Phosphorylation, disorder, and phase separation govern the behavior of Frequency in the fungal circadian clock

Circadian clocks are composed of transcription-translation negative feedback loops that pace rhythms of gene expression to the diurnal cycle. In the filamentous fungus Neurospora crassa, the proteins Frequency (FRQ), the FRQ-interacting RNA helicase (FRH), and Casein-Kinase I (CK1) form the FFC complex that represses expression of genes activated by the white-collar complex (WCC). FRQ orchestrates key molecular interactions of the clock despite containing little predicted tertiary structure. Spin labeling and pulse-dipolar electron spin resonance spectroscopy provide domain-specific structural insights into the 989-residue intrinsically disordered FRQ and the FFC. FRQ contains a compact core that associates and organizes FRH and CK1 to coordinate their roles in WCC repression. FRQ phosphorylation increases conformational flexibility and alters oligomeric state, but the changes in structure and dynamics are non-uniform. Full-length FRQ undergoes liquid-liquid phase separation (LLPS) to sequester FRH and CK1 and influence CK1 enzymatic activity. Although FRQ phosphorylation favors LLPS, LLPS feeds back to reduce FRQ phosphorylation by CK1 at higher temperatures. Live imaging of Neurospora hyphae reveals FRQ foci characteristic of condensates near the nuclear periphery. Analogous clock repressor proteins in higher organisms share little position-specific sequence identity with FRQ; yet, they contain amino acid compositions that promote LLPS. Hence, condensate formation may be a conserved feature of eukaryotic clocks.

Complex interplay between FMRP and DHX9 during DNA replication stress

Mutations in, or deficiency of, fragile X messenger ribonucleoprotein (FMRP) is responsible for the Fragile X syndrome (FXS), the most common cause for inherited intellectual disability. FMRP is a nucleocytoplasmic protein, primarily characterized as a translation repressor with poorly understood nuclear function(s). We recently reported that FXS patient cells lacking FMRP sustain higher level of DNA double-strand breaks (DSBs) than normal cells, specifically at sequences prone to forming R-loops, a phenotype further exacerbated by DNA replication stress. Moreover, expression of FMRP, and not an FMRPI304N mutant known to cause FXS, reduced R-loop-associated DSBs. We subsequently reported that recombinant FMRP directly binds R-loops, primarily through the carboxyl terminal intrinsically disordered region. Here, we show that FMRP directly interacts with an RNA helicase, DHX9. This interaction, which is mediated by the amino terminal structured domain of FMRP, is reduced with FMRPI304N. We also show that FMRP inhibits DHX9 helicase activity on RNA:DNA hybrids and the inhibition is also dependent on the amino terminus. Furthermore, the FMRPI304N mutation causes both FMRP and DHX9 to persist on the chromatin in replication stress. These results suggest an antagonistic relationship between FMRP and DHX9 at the chromatin, where their proper interaction leads to dissociation of both proteins from the fully resolved R-loop. We propose that the absence or the loss of function of FMRP leads to persistent presence of DHX9 or both proteins, respectively, on the unresolved R-loop, ultimately leading to DSBs. Our study sheds new light on our understanding of the genome functions of FMRP.

Delineating Structural Propensities of the 4E-BP2 Protein via Integrative Modeling and Clustering

The intrinsically disordered 4E-BP2 protein regulates mRNA cap-dependent translation through interaction with the predominantly folded eukaryotic initiation factor 4E (eIF4E). Phosphorylation of 4E-BP2 dramatically reduces the level of eIF4E binding, in part by stabilizing a binding-incompatible folded domain. Here, we used a Rosetta-based sampling algorithm optimized for IDRs to generate initial ensembles for two phospho forms of 4E-BP2, non- and 5-fold phosphorylated (NP and 5P, respectively), with the 5P folded domain flanked by N- and C-terminal IDRs (N-IDR and C-IDR, respectively). We then applied an integrative Bayesian approach to obtain NP and 5P conformational ensembles that agree with experimental data from nuclear magnetic resonance, small-angle X-ray scattering, and single-molecule Förster resonance energy transfer (smFRET). For the NP state, inter-residue distance scaling and 2D maps revealed the role of charge segregation and pi interactions in driving contacts between distal regions of the chain (∼70 residues apart). The 5P ensemble shows prominent contacts of the N-IDR region with the two phosphosites in the folded domain, pT37 and pT46, and, to a lesser extent, delocalized interactions with the C-IDR region. Agglomerative hierarchical clustering led to partitioning of each of the two ensembles into four clusters with different global dimensions and contact maps. This helped delineate an NP cluster that, based on our smFRET data, is compatible with the eIF4E-bound state. 5P clusters were differentiated by interactions of C-IDR with the folded domain and of the N-IDR with the two phosphosites in the folded domain. Our study provides both a better visualization of fundamental structural poses of 4E-BP2 and a set of falsifiable insights on intrachain interactions that bias folding and binding of this protein.

