Spike Structure Research Articles

The SARS-CoV-2 Spike Glycoprotein Biosynthesis, Structure, Function, and Antigenicity: Implications for the Design of Spike-Based Vaccine Immunogens.

The ongoing pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), poses a grave threat to global public health and imposes a severe burden on the entire human society. Like other coronaviruses, the SARS-CoV-2 genome encodes spike (S) glycoproteins, which protrude from the surface of mature virions. The S glycoprotein plays essential roles in virus attachment, fusion and entry into the host cell. Surface location of the S glycoprotein renders it a direct target for host immune responses, making it the main target of neutralizing antibodies. In the light of its crucial roles in viral infection and adaptive immunity, the S protein is the focus of most vaccine strategies as well as therapeutic interventions. In this review, we highlight and describe the recent progress that has been made in the biosynthesis, structure, function, and antigenicity of the SARS-CoV-2 S glycoprotein, aiming to provide valuable insights into the design and development of the S protein-based vaccines as well as therapeutics.

CoV3D: a database of high resolution coronavirus protein structures.

SARS-CoV-2, the etiologic agent of COVID-19, exemplifies the general threat to global health posed by coronaviruses. The urgent need for effective vaccines and therapies is leading to a rapid rise in the number of high resolution structures of SARS-CoV-2 proteins that collectively reveal a map of virus vulnerabilities. To assist structure-based design of vaccines and therapeutics against SARS-CoV-2 and other coronaviruses, we have developed CoV3D, a database and resource for coronavirus protein structures, which is updated on a weekly basis. CoV3D provides users with comprehensive sets of structures of coronavirus proteins and their complexes with antibodies, receptors, and small molecules. Integrated molecular viewers allow users to visualize structures of the spike glycoprotein, which is the major target of neutralizing antibodies and vaccine design efforts, as well as sets of spike-antibody complexes, spike sequence variability, and known polymorphisms. In order to aid structure-based design and analysis of the spike glycoprotein, CoV3D permits visualization and download of spike structures with modeled N-glycosylation at known glycan sites, and contains structure-based classification of spike conformations, generated by unsupervised clustering. CoV3D can serve the research community as a centralized reference and resource for spike and other coronavirus protein structures, and is available at: https://cov3d.ibbr.umd.edu.

Impact of glycan cloud on the B-cell epitope prediction of SARS-CoV-2 Spike protein

The SARS-CoV-2 outbreak originated in China in late 2019 and has since spread to pandemic proportions. Diagnostics, therapeutics and vaccines are urgently needed. We model the trimeric Spike protein, including flexible loops and all N-glycosylation sites, in order to elucidate accessible epitopes for antibody-based diagnostics, therapeutics and vaccine development. Based on published experimental data, six homogeneous glycosylation patterns and two heterogeneous ones were used for the analysis. The glycan chains alter the accessible surface areas on the S-protein, impeding antibody-antigen recognition. In presence of glycan, epitopes on the S1 subunit, that notably contains the receptor binding domain, remain mostly accessible to antibodies while those present on the S2 subunit are predominantly inaccessible. We identify 28 B-cell epitopes in the Spike structure and group them as non-affected by the glycan cloud versus those which are strongly masked by the glycan cloud, resulting in a list of favourable epitopes as targets for vaccine development, antibody-based therapy and diagnostics.

The Architecture of Inactivated SARS-CoV-2 with Postfusion Spikes Revealed by CryoEM and CryoET

The outbreak of SARS-CoV-2 in December 2019, led to the ongoing global pandemic of coronavirus disease 2019 (COVID‑19), which has claimed more than a half million lives in a few months. Enormous efforts are being made in developing vaccines and therapeutic treatment to fight against COVID-19. Inactivated SARS-CoV-2 viruses are currently used as vaccine candidates; therefore, it is important to understand the architecture of SARS-CoV-2. We have propagated and purified a clinical strain of SARS-CoV-2 and genetically and structurally characterized β-propiolactone inactivated viruses. We observed that the virus particles are roughly spherical or moderately pleiomorphic. Although a small fraction of prefusion spikes are observed, the majority of viral spikes appear nail-shaped resembling a postfusion state, where S1 protein of the spike has disassociated. Cryo-electron tomography and subtomogram averaging of these spikes yielded a density map which closely matches the overall structure of SARS-CoV S2 spike and their corresponding glycosylation sites. Our findings have major implications in SARS-CoV-2 vaccine design owing to the critical importance of prefusion immunogens.Funding: This work was supported by the Science and Technology Innovation Committee of Shenzhen Municipality(202002073000002), the National Institutes of Health grant P50AI150481 (P.Z.), the UK Wellcome Trust Investigator Award 206422/Z/17/Z(P.Z.), and the UK Biotechnology and Biological Sciences Research Council grant BB/S003339/1 (P.Z.). Conflict of Interest: The authors declare no competing financial or non-financial interests. Ethical Approval: The research received approval from the Research Ethics Committee of Shenzhen Third People's Hospital, China (approval number: 2020-038). The Research Ethics Committee waived the requirement informed consent before the study started because of the urgent need to collect epidemiological and clinical data. We analyzed the data anonymously.

