Dual-wield NTPases: A novel protein family mined from AlphaFold DB

AlphaFold protein structure database (AlphaFold DB) archives a vast number of predicted models. We conducted systematic data mining against AlphaFold DB and discovered an uncharacterized P-loop NTPase family. The structure of the protein family was surprisingly novel, showing an atypical topology for P-loop NTPases, noticeable twofold symmetry, and two pairs of independent putative active sites. Our findings show that structural data mining is a powerful approach to identifying undiscovered protein families.

Elastic network model reveals distinct flexibilities of capping proteins bound to CARMIL and twinfilin-tail

Capping protein (CP) binds to the barbed end of an actin-filament and inhibits its elongation. CARMIL binds CP and dissociates it from the barbed end of the actin-filament. The binding of CARMIL peptide alters the flexibility of CP, which is considered to facilitate the dissociation. Twinfilin also binds to CP through its C-terminal tail. The complex structures of the CP/twinfilin-tail (TW-tail) peptide indicate that the binding sites of CARMIL and TW-tail overlap. However, TW-tail binding does not facilitate the dissociation of CP from the barbed end. We extensively investigated the flexibilities of CP in the CP/TW-tail or CP/CARMIL complexes using an elastic network model and concluded that TW-tail binding does not alter the flexibility of CP. Our extensive analysis also highlighted that the strong contacts of peptides with the two domains of CP, that is, the CP-L and CP-S domains, are key to changing the flexibilities of CP. CARMIL peptides can interact strongly with both of the domains, while TW-tail peptides exclusively interact with the CP-S domain because the binding site of TW-tail on CP relatively shifts to the CP-S domain compared with that of CP/CARMIL. This result supports our hypothesis that the dissociation of CP from the barbed end is regulated by the flexibility of CP.

Prediction of chaperonin GroE substrates using small structural patterns of proteins

Molecular chaperones are indispensable proteins that assist the folding of aggregation-prone proteins into their functional native states, thereby maintaining organized cellular systems. Two of the best-characterized chaperones are the Escherichia coli chaperonins GroEL and GroES (GroE), for which in vivo obligate substrates have been identified by proteome-wide experiments. These substrates comprise various proteins but exhibit remarkable structural features. They include a number of α/β proteins, particularly those adopting the TIM β/α barrel fold. This observation led us to speculate that GroE obligate substrates share a structural motif. Based on this hypothesis, we exhaustively compared substrate structures with the MICAN alignment tool, which detects common structural patterns while ignoring the connectivity or orientation of secondary structural elements. We selected four (or five) substructures with hydrophobic indices that were mostly included in substrates and excluded in others, and developed a GroE obligate substrate discriminator. The substructures are structurally similar and superimposable on the 2-layer 2α4β sandwich, the most popular protein substructure, implying that targeting this structural pattern is a useful strategy for GroE to assist numerous proteins. Seventeen false positives predicted by our methods were experimentally examined using GroE-depleted cells, and 9 proteins were confirmed to be novel GroE obligate substrates. Together, these results demonstrate the utility of our common substructure hypothesis and prediction method.

How AlphaFold2 Predicts Conditionally Folding Regions Annotated in an Intrinsically Disordered Protein Database, IDEAL

AlphaFold2 (AF2) is a protein structure prediction program which provides accurate models. In addition to predicting structural domains, AF2 assigns intrinsically disordered regions (IDRs) by identifying regions with low prediction reliability (pLDDT). Some regions in IDRs undergo disorder-to-order transition upon binding the interaction partner. Here we assessed model structures of AF2 based on the annotations in IDEAL, in which segments with disorder-to-order transition have been collected as Protean Segments (ProSs). We non-redundantly selected ProSs from IDEAL and classified them based on the root mean square deviation to the corresponding region of AF2 models. Statistical analysis identified 11 structural and sequential features, possibly contributing toward the prediction of ProS structures. These features were categorized into two groups: one that contained pLDDT and the other that contained normalized radius of gyration. The typical ProS structures in the former group comprise a long α helix or a whole or part of the structural domain and those in the latter group comprise a short α helix with terminal loops.