Coevolution of the Ess1-CTD axis in polar fungi suggests a role for phase separation in cold tolerance

Most of the world's biodiversity lives in cold (-2° to 4°C) and hypersaline environments. To understand how cells adapt to such conditions, we isolated two key components of the transcription machinery from fungal species that live in extreme polar environments: the Ess1 prolyl isomerase and its target, the carboxy-terminal domain (CTD) of RNA polymerase II. Polar Ess1 enzymes are conserved and functional in the model yeast, Saccharomyces cerevisiae. By contrast, polar CTDs diverge from the consensus (YSPTSPS)₂₆ and are not fully functional in S. cerevisiae. These CTDs retain the critical Ess1 Ser-Pro target motifs, but substitutions at Y1, T4, and S7 profoundly affected their ability to undergo phase separation in vitro and localize in vivo. We propose that environmentally tuned phase separation by the CTD and other intrinsically disordered regions plays an adaptive role in cold tolerance by concentrating enzymes and substrates to overcome energetic barriers to metabolic activity.

Multisite phosphorylation and binding alter conformational dynamics of the 4E-BP2 protein

Intrinsically disordered proteins (IDPs) play critical roles in regulatory protein interactions, but detailed structural/dynamic characterization of their ensembles remain challenging, both in isolation and when they form dynamic "fuzzy" complexes. Such is the case for mRNA cap-dependent translation initiation, which is regulated by the interaction of the predominantly folded eukaryotic initiation factor 4E (eIF4E) with the intrinsically disordered eIF4E binding proteins (4E-BPs) in a phosphorylation-dependent manner. Single-molecule Förster resonance energy transfer showed that the conformational changes of 4E-BP2 induced by binding to eIF4E are non-uniform along the sequence; while a central region containing both motifs that bind to eIF4E expands and becomes stiffer, the C-terminal region is less affected. Fluorescence anisotropy decay revealed a non-uniform segmental flexibility around six different labeling sites along the chain. Dynamic quenching of these fluorescent probes by intrinsic aromatic residues measured via fluorescence correlation spectroscopy report on transient intra- and inter-molecular contacts on nanosecond-to-microsecond timescales. Upon hyperphosphorylation, which induces folding of ∼40 residues in 4E-BP2, the quenching rates decreased at most labeling sites. The chain dynamics around sites in the C-terminal region far away from the two binding motifs significantly increased upon binding to eIF4E, suggesting that this region is also involved in the highly dynamic 4E-BP2:eIF4E complex. Our time-resolved fluorescence data paint a sequence-level rigidity map of three states of 4E-BP2 differing in phosphorylation or binding status and distinguish regions that form contacts with eIF4E. This study adds complementary structural and dynamics information to recent studies of 4E-BP2, and it constitutes an important step toward a mechanistic understanding of this important IDP via integrative modeling.

Abstract 2364: ABI1 regulates transcriptional activity of STAT3

Background: Prostate cancer (PCa) is characterized by the complexity of oncogenic signaling and heterogeneity of transcriptional landscapes. Adaptor protein ABI1 is a tumor suppressor in PCa as evidenced by its loss or downregulation in high grade and metastatic tumors. STAT3 activation is a hallmark of high-risk prostate tumors. ABI1 loss is associated with STAT3 activation leading to transcriptional reprogramming and epithelial-mesenchymal-transition (EMT) of prostate cancer cells (Nath, Li et al. 2019 Cell Commun Signal). EMT changes involve several homeobox transcription factors. The fact that ABI1 contains a homeobox homology region (HHR) suggested the possibility that it plays a role in EMT through directly regulating transcriptional activity by DNA binding.

