the base acid ratio and fouling index were improved from high slagging and fouling risk(1.7 and 90.8)of the original organic solid waste to low and medium risk(0.4 and 3.5),respectively.All these results signified the contributing effect of proposed semi-continuous water washing method on the combustion of agricultural organic solid waste.In a word,this study provided a promising method for fouling and slagging inhibition during the agricultural organic solid waste combustion.

Comparing T-and B-cell responses to COVID-19 vaccines across varied immune backgrounds

The emergence of adapted variants of the SARS-CoV-2 virus has led to a surge in breakthrough infections worldwide.A recent analysis of immune responses in people who received inactivated vaccines has revealed that individuals with no prior infection have limited resistance to Omicron and its sub-lineages,while those with previous infections exhibit a significant amount of neutralizing antibodies and memory B cells.However,specific T-cell responses remain largely unaffected by the mutations,indicating that T-cell-mediated cellular immunity can still provide protection.Moreover,the administration of a third dose of vaccine has resulted in a marked increase in the spectrum and duration of neutralizing antibodies and memory B cells in vivo,which has enhanced resistance to emerging variants such as BA.2.75 and BA.2.12.1.These results highlight the need to consider booster immunization for previously infected individuals and the development of novel vaccination strategies.The rapid spread of adapted variants of the SARS-CoV-2 virus presents a significant challenge to global health.The findings from this study underscore the importance of tailoring vaccination strategies based on individual immune backgrounds and the potential need for booster shots to combat emerging variants.Continued research and development are crucial to discovering new immunization strategies that will effectively protect public health against the evolving virus.

Molecular mechanism of SCARB2-mediatec attachment and uncoating of EV71

Unlike the well-established picture for the entry of enveloped viruses, the mechanism of cellular entry of non-enveloped eukaryotic viruses remains largely mysterious. Picornaviruses are representative models for such viruses, and initiate this entry process by their functional receptors. Here we present the structural and functional studies of SCARB2, a functional receptor of the important human enterovirus 71 （EV71）. SCARB2 is responsible for attachment as well as uncoating of EV71. Differences in the structures of SCARB2 under neutral and acidic conditions reveal that SCARB2 undergoes a pivotal pH-dependent conformational change which opens a lipid-transfer tunnel to mediate the expulsion of a hydrophobic pocket factor from the virion, a pre-requisite for uncoating. We have also identified the key residues essential for attachment to SCARB2, identifying the canyon region of EV71 as mediating the receptor interaction. Together these results provide a clear understanding of cellular attachment and initiation of uncoating for enteroviruses.

The binding of a monoclonal antibody to the apical region of SCARB2 blocks EV71 infection

Entero virus 71 （EV71） causes hand, foot, and mouth disease （HFMD） and occasionally leads to severe neurological complications and even death. Scavenger receptor class B member 2 （SCARB2） is a functional receptor for EV71, that mediates viral attachment, internalization, and uncoating. However, the exact binding site of EV71 on SCARB2 is unknown. In this study, we generated a monoclonal antibody （mAb） that binds to human but not mouse SCARB2. It is named JL2, and it can effectively inhibit EV71 infection of target cells. Using a set of chimeras of human and mouse SCARB2, we identified that the region containing residues 77-113 of human SCARB2 contributes significantly to JL2 binding. The structure of the SCARB2-JL2 complex revealed that JL2 binds to the apical region of SCARB2 involving a-helices 2, 5, and 14. Our results provide new insights into the potential binding sites for EV71 on SCARB2 and the molecular mechanism of EV71 entry.

Ultrafine Sn_(4)P_(3)nanocrystals from chloride reduction on mechanically activated Na surface for sodium/lithium ion batteries

Nanostructured metal phosphides are very attractive materials in energy storage and conversion,but their applications are severely limited by complicated preparation steps,harsh conditions and large excess of highly toxic phosphorus source.Here we develop a highly efficient one-step method to synthesize Sn_(4)P_(3)nanostructure based on simultaneous reduction of SnCl_(4)and PCl_(3)on mechanically activated Na surface and in situ phosphorization.The low-toxic PCl3 displays a very high phosphorizing efficiency(100%).Furthermore,this simple method is powerful to control phosphide size.Ultrafine Sn_(4)P_(3)nanocrystals(<5 nm)supported on carbon sheets(Sn_(4)P_(3)/C)are obtained,which is due to the unique bottom-up surface-limited reaction.As the anode material for sodium/lithium ion batteries(SIBs/LIBs),the Sn_(4)P_(3)/C shows profound sodiation/lithiation extents,good phase-conversion reversibility,excellent rate performance and long cycling stability,retaining high capacities of 420 mAh/g for SIBs and 760 mAh/g for LIBs even after 400 cycles at 1.0 A/g.Combining simple and efficient preparation,low-toxic and high-efficiency phosphorus source and good control of nanosize,this method is very promising for low-cost and scalable preparation of high-performance Sn_(4)P_(3)anode.