Computational Methods to Predict Intrinsically Disordered Regions and Functional Regions in Them

Intrinsically disordered regions (IDRs) are protein regions that do not adopt fixed tertiary structures. Since these regions lack ordered three-dimensional structures, they should be excluded from the target portions of homology modeling. IDRs can be predicted from the amino acid sequences, because their amino acid compositions are different from that of the structured domains. This chapter provides a review of the prediction methods of IDRs and a case study of IDR prediction.

Classification of proteins inducing liquid-liquid phase separation: sequential, structural and functional characterization

Liquid-liquid phase separation (LLPS) within the cell can form biological condensates, which are increasingly recognized to play important roles in various biological processes. Most proteins involved in LLPS are known to be intrinsically disordered proteins containing intrinsically disordered regions (IDRs) with low complexity regions (LCRs). The proteins driving LLPS were selected from databases of LLPS-related proteins and then classified into three classes according to the components in the condensates. Through in silico analyses, we found that proteins in the homo class, those that induce LLPS without partner molecules, have different IDRs and LCRs compared with the reference proteome. In contrast, proteins in the other classes, those that induce LLPS with partner proteins (the hetero class) or nucleic acids (the mixed class), did not show a clear difference to the reference proteome in IDRs and LCRs. The hetero-class proteins contained structural domains to serve protein-protein interactions, and the mixed-class ones had the structural domains associated with nucleic acids. These results suggest that IDRs in the homo-class proteins have unique IDRs, which provide multivalent interaction sites required for LLPS, whereas the hetero- and mixed-class proteins can induce LLPS through the combination of the interaction among LCRs, structural domains, and nucleic acids.

Causes of pre-treatment loss to follow-up in patients with TB

SETTING

Five urban TB diagnostic centres in Lusaka, Zambia.

OBJECTIVE

To determine the proportion of bacteriologically confirmed pre-treatment lost to follow-up (LTFU) patients with TB found at the study settings in 2020.

DESIGN

This was a retrospective cohort study in which the TB laboratory and treatment registers at the study sites were cross-matched.

RESULTS

A total of 1,085 bacteriologically confirmed patients with TB were found in the laboratory TB registers at the study settings. Of these, 809 (74.6%) were males, whereas 8 (0.7%) were children, 1,005 (92.6%) were diagnosed using Xpert, 78 (7.2%) by microscopy. A total of 91 (8.4%, 95% CI 6.8-10.2) were determined to be pre-treatment LTFU. Those who had very low (14.0%, 95% CI 8.5-21.2) and low (11.8%, 95% CI 8.4-16.0) results on Xpert were respectively 3.1 (95% CI 1.6-6.0) and 2.6 (95% CI 1.4-4.8) times more likely to become pre-treatment LTFU than those who had medium (4.5%, 95% CI 2.5-7.4) results. The proportions of pre-treatment LTFU varied among the study sites from 0.7% to 16.1%.

CONCLUSION

Health facilities should strive to account for every patient with TB, with particular attention to those who are bacteriologically confirmed.

TB-related technical enquiries received in Japan, 2017-2019

SETTING

Japan, an intermediate TB burden country.

OBJECTIVE

To review TB-related technical enquiries received at the Research Institute of Tuberculosis, Japan, from January 2017 to December 2019.

DESIGN

This was a cohort study.

RESULTS

A total of 2,197 enquiries were analysed. On average, 61.0 enquiries/month (range: 42-81) were received. The enquiry rates were highest for the Yamanashi (4.65/100,000 population) and Ishikawa (4.55) Prefectures, and lowest in the Yamagata (0.46) and Tochigi (0.56) Prefectures. The main organisations the enquirers belonged to were local governments (n = 1,585, 72.1%) and healthcare facilities (n = 307, 14.0%). The enquirers were medical doctors (n = 391, 17.8%), nurses (n = 1,207, 54.9%), other healthcare professionals (n = 57, 2.6%), the general public (n = 168, 7.6%) and others/unknown (n = 374, 17.0%). The most frequent enquiries were about TB diagnosis and treatment (n = 501, 22.8%), including laboratory diagnosis (n = 88, 4.0%), TB treatment in general (n = 93, 4.2%) and management of comorbidities (n = 86, 3.9%), followed by contact investigations (n = 385, 17.5%) and TB in foreigners (n = 344, 15.7%).

CONCLUSION

As the most frequent enquiries were about diagnosis and treatment of TB, the health ministry of Japan should maintain a few specialised TB institutions with TB physicians to provide technical assistance.

