Generation of antibodies to an extracellular region of the transporters Glut1/Glut4 by immunization with a designed antigen.

Monoclonal antibodies are one of the fastest growing class of drugs. Nevertheless, relatively few biologics target multispanning membrane proteins because of technical challenges. To target relatively small extracellular regions of multiple membrane-spanning proteins, synthetic peptides, which are composed of amino acids corresponding to an extracellular region of a membrane protein, are often utilized in antibody discovery. However, antibodies to these peptides often do not recognize parental membrane proteins. In this study, we designed fusion proteins in which an extracellular helix of the membrane protein glucose transporter 1 (Glut1) was grafted onto the scaffold protein Adhiron. In the initial design, the grafted fragment did not form a helical conformation. Molecular dynamics simulations of full-length Glut1 suggested the importance of intramolecular interactions formed by surrounding residues in the formation of the helical conformation. A fusion protein designed to maintain such intramolecular interactions did form the desired helical conformation in the grafted region. We then immunized an alpaca with the designed fusion protein and obtained VHH (variable region of heavy-chain antibodies) using the phage display method. The binding of these VHH antibodies to the recombinant Glut1 protein was evaluated by surface plasmon resonance, and their binding to Glut1 on the cell membrane was further validated by flow cytometry. Furthermore, we also succeeded in the generation of a VHH against another integral membrane protein, glucose transporter 4 (Glut4) with the same strategy. These illustrates that our combined biochemical and computational approach can be applied to designing other novel fusion proteins for generating site-specific antibodies.

Experimental modification in thermal stability of oligomers by alanine substitution and site saturation mutagenesis of interfacial residues.

For certain industrial applications, the stability of protein oligomers is important. In this study, we demonstrated an efficient method to improve the thermal stability of oligomers using the trimeric protein chloramphenicol acetyltransferase (CAT) as the model. We substituted all interfacial residues of CAT with alanine to detect residues critical for oligomer stability. Mutation of six of the forty-nine interfacial residues enhanced oligomer thermal stability. Site saturation mutagenesis was performed on these six residues to optimize the side chains. About 15% of mutations enhanced thermal stability by more than 0.5 °C and most did not disrupt activity of CAT. Certain combinations of mutations further improved thermal stability and resistance against heat treatment. The quadruple mutant, H17V/N34S/F134A/D157C, retained the same activity as the wild-type after heat treatment at 9 °C higher temperature than the wild-type CAT. Furthermore, combinations with only alanine substitutions also improved thermal stability, suggesting the method we developed can be used for rapid modification of industrially important proteins.

Conformational features and interaction mechanisms of VH H antibodies with ß-hairpin CDR3: A case of Nb8-HigB2 interaction.

The ß-hairpin conformation is regarded as an important basic motif to form and regulate protein-protein interactions. Single-domain VH H antibodies are potential therapeutic and diagnostic tools, and the third complementarity-determining regions of the heavy chains (CDR3s) of these antibodies are critical for antigen recognition. Although the sequences and conformations of the CDR3s are diverse, CDR3s sometimes adopt ß-hairpin conformations. However, characteristic features and interaction mechanisms of ß-hairpin CDR3s remain to be fully elucidated. In this study, we investigated the molecular recognition of the anti-HigB2 VH H antibody Nb8, which has a CDR3 that forms a ß-hairpin conformation. The interaction was analyzed by evaluation of alanine-scanning mutants, molecular dynamics simulations, and hydrogen/deuterium exchange mass spectrometry. These experiments demonstrated that positions 93 and 94 (Chothia numbering) in framework region 3, which is right outside CDR3 by definition, play pivotal roles in maintaining structural stability and binding properties of Nb8. These findings will facilitate the design and optimization of single-domain antibodies.

High-throughput analysis system of interaction kinetics for data-driven antibody design.

Surface plasmon resonance (SPR) is widely used for antigen-antibody interaction kinetics analysis. However, it has not been used in the screening phase because of the low throughput of measurement and analysis. Herein, we proposed a high-throughput SPR analysis system named "BreviA" using the Brevibacillus expression system. Brevibacillus was transformed using a plasmid library containing various antibody sequences, and single colonies were cultured in 96-well plates. Sequence analysis was performed using bacterial cells, and recombinant antibodies secreted in the supernatant were immobilized on a sensor chip to analyze their interactions with antigens using high-throughput SPR. Using this system, the process from the transformation to 384 interaction analyses can be performed within a week. This system utility was tested using an interspecies specificity design of an anti-human programmed cell death protein 1 (PD-1) antibody. A plasmid library containing alanine and tyrosine mutants of all complementarity-determining region residues was generated. A high-throughput SPR analysis was performed against human and mouse PD-1, showing that the mutation in the specific region enhanced the affinity for mouse PD-1. Furthermore, deep mutational scanning of the region revealed two mutants with > 100-fold increased affinity for mouse PD-1, demonstrating the potential efficacy of antibody design using data-driven approach.