Methods: To examine this hypothesis we set out to analyze ABI1-DNA binding. We purified ABI1 HHR and demonstrated its in vitro interactions with different homeobox DNA-binding consensus of double-stranded DNA sequences. We created DU145 ABI1 CRISPR KO cell line and rescue ABI1 expression using retroviral transfection with either ABI1 wild type or Abi1 HHR mutants. DU145 cell lines STAT3 cellular localization was studied by Immunofluorescence staining and the STAT3 transcription activities was studied by Firefly Luciferase Assays with STAT3 specific luciferase reporter plasmid.

Results: We found that the presence of alternatively spliced Exon 4-encoded sequence, located in the C-terminus of HHR, regulates binding of ABI1 to DNA. Structural NMR studies confirmed ABI1 binding to DNA. Subsequent functional studies using DU145 CRISPR KO cell lines expressing wild type or HHR mutants of ABI1 demonstrated that HHR regulates the nuclear localization and transcriptional activity of STAT3.

Conclusion: We propose that ABI1 is a critical regulator of STAT3 activity during prostate cancer progression by the ABI1 HHR mediated DNA binding mechanism.

Funding resources: NCI R01 CA161018; R21 CA260381

Conflicts of Interest Disclosure Statement: The authors declare no conflicts of interest.

Citation Format: Xiang Li, Baylee Porter, Allysa Kemraj, Alaji Bah, Marcin Kortylewski, Leszek Kotula. ABI1 regulates transcriptional activity of STAT3 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2364.

Abstract 2367: Characterizing the reciprocal regulation of an ABI1-dependent androgen receptor axis in prostate cancer

Background: Prostate cancer (PCa) affects nearly 50% of males over 60. Therapies for advanced PCa primarily target the androgen receptor (AR), a ligand-activated transcription factor, which is a key driver of PCa tumor growth. Our previous research demonstrated that ABI1 acts as a tumor suppressor in PCa. ABI1 is a scaffold protein for the WAVE Regulatory Complex, positively regulates cell adhesion, and inhibits integrin activation through sequestering key kinases. We have observed a physical interaction between AR and ABI1. In this study, we aim to characterize the ABI1-dependent AR regulation in PCa.

Method: We generated an ABI1 KO cell line model in LNCaP cells using CRISPR-Cas9. We then used mutagenesis to develop ABI1 binding mutants (W485N and ∆SH3) and generated ABI1 rescue cell lines in ABI1-KO. We performed qPCR, co-immunoprecipitation, subcellular fractionation, western blotting, in vitro assay, live-cell imaging, and PLA. We purified both AR and ABI1 proteins for in vitro analysis, performed turbidity and liquid-liquid droplet formation assays under DIC.

Results: In cellulo binding assays indicate interaction of AR-NTD with the ABI1-SH3 domain. Expression of ABI1-W485N in KO cell line showed decreased binding, while ABI1-∆SH3 showed no observable binding to AR in co-IP assays compared to wildtype control. We then performed subcellular fractionation assays and saw decreased AR nuclear localization compared to ABI1-WT control. Decreased nuclear localization in ABI1-W485N was associated with decreased mRNA expression of hallmark AR target genes, KLK3 and FKBP5. In vitro turbidity assays indicated the conditions in which AR and ABI1 have propensity to phase separate. We then performed a liquid-liquid droplet assay. AR and ABI1 formed liquid-liquid droplets individually. We labeled ABI1 with Alexaflour 488 and saw that ABI1 was recruited to AR droplets indicating that AR and ABI1 can co-phase separate. PLA assays in cellulo and in vivo patient tumor samples showed positive interactions of AR-ABI1 in the nucleus. We then used live-cell observation and saw co-localization of biomolecular condensates for AR and ABI1.

Conclusions: Our studies demonstrate that ABI1 plays a role in AR transcriptional pathway. Loss of ABI1 resulted in decreased nuclear AR and subsequent decrease in mRNA expression of AR target genes. Due to the intrinsically disordered structure of AR and ABI1, they were both able to phase separate individually as well as together. AR stimulation increased PLA interactions in nucleus of cells. The co-localization of AR and ABI1 in biomolecular condensates was changed upon androgen deprivation conditions. Future studies will investigate if anti-AR treatments could lead to the dysregulation of ABI1 and promote reactivation of AR pathway through ABI1-AR axis. Findings will allow for novel insights into the mechanisms underlying AR and ABI1 in prostate metastatic progression.

