Evolving cellular automata schemes for protein folding modeling using the Rosetta atomic representation

Protein folding is the dynamic process by which a protein folds into its final native structure. This is different to the traditional problem of the prediction of the final protein structure, since it requires a modeling of how protein components interact over time to obtain the final folded structure. In this study we test whether a model of the folding process can be obtained exclusively through machine learning. To this end, protein folding is considered as an emergent process and the cellular automata tool is used to model the folding process. A neural cellular automaton is defined, using a connectionist model that acts as a cellular automaton through the protein chain to define the dynamic folding. Differential evolution is used to automatically obtain the optimized neural cellular automata that provide protein folding. We tested the methods with the Rosetta coarse-grained atomic model of protein representation, using different proteins to analyze the modeling of folding and the structure refinement that the modeling can provide, showing the potential advantages that such methods offer, but also difficulties that arise.

Miniaturized Dual-Band Bandpass Filter Using T-Shaped Line Based on Stepped Impedance Resonator with Meander Line and Folded Structure

A stepped impedance resonator (SIR) is suitable for designing a dual-band bandpass filter (BPF) that can be adjusted to reject spurious bands. A BPF is proposed using an SIR T-shaped meander line and folded structure. The BPF mainly comprises a meander line, a folded structure, and a T-shaped line. A novel BPF is used for the T-shaped line, which operates as a band-stop filter connecting to the center of the BPF. As a result, the complete BPF enables dual-band operation. The insertion and return losses of the first frequency passband (f01) are 0.024 and 17.3 dB, respectively, with a bandwidth of 46% at a center frequency of 2.801 GHz (2.2–3.48 GHz). The insertion and return losses of the second frequency passband (f02) are 0.026 and 17.2 dB, respectively, with a bandwidth of 10% at a center frequency of 4.351 GHz (4.13–4.55 GHz). The proposed BPF provides low loss, a simple structure, and a small size of only 4.29 × 4.08 mm, and it can be integrated into mobile communications systems.

POINTS IN A FOLD

When a page, represented by the interval $[0,1],$ is folded right over left $ n$ times, the right-hand fold contains a sequence of points. We specify these points and the order in which they appear in each fold. We also determine exactly where in the folded structure any point in $[0,1]$ appears and, given any point on the bottom line of the structure, which point lies at each level above it.

Aptamer Conjugated Indium Phosphide Quantum Dots with a Zinc Sulphide Shell as Photoluminescent Labels for Acinetobacter baumannii

Acinetobacter baumannii is a remarkable microorganism known for its diversity of habitat and its multi-drug resistance, resulting in hard-to-treat infections. Thus, a sensitive method for the identification and detection of Acinetobacter baumannii is vital. However, current methods used for the detection of pathogens have not improved in the past decades and suffer from long process times and low detection limits. A cheap, quick, and easy detection mechanism is needed. In this work, we successfully prepared indium phosphide quantum dots with a zinc sulphide shell, conjugated to a targeting aptamer ligand, to specifically label Acinetobacter baumannii. The system retained both the photophysical properties of the quantum dots and the folded structure and molecular recognition function of the aptamer, therefore successfully targeting Acinetobacter baumannii. Confocal microscopy and transmission electron microscopy showed the fluorescent quantum dots surrounding the Acinetobacter baumannii cells confirming the specificity of the aptamer conjugated to indium phosphide quantum dots with a zinc sulphide shell. Controls were undertaken with a different bacteria species, showing no binding of the aptamer conjugated quantum dots. Our strategy offers a novel method to detect bacteria and engineer a scalable platform for fluorescence detection, therefore improving current methods and allowing for better treatment.

Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants

Glycan-masking the vaccine antigen by mutating the undesired antigenic sites with an additional N-linked glycosylation motif can refocus B-cell responses to desired epitopes, without affecting the antigen’s overall-folded structure. This study examined the impact of glycan-masking mutants of the N-terminal domain (NTD) and receptor-binding domain (RBD) of SARS-CoV-2, and found that the antigenic design of the S protein increases the neutralizing antibody titers against the Wuhan-Hu-1 ancestral strain and the recently emerged SARS-CoV-2 variants Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617.2). Our results demonstrated that the use of glycan-masking Ad-S-R158N/Y160T in the NTD elicited a 2.8-fold, 6.5-fold, and 4.6-fold increase in the IC-50 NT titer against the Alpha (B.1.1.7), Beta (B.1.351) and Delta (B.1.617.2) variants, respectively. Glycan-masking of Ad-S-D428N in the RBD resulted in a 3.0-fold and 2.0-fold increase in the IC-50 neutralization titer against the Alpha (B.1.1.7) and Beta (B.1.351) variants, respectively. The use of glycan-masking in Ad-S-R158N/Y160T and Ad-S-D428N antigen design may help develop universal COVID-19 vaccines against current and future emerging SARS-CoV-2 variants.

Mesoscopic Quantification of Cortical Architecture in the Living Human Brain

Mesoscopic (0.1-0.5 mm) interrogation of the living human brain is critical for a comprehensive understanding of brain structure and function. However, in vivo techniques for mesoscopic imaging have been hampered by the sensitivity challenges of acquiring data at very high resolutions and the lack of analysis tools that can retain fine-scale detail while also accurately positioning measurements relative to the complex folded structure of the cerebral cortex. Here, we present an experimental dataset in which we image the anatomical structure of the visual and auditory cortices of five participants at 0.35 × 0.35 × 0.35 mm3 resolution. To analyze this challenging dataset, we design and implement two sets of novel methodology: a method for mitigating imaging artifacts related to blood motion and a suite of software tools for accurate quantification and visualization of the mesoscopic structure of the cortical surface. Applying these methods, we demonstrate the ability to clearly identify structures that are visible only at the mesoscopic scale, including cortical layers and intracortical blood vessels. We freely share our dataset and tools with the research community, thereby enabling investigations of fine-scale neurobiological structures in both the current and future datasets. Overall, our results demonstrate the viability of mesoscopic imaging as a quantitative tool for studying the living human brain.

Glycan-masking spike antigen in NTD and RBD elicits broadly neutralizing antibodies against SARS-CoV-2 variants

Glycan-masking the vaccine antigen by mutating the undesired antigenic sites with an additional N-linked glycosylation motif can refocus B-cell responses to desired/undesired epitopes, without affecting the antigen overall-folded structure. This study examine the impact of glycan-masking mutants of the N-terminal domain (NTD) and receptor-binding domain (RBD) of SARS-CoV-2, and found that the antigenic design of the S protein increases the neutralizing antibody titers against the Wuhan-Hu-1 ancestral strain and the recently emerged SARS-CoV-2 variants Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617.2). Our results demonstrated that the use of glycan-masking Ad-S-R158N-Y160T in the NTD elicited a 2.8-fold, 6.5-fold, and 4.6-fold increase in the IC-50 NT titer against the Alpha (B.1.1.7), Beta (B.1.351) and Delta (B.1.617.2) variants, respectively. Glycan-masking of Ad-S-D428N in the RBD resulted in a 3.0-fold and 2.0-fold increase in the IC50 neutralization titer against the Alpha (B.1.1.7) and Beta (B.1.351) variants, respectively. The use of glycan-masking in Ad-S-R158N-Y160T and Ad-S-D428N antigen design may help develop universal COVID-19 vaccines against current and future emerging SARS-CoV-2 variants.

The deep structure of the Salair fold-cover structure according to magnetotelluric studies

The results of magnetotelluric studies (MTS) performed within the Salair cover-folded structure on two profiles are considered: the Zabrodino village – the Rodnikovy village (1) and the Smaznevo village – the Kotino village (2). The profiles are oriented crosswise along the main structures and intersect Salair and the western part of the Kuznetskiy trough. The analysis of the obtained data showed that a subhorizontal underlying conducting zone is distinguished in the Earth’s crust of the Salair fold-cover structure, such zone is typical for intracontinental orogens. The zone is considered as a deep separation failure. The nature of the electrical resistance values distribution confirms the presence of the Salair thrust on the Kuznetskiy deflection. The Alambay ophiolite zone on the geoelectric section corresponds to a highly gradient region, indicating the suture zone of this structure. High resistivity values in the northern part of the Khmelevskoy trough are associated with the widespread development of granitoid massifs that are not covered by erosion.

Optimised production of disulfide-bonded fungal effectors in E. coli using CyDisCo and FunCyDisCo co-expression approaches

Effectors are a key part of the arsenal of plant pathogenic fungi and promote pathogen virulence and disease. Effectors typically lack sequence similarity to proteins with known functional domains and motifs, limiting our ability to predict their functions and understand how they are recognised by plant hosts. As a result, cross-disciplinary approaches involving structural biology and protein biochemistry are often required to decipher and better characterise effector function. These approaches are reliant on high yields of relatively pure protein, which often requires protein production using a heterologous expression system. For some effectors, establishing an efficient production system can be difficult, particularly those that require multiple disulfide bonds to achieve their naturally folded structure. Here, we describe the use of a co-expression system within the heterologous host E. coli termed CyDisCo (cytoplasmic disulfide bond formation in E. coli) to produce disulfide bonded fungal effectors. We demonstrate that CyDisCo and a naturalised co-expression approach termed FunCyDisCo (Fungi-CyDisCo) can significantly improve the production yields of numerous disulfide bonded effectors from diverse fungal pathogens. The ability to produce large quantities of functional recombinant protein has facilitated functional studies and crystallisation of several of these reported fungal effectors. We suggest this approach could be broadly useful in the investigation of the function and recognition of a broad range of disulfide-bond containing effectors.

Multiple Roles of Flagellar Export Chaperones for Efficient and Robust Flagellar Filament Formation in Salmonella

FlgN, FliS, and FliT are flagellar export chaperones specific for FlgK/FlgL, FliC, and FliD, respectively, which are essential component proteins for filament formation. These chaperones facilitate the docking of their cognate substrates to a transmembrane export gate protein, FlhA, to facilitate their subsequent unfolding and export by the flagellar type III secretion system (fT3SS). Dynamic interactions of the chaperones with FlhA are thought to determine the substrate export order. To clarify the role of flagellar chaperones in filament assembly, we constructed cells lacking FlgN, FliS, and/or FliT. Removal of either FlgN, FliS, or FliT resulted in leakage of a large amount of unassembled FliC monomers into the culture media, indicating that these chaperones contribute to robust and efficient filament formation. The ∆flgN ∆fliS ∆fliT (∆NST) cells produced short filaments similarly to the ∆fliS mutant. Suppressor mutations of the ∆NST cells, which lengthened the filament, were all found in FliC and destabilized the folded structure of FliC monomer. Deletion of FliS inhibited FliC export and filament elongation only after FliC synthesis was complete. We propose that FliS is not involved in the transport of FliC upon onset of filament formation, but FliS-assisted unfolding of FliC by the fT3SS becomes essential for its rapid and efficient export to form a long filament when FliC becomes fully expressed in the cytoplasm.