Biophysical insight into protein-protein interactions in the Interleukin-11/Interleukin-11Rα/glycoprotein 130 signaling complex.

Interleukin-11 (IL-11) is a member of the interleukin-6 (IL-6) family of cytokines. IL-11 is a regulator of multiple events in hematopoiesis, and IL-11-mediated signaling is implicated in inflammatory disease, cancer, and fibrosis. All IL-6 family cytokines signal through the signal-transducing receptor, glycoprotein 130 (gp130), but these cytokines have distinct as well as overlapping biological functions. To understand IL-11 signaling at the molecular level, we performed a comprehensive interaction analysis of the IL-11 signaling complex, comparing it with the IL-6 complex, one of the best-characterized cytokine complexes. Our thermodynamic analysis revealed a clear difference between IL-11 and IL-6. Surface plasmon resonance analysis showed that the interaction between IL-11 and IL-11 receptor α (IL-11Rα) is entropy driven, whereas that between IL-6 and IL-6 receptor α (IL-6Rα) is enthalpy driven. Our analysis using isothermal titration calorimetry revealed that the binding of gp130 to the IL-11/IL-11Rα complex results in entropy loss, but that the interaction of gp130 with the IL-6/IL-6Rα complex results in entropy gain. Our hydrogen-deuterium exchange mass spectrometry experiments suggested that the D2 domain of gp130 was not involved in IL-6-like interactions in the IL-11/IL-11Rα complex. It has been reported that IL-6 interaction with gp130 in the signaling complex was characterized through the hydrophobic interface located in its D2 domain of gp130. Our findings suggest that unique interactions of the IL-11 signaling complex with gp130 are responsible for the distinct biological activities of IL-11 compared to IL-6.

Anti-InlA single-domain antibodies that inhibit the cell invasion of Listeria monocytogenes.

Listeriosis, caused by infection with Listeria monocytogenes, is a severe disease with a high mortality rate. The L. monocytogenes virulence factor, internalin family protein InlA, which binds to the host receptor E-cadherin, is necessary to invade host cells. Here, we isolated two single-domain antibodies (VHHs) that bind to InlA with picomolar affinities from an alpaca immune library using the phage display method. These InlA-specific VHHs inhibited the binding of InlA to the extracellular domains of E-cadherin in vitro as shown by biophysical interaction analysis. Furthermore, we determined that the VHHs inhibited the invasion of L. monocytogenes into host cells in culture. High-resolution X-ray structure analyses of the complexes of VHHs with InlA revealed that the VHHs bind to the same binding site as E-cadherin against InlA. We conclude that these VHHs have the potential for use as drugs to treat listeriosis.

Impact of the COVID-19 Pandemic on Injury Incidence in Japanese Male Professional Soccer Players.

Background: The outbreak of the 2019 novel coronavirus disease (COVID-19) led to an enforced quarantine period and limited training and match activities for athletes. Purpose: To report the influence of the COVID-19 pandemic on the occurrence of injury in Japanese male professional soccer players. Study Design: Descriptive epidemiology study. Methods: In total, 21 clubs in the 2019 season and 28 clubs in the 2020 season from the Japan Professional Football League were prospectively followed, and 16 clubs in 2019 and 24 clubs in 2020 were analyzed in this study. Individual training, match exposure, and time-loss injuries were recorded using an electronic data capture system. The influence of COVID-19-related suspension during the 2020 season was retrospectively investigated via comparisons with the 2019 season. Results: Total activity time included 114,001 hours in training and 16,339 hours in matches in 2019 and 170,798 hours in training and 25,411 hours in matches in 2020. The mean training interruption period caused by COVID-19 in 2020 was 39.9 days (range, 3-65 days), and the mean game-interruption period was 70.1 days (range, 58-79 days). The total number of injuries was 1495 in 2019 and 1701 in 2020. The overall injury incidence per 1000 hours of exposure was 5.7 in 2019 and 5.8 in 2020. The overall injury burden per 1000 hours of exposure was 155.5 days in 2019 and 130.2 days in 2020. The muscle injury incidence was highest in May 2020, immediately after the suspension period. Conclusion: The overall injury incidence did not differ between 2019 and 2020. However, muscle injury incidence notably increased in the 2 months after the COVID-19 pandemic suspension period.

Training Practices of Football Players During the Early COVID-19 Lockdown Worldwide.