Citation Format: Baylee A. Porter-Hansen, Alaji Bah, Alfonso Urbanucci, Konsta Kukkonen, Fan Zhang, Sonia Kung, Ladan Fazli, Martin E. Gleave, Gennady Bratslavsky, Leszek Kotula. Characterizing the reciprocal regulation of an ABI1-dependent androgen receptor axis in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2367.

[Covid-19 And Surgical Pathologies In General Surgery Of CHU Gabriel Toure Of Bamako]

INTRODUCTION

The pure digestive form of COVID-19 is possible and initially considered rare. Our objectives were to determine the frequency of COVID-19 in patients treated in general surgery, identify the circumstances of COVID-19 discoveries in surgery, describe the post-operative complications in patients operated on COVID-1919 and describe the reorganization of post-operative COVID-19 diagnosis management.

MATERIALS AND METHODS

We conducted a prospective descriptive study from March 2020 to August 2021 (18 months). All patients who have been operated on, hospitalized or consulted in the department, the Emergency Department (ERS) or other CHU-GT departments for surgical pathology with COVID-19 or infected with COVID-19 while hospitalized were included in the study.

RESULTS

23 cases collected, representing 8.91% (23/258) of COVID-19 cases identified, a frequency of 1.27/month. The age group 66-75 was the most affected, the average age was 49.13 18.75 years, the predominance was male (sex ratio of 1.3). More than 34.78% were recruited at the SAU, 16 patients (69.56%) consulted in emergency, and digestive signs of COVID-19 were: Abdominal pain 20 cases (89.96%), anorexia 19 cases (82.61%), vomiting 8 cases (34.78%) and diarrhea 3 cases (13.04%). The pulmonary signs of COVID-19 were: Cough 18 cases (78.26%), chest pain 15 cases (65.22%), and dyspnea 9 cases (39.13%). Manifestations of COVID-19 were: pulmonary 9 cases, digestive 9 cases, associated 3 cases, incidental discovery 2 cases. The diagnostic mean was Thoracic CT (100%), Test-PCR 14 cases (60.86%) with a positive PCR test in 50% of cases. Surgical pathologies were surgical emergencies in 7 cases (30.43%), cancers in 6 cases (26.09%), COVID-19 digestive event (30.43%) and other 3 cases (13.04%). More than half of patients were operated on 12 cases (52.17%). The overall mortality was 60.87% and the mortality of surgical patients was 41.67%.

CONCLUSION

The infectious risk of COVID-19 during hospitalization, during or after digestive surgery is a real and potentially serious risk for the patient and caregivers.

Interleukin-2-inducible T-cell kinase (Itk) signaling regulates potent noncanonical regulatory T cells

Regulatory T cells (Tregs) play an important role in controlling autoimmunity and limiting tissue damage and inflammation. IL2-inducible T cell kinase (Itk) is part of the Tec family of tyrosine kinases and is a critical component of T cell receptor mediated signaling. Here, we showed that either genetic ablation of Itk signaling or inhibition of Itk signaling pathways resulted in increased frequency of "noncanonical" CD4+ CD25- FOXP3+ Tregs (ncTregs), as well as of "canonical" CD4+ CD25+ FOXP3+ Tregs (canTregs). Using in vivo models, we showed that ncTregs can avert the formation of acute graft-versus-host disease (GVHD), in part by reducing conventional T cell proliferation, proinflammatory cytokine production, and tissue damage. This reduction in GVHD occurred without disruption of graft-versus-leukaemia (GVL) effects. RNA sequencing revealed that a number of effector, cell adhesion, and migration molecules were upregulated in Itk-/- ncTregs. Furthermore, disrupting the SLP76: ITK interaction using a specific peptide inhibitor led to enhanced Treg development in both mouse and primary human cells. This peptide inhibitor also significantly reduced inflammatory cytokine production in primary GVHD patient samples and mouse T cells without causing cell death or apoptosis. We provide evidence that specifically targeting Itk signaling could be a therapeutic strategy to treat autoimmune disorders.

