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Epitopes, the basic functional units of antigens, hold great significance in the field of immunology. However, the structure and composition of epitopes and their interactions with antibodies remain unclear, which limits in‐depth studies on epitopes and the development of subunit vaccines. In a previous study on the localization of anti‐influenza HA monoclonal antibodies (mAbs), three strains with different characteristics reacted with the same peptide. In this study, by conventional immunological assays, computer homology modeling, and molecular docking simulations, we found that (1) the peptide could bind to three strains of mAbs with different reaction characteristics utilizing different combinations of immunodominant groups. (2) By computer molecular docking and simulation methods, the immunodominant groups on the two peptides could be combined into a multi‐epitope peptide bound to six strains of mAbs. We established a method for multi‐epitope peptide recombination from these immunodominant groups. (3) The immune effect of the recombinant multi‐epitope peptide was better than that of a single peptide. Our findings facilitate the understanding of the composition of antigen epitopes and provide a theoretical and experimental basis for developing polyvalent vaccines and understanding immune responses at the molecular level. [ABSTRACT FROM AUTHOR]

In immunology, cross‐reaction between antigens and antibodies are commonly observed. Prior research has shown that various monoclonal antibodies (mAbs) can recognize a broad spectrum of epitopes related to influenza viruses. However, existing theories on cross‐reactions fall short in explaining the phenomena observed. This study explored the interaction characteristics of H1‐74 mAb with three peptides: two natural peptides, LVLWGIHHP and LPFQNI, derived from the hemagglutinin (HA) antigen of the H1N1 influenza virus, and one synthetic peptide, WPFQNY. Our findings indicate that the complementarity‐determining region (CDR) of H1‐74 mAb comprised five antigen‐binding sites, containing eight key amino acid residues from the light chain variable region and 16 from the heavy chain variable region. These critical residues formed distinct hydrophobic or hydrophilic clusters and functional groups within the binding sites, facilitating interaction with antigen epitopes through hydrogen bonding, salt bridge formation, and π–π stacking. The study revealed that the formation of the antibody molecule led to the creation of binding groups and small units in the CDR, allowing the antibody to attach to a variety of antigen epitopes through diverse combinations of these small units and functional groups. This unique ability of the antibody to bind with antigen epitopes provides a new molecular basis for explaining the phenomenon of antibody cross‐reaction. [ABSTRACT FROM AUTHOR]

The Coronavirus Disease 2019 (COVID-19) has become an international public health emergency, posing a serious threat to human health and safety around the world. The 2019-nCoV coronavirus spike protein was confirmed to be highly susceptible to various mutations, which can trigger apparent changes of virus transmission capacity and the pathogenic mechanism. In this article, the binding interface was obtained by analyzing the interaction modes between 2019-nCoV coronavirus and the human ACE2. Based on the “SIFT server” and the “bubble” identification mechanism, 9 amino acid sites were selected as potential mutation-sites from the 2019-nCoV-S1-ACE2 binding interface. Subsequently, a total number of 171 mutant systems for 9 mutation-sites were optimized for binding-pattern comparsion analysis, and 14 mutations that may improve the binding capacity of 2019-nCoV-S1 to ACE2 were selected. The Molecular Dynamic Simulations were conducted to calculate the binding free energies of all the 14 mutant systems. Finally, we found that most of the 14 mutations on the 2019-nCoV-S1 protein could enhance the binding ability between 2019-nCoV coronavirus and human ACE2. Among which, the binding capacities for G446R, Y449R and F486Y mutations could be increased by 20 percent, and that for S494R mutant increased even by 38.98 percent. We hope this research could provide significant help for the future epidemic detection, drug and vaccine development. [ABSTRACT FROM AUTHOR]