Efficient Naphthalene Imide-Based Interface Engineering Materials for Enhancing Perovskite Photovoltaic Performance and Stability.

The ways to overcome surface charge recombination and poor interface contact are still the central challenges for the development of inorganic-organic hybrid halide perovskite solar cells (PSCs). [6,6]-Phenyl C61 butyric acid methyl ester (PCBM) is commonly employed in PSCs, but it has some disadvantages including high charge recombination and poor surface coverage. Therefore, the addition of an interfacial engineering layer showing efficient surface passivation, electron extraction, and excellent interface contact can solve the above problems. Furthermore, by employing interface engineering with a spike structure of the energy levels, the reduced energy losses are beneficial to elevating the open-circuit voltage (Voc) in PSCs. Herein, the linear naphthalene imide dimer containing an indacenodithiophene unit (IDTT2NPI) has been developed as an excellent interface engineering material to strengthen the perovskite performance. The introduction of a spike interface on the top of a methylammonium lead triiodide (MAPbI3) film resulted in a high Voc of 1.12 V with the optimal efficiency reaching 20.2%. The efficiency enhancement can be traced to the efficient surface passivation and enhanced interface contact. The mechanism of IDTT2NPI as the interface engineering layer was investigated by both experiments and theoretical calculations. This work provides a promising naphthalene imide-based interfacial material for high-efficiency and stable PSCs.

Structure of the Pandemic

During global pandemics, the spread of information needs to be faster than the spread of the virus in order to ensure the health and safety of human populations worldwide. In our current crisis, the demand for SARS-CoV-2 drugs and vaccines highlights the importance of biological targets and their three-dimensional shape. In particular, structural biology as a field was poised to quickly respond to crises due to previous experience and expertise and because of its early adoption of open access practices.

ACE2, Metformin, and COVID-19.

SummaryCOVID-19 is becoming a leading cause of mortality throughout the world, and few effective therapies are currently available. Angiotensin converting enzyme 2 (ACE2) is essential to COVID-19 pathogenesis, as the binding of SARS-CoV-2 spike protein (S protein) is required for viral entry and development of COVID-19. ACE2 regulates the protective arm of the renin-angiotensin-aldosterone system (RAAS) that endows anti-hypertensive and anti-inflammatory effects in the cardiovascular and pulmonary systems. Preclinical data suggest ACE2 might be downregulated after SARS-CoV-2 binding, and treatments that increase ACE2 may prevent cardiopulmonary injury. Development, testing, and mass production of novel ACE2 therapies may take years, whereas more effective treatments for COVID-19 are needed urgently. Metformin is a widely available anti-diabetic agent that has an excellent safety profile, and clinical and preclinical data suggest metformin may offer cardiopulmonary protection in COVID-19 via enhanced ACE2 expression.

Considerations around the SARS-CoV-2 Spike Protein with Particular Attention to COVID-19 Brain Infection and Neurological Symptoms.

Spike protein (S protein) is the virus “key” to infect cells and is able to strongly bind to the human angiotensin-converting enzyme2 (ACE2), as has been reported. In fact, Spike structure and function is known to be highly important for cell infection as well as for entering the brain. Growing evidence indicates that different types of coronaviruses not only affect the respiratory system, but they might also invade the central nervous system (CNS). However, very little evidence has been so far reported on the presence of COVID-19 in the brain, and the potential exploitation, by this virus, of the lung to brain axis to reach neurons has not been completely understood. In this Article, we assessed the SARS-CoV and SARS-CoV-2 Spike protein sequence, structure, and electrostatic potential using computational approaches. Our results showed that the S proteins of SARS-CoV-2 and SARS-CoV are highly similar, sharing a sequence identity of 77%. In addition, we found that the SARS-CoV-2 S protein is slightly more positively charged than that of SARS-CoV since it contains four more positively charged residues and five less negatively charged residues which may lead to an increased affinity to bind to negatively charged regions of other molecules through nonspecific and specific interactions. Analysis the S protein binding to the host ACE2 receptor showed a 30% higher binding energy for SARS-CoV-2 than for the SARS-CoV S protein. These results might be useful for understanding the mechanism of cell entry, blood-brain barrier crossing, and clinical features related to the CNS infection by SARS-CoV-2.

Coronavirus Disease 2019 and Hypertension: The Role of Angiotensin-Converting Enzyme 2 and the Renin-Angiotensin System.

Hypertension emerged from early reports as a potential risk factor for worse outcomes for persons with coronavirus disease 2019 (COVID-19). Among the putative links between hypertension and COVID-19 is a key counter-regulatory component of the renin-angiotensin system (RAS): angiotensin-converting enzyme 2 (ACE2). ACE2 facilitates entry of severe acute respiratory syndrome coronavirus 2, the virus responsible for COVID-19, into host cells. Because RAS inhibitors have been suggested to increase ACE2 expression, health-care providers and patients have grappled with the decision of whether to discontinue these medications during the COVID-19 pandemic. However, experimental models of analogous viral pneumonias suggest RAS inhibitors may exert protective effects against acute lung injury. We review how RAS and ACE2 biology may affect outcomes in COVID-19 through pulmonary and other systemic effects. In addition, we briefly detail the data for and against continuation of RAS inhibitors in persons with COVID-19 and summarize the current consensus recommendations from select specialty organizations.

On the structure of spikes

Spikes are an important class of 3-connected matroids. For an integer , there is a unique binary r-spike denoted by Zr. When a circuit-hyperplane of Zr is relaxed, we obtain another spike and repeating this procedure will produce other non-binary spikes. The es-splitting operation on a binary spike of rank r, may not yield a spike. In this paper, we give a necessary and sufficient condition for the es-splitting operation to construct Zr+1 directly from Zr. Indeed, all binary spikes and many of non-binary spikes of each rank can be derived from the spike Z3 by a sequence of the es-splitting operations and circuit-hyperplane relaxations.

Scale-dependent Rayleigh–Taylor dynamics with variable acceleration by group theory approach

Rayleigh–Taylor instability (RTI) has critical importance for a broad range of plasma processes, from supernovae to fusion. In most instances, RTI is driven by variable acceleration, whereas the bulk of existing studies have considered only constant and impulsive acceleration. This work focuses on RTI driven by acceleration with a power-law time-dependence. We review the existing theoretical approaches, apply the group theory approach to solve this long-standing problem, and yield the unified framework for the scale-dependent dynamics of Rayleigh–Taylor (RT) bubbles and RT spikes. For the early-time linear dynamics, we provide the dependence of RTI evolution on the acceleration parameters and the initial conditions. For the late-time nonlinear dynamics, we find a continuous family of asymptotic solutions, directly link the interface velocity to the interface morphology and the interfacial shear, derive solutions for the regular bubbles and for the singular spikes, and study the stability of these solutions. The properties of special nonlinear solutions in the RT family are scrupulously described, including the critical, Taylor, Layzer-drag, and Atwood solutions. It is shown that the fastest Atwood bubble is regular and stable, and the fastest Atwood spike is singular and unstable. The essentially multi-scale and interfacial character of RT dynamics is demonstrated. The former can be understood by viewing the RT coherent structure of bubbles and spikes as a standing wave with the growing amplitude. The latter implies that RT flow has effectively no motion of the fluids away from the interface and has intense motion of the fluids near the interface, with shear-driven vortical structures appearing at the interface. Our theory agrees with available observations and elaborates extensive benchmarks for future research and for better understanding of RT driven phenomena in plasmas.

Energy level engineering of charge selective contact and halide perovskite by modulating band offset: Mechanistic insights

Mixed cation and anion based perovskites solar cells exhibited enhanced stability under outdoor conditions, however, it yielded limited power conversion efficiency when TiO2 and Spiro-OMeTAD were employed as electron and hole transport layer (ETL/HTL) respectively. The inevitable interfacial recombination of charge carriers at ETL/perovskite and perovskite/HTL interface diminished the efficiency in planar (n-i-p) perovskite solar cells. By employing computational approach for uni-dimensional device simulator, the effect of band offset on charge recombination at both interfaces was investigated. We noted that it acquired cliff structure when the conduction band minimum of the ETL was lower than that of the perovskite, and thus maximized interfacial recombination. However, if the conduction band minimum of ETL is higher than perovskite, a spike structure is formed, which improve the performance of solar cell. An optimum value of conduction band offset allows to reach performance of 25.21%, with an open circuit voltage (Voc) of 1231 mV, a current density Jsc of 24.57 mA/cm2 and a fill factor of 83.28%. Additionally, we found that beyond the optimum offset value, large spike structure could decrease the performance. With an optimized energy level of Spiro-OMeTAD and the thickness of mixed-perovskite layer performance of 26.56% can be attained. Our results demonstrate a detailed understanding about the energy level tuning between the charge selective layers and perovskite and how the improvement in PV performance can be achieved by adjusting the energy level offset.

Bionic research on spikes based on the tractive characteristics of ostrich foot toenail

Inspired by the superior fixed and traction characteristics of ostrich foot toenails, we devised, optimized and manufactured the single structure and group arrangement of a new-style bionic spike for sprint shoes to improve athletic performance. The tractive performance of the bionic spike was tested by finite element analysis and experimental verification. The optimized single structure of the bionic spike had a top slope angle of 13° and the radius of the medial groove of 7.3 mm. Compared with the conventional conic spike, the maximal and stable extrusion resistances of the single bionic spike decreased by about 25% and 40% respectively, while the maximal and stable horizontal thrusts increased by about 16% and 10%, respectively. In addition, the arrangement of the bionic spikes was also optimized. Compared with the conventional spike group, the maximal and stable extrusion resistances of the bionic spike group decreased by 11.0% and 6.2%, respectively, while the maximal and stable horizontal thrusts increased by 20.0% and 16.0%, respectively. The current results may provide useful mechanical information that can help develop a better design of athletic shoes with the potential for advanced performance.

The immunology of COVID-19: is immune modulation an option for treatment?

SummaryIn December, 2019, an outbreak of COVID-19 emerged in Wuhan, China and quickly spread globally. As of May 7, 2020, there were 3 672 238 confirmed infections and 254 045 deaths attributed to COVID-19. Evidence has shown that there are asymptomatic carriers of COVID-19 who can transmit the disease to others. The virus incubation time shows a wide range (0–24 days) and the virus displays a high infectivity. It is therefore urgent to develop an effective therapy to treat patients with COVID-19 and to control the spread of the causative agent, severe respiratory syndrome coronavirus 2. Repurposing of approved drugs is widely adopted to fight newly emerged diseases such as COVID-19, as these drugs have known pharmacokinetic and safety profiles. As pathological examination has confirmed the involvement of immune hyperactivation and acute respiratory distress syndrome in fatal cases of COVID-19, several disease-modifying anti-rheumatic drugs (DMARDS), such as hydroxychloroquine and tocilizumab, have been proposed as potential therapies for the treatment of COVID-19. In this Review, we discuss the immunological aspects of COVID-19 and the potential implication of DMARDs in treating this disease.

SARS-CoV-2 infection of the liver directly contributes to hepatic impairment in patients with COVID-19

Background & AimsLiver enzyme abnormalities are common in patients with coronavirus disease 2019 (COVID-19). Whether or not severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can lead to liver damage per se remains unknown. Herein, we reported the clinical characteristics and liver pathological manifestations of COVID-19 patients with liver enzyme abnormalities.MethodsWe analyzed 156 patients diagnosed with COVID-19 from 2 designated centers in China and compared clinical features between patients with or without elevated aminotransferases. Postmortem liver biopsies were obtained from 2 cases who had elevated aminotransferases. We investigated the patterns of liver impairment by electron microscopy, immunohistochemistry, TUNEL assay and pathological studies.ResultsSixty-four out of 156 (41.0%) patients with COVID-19 had elevated aminotransferases. The median levels of alanine aminotransferase were 50 U/L vs. 19 U/L, respectively, aspartate aminotransferase were 45.5 U/L vs. 24 U/L, respectively in abnormal and normal aminotransferase groups. Liver enzyme abnormalities were associated with disease severity, as well as a series of laboratory tests including higher alveolar-arterial oxygen partial pressure difference, higher gamma-glutamyltransferase, lower albumin, decreased CD4+ T cells and B lymphocytes. Ultrastructural examination identified typical coronavirus particles, characterized by spike structures, in the cytoplasm of hepatocytes in 2 COVID-19 cases. SARS-CoV-2-infected hepatocytes displayed conspicuous mitochondrial swelling, endoplasmic reticulum dilatation and glycogen granule decrease. Histologically, massive hepatic apoptosis and some binuclear hepatocytes were observed. Taken together, both ultrastructural and histological evidence indicated a typical lesion of viral infection. Immunohistochemical results showed scarce CD4+ and CD8+ lymphocytes. No obvious eosinophil infiltration, cholestasis, fibrin deposition, granuloma, massive central necrosis, or interface hepatitis were observed.ConclusionsSARS-CoV-2 infection in the liver directly contributes to hepatic impairment in patients with COVID-19. Hence, a surveillance of viral clearance in liver and long-term outcome of COVID-19 is required.Lay summaryLiver enzyme abnormalities are common in patients with coronavirus disease 2019 (COVID-19). We reported the clinical characteristics and liver pathological manifestations of COVID-19 patients with elevated liver enzymes. Our findings suggested that SARS-CoV-2 infection of the liver is a crucial factor contributing to hepatic impairment in patients with COVID-19.

The Degree of Nesting between Spindles and Slow Oscillations Modulates Neural Synchrony.

Spindles and slow oscillations (SOs) both appear to play an important role in memory consolidation. Spindle and SO "nesting," or the temporal overlap between the two events, is believed to modulate consolidation. However, the neurophysiological processes modified by nesting remain poorly understood. We thus recorded activity from the primary motor cortex of 4 male sleeping rats to investigate how SO and spindles interact to modulate the correlation structure of neural firing. During spindles, primary motor cortex neurons fired at a preferred phase, with neural pairs demonstrating greater neural synchrony, or correlated firing, during spindle peaks. We found a direct relationship between the temporal proximity between SO and spindles, and changes to the distribution of neural correlations; nesting was associated with narrowing of the distribution, with a reduction in low- and high-correlation pairs. Such narrowing may be consistent with greater exploration of neural states. Interestingly, after animals practiced a novel motor task, pairwise correlations increased during nested spindles, consistent with targeted strengthening of functional interactions. These findings may be key mechanisms through which spindle nesting supports memory consolidation.SIGNIFICANCE STATEMENT Our analysis revealed changes in cortical spiking structure that followed the waxing and waning of spindles; firing rates increased, spikes were more phase-locked to spindle-band local field potential, and synchrony across units peaked during spindles. Moreover, we showed that the degree of nesting between spindles and slow oscillations modified the correlation structure across units by narrowing the distribution of pairwise correlations. Finally, we demonstrated that engaging in a novel motor task increased pairwise correlations during nested spindles. These phenomena suggest key mechanisms through which the interaction of spindles and slow oscillations may support sensorimotor learning. More broadly, this work helps link large-scale measures of population activity to changes in spiking structure, a critical step in understanding neuroplasticity across multiple scales.

Rational Vaccine Design in the Time of COVID-19

As scientists consider SARS-CoV-2 vaccine design, we discuss problems that may be encountered and how to tackle them by what we term “rational vaccine design.” We further discuss approaches to pan-coronavirus vaccines. We draw on experiences from recent research on several viruses including HIV and influenza, as well as coronaviruses.

Bearing characteristic of journal bearing applied biomimetics

Journal bearings have been improved by reducing friction and increasing stability via various methods. However, if future applications require even better performance, a new approach will be required. In this study, we aimed to improve the bearing characteristics of journal bearings by incorporating biomimetics. To that end, we applied a texture to the journal bearing that was inspired by the micro-spike structure on a dragonfly wing, and we verified its effect by measuring friction torque and shaft center locus. Furthermore, the effect of the spike structure on oil film formation was confirmed by photographing the oil film distribution through X-ray computed tomography. The results showed that the microbubbles generated by the spikes expanded the gas-phase region and reduced friction and whirling.

COVID-19, diabetes mellitus and ACE2: The conundrum

COVID-19, diabetes mellitus and ACE2: The conundrum

Structure of mouse coronavirus spike protein complexed with receptor reveals mechanism for viral entry.

Coronaviruses recognize a variety of receptors using different domains of their envelope-anchored spike protein. How these diverse receptor recognition patterns affect viral entry is unknown. Mouse hepatitis coronavirus (MHV) is the only known coronavirus that uses the N-terminal domain (NTD) of its spike to recognize a protein receptor, CEACAM1a. Here we determined the cryo-EM structure of MHV spike complexed with mouse CEACAM1a. The trimeric spike contains three receptor-binding S1 heads sitting on top of a trimeric membrane-fusion S2 stalk. Three receptor molecules bind to the sides of the spike trimer, where three NTDs are located. Receptor binding induces structural changes in the spike, weakening the interactions between S1 and S2. Using protease sensitivity and negative-stain EM analyses, we further showed that after protease treatment of the spike, receptor binding facilitated the dissociation of S1 from S2, allowing S2 to transition from pre-fusion to post-fusion conformation. Together these results reveal a new role of receptor binding in MHV entry: in addition to its well-characterized role in viral attachment to host cells, receptor binding also induces the conformational change of the spike and hence the fusion of viral and host membranes. Our study provides new mechanistic insight into coronavirus entry and highlights the diverse entry mechanisms used by different viruses.