The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus is causing a global pandemic, and cases continue to rise. Most infected individuals experience mildly symptomatic coronavirus ...disease 2019 (COVID-19), but it is unknown whether this can induce persistent immune memory that could contribute to immunity. We performed a longitudinal assessment of individuals recovered from mild COVID-19 to determine whether they develop and sustain multifaceted SARS-CoV-2-specific immunological memory. Recovered individuals developed SARS-CoV-2-specific immunoglobulin (IgG) antibodies, neutralizing plasma, and memory B and memory T cells that persisted for at least 3 months. Our data further reveal that SARS-CoV-2-specific IgG memory B cells increased over time. Additionally, SARS-CoV-2-specific memory lymphocytes exhibited characteristics associated with potent antiviral function: memory T cells secreted cytokines and expanded upon antigen re-encounter, whereas memory B cells expressed receptors capable of neutralizing virus when expressed as monoclonal antibodies. Therefore, mild COVID-19 elicits memory lymphocytes that persist and display functional hallmarks of antiviral immunity.
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•Longitudinal analysis of multifaceted immune memory following mild COVID-19•Antibodies capable of neutralizing virus persist for at least 3 months in most subjects•Virus-specific memory B and T cells display hallmarks of anti-viral immunity•MBCs increase in number and express antibodies capable of neutralizing SARS-CoV-2
Longitudinal analysis of immune memory following mild COVID-19 elicits memory lymphocytes that persist and display functional hallmarks of antiviral immunity.
Targeting the interaction between the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein and the human angiotensin-converting enzyme 2 (ACE2) receptor is a promising ...therapeutic strategy. We designed inhibitors using two de novo design approaches. Computer-generated scaffolds were either built around an ACE2 helix that interacts with the spike receptor binding domain (RBD) or docked against the RBD to identify new binding modes, and their amino acid sequences were designed to optimize target binding, folding, and stability. Ten designs bound the RBD, with affinities ranging from 100 picomolar to 10 nanomolar, and blocked SARS-CoV-2 infection of Vero E6 cells with median inhibitory concentration (IC
) values between 24 picomolar and 35 nanomolar. The most potent, with new binding modes, are 56- and 64-residue proteins (IC
~ 0.16 nanograms per milliliter). Cryo-electron microscopy structures of these minibinders in complex with the SARS-CoV-2 spike ectodomain trimer with all three RBDs bound are nearly identical to the computational models. These hyperstable minibinders provide starting points for SARS-CoV-2 therapeutics.
Proteins fold into unique native structures stabilized by thousands of weak interactions that collectively overcome the entropic cost of folding. Although these forces are “encoded” in the thousands ...of known protein structures, “decoding” them is challenging because of the complexity of natural proteins that have evolved for function, not stability. We combined computational protein design, next-generation gene synthesis, and a high-throughput protease susceptibility assay to measure folding and stability for more than 15,000 de novo designed miniproteins, 1000 natural proteins, 10,000 point mutants, and 30,000 negative control sequences. This analysis identified more than 2500 stable designed proteins in four basic folds—a number sufficient to enable us to systematically examine how sequence determines folding and stability in uncharted protein space. Iteration between design and experiment increased the design success rate from 6% to 47%, produced stable proteins unlike those found in nature for topologies where design was initially unsuccessful, and revealed subtle contributions to stability as designs became increasingly optimized. Our approach achieves the long-standing goal of a tight feedback cycle between computation and experiment and has the potential to transform computational protein design into a data-driven science.
