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Molecular systems with coincident cyclic and superhelical symmetry axes have considerable advantages for materials design as they can be readily lengthened or shortened by changing the length of the constituent monomers. Among proteins, alpha-helical coiled coils have such symmetric, extendable architectures, but are limited by the relatively fixed geometry and flexibility of the helical protomers. Here we describe a systematic approach to generating modular and rigid repeat protein oligomers with coincident C2 to C8 and superhelical symmetry axes that can be readily extended by repeat propagation. From these building blocks, we demonstrate that a wide range of unbounded fibres can be systematically designed by introducing hydrophilic surface patches that force staggering of the monomers; the geometry of such fibres can be precisely tuned by varying the number of repeat units in the monomer and the placement of the hydrophilic patches.

Targeted intracellular delivery via receptor-mediated endocytosis requires the delivered cargo to escape the endosome to prevent lysosomal degradation. This can in principle be achieved by membrane lysis tightly restricted to endosomal membranes upon internalization to avoid general membrane insertion and lysis. Here, we describe the design of small monomeric proteins with buried histidine containing pH-responsive hydrogen bond networks and membrane permeating amphipathic helices. Of the 30 designs that were experimentally tested, all expressed in Escherichia coli, 13 were monomeric with the expected secondary structure, and 4 designs disrupted artificial liposomes in a pH-dependent manner. Mutational analysis showed that the buried histidine hydrogen bond networks mediate pH-responsiveness and control lysis of model membranes within a very narrow range of pH (6.0-5.5) with almost no lysis occurring at neutral pH. These tightly controlled lytic monomers could help mediate endosomal escape in designed targeted delivery platforms.

Computationally designed protein nanoparticles have recently emerged as a promising platform for the development of new vaccines and biologics. For many applications, secretion of designed nanoparticles from eukaryotic cells would be advantageous, but in practice, they often secrete poorly. Here we show that designed hydrophobic interfaces that drive nanoparticle assembly are often predicted to form cryptic transmembrane domains, suggesting that interaction with the membrane insertion machinery could limit efficient secretion. We develop a general computational protocol, the Degreaser, to design away cryptic transmembrane domains without sacrificing protein stability. The retroactive application of the Degreaser to previously designed nanoparticle components and nanoparticles considerably improves secretion, and modular integration of the Degreaser into design pipelines results in new nanoparticles that secrete as robustly as naturally occurring protein assemblies. Both the Degreaser protocol and the nanoparticles we describe may be broadly useful in biotechnological applications.

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 scaffolds1,2, 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 diphenylterazine3 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 (kcat/Km = 106 M-1 s-1) 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.

We designed a protein biosensor that uses thermodynamic coupling for sensitive and rapid detection of neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in serum. The biosensor is a switchable, caged luciferase-receptor-binding domain (RBD) construct that detects serum-antibody interference with the binding of virus RBD to angiotensin-converting enzyme 2 (ACE-2) as a proxy for neutralization. Our coupling approach does not require target modification and can better distinguish sample-to-sample differences in analyte binding affinity and abundance than traditional competition-based assays.

New variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to arise and prolong the coronavirus disease 2019 (COVID-19) pandemic. Here, we used a cell-free expression workflow to rapidly screen and optimize constructs containing multiple computationally designed miniprotein inhibitors of SARS-CoV-2. We found the broadest efficacy was achieved with a homotrimeric version of the 75-residue angiotensin-converting enzyme 2 (ACE2) mimic AHB2 (TRI2-2) designed to geometrically match the trimeric spike architecture. Consistent with the design model, in the cryo-electron microscopy structure TRI2-2 forms a tripod at the apex of the spike protein that engaged all three receptor binding domains simultaneously. TRI2-2 neutralized Omicron (B.1.1.529), Delta (B.1.617.2), and all other variants tested with greater potency than the monoclonal antibodies used clinically for the treatment of COVID-19. TRI2-2 also conferred prophylactic and therapeutic protection against SARS-CoV-2 challenge when administered intranasally in mice. Designed miniprotein receptor mimics geometrically arrayed to match pathogen receptor binding sites could be a widely applicable antiviral therapeutic strategy with advantages over antibodies in greater resistance to viral escape and antigenic drift, and advantages over native receptor traps in lower chances of autoimmune responses.

Through the efforts of many groups, a wide range of fluorescent protein reporters and sensors based on green fluorescent protein and its relatives have been engineered in recent years. Here we explore the incorporation of sensing modalities into de novo designed fluorescence-activating proteins, called mini-fluorescence-activating proteins (mFAPs), that bind and stabilize the fluorescent cis-planar state of the fluorogenic compound DFHBI. We show through further design that the fluorescence intensity and specificity of mFAPs for different chromophores can be tuned, and the fluorescence made sensitive to pH and Ca2+ for real-time fluorescence reporting. Bipartite split mFAPs enable real-time monitoring of protein-protein association and (unlike widely used split GFP reporter systems) are fully reversible, allowing direct readout of association and dissociation events. The relative ease with which sensing modalities can be incorporated and advantages in smaller size and photostability make de novo designed fluorescence-activating proteins attractive candidates for optical sensor engineering.

BACKGROUND:It is not common for people to come across a living kidney donor, let alone consider whether they would ever donate a kidney themselves while they are alive. Narrative storytelling, the sharing of first-person narratives based on lived experience, may be an important way to improve education about living donor kidney transplants (LDKTs). Developing ways to easily standardize and disseminate diverse living donor stories using digital technology could inspire more people to consider becoming living donors and reduce the kidney shortage nationally. OBJECTIVE:This paper aimed to describe the development of the Living Donation Storytelling Project, a web-based digital library of living donation narratives from multiple audiences using video capture technology. Specifically, we aimed to describe the theoretical foundation and development of the library, a protocol to capture diverse storytellers, the characteristics and experiences of participating storytellers, and the frequency with which any ethical concerns about the content being shared emerged. METHODS:This study invited kidney transplant recipients who had received LDKTs, living donors, family members, and patients seeking LDKTs to record personal stories using video capture technology by answering a series of guided prompts on their computer or smartphone and answering questions about their filming experience. The digital software automatically spliced responses to open-ended prompts, creating a seamless story available for uploading to a web-based library and posting to social media. Each story was reviewed by a transplant professional for the disclosure of protected health information (PHI), pressuring others to donate, and medical inaccuracies. Disclosures were edited. RESULTS:This study recruited diverse storytellers through social media, support groups, churches, and transplant programs. Of the 137 storytellers who completed the postsurvey, 105/137 (76.6%) were white and 99/137 (72.2%) were female. They spent 62.5 min, on average, recording their story, with a final median story length of 10 min (00:46 seconds to 32:16 min). A total of 94.8% (130/137) of storytellers were motivated by a desire to educate the public; 78.1% (107/137) were motivated to help more people become living donors; and 75.9% (104/137) were motivated to dispel myths. The ease of using the technology and telling their story varied, with the fear of being on film, emotional difficulty talking about their experiences, and some technological barriers being reported. PHI, most commonly surnames and transplant center names, was present in 62.9% (85/135) of stories and was edited out. CONCLUSIONS:With appropriate sensitivity to ensure diverse recruitment, ethical review of content, and support for storytellers, web-based storytelling platforms may be a cost-effective and convenient way to further engage patients and increase the curiosity of the public in learning more about the possibility of becoming living donors.

The plasticity of naturally occurring protein structures, which can change shape considerably in response to changes in environmental conditions, is critical to biological function. While computational methods have been used for de novo design of proteins that fold to a single state with a deep free-energy minimum [P.-S. Huang, S. E. Boyken, D. Baker, Nature 537, 320-327 (2016)], and to reengineer natural proteins to alter their dynamics [J. A. Davey, A. M. Damry, N. K. Goto, R. A. Chica, Nat. Chem. Biol. 13, 1280-1285 (2017)] or fold [P. A. Alexander, Y. He, Y. Chen, J. Orban, P. N. Bryan, Proc. Natl. Acad. Sci. U.S.A. 106, 21149-21154 (2009)], the de novo design of closely related sequences which adopt well-defined but structurally divergent structures remains an outstanding challenge. We designed closely related sequences (over 94% identity) that can adopt two very different homotrimeric helical bundle conformations-one short (∼66 Å height) and the other long (∼100 Å height)-reminiscent of the conformational transition of viral fusion proteins. Crystallographic and NMR spectroscopic characterization shows that both the short- and long-state sequences fold as designed. We sought to design bistable sequences for which both states are accessible, and obtained a single designed protein sequence that populates either the short state or the long state depending on the measurement conditions. The design of sequences which are poised to adopt two very different conformations sets the stage for creating large-scale conformational switches between structurally divergent forms.

1p36 deletion syndrome is a well-described condition with a recognizable phenotype, including cognitive impairment, seizures, and structural brain anomalies such as periventricular leukomalacia (PVL). In a large series of these individuals by Battaglia et al., "birth history was notable in 50% of the cases for varying degrees of perinatal distress." Given the potential for perinatal distress, seizures and PVL, we questioned if this disorder has clinical overlap with hypoxic ischemic encephalopathy (HIE). We reviewed the medical records of 69 individuals with 1p36 deletion to clarify the perinatal phenotype of this disorder and determine if there is evidence of perinatal distress and/or hypoxic injury. Our data provides evidence that these babies have signs of perinatal distress. The majority (59% term; 75% preterm) needed resuscitation and approximately 18% had cardiac arrest. Most had abnormal brain imaging (84% term; 73% preterm) with abnormal white matter findings in over half of patients. PVL or suggestion of "hypoxic insult" was present in 18% of term and 45% of preterm patients. In conclusion, individuals with 1p36 deletion have evidence of perinatal distress, white matter changes, and seizures, which can mimic HIE but are likely related to their underlying chromosome disorder.

Racist rhetoric blaming the Asian, Asian American, and Pacific Islander (AAAPI) community for the COVID-19 pandemic has precipitated a surge of violence against the AAAPI community in the United States, including the Atlanta mass shooting on March 16, 2021. These incidents resurfaced the ongoing racism against AAAPIs that has largely been unaddressed despite lasting almost 2 centuries. The erasure of AAAPIs' historical oppression, unique cultures, languages, immigration experiences, and contributions to scientific and social justice advancement in the United States has hindered AAAPI voices from being heard. School psychologists are ethically bound to promote equity and dismantle racism; it is imperative to increase visibility of AAAPIs' experiences across training levels (P-12 and graduate programs), settings, and systems. In this unified statement, school psychology organizations have come together to reaffirm the field's commitment to anti-racism by offering proactive strategies to effectively promote visibility and equity for AAAPI students, families, and communities.

Background: Persistent symptoms have been reported in up to 50% of the 27 million people with mild traumatic brain injuries (mTBI) every year. MRI findings are currently limited by low diagnostic and prognostic sensitivities, constraining the value of imaging in the stratification of patients following mTBI. Limbic system structures are promising brain regions in offering prognostic factors for symptom persistence following mTBI. The objective of this study was to associate volume and symmetry of limbic system structures with the presence and persistence of common symptoms in patients with mTBI. Methods: This study focused on 524 adults (aged 18–82), 58% female, with 82% injured in motor vehicle accidents and 28% reporting loss of consciousness (LOC). Magnetic resonance imaging (MRI) data included a sagittal 3D T1-weighted sequence with 1.2 mm slice thickness, with voxel sizes of 0.93 mm × 0.93 mm × 1.2 mm, obtained a median of 156 days after injury. Symptom diagnosis and persistence were collected retrospectively from patient medical records. Intracranial volume-adjusted regional volumes per side utilizing automated volumetric analysis (NeuroQuant®) were used to calculate total volume, laterality index, and side-independent asymmetry. Covariates included age, sex, LOC, and days from injury. Limbic volumetrics did not relate to symptom presentation, except the (-) association between headache presence and thalamus volume (adjusted odds ratio = 0.51, 95% confidence interval = 0.32, 0.85). Headache, balance problems, anxiety, and depression persistence was (-) associated with thalamus volume (hazard ratio (HR) 1.25 to 1.94). Longer persistence of balance problems was associated with (-) lateral orbitofrontal cortex volume (HR = 1.33) and (+) asymmetry of the hippocampus (HR = 0.27). Persistence of cognitive deficits was associated with (+) asymmetry in the caudal anterior cingulate (HR = 0.67). Depression persistence was associated with (+) asymmetry in the isthmus of the cingulate gyrus (HR = 5.39). Persistence of anxiety was associated with (-) volume of the parahippocampal gyrus (HR = 1.67), orbitofrontal cortex (HR > 1.97), and right-biased laterality of the entorhinal cortex (HR = 0.52). Conclusions: Relative volume and asymmetry of the limbic system structures in patients with mTBI are associated with the persistence of symptoms, particularly anxiety. The conclusions of this study are limited by the absence of a reference group with no mTBI. [ABSTRACT FROM AUTHOR]

There has been considerable recent progress in protein structure prediction using deep neural networks to predict inter-residue distances from amino acid sequences.sup.1-3. Here we investigate whether the information captured by such networks is sufficiently rich to generate new folded proteins with sequences unrelated to those of the naturally occurring proteins used in training the models. We generate random amino acid sequences, and input them into the trRosetta structure prediction network to predict starting residue-residue distance maps, which, as expected, are quite featureless. We then carry out Monte Carlo sampling in amino acid sequence space, optimizing the contrast (Kullback-Leibler divergence) between the inter-residue distance distributions predicted by the network and background distributions averaged over all proteins. Optimization from different random starting points resulted in novel proteins spanning a wide range of sequences and predicted structures. We obtained synthetic genes encoding 129 of the network-'hallucinated' sequences, and expressed and purified the proteins in Escherichia coli; 27 of the proteins yielded monodisperse species with circular dichroism spectra consistent with the hallucinated structures. We determined the three-dimensional structures of three of the hallucinated proteins, two by X-ray crystallography and one by NMR, and these closely matched the hallucinated models. Thus, deep networks trained to predict native protein structures from their sequences can be inverted to design new proteins, and such networks and methods should contribute alongside traditional physics-based models to the de novo design of proteins with new functions. The trRosetta neural network was used to iteratively optimise model proteins from random 100-amino-acid sequences, resulting in 'hallucinated' proteins, which when expressed in bacteria closely resembled the model structures., Author(s): Ivan Anishchenko [sup.1] [sup.2] , Samuel J. Pellock [sup.1] [sup.2] , Tamuka M. Chidyausiku [sup.1] [sup.2] , Theresa A. Ramelot [sup.3] [sup.4] , Sergey Ovchinnikov [sup.5] , Jingzhou Hao [...]

The regular arrangements of β-strands around a central axis in β-barrels and of α-helices in coiled coils contrast with the irregular tertiary structures of most globular proteins, and have fascinated structural biologists since they were first discovered. Simple parametric models have been used to design a wide range of α-helical coiled-coil structures, but to date there has been no success with β-barrels. Here we show that accurate de novo design of β-barrels requires considerable symmetry-breaking to achieve continuous hydrogen-bond connectivity and eliminate backbone strain. We then build ensembles of β-barrel backbone models with cavity shapes that match the fluorogenic compound DFHBI, and use a hierarchical grid-based search method to simultaneously optimize the rigid-body placement of DFHBI in these cavities and the identities of the surrounding amino acids to achieve high shape and chemical complementarity. The designs have high structural accuracy and bind and fluorescently activate DFHBI in vitro and in Escherichia coli, yeast and mammalian cells. This de novo design of small-molecule binding activity, using backbones custom-built to bind the ligand, should enable the design of increasingly sophisticated ligand-binding proteins, sensors and catalysts that are not limited by the backbone geometries available in known protein structures.