Abstract 2470: Defining the reciprocal regulation of Abi1 and the androgen receptor in prostate cancer

Background: Prostate cancer (PCa) is a slowly progressing disease that affects nearly 50% of males over the age of 60. Current therapies for patients diagnosed with advanced PCa include Androgen Deprivation Therapy (ADT) and anti-androgen receptor (Anti-AR) treatment. PCa treatment primarily targets the androgen receptor (AR), a ligand-activated transcription factor, which is a key driver of PCa tumor growth. Our previous research has demonstrated that ABI1, acts as a tumor suppressor in PCa. ABI1 is a scaffold protein and an integral member of the WAVE Regulatory Complex (WRC), a nucleation promoting factor. UCSC database indicates there is an AR binding site within the ABI1 gene, suggesting AR plays a role in the transcriptional regulation of ABI1. In this study, we aim to characterize the ABI1-dependent AR regulation in PCa.

Method: We generated an ABI1 KO cell line model in LNCaP cells using CRISPR-Cas9. The efficiency of CRISPR-Cas9 was evaluated by Western Blotting and genomic alterations confirmed by DNA sequencing. In addition, we have generated ABI1 Isoform-specific rescue cell lines in our LNCaP ABI1 KO cell line with a binding mutation in the SH3 domain (ABI1-W485N) and an SH3 domain deleted (Abi1-ΔSH3) ABI1 protein. To understand AR and ABI1 dependent pathways we performed qPCR, co-immunoprecipitation, Western Blotting, ChIP, in vitro fluorescence spectra assay, immunofluorescence, proximity ligation assays. Results: In vitro binding assays indicate the interaction of AR, NTD poly-proline region, with the ABI1 SH3 domain. Expression of ABI1- W485N in our ABI1 CRISPR KO cell line showed decrease binding, while ABI1-ΔSH3 showed no binding to AR in co-IP assays compared to our control. Consequently, we saw decreased AR nuclear localization compared to our ABI1-WT control. Furthermore, decreased nuclear localization in our ABI1-W485N mutant was associated with decreased mRNA expression of hallmark AR target genes, Prostate-Specific-Antigen (KLK3), and TMPRSS2. ABI1 is an AR responsive gene and was confirmed with ChIP assays in an AR overexpression cell line. Further, the stimulation of AR transcriptional activity increased cell-cell adhesion in an ABI1 dependent system.

Conclusions: Our preliminary studies demonstrate that AR and ABI1 have a negative feedback pathway. The loss of ABI1 resulted in a decrease of nuclear AR and a subsequent decrease in mRNA expression of AR target genes. AR can also modulate ABI1 expression on a transcriptional level as needed for this pathway to function. Future studies will investigate if anti-AR treatments could lead to the dysregulation of ABI1 and promote EMT through STAT3 activation until AR transcriptional regulation on ABI1 is restored. These findings will allow for novel insights into the mechanisms underlying AR and ABI1 relationship in neoplastic progression.

Citation Format: Baylee A. Porter, Alaji Bah, Alfonso Urbanucci, Fan Zhang, Sonia Kung, Ladan Fazli, Martin Gleave, Gennady Bratslavsky, Leszek Kotula. Defining the reciprocal regulation of Abi1 and the androgen receptor in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2470.

Src family kinases, adaptor proteins and the actin cytoskeleton in epithelial-to-mesenchymal transition

Over a century of scientific inquiry since the discovery of v-SRC but still no final judgement on SRC function. However, a significant body of work has defined Src family kinases as key players in tumor progression, invasion and metastasis in human cancer. With the ever-growing evidence supporting the role of epithelial-mesenchymal transition (EMT) in invasion and metastasis, so does our understanding of the role SFKs play in mediating these processes. Here we describe some key mechanisms through which Src family kinases play critical role in epithelial homeostasis and how their function is essential for the propagation of invasive signals. Video abstract.

A Tale of Loops and Tails: The Role of Intrinsically Disordered Protein Regions in R-Loop Recognition and Phase Separation