The COVID-19 lockdown challenged the training options of athletes worldwide, including players from the most popular sport globally, football/soccer. PURPOSE: The authors explored the training practices of football players worldwide during the COVID-19 lockdown. METHODS: Football players (N = 2482, 30% professional, 22% semipro, and 48% amateur) completed an online survey (May-July 2020) on their training practices before versus during lockdown (March-June 2020). Questions were related to training frequency and session duration, as well as training knowledge and attitudes. RESULTS: Before lockdown, more professional (87%) than semipro (67%) and amateur (65%) players trained ≥5 sessions/wk, but this proportion decreased during the lockdown to 55%, 35%, and 42%, respectively. Players (80%-87%) trained ≥60 minutes before lockdown, but this proportion decreased to 45% in professionals, 43% in amateurs, and 36% in semipros during lockdown. At home, more than two-thirds of players had training space (73%) and equipment (66%) for cardiorespiratory training, while availability of equipment for technical and strength training was <50% during lockdown. Interactions between coach/trainer and player were more frequent (ie, daily) among professional (27%) than amateur (11%) and semipro (17%) players. Training load monitoring, albeit limited, was mostly performed by fitness coaches, more so with professionals (35%) than amateurs (13%) and semipros (17%). The players' training knowledge and attitudes/beliefs toward training were relatively modest (50%-59%). CONCLUSION: COVID-19 lockdown negatively affected training practices of football players worldwide, especially amateurs and semipros, for example, in training frequency, duration, intensity, technical, recovery, and other fitness training and coaching-related aspects. During lockdown-like situations, players should be monitored closely and provided appropriate support to facilitate their training.

Unveiling the affinity-stability relationship in anti-measles virus antibodies: a computational approach for hotspots prediction.

Recent years have seen an uptick in the use of computational applications in antibody engineering. These tools have enhanced our ability to predict interactions with antigens and immunogenicity, facilitate humanization, and serve other critical functions. However, several studies highlight the concern of potential trade-offs between antibody affinity and stability in antibody engineering. In this study, we analyzed anti-measles virus antibodies as a case study, to examine the relationship between binding affinity and stability, upon identifying the binding hotspots. We leverage in silico tools like Rosetta and FoldX, along with molecular dynamics (MD) simulations, offering a cost-effective alternative to traditional in vitro mutagenesis. We introduced a pattern in identifying key residues in pairs, shedding light on hotspots identification. Experimental physicochemical analysis validated the predicted key residues by confirming significant decrease in binding affinity for the high-affinity antibodies to measles virus hemagglutinin. Through the nature of the identified pairs, which represented the relative hydropathy of amino acid side chain, a connection was proposed between affinity and stability. The findings of the study enhance our understanding of the interactions between antibody and measles virus hemagglutinin. Moreover, the implications of the observed correlation between binding affinity and stability extend beyond the field of anti-measles virus antibodies, thereby opening doors for advancements in antibody research.

Addition of arginine hydrochloride and proline to the culture medium enhances recombinant protein expression in Brevibacillus choshinensis: The case of RBD of SARS-CoV-2 spike protein and its antibody.

Brevibacillus choshinensis is a gram-positive bacterium that is known to efficiently secrete recombinant proteins. However, the expression of these proteins is often difficult depending upon the expressed protein. In this study, we demonstrated that the addition of arginine hydrochloride and proline to the culture medium dramatically increased protein expression. By culturing bacterial cells in 96-well plates, we were able to rapidly examine the expression conditions and easily scale up to 96 mL of culture for production. Although functional expression of the receptor binding domain (RBD) of the SARS-CoV-2 spike protein without any solubility-enhancing tag in bacterial strains (including Escherichia coli) has not been reported to date, we succeeded in efficiently producing RBD which showed a similar CD spectrum to that of RBD produced by eukaryotic cell expression systems. Furthermore, RBD from the omicron variant (B.1.1.529) was also produced. Physicochemical analyses indicated that omicron RBD exhibited markedly increased instability compared to the wild-type. We also revealed that the Fab format of the anti-SARS-CoV-2 antibody C121 can be produced in large quantities using the same expression system. The obtained C121 Fab bound to wild-type RBD but not to omicron RBD. These results strongly suggest that the Brevibacillus expression system is useful for facilitating the efficient expression of proteins that are difficult to fold and will thus contribute to the rapid physicochemical evaluation of functional proteins.

A new method for diagnosing biochemical abnormalities of anterior cruciate ligament (ACL) in human knees: A Raman spectroscopic study.