De novo protein design holds promise for creating small stable proteins with shapes customized to bind therapeutic targets. We describe a massively parallel approach for designing, manufacturing and screening mini-protein binders, integrating large-scale computational design, oligonucleotide synthesis, yeast display screening and next-generation sequencing. We designed and tested 22,660 mini-proteins of 37-43 residues that target influenza haemagglutinin and botulinum neurotoxin B, along with 6,286 control sequences to probe contributions to folding and binding, and identified 2,618 high-affinity binders. Comparison of the binding and non-binding design sets, which are two orders of magnitude larger than any previously investigated, enabled the evaluation and improvement of the computational model. Biophysical characterization of a subset of the binder designs showed that they are extremely stable and, unlike antibodies, do not lose activity after exposure to high temperatures. The designs elicit little or no immune response and provide potent prophylactic and therapeutic protection against influenza, even after extensive repeated dosing.

There is an increasing recognition of the importance of diagnosing genetic conditions with an ever‐growing list of genetic testing options. However, most providers do not have formal genetics training, which makes choosing the most appropriate test to order challenging. Our project sought to improve cytogenetic testing utilization in a tertiary care neonatal intensive care unit (NICU) through utilizing quality improvement techniques, specifically the Model for Improvement framework with rapid Plan‐Do‐Study‐Act cycles. Our project utilized various interventions including the implementation of a NICU genetic testing algorithm. Interventions demonstrated improvement in all areas, specifically a 92% reduction in unnecessary cytogenetic testing with improvement in the diagnostic rate. Our work also resulted in a 59% decrease in charges with an estimated projected savings of $21,000 per year. Quality improvement can minimize redundancies and inefficiencies in genetic testing in a Level IV NICU in a large tertiary care children's hospital and result in substantial cost‐savings. [ABSTRACT FROM AUTHOR]

The Atlantic mackerel (Scomber scombrus) is a migratory, small pelagic species that supports important fisheries throughout the North Atlantic Ocean. In recent decades, the majority of worldwide landings of Atlantic [...]

Research Findings: This study explored the quality of teacher-child interactions within the context of a newly developed standardized task, Teacher-Child Structured Play Task (TC-SPT). A sample of 146 teachers and 345 children participated. Children who displayed the highest disruptive behaviors within each classroom were selected to participate. Teacher-child dyads (n = 345) participated in a play session that included free play and clean-up tasks. We adapted two coding schemes to assess the quality of both teachers' and children's interactive behaviors during these two tasks. The coding schemes exhibited internal and inter-rater reliability. Significant associations with classroom-level teacher-child interactions and children's observed classroom engagement provide support for the measure's validity. Differences in teacher and child-interactive behaviors across the two tasks (free play versus clean-up) suggest that task features may affect the quality of teacher-child interactive behaviors. Practice and Policy: Examining the interactions of different teacher-child dyads within the same standardized context will allow researchers to better understand the child and teacher factors that contribute to the quality of those interactions. Thus, use of this task in future field-based research may help to assess the impact of early interventions and professional development efforts that target improvement in the quality of teacher-child interactions.

We describe a screening protocol for making clinical decisions about the fading of protective equipment worn by children with intellectual disability (ID) who injure themselves. The Protective Equipment Screening Protocol includes information sources derived from research publications and is presented in a format conducive to review and completion by treatment teams. An accompanying case report illustrates protocoldriven protective equipment fading procedures implemented with a self-injurious student. Using the screening protocol in a clinical context and research directions are discussed. [ABSTRACT FROM AUTHOR]

The current investigation tested the effectiveness of an online student research project designed to supplement traditional methods (e.g., lectures, discussions, and assigned readings) of teaching research methods in a large-enrollment Introduction to Psychology course. Over the course of the semester, students completed seven assignments, each representing a stage of the research process. Students formed hypotheses, tested their hypotheses using data from the class, interpreted their results, generated future directions, created PowerPoint slides summarizing their projects, and presented their results in a poster session. We found support for the hypothesis that the research methods intervention would lead to better performance on a research methods quiz compared to students in a nonintervention section taught by the same instructor. This intervention demonstrated that it is feasible to use project-oriented active-learning techniques to foster understanding of research methods in large classes.