Architecture of the herpesvirus genomepackaging complex and implications for DNA translocation

Genome packaging is a fundamental process in a viral life cycle and a prime target of antiviral drugs.Herpesviruses use an ATP-driven packaging motor/terminase complex to translocate and cleave concatemeric dsDNA into procapsids but its molecular architecture and mechanism are unknown.We report atomic structures of a herpesvirus hexameric terminase complex in both the apo and ADP·BeF3-bound states.Each subunit of the hexameric ring comprises three components-the ATPase/terminase pUL15 and two regulator/fixer proteins,pUL28 and pUL33-unlike bacteriophage terminases.Distal to the nuclease domains,six ATPase domains form a central channel with conserved basicpatches conducive to DNA binding and trans-acting arginine fingers are essential to ATP hydrolysis and sequential DNA translocation.Rearrangement of the nuclease domains mediated by regulatory domains converts DNA translocation mode to cleavage mode.Our structures favor a sequential revolution model for DNA translocation and suggest mechanisms for concerted domain rearrangements leading to DNA cleavage.

TIM-1 acts a dual-attachment receptor for Ebolavirus by interacting directly with viral GP and the PS on the viral envelope

Ebolavirus can cause hemorrhagic fever in humans with a mortality rate of 50%-90%. Currently, no approved vaccines and antiviral therapies are available. Human TIM1 is considered as an attachment factor for EBOV, enhancing viral infection through interaction with PS located on the viral envelope. However, reasons under- lying the preferable usage of hTIM-1, but not other PS binding receptors by filovirus, remain unknown. We firstly demonstrated a direct interaction between hTIM-1 and EBOV GP in vitro and determined the crystal structures of the Ig V domains of hTIM-1 and hTIM-4. The binding region in hTIM-1 to EBOV GP was mapped by chimeras and mutation assays, which were designed based on structural analysis. Pseudovirion infection assays performed using hTIM-1 and its homologs as well as point mutants verified the location of the GP binding site and the importance of EBOV GP-hTIM-1 interaction in EBOV cellular entry.

Sequential immunizations confer cross-protection against variants of SARS-CoV-2,including Omicron in Rhesus macaques

Variants of concern(VOCs)like Delta and Omicron,harbor a high number of mutations,which aid these viruses in escaping a majority of known SARS-CoV-2 neutralizing antibodies(NAbs).In this study,Rhesus macaques immunized with 2-dose inactivated vaccines(Coronavac)were boosted with an additional dose of homologous vaccine or an RBD-subunit vaccine,or a bivalent inactivated vaccine(Beta and Delta)to determine the effectiveness of sequential immunization.The booster vaccination significantly enhanced the duration and levels of neutralizing antibody titers against wild-type.

Structural and molecular basis for foot-andmouth disease virus neutralization by two potent protective antibodies

Dear Editor,Foot-and-mouth disease(FMD)is an economically devastating and highly contagious viral disease of cloven-hoofed animals with a global distribution.The causative agent,FMD virus(FMDV)is a small non-enveloped RNA virus,belonging to the Aphthoviruses genus within Picornaviridae family(Tuthill et al.,2010).Control of FMD has been largely reliant on vaccinations with inactivated virus vaccines.However,significant antigenic diversity within FMDV serotypes and inability of the vaccines to induce immune protection for a long duration of time impinge on the efficacy of available vaccines.The roles of neutralizing antibodies(NAbs)as the principal protective components of the immune responses to FMDV vaccination or infection have been well established(Pay and Hingley,1987;Juleff et al.,2009).Passive immunization of NAbs has also been demonstrated to be effective in curing FMD and many viral diseases(Harmsen et al.,2007;Qiu et al.,2018).A deep understanding of the molecular basis for viral neutralization by antibodies and the identification of key viral epitopes would aid in the development of potent rationally designed broad-spectrum vaccine.

An open conformation determined by a structural switch for 2A protease from coxsackievirus A16

Coxsackievirus A16 belongs to the family Picornaviridae,and is a major agent of hand-foot-and-mouth disease that infects mostly children,and to date no vaccines or antivi-ral therapies are available.2A protease of enterovirus is a nonstructural protein and possesses both self-cleavage activity and the ability to cleave the eukaryotic translation initiation factor 4G.Here we present the crystal structure of coxsackievirus A162A protease,which interestingly forms hexamers in crystal as well as in solution.This structure shows an open conformation,with its active site accessible,ready for substrate binding and cleav-age activity.In conjunction with a previously reported“closed”state structure of human rhinovirus 2,we were able to develop a detailed hypothesis for the conforma-tional conversion triggered by two“switcher”residues Glu88 and Tyr89 located within the bll2-cII loop.Substrate recognition assays revealed that amino acid residues P1′,P2 and P4 are essential for substrate specificity,which was verifi ed by our substrate binding model.In addition,we compared the in vitro cleavage effi ciency of 2A pro-teases from coxsackievirus A16 and enterovirus 71 upon the same substrates by fl uorescence resonance energy transfer(FRET),and observed higher protease activity of enterovirus 71 compared to that of coxsackievirus A16.In conclusion,our study shows an open conformation of coxsackievirus A162A protease and the underlying mechanisms for conformational conversion and substrate specifi city.These new insights should facilitate the future rational design of effi cient 2A protease inhibitors.