Anterior cruciate ligament (ACL) plays an essential role in knee joint stability and kinematics. The microstructural irregularities such as cellular changes and disorganization of the extracellular matrix (ECM) alter the mechanical properties of the ligament, leading to a significant knee functional instability and progression of osteoarthritis (OA). So far, the identification of the local abnormality in ACL has routinely relied on invasive analytical techniques such as histology or biochemical assays. The non-invasive diagnosis using magnetic resonance imaging (MRI) is still limited to identifying the presence/absence of partial/complete ruptures and mucoid degeneration. In this study, laser micro-Raman spectroscopy with near-infrared excitation (785 nm) was applied to human ACL in order to establish optical algorithms for non-destructively diagnosing a degeneration state at molecular level. Raman spectra were obtained from 44 ex-vivo ACL specimens, and these were subsequently classified as an early (subclinical) and advanced (clinical) level of tissue degradation based on the histopathological scoring system. The significant differences in Raman peak intensities were found between the different degeneration groups, which were assigned to the vibrational modes of nucleic acids in cells, collagens, and phospholipids. Linear discriminant analysis (LDA) was performed to identify cut-off values for the distributions of Raman intensity and intensity ratios, which enable to best discriminate between the early and advanced degenerated tissues. Raman intensity algorithms derived from I1101/I1749, [I1002/I1516vs. I1101/I1749], and [I1002/I1749vs. I1101/I1749], yielded a maximum diagnostic sensitivity of 100%, specificity of 80%, and accuracy of 91% for discriminating the degeneration severity. STATEMENT OF SIGNIFICANCE: In this study, laser micro-Raman spectroscopy was applied to human anterior cruciate ligament (ACL) to establish optical algorithms for non-destructively diagnosing the tissue degeneration at molecular level. To our knowledge, this is the first report on Raman diagnosis for human ACL. Linear discriminant analysis (LDA) was performed to identify cut-off values for Raman intensity and intensity ratios, which enable to best discriminate between an early (subclinical) and advanced (clinical) level of ACL degeneration. The intensity ratios of I1101/I1749, [I1002/I1516vs. I1101/I1749], and [I1002/I1749vs. I1101/I1749] yielded a maximum diagnostic sensitivity of 100%, specificity of 80%, and accuracy of 91% for discriminating the ACL degeneration. The present findings might contribute to expanding clinical diagnostic possibilities for non-invasively identifying tissue degeneration.

Hyperthin nanochains composed of self-polymerizing protein shackles.

Protein fibrils are expected to have applications as functional nanomaterials because of their sophisticated structures; however, nanoscale ordering of the functional units of protein fibrils remains challenging. Here we design a series of self-polymerizing protein monomers, referred to as protein shackles, derived from modified recombinant subunits of pili from Streptococcus pyogenes. The monomers polymerize into nanochains through spontaneous irreversible covalent bond formation. We design the protein shackles so that their reactions can be controlled by altering redox conditions, which affect disulphide bond formation between engineered cysteine residues. The interaction between the monomers improves their polymerization reactivity and determines morphologies of the polymers. In addition, green fluorescent protein-tagged protein shackles can polymerize, indicating proteins can be stably attached to the nanochains with its functionality preserved. Furthermore we demonstrate that a molecular-recognizable nanochain binds to its partner with an enhanced binding ability in solution. These characteristics are expected to be applied for novel protein nanomaterials.

Bidirectional binding property of high glycine-tyrosine keratin-associated protein contributes to the mechanical strength and shape of hair.

Since their first finding in wool 50years ago, keratin-associated proteins (KAPs), which are classified into three groups; high sulfur (HS) KAPs, ultra high sulfur (UHS) KAPs, and high glycine-tyrosine (HGT) KAPs, have been the target of curiosity for scientists due to their characteristic amino acid sequences. While HS and UHS KAPs are known to function in disulfide bond crosslinking, the function of HGT KAPs remains unknown. To clarify the function as well as the binding partners of HGT KAPs, we prepared KAP8.1 and other KAP family proteins, the trichocyte intermediate filament proteins (IFP) K85 and K35, the head domain of K85, and the C subdomain of desmoplakin C-terminus (DPCT-C) and investigated the interactions between them in vitro. Western blot analysis and isothermal titration calorimetry (ITC) indicate that KAP8.1 binds to the head domain of K85, which is helically aligned around the axis of the intermediate filament (IF). From these results and transmission electron microscopy (TEM) observations of bundled filament complex in vitro, we propose that the helical arrangement of IFs found in the orthocortex, which is uniquely distributed on the convex fiber side of the hair, is regulated by KAP8.1. Structure-dependent binding of DPCT-C to trichocyte IFP was confirmed by Western blotting, ITC, and circular dichroism. Moreover, DPCT-C also binds to some HGT KAPs. It is probable that such bidirectional binding property of HGT KAPs contribute to the mechanical robustness of hair.