The Novel Coronavirus Disease 2019 (COVID-19) has become an international public health emergency, which poses the most serious threat to the human health around the world. Accumulating evidences have shown that the new coronavirus could not only infect human beings, but also can infect other species which might result in the cross-species infections. In this research, 1056 ACE2 protein sequences are collected from the NCBI database, and 173 species with >60% sequence identity compared with that of human beings are selected for further analysis. We find 14 polar residues forming the binding interface of ACE2/2019-nCoV-Spike complex play an important role in maintaining protein–protein stability. Among them, 8 polar residues at the same positions with that of human ACE2 are highly conserved, which ensure its basic binding affinity with the novel coronavirus. 5 of other 6 unconserved polar residues (positions at human ACE2: Q24, D30, K31, H34 and E35) are proved to have an effect on the binding patterns among species. We select 21 species keeping close contacts with human beings, construct their ACE2 three-dimensional structures by Homology Modeling method and calculate the binding free energies of their ACE2/2019-nCoV-Spike complexes. We find the ACE2 from all the 21 species possess the capabilities to bind with the novel coronavirus. Compared with the human beings, 8 species (cow, deer, cynomys, chimpanzee, monkey, sheep, dolphin and whale) present almost the same binding abilities, and 3 species (bat, pig and dog) show significant improvements in binding affinities. We hope this research could provide significant help for the future epidemic detection, drug and vaccine development and even the global eco-system protections. [ABSTRACT FROM AUTHOR]

The vast majority of data obtained from sequence analysis of influenza A viruses (IAVs) have revealed that nonstructural 1 (NS1) proteins from H1N1 swine, H3N8 equine, H3N2 avian and the correspondent subtypes from dogs have a conserved four C-terminal amino acid motif when independent cross-species transmission occurs between these species. To test the influence of the C-terminal amino acid motifs of NS1 protein on the replication and virulence of IAVs, we systematically generated 7 recombinants, which carried naturally truncated NS1 proteins, and their last four C-terminal residues were replaced with PEQK and SEQK (for H1N1), EPEV and KPEI (for H3N8) and ESEV and ESEI (for H3N2) IAVs. Another recombinant was generated by removing the C-terminal residues by reverse genetics. Remarkably, the ESEI and KPEI motifs circulating in canines largely contributed efficient replication in cultured cells and these had enhanced virulence. In contrast, the avian ESEV motif was only responsible for high pathogenicity in mice. We examined the effects of these motifs upon interferon (IFN) induction. The 7 mutant viruses replicated in vitro in an IFN-independent manner, and the canine SEQK motif was able to induced higher levels of IFN-β in human cell lines. These findings shed further new light on the role of the four C-terminal residues in replication and virulence of IAVs and suggest that these motifs can modulate viral replication in a species-specific manner.

The m-pyridine urea (mPU) oligomer was constructed by using the intramolecular hydrogen bond formed by the pyridine nitrogen atom and the NH of urea and the intermolecular hydrogen bond of the terminal carbonyl group and the NH of urea. Due to the synergistic effect of hydrogen bonds, mPU oligomer folds and exhibits strong self-assembly behaviour. Affected by folding, mPU oligomer generates a twisted plane, and one of its important features is that the carbonyl group of the urea group orientates outwards from the twisted plane, while the NHs tend to direct inward. This feature is beneficial to NH attraction for electron-rich species. Among them, the trimer self-assembles into helical nanotubes, and can efficiently transport chloride ions. This study provides a novel and efficient strategy for constructing self-assembled biomimetic materials for electron-rich species transmission., (© 2021 Wiley-VCH GmbH.)

The human ether-à-go-go-related gene (hERG) potassium channel mediates the repolarization of ventricular action potentials. Mutations in the KCNH2 cause long QT syndrome (LQTS) and are associated with cardiac arrhythmias and sudden death. Here, we functionally analyzed a mutation of hERG potassium channel (p.L51P), gaining novel insights into clinical genotype-phenotype relationships. Potassium currents were recorded by whole-cell patch clamping in HEK293 cells transiently transfected with wild-type and/or mutant hERG potassium channel. Immunofluorescence assay and confocal imaging were undertaken to study the effects of L51P mutation on channel trafficking. The models of the protein structure of hERG and its mutations are predicted by Amber16 software. Molecular dynamics (MD) of individual protein were performed with Particle Mesh Ewald (PME). The production of MD simulations of hERG-WT and hERG-Mut at constant pressure and temperature were carried out with SHAKE. L51 was a conservative amino acid, located in the Per-Arnt-Sim (PAS) domain of the amino terminus. L51P caused loss of function via impairing channel activation. L51P was predicted to destroy hydrophobic structure in the PAS domain, thus causing the failure of channel opening. In summary, the present study identifies L51P as a novel mutation of hERG potassium channel. L51P mutation mechanistically impairs channel activation, reducing channel functionality., Competing Interests: None., (AJTR Copyright © 2020.)