High-power laser experiment on developing supercritical shock propagating in homogeneously magnetized plasma of ambient gas origin

A developing supercritical collisionless shock propagating in a homogeneously magnetized plasma of ambient gas origin having higher uniformity than the previous experiments is formed by using high-power laser experiment. The ambient plasma is not contaminated by the plasma produced in the early time after the laser shot. While the observed developing shock does not have stationary downstream structure, it possesses some characteristics of a magnetized supercritical shock, which are supported by a one-dimensional full particle-in-cell simulation taking the effect of finite time of laser-target interaction into account.

Direct observations of pure electron outflow in magnetic reconnection

Magnetic reconnection is a universal process in space, astrophysical, and laboratory plasmas. It alters magnetic field topology and results in energy release to the plasma. Here we report the experimental results of a pure electron outflow in magnetic reconnection, which is not accompanied with ion flows. By controlling an applied magnetic field in a laser produced plasma, we have constructed an experiment that magnetizes the electrons but not the ions. This allows us to isolate the electron dynamics from the ions. Collective Thomson scattering measurements reveal the electron Alfvénic outflow without ion outflow. The resultant plasmoid and whistler waves are observed with the magnetic induction probe measurements. We observe the unique features of electron-scale magnetic reconnection simultaneously in laser produced plasmas, including global structures, local plasma parameters, magnetic field, and waves.

OP0110 CELL-TYPE-SPECIFIC TRANSCRIPTOME ARCHITECTURE UNDERLYING THE ESTABLISHMENT AND EXACERBATION OF SYSTEMIC LUPUS ERYTHEMATOSUS

Background

Systemic lupus erythematosus (SLE) is a complex autoimmune disease with unknown etiology involving multiple immune cells and has diverse clinical phenotypes. This heterogeneous nature has hampered a better understanding of SLE pathogenesis and the development of effective therapeutic agents. While recent single-cell RNA sequencing studies of SLE identified several important cell subpopulations, they were limited by sparse expression information at single-cell level and small sample sizes.

Objectives

This study aimed to elucidate the dysregulated gene expression pattern linked to multiple clinical statuses of SLE with a fine cellular resolution and higher sensitivity. We also attempted to resolve a complex interaction between risk variants and the transcriptome dysregulation seen in SLE patients.

Methods

We conducted a large-scale bulk transcriptome study of 6,386 RNA-sequencing data including 27 purified immune cell types in peripheral blood from 136 SLE and 89 healthy donors in the Immune Cell Gene Expression Atlas from the University of Tokyo (ImmuNexUT) cohort1. At enrollment, SLE patients had diverse clinical manifestations (disease activity, organ involvement and treatment profiles) and 22 patients were re-evaluated after belimumab treatment.

Results

We first profiled two distinct cell-type-specific transcriptomic signatures: disease-state and disease-activity signatures, reflecting disease establishment and exacerbation, respectively.

After confirming the high replicability of both signatures in independent cohorts, we identified candidates of biological processes unique to each signature: e.g., upregulated E2F transcriptional activity in Th1, CD8+ memory T-lineage and NK cells, and dynamic increase of IL21 and CXCL13 in Th1 cells in an active phase of SLE. Pathway analysis highlighted the importance of immunometabolic process for SLE (e.g., oxidative phosphorylation) in cell-type-specific resolution.

Moreover, we demonstrated cell-type-specific contributions to diverse organ involvement, e.g., Th1 for mucocutaneous, monocyte-lineage cells for musculoskeletal, neutrophil-lineage cells for renal activity, respectively.

We also observed the strong associations of disease-activity signatures with treatment effect: (i) belimumab suppressed activity signatures from B-lineage cells, especially in good responders and (ii) mycophenolate mofetil substantially suppressed activity signatures from plasmablast, Th1, and central memory CD8 cells.

However, through stratified LD score regression using large-scale SLE-GWASs, we revealed that disease-activity signatures were less enriched around SLE risk variants than disease-state signatures. Consistent with this result, the directions of SLE risk alleles’ expression quantitative trait locus (eQTL) effects were significantly concordant with the directions of disease-state signatures, but not with those of activity signatures. These findings suggested that the current genetic case-control studies may not well capture clinically vital biology linked to drug target discovery for SLE. Meanwhile, we also detected some examples of activity signatures that might contribute to the disease risk by modulating risk allele’s eQTL effects.

Figure 1.

Conclusion

We identified comprehensive gene signatures reflecting the establishment and exacerbation of SLE, which provide essential foundations for future genomic, genetic, and clinical studies.

References

[1]Ota, M. et al. Dynamic landscape of immune cell-specific gene regulation in immune-mediated diseases. Cell 2021;184:3006-21.e17.

Acknowledgements

This study was supported by Chugai Pharmaceutical Co., Ltd., Tokyo, Japan; the Ministry of Education, Culture, Sports; and the Japan Agency for Medical Research and Development (AMED) (JP21tm0424221 and JP21zf0127004).

Disclosure of Interests

Masahiro Nakano: None declared, Mineto Ota Grant/research support from: Mineto Ota belongs to the Social Cooperation Program, Department of functional genomics and immunological diseases, supported by Chugai Pharmaceutical., Yusuke Takeshima Grant/research support from: Yusuke Takeshima belonged to the Social Cooperation Program, Department of functional genomics and immunological diseases, supported by Chugai Pharmaceutical., Yukiko Iwasaki: None declared, Hiroaki Hatano: None declared, Yasuo Nagafuchi Grant/research support from: Yasuo Nagafuchi belongs to the Social Cooperation Program, Department of functional genomics and immunological diseases, supported by Chugai Pharmaceutical., Kwangwoo Kim: None declared, So-Young Bang: None declared, Hye Soon Lee: None declared, Hirofumi Shoda: None declared, Xuejun Zhang: None declared, Sang-Cheol Bae: None declared, Chikashi Terao: None declared, Kazuhiko Yamamoto: None declared, Tomohisa Okamura Grant/research support from: Tomohisa Okamura belongs to the Social Cooperation Program, Department of functional genomics and immunological diseases, supported by Chugai Pharmaceutical., Kazuyoshi Ishigaki: None declared, Keishi Fujio Speakers bureau: Keishi Fujio receives speaker fees from Chugai Pharmaceutical., Consultant of: Keishi Fujio receives consulting honoraria from Chugai Pharmaceutical., Grant/research support from: Keishi Fujio receives research support from Chugai Pharmaceutical.

High-power laser experiment forming a supercritical collisionless shock in a magnetized uniform plasma at rest

We present an experimental method to generate quasiperpendicular supercritical magnetized collisionless shocks. In our experiment, ambient nitrogen (N) plasma is at rest and well magnetized, and it has uniform mass density. The plasma is pushed by laser-driven ablation aluminum (Al) plasma. Streaked optical pyrometry and spatially resolved laser collective Thomson scattering clarify structures of plasma density and temperatures, which are compared with one-dimensional particle-in-cell simulations. It is indicated that just after the laser irradiation, the Al plasma is magnetized by a self-generated Biermann battery field, and the plasma slaps the incident N plasma. The compressed external field in the N plasma reflects N ions, leading to counterstreaming magnetized N flows. Namely, we identify the edge of the reflected N ions. Such interacting plasmas form a magnetized collisionless shock.

Evaluating cepharanthine analogues as natural drugs against SARS-CoV-2

Cepharanthine (CEP) is a natural biscoclaurine alkaloid of plant origin and was recently demonstrated to have anti‐severe acute respiratory syndrome coronavirus 2 (anti‐SARS‐CoV‐2) activity. In this study, we evaluated whether natural analogues of CEP may act as potential anti‐coronavirus disease 2019 drugs. A total of 24 compounds resembling CEP were extracted from the KNApSAcK database, and their binding affinities to target proteins, including the spike protein and main protease of SARS‐CoV‐2, NPC1 and TPC2 in humans, were predicted via molecular docking simulations. Selected analogues were further evaluated by a cell‐based SARS‐CoV‐2 infection assay. In addition, the efficacies of CEP and its analogue tetrandrine were assessed. A comparison of the docking conformations of these compounds suggested that the diphenyl ester moiety of the molecules was a putative pharmacophore of the CEP analogues.

Current status of structure-based drug repurposing against COVID-19 by targeting SARS-CoV-2 proteins

More than one and half years have passed, as of August 2021, since the COVID-19 caused by the novel coronavirus named SARS-CoV-2 emerged in 2019. While the recent success of vaccine developments likely reduces the severe cases, there is still a strong requirement of safety and effective therapeutic drugs for overcoming the unprecedented situation. Here we review the recent progress and the status of the drug discovery against COVID-19 with emphasizing a structure-based perspective. Structural data regarding the SARS-CoV-2 proteome has been rapidly accumulated in the Protein Data Bank, and up to 68% of the total amino acid residues encoded in the genome were covered by the structural data. Despite a global effort of in silico and in vitro screenings for drug repurposing, there is only a limited number of drugs had been successfully authorized by drug regulation organizations. Although many approved drugs and natural compounds, which exhibited antiviral activity in vitro, were considered potential drugs against COVID-19, a further multidisciplinary investigation is required for understanding the mechanisms underlying the antiviral effects of the drugs.

Analysis of 605 tuberculosis outbreaks in Japan, 1993-2015: time, place and transmission site

Since 1993, reports on tuberculosis (TB) outbreaks have been collected in Japan; however, there has never been an overall analysis of these TB outbreaks. We aim to provide one here. The TB outbreak data were obtained from the Ministry of Health, Labour and Welfare and are described in terms of time, place and transmission site. The average number of TB cases and latent tuberculosis infection (LTBI) were compared by the transmission site. Some 605 TB outbreaks with 3491 TB cases were reported in 1993-2015 with an increasing trend (r = 0.45), during which time 728 777 TB cases were reported nationwide. On an average, TB outbreaks occurred more often in April to May (5.5 outbreaks per 2 months) than in December to January (3.4). The most common transmission sites were workplaces (n = 255), followed by health facilities (n = 144), schools (n = 60) and welfare facilities (n = 48). Psychiatric hospitals and nursing homes had the highest average number of TB cases per outbreak (8.5 each), whereas schools and prisons had the highest numbers of LTBI cases (29.1 and 38.9, respectively). Countries, particularly those that have resources to investigate TB outbreaks, should collect and analyse findings of TB outbreaks, as it informs surveillance systems and eventually strengthens general health systems.

Re-evaluated treatment outcomes of bacteriologically positive TB patients registered at a clinic in Lusaka, Zambia in 2018

SETTING

An urban TB diagnostic centre in Lusaka, Zambia.

OBJECTIVE

To re-evaluate treatment outcomes of all bacteriologically confirmed TB patients registered in 2018.

DESIGN

This was a retrospective cohort study on TB patients. Treatment outcomes of patients who were transferred out were retrieved.

RESULTS

A total of 182 patients were registered, 26 of whom had missing documents; these were excluded from the study. Of the remaining 156 patients who were reviewed, 86 (55.1%) were correctly evaluated by the centre, 35 (22.4%) were incorrectly evaluated and 35 (22.4%) were 'transferred out' (not evaluated). As a result of this review, the number of evaluated patients increased from 86 (55.1%) to 150 (96.2%). The cure and treatment success rates rose from 43.6% and 44.2%, respectively, to 57.7% and 73.1%, respectively. Of note, 14 of the 35 patients who were initially declared 'transferred out' did not actually reach their treatment facilities and ended up being lost to follow-up.

CONCLUSION

This study shows that it is possible to evaluate almost all TB patients. Re-evaluation of treatment outcomes of TB patients revealed the problems in the TB services that need to be improved in the future.

Structural Insights into the Regulation of Actin Capping Protein by Twinfilin C-terminal Tail

Twinfilin is a conserved actin regulator that interacts with actin capping protein (CP) via C terminus residues (TWtail) that exhibits sequence similarity with the CP interaction (CPI) motif of CARMIL. Here we report the crystal structure of TWtail in complex with CP. Our structure showed that although TWtail and CARMIL CPI bind CP to an overlapping surface via their middle regions, they exhibit different CP-binding modes at both termini. Consequently, TWtail and CARMIL CPI restrict the CP in distinct conformations of open and closed forms, respectively. Interestingly, V-1, which targets CP away from the TWtail binding site, also favors the open-form CP. Consistently, TWtail forms a stable ternary complex with CP and V-1, a striking contrast to CARMIL CPI, which rapidly dissociates V-1 from CP. Our results demonstrate that TWtail is a unique CP-binding motif that regulates CP in a manner distinct from CARMIL CPI.