De novo enzyme design has sought to introduce active sites and substrate-binding pockets that are predicted to catalyse a reaction of interest into geometrically compatible native scaffolds
, but has ...been limited by a lack of suitable protein structures and the complexity of native protein sequence-structure relationships. Here we describe a deep-learning-based 'family-wide hallucination' approach that generates large numbers of idealized protein structures containing diverse pocket shapes and designed sequences that encode them. We use these scaffolds to design artificial luciferases that selectively catalyse the oxidative chemiluminescence of the synthetic luciferin substrates diphenylterazine
and 2-deoxycoelenterazine. The designed active sites position an arginine guanidinium group adjacent to an anion that develops during the reaction in a binding pocket with high shape complementarity. For both luciferin substrates, we obtain designed luciferases with high selectivity; the most active of these is a small (13.9 kDa) and thermostable (with a melting temperature higher than 95 °C) enzyme that has a catalytic efficiency on diphenylterazine (k
/K
= 10
M
s
) comparable to that of native luciferases, but a much higher substrate specificity. The creation of highly active and specific biocatalysts from scratch with broad applications in biomedicine is a key milestone for computational enzyme design, and our approach should enable generation of a wide range of luciferases and other enzymes.
Objective
Atypical anorexia nervosa (AAN) is defined by the symptoms of anorexia nervosa in the presence of “significant weight loss” in individuals who are not underweight. Description of current ...weight in AAN has been limited, significant weight loss has not been defined, and the distinction between having AAN versus having weight suppression has not been examined.
Method
Secondary analyses were conducted with data from an epidemiological study of women (n = 1,640) and men (n = 794). Three definitions of significant weight loss (5, 10, and 15%) for AAN were tested in comparisons with controls and a DSM‐5 eating disorder group (DSM‐5 ED) on measures of eating pathology and clinical significance using ANCOVA and logistic regression, controlling for age and body mass index. Secondary analyses compared AAN to a weight suppressed group (WS‐only) and a cognitive concerns group (COG‐only).
Results
Across weight loss thresholds, ≥25% of adults with AAN were currently overweight/obese. At the 5% and 10% definitions, AAN was associated with elevated eating pathology and distress relative to controls, WS‐only, and COG‐only in women and men. Women with AAN endorsed less eating pathology and distress than DSM‐5 ED at some weight loss definitions, whereas men with AAN did not differ from DSM‐5 ED in eating pathology or distress.
Discussion
Results support that even a 5% weight loss, combined with cognitive concerns, may produce a group with a clinically significant eating disorder. AAN was observed in both healthy weight and overweight/obese adults, highlighting the importance of screening for restrictive eating disorders at all weights.
To create new enzymes and biosensors from scratch, precise control over the structure of small-molecule binding sites is of paramount importance, but systematically designing arbitrary protein pocket ...shapes and sizes remains an outstanding challenge. Using the NTF2-like structural superfamily as a model system, we developed an enumerative algorithm for creating a virtually unlimited number of de novo proteins supporting diverse pocket structures. The enumerative algorithm was tested and refined through feedback from two rounds of large-scale experimental testing, involving in total the assembly of synthetic genes encoding 7,896 designs and assessment of their stability on yeast cell surface, detailed biophysical characterization of 64 designs, and crystal structures of 5 designs. The refined algorithm generates proteins that remain folded at high temperatures and exhibit more pocket diversity than naturally occurring NTF2-like proteins. We expect this approach to transform the design of smallmolecule sensors and enzymes by enabling the creation of binding and active site geometries much more optimal for specific design challenges than is accessible by repurposing the limited number of naturally occurring NTF2-like proteins.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission leads to the emergence of variants, including the B.1.617.2 (Delta) variant of concern that is causing a new wave of ...infections and has become globally dominant. We show that these variants dampen the in vitro potency of vaccine-elicited serum neutralizing antibodies and provide a structural framework for describing their immune evasion. Mutations in the B.1.617.1 (Kappa) and Delta spike glycoproteins abrogate recognition by several monoclonal antibodies via alteration of key antigenic sites, including remodeling of the Delta amino-terminal domain. The angiotensin-converting enzyme 2 binding affinities of the Kappa and Delta receptor binding domains are comparable to the Wuhan-Hu-1 isolate, whereas B.1.617.2+ (Delta+) exhibits markedly reduced affinity.