R-loops are non-canonical, three-stranded nucleic acid structures composed of a DNA:RNA hybrid, a displaced single-stranded (ss)DNA, and a trailing ssRNA overhang. R-loops perform critical biological functions under both normal and disease conditions. To elucidate their cellular functions, we need to understand the mechanisms underlying R-loop formation, recognition, signaling, and resolution. Previous high-throughput screens identified multiple proteins that bind R-loops, with many of these proteins containing folded nucleic acid processing and binding domains that prevent (e.g., topoisomerases), resolve (e.g., helicases, nucleases), or recognize (e.g., KH, RRMs) R-loops. However, a significant number of these R-loop interacting Enzyme and Reader proteins also contain long stretches of intrinsically disordered regions (IDRs). The precise molecular and structural mechanisms by which the folded domains and IDRs synergize to recognize and process R-loops or modulate R-loop-mediated signaling have not been fully explored. While studying one such modular R-loop Reader, the Fragile X Protein (FMRP), we unexpectedly discovered that the C-terminal IDR (C-IDR) of FMRP is the predominant R-loop binding site, with the three N-terminal KH domains recognizing the trailing ssRNA overhang. Interestingly, the C-IDR of FMRP has recently been shown to undergo spontaneous Liquid-Liquid Phase Separation (LLPS) assembly by itself or in complex with another non-canonical nucleic acid structure, RNA G-quadruplex. Furthermore, we have recently shown that FMRP can suppress persistent R-loops that form during transcription, a process that is also enhanced by LLPS via the assembly of membraneless transcription factories. These exciting findings prompted us to explore the role of IDRs in R-loop processing and signaling proteins through a comprehensive bioinformatics and computational biology study. Here, we evaluated IDR prevalence, sequence composition and LLPS propensity for the known R-loop interactome. We observed that, like FMRP, the majority of the R-loop interactome, especially Readers, contains long IDRs that are highly enriched in low complexity sequences with biased amino acid composition, suggesting that these IDRs could directly interact with R-loops, rather than being “mere flexible linkers” connecting the “functional folded enzyme or binding domains”. Furthermore, our analysis shows that several proteins in the R-loop interactome are either predicted to or have been experimentally demonstrated to undergo LLPS or are known to be associated with phase separated membraneless organelles. Thus, our overall results present a thought-provoking hypothesis that IDRs in the R-loop interactome can provide a functional link between R-loop recognition via direct binding and downstream signaling through the assembly of LLPS-mediated membrane-less R-loop foci. The absence or dysregulation of the function of IDR-enriched R-loop interactors can potentially lead to severe genomic defects, such as the widespread R-loop-mediated DNA double strand breaks that we recently observed in Fragile X patient-derived cells.

Targeting SLP76:ITK interaction separates GVHD from GVL in allo-HSCT

Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a curative therapy for hematological malignancies, due to graft-versus-leukemia (GVL) activity mediated by alloreactive donor T cells. However, graft-versus-host disease (GVHD) is also mediated by these cells. Here, we assessed the effect of attenuating TCR-mediated SLP76:ITK interaction in GVL vs. GVHD effects after allo-HSCT. CD8+ and CD4+ donor T cells from mice expressing a Y145F mutation in SLP-76 did not cause GVHD but preserved GVL effects against B-ALL cells. SLP76Y145FKI CD8+ and CD4+ donor T cells also showed less inflammatory cytokine production and migration to GVHD target organs. We developed a novel peptide to specifically inhibit SLP76:ITK interactions, resulting in decreased phosphorylation of PLCγ1 and ERK, decreased cytokine production in human T cells, and separation of GVHD from GVL effects. Altogether, our data suggest that inhibiting SLP76:ITK interaction could be a therapeutic strategy to separate GVHD from GVL effects after allo-HSCT treatment.

Bok binds to a largely disordered loop in the coupling domain of type 1 inositol 1,4,5-trisphosphate receptor

Bcl-2-related ovarian killer (Bok) binds tightly to inositol 1,4,5-trisphosphate receptors (IP₃Rs). To better understand this interaction, we sought to elucidate the Bok binding determinants in IP₃R1, focusing on the ∼75 amino acid loop (residues 1882-1957) between α helices 72 and 73. Bioinformatic analysis revealed that the majority of this loop is intrinsically disordered, with two flanking regions of high disorder next to a low disorder central region (∼residues 1914-1926) that is predicted to contain two fused, disjointed transient helical elements. Experiments with IP₃R1 mutants, combined with computational analysis, indicated that small deletions in this central region block Bok binding due to perturbation of the helical elements. Studies in vitro with purified Bok and IP₃R1-derived peptides revealed high affinity binding to amino acids 1898-1940 of IP₃R1 (K_d ∼65 nM) and that binding affinity is also dependent upon both of the high disorder flanking regions. The strength of the Bok-IP₃R1 interaction was demonstrated by the ability of IP₃R1 or Bok to recruit transmembrane domain-free Bok or IP₃R1 mutants, respectively, to membranes in intact cells, and that these two mutants can bind in the cytosol independently of membrane association. Overall, we show that Bok binding to IP₃R1 occurs within a largely disordered loop between α helices 72 and 73 and that high affinity binding is mediated by multivalent interactions.