Structures of the portal vertex reveal essential protein-protein interactions for Herpesvirus assembly and maturation

Dear Editor,Herpesviridae is a large family of double-stranded DNA(dsDNA)viruses that cause a variety of human diseases ranging from cold sores and chicken pox to congenital defects,blindness and cancer(Chayavichitsilp et al.,2009;Wang et al.,2018).In the past 70 years,substantial advances in our knowledge of the molecular biology of herpesviruses have led to insights into disease pathogenesis and management.However,the mechanism for capsid assembly that requires the ordered packing of about 4,000 protein subunits into the hexons,pentons and triplexes remains elusive.It is still a puzzle how initially identical subunits adopt both hexameric and pentameric conformations in the capsid and select the correct locations needed to form closed shells of the proper size.Biochemical and genetic studies have shown that the portal is involved in initiation of capsid assembly(Newcomb et al.,2005)and functions akin to a DNA-sensor coupling genome-packaging achieved by a genome-packaging machinery-“terminase complex”(Chen et al.,2020;Yunxiang Yang,2020)with icosahedral capsid maturation(Lokareddy et al.,2017).Structural investigations of the herpesvirus portal have proven challenging due to the small size of this dodecamer,which accounts for less than 1%of the total mass of the capsid protein layer and the technical difficulties involved in resolving non-icosahedral components of such large icosahedral viruses(diameter is∼1,250Å).Efforts of many investigators over two decades have made to reconstruct the cryo-electron microscopy(cryo-EM)structure of herpesvirus portal vertex and more recently near-atomic structures of two herpesvirus(herpes simplex virus type 1(HSV-1)and Kaposi’s sarcoma-associated herpesvirus(KSHV))portal vertices were reported(McElwee et al.,2018;Gong et al.,2019;Liu et al.,2019).

A highly immunogenic live-attenuated vaccine candidate prevents SARS-CoV-2 infection and transmission in hamsters

The highly pathogenic and readily transmissible SARS-CoV-2 has caused a global coronavirus pandemic,urgently requiring effective countermeasures against its rapid expansion.All available vaccine platforms are being used to generate safe and effective COVID-19 vaccines.Here,we generated a live-attenuated candidate vaccine strain by serial passaging of a SARSCoV-2 clinical isolate in Vero cells.

Structure analysis of the extracellular domain reveals disulfide bond forming-protein properties of Mycobacterium tuberculosis Rv2969c

Disulfide bond-forming(Dsb)protein is a bacterial periplasmic protein that is essential for the correct folding and disulfide bond formation of secreted or cell wallassociated proteins.DsbA introduces disulfi de bonds into folding proteins,and is re-oxidized through interaction with its redox partner DsbB.Mycobacterium tuberculosis,a Gram-positive bacterium,expresses a DsbA-like protein(Rv2969c),an extracellular protein that has its Nterminus anchored in the cell membrane.Since Rv2969c is an essential gene,crucial for disulfi de bond formation,research of DsbA may provide a target of a new class of anti-bacterial drugs for treatment of M.tuberculosis infection.In the present work,the crystal structures of the extracellular region of Rv2969c(Mtb DsbA)were determined in both its reduced and oxidized states.The overall structure of Mtb DsbA can be divided into two domains:a classical thioredoxin-like domain with a typical CXXC active site,and anα-helical domain.It largely resembles its Escherichia coli homologue EcDsbA,however,it possesses a truncated binding groove;in addition,its active site is surrounded by an acidic,rather than hydrophobic surface.In our oxidoreductase activity assay,Mtb DsbA exhibited a different substrate specifi city when compared to EcDsbA.Moreover,structural analysis revealed a second disulfi de bond in Mtb DsbA,which is rare in the previously reported DsbA structures,and is assumed to contribute to the overall stability of Mtb DsbA.To investigate the disulphide formation pathway in M.tuberculosis,we modeled Mtb Vitamin K epoxide reductase(Mtb VKOR),a binding partner of Mtb DsbA,to Mtb DsbA.

Cross-reactivity of eight SARS-CoV-2 variants rationally predicts immunogenicity clustering in sarbecoviruses

A steep rise in Omicron reinfection cases suggests that this variant has increased immune evasion ability.To evaluate its antigenicity relationship with other variants,antisera from guinea pigs immunized with spike protein of SARS-CoV-2 variants of concern(VOCs)and variants of interest(VOIs)were cross-tested against pseudotyped variants.The neutralization activity against Omicron was markedly reduced when other VOCs or VOIs were used as immunogens,and Omicron(BA.1)-elicited sera did not efficiently neutralize the other variants.However,a Beta or Omicron booster,when administered as the 4th dose 3-months after the 3rd dose of any of the variants,could elicit broad neutralizing antibodies against all of the current variants including Omicron BA.1.Further analysis with 280 available antigen–antibody structures and quantification of immune escape from 715 reported neutralizing antibodies provide explanations for the observed differential immunogenicity.Three distinct clades predicted using an in silico algorithm for clustering of sarbecoviruses based on immune escape provide key information for rational design of vaccines.