Respiratory syncytial virus (RSV) is a worldwide public health concern for which no vaccine is available. Elucidation of the prefusion structure of the RSV F glycoprotein and its identification as ...the main target of neutralizing antibodies have provided new opportunities for development of an effective vaccine. Here, we describe the structure-based design of a self-assembling protein nanoparticle presenting a prefusion-stabilized variant of the F glycoprotein trimer (DS-Cav1) in a repetitive array on the nanoparticle exterior. The two-component nature of the nanoparticle scaffold enabled the production of highly ordered, monodisperse immunogens that display DS-Cav1 at controllable density. In mice and nonhuman primates, the full-valency nanoparticle immunogen displaying 20 DS-Cav1 trimers induced neutralizing antibody responses ∼10-fold higher than trimeric DS-Cav1. These results motivate continued development of this promising nanoparticle RSV vaccine candidate and establish computationally designed two-component nanoparticles as a robust and customizable platform for structure-based vaccine design.
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•Design of a self-assembling protein immunogen displaying 20 copies of prefusion RSV F•In vitro assembly yields highly ordered immunogens with tunable antigen density•The nanoparticle immunogens induce potent neutralizing antibody responses•Fusion of DS-Cav1 to the trimeric nanoparticle subunit stabilizes the antigen
A computationally designed self-assembling nanoparticle that displays 20 copies of a trimeric viral protein induces potent neutralizing antibody responses.
The COVID-19 pandemic has completely disrupted and possibly permanently changed the way humans travel. In Puerto Rico, major travel restrictions to the island have persisted at different levels since ...March 2020, which heavily influenced residents' travel behaviors. However, it remains unclear about how big the impact is and how inequitable it might be. The goal of this study is to evaluate COVID-19's impacts on Puerto Rican's travel behaviors by analyzing travel flows from Puerto Rico to the contiguous US with a modified gravity model. The roles of socioeconomic factors regarding the Puerto Rican travelers and COVID-19 factors regarding the destination US states have been assessed. COVID-19 was a strong deterring factor of travel at the beginning of the pandemic and also in the winter of 2020, but it did not keep Puerto Ricans from traveling during the summer 2020 when most travel restrictions were lifted. We found that the elderly population of Puerto Rico, despite being more vulnerable to COVID-19, were much more likely to travel during the pandemic. We also found that, during the holiday season in 2020, some socioeconomically disadvantaged populations were more likely to be traveling, a direct contradiction to their travel flows the year prior. These findings shed light on about how disproportionately affected populations behavior changed from pre-pandemic to after the pandemic started. With the continuance of the pandemic, this information is extremely valuable for future planning with respect to emergency management, travel regulation, and social benefit.
Specificity of interactions between two DNA strands, or between protein and DNA, is often achieved by varying bases or side chains coming off the DNA or protein backbone-for example, the bases ...participating in Watson-Crick pairing in the double helix, or the side chains contacting DNA in TALEN-DNA complexes. By contrast, specificity of protein-protein interactions usually involves backbone shape complementarity
, which is less modular and hence harder to generalize. Coiled-coil heterodimers are an exception, but the restricted geometry of interactions across the heterodimer interface (primarily at the heptad a and d positions
) limits the number of orthogonal pairs that can be created simply by varying side-chain interactions
. Here we show that protein-protein interaction specificity can be achieved using extensive and modular side-chain hydrogen-bond networks. We used the Crick generating equations
to produce millions of four-helix backbones with varying degrees of supercoiling around a central axis, identified those accommodating extensive hydrogen-bond networks, and used Rosetta to connect pairs of helices with short loops and to optimize the remainder of the sequence. Of 97 such designs expressed in Escherichia coli, 65 formed constitutive heterodimers, and the crystal structures of four designs were in close agreement with the computational models and confirmed the designed hydrogen-bond networks. In cells, six heterodimers were fully orthogonal, and in vitro-following mixing of 32 chains from 16 heterodimer designs, denaturation in 5 M guanidine hydrochloride and reannealing-almost all of the interactions observed by native mass spectrometry were between the designed cognate pairs. The ability to design orthogonal protein heterodimers should enable sophisticated protein-based control logic for synthetic biology, and illustrates that nature has not fully explored the possibilities for programmable biomolecular interaction modalities.
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