Complex data labeling with deep learning methods: Lessons from fisheries acoustics

Quantitative and qualitative analysis of acoustic backscattered signals from the seabed bottom to the sea surface is used worldwide for fish stocks assessment and marine ecosystem monitoring. Huge amounts of raw data are collected yet require tedious expert labeling. This paper focuses on a case study where the ground truth labels are non-obvious: echograms labeling, which is time-consuming and critical for the quality of fisheries and ecological analysis. We investigate how these tasks can benefit from supervised learning algorithms and demonstrate that convolutional neural networks trained with non-stationary datasets can be used to stress parts of a new dataset needing human expert correction. Further development of this approach paves the way toward a standardization of the labeling process in fisheries acoustics and is a good case study for non-obvious data labeling processes.

Targeting Interleukin-2-Inducible T-Cell Kinase (ITK) Differentiates GVL and GVHD in Allo-HSCT

Allogeneic hematopoietic stem cell transplantation is a potentially curative procedure for many malignant diseases. Donor T cells prevent disease recurrence via graft-versus-leukemia (GVL) effect. Donor T cells also contribute to graft-versus-host disease (GVHD), a debilitating and potentially fatal complication. Novel treatment strategies are needed which allow preservation of GVL effects without causing GVHD. Using murine models, we show that targeting IL-2-inducible T cell kinase (ITK) in donor T cells reduces GVHD while preserving GVL effects. Both CD8⁺ and CD4⁺ donor T cells from Itk^-/- mice produce less inflammatory cytokines and show decrease migration to GVHD target organs such as the liver and small intestine, while maintaining GVL efficacy against primary B-cell acute lymphoblastic leukemia (B-ALL). Itk^-/- T cells exhibit reduced expression of IRF4 and decreased JAK/STAT signaling activity but upregulating expression of Eomesodermin (Eomes) and preserve cytotoxicity, necessary for GVL effect. Transcriptome analysis indicates that ITK signaling controls chemokine receptor expression during alloactivation, which in turn affects the ability of donor T cells to migrate to GVHD target organs. Our data suggest that inhibiting ITK could be a therapeutic strategy to reduce GVHD while preserving the beneficial GVL effects following allo-HSCT treatment.

Co-chaperones TIMP2 and AHA1 Competitively Regulate Extracellular HSP90:Client MMP2 Activity and Matrix Proteolysis

The extracellular molecular chaperone heat shock protein 90 (eHSP90) stabilizes protease client the matrix metalloproteinase 2 (MMP2), leading to tumor cell invasion. Although co-chaperones are critical modulators of intracellular HSP90:client function, how the eHSP90:MMP2 complex is regulated remains speculative. Here, we report that the tissue inhibitor of metalloproteinases-2 (TIMP2) is a stress-inducible extracellular co-chaperone that binds to eHSP90, increases eHSP90 binding to ATP, and inhibits its ATPase activity. In addition to disrupting the eHSP90:MMP2 complex and terminally inactivating MMP2, TIMP2 loads the client to eHSP90, keeping the protease in a transient inhibitory state. Secreted activating co-chaperone AHA1 displaces TIMP2 from the complex, providing a "reactivating" mechanism for MMP2. Gene knockout or blocking antibodies targeting TIMP2 and AHA1 released by HT1080 cancer cells modify their gelatinolytic activity. Our data suggest that TIMP2 and AHA1 co-chaperones function as a molecular switch that determines the inhibition and reactivation of the eHSP90 client protein MMP2.

[Health care-associated infections in teaching hospital Gabriel TOURE]

OBJECTIVES

To study health care-associated infections (HCAI) in teaching hospital Gabriel TOURE.

METHODOLOGY

This was a prospective study of 6 months (from April to September 2016) which included patients admitted to the General Surgery Department, operated or not, except those who had undergone a necrosectomy. The criteria used for the diagnosis of the infection were those of the CDC of Atlanta.

RESULTS

A total of 200 patients were included in the study. Twenty one patients developed IAS that is a frequency of 10.5%. There were 11 men and 10 women with a mean age of 37.7 years with a standard deviation of 17.6 years. Surgical site infection was the most common HCAI (77.3%) followed by urinary tract infection (13.6%) and burn infection (9.1%). The influencing factors were those related to the patients (nutritional status p = 0.004, anemia RR = 3.1 IC p = 0.003 and diabetes), those related to the surgical intervention (the duration of the intervention ≥ 2H, p = 0,0001, the Altemeier class 3 and 4, RR = 4.24, IC p = 0.005, the number of interveners in the blocks ≥7, p = 0.000, the NNISS score 1 and 2 p = 0.0009), invasive procedures (bladder catheter ≥ 4 days p = 0.0000). Escherichia coli was the most isolated microorganism (31.2%) followed by Klebsiella pneumonia and A baumannii (18.7%). The treatment was local (twice-daily dressing with antiseptics), surgical (necrosectomy 16% and re-intervention 10%) and general (adapted to the antibiogram). The consequences of HCAI were an extension of total hospital stay (greater than 7 days) with p = 0.0000, morbidity 3% and mortality 5%.

CONCLUSION

HCAI remains a concern in our country and globally. They prolong the hospital stay. The implementation of a prevention, control and surveillance program will improve the quality of care by significantly reducing HCAI.

[Foreskin Cyst After Circumcision At The Hospital Of Sikasso (MALI)]

Cyst scar post circumcision of the stump of the prepuce is pathology of which we have not found any cases in the literature. The circumcision traditional is still practiced in our regions with its attendant complications, in particular, the high section, the whole or part of the gland, infections. The case we report concerns a patient 24 years of age, having a large cyst of 8cm diameter, evolving for the past 17 years. The patient has not informed his parents that when the desire to marry has become very pressing. The consultation was motivated by the psychological trauma, the discomfort and the pain caused by the infection, and the fistulisation. The treatment was surgical with bedroom suites. This observation underscores the importance of the knowledge of good surgical technique in order to minimize complications; it also sheds light on the taboo side of the pathologies the sphere uro-genitale.

Theoretical assessment of the impact of desert aerosols on the dynamical transmission of meningitidis serogroup A

This paper has been motivated by the following biological question: how influential are desert aerosols in the transmission of meningitidis serogroup A (MenA)? A mathematical model for the dynamical transmission of MenA is considered, with the aim of investigating the impact of desert aerosols. Sensitivity analysis of the model has been performed in order to determine the impact of related parameters on meningitis outbreak. We derive the basic reproduction number [Formula: see text]. We prove that there exists a threshold parameter [Formula: see text] such that when [Formula: see text], the disease-free equilibrium is globally asymptotically stable (GAS). However, when [Formula: see text], the model exhibits the phenomenon of backward bifurcation. At the endemic level, we show that the number of infectious individuals in the presence of desert aerosols is larger than the corresponding number without the presence of desert aerosols. In conjunction with the inequality [Formula: see text] where [Formula: see text] is the basic reproduction number without desert aerosols, we found that the ingestion of aerosols by carriers will increase the endemic level, and the severity of the outbreak. This suggests that the control of MenA passes through a combination of a large coverage vaccination of young susceptible individuals and the production of a vaccine with a high level of efficacy as well as respecting the hygienic rules to avoid the inhalation of desert aerosols. Theoretical results are supported by numerical simulations.

Theoretical assessment of the impact of environmental contamination on the dynamical transmission of polio

A mathematical model for the dynamical transmission of polio is considered, with the aim of investigating the impact of environment contamination. The model captures two infection pathways through both direct human-to-human transmission and indirect human-to-environment-to-human transmission by incorporating the environment as a transition and/or reservoir of viruses. We derive the basic reproduction number [Formula: see text]. We show that the disease free equilibrium is globally asymptotically stable (GAS) if [Formula: see text], while if [Formula: see text], there exists a unique endemic equilibrium which is locally asymptotically stable (LAS). Similar results hold for environmental contamination free sub-model (without the incorporation of the indirect transmission). At the endemic level, we show that the number of infected individuals for the model with the environmental-related contagion is greater than the corresponding number for the environmental contamination free sub-model. In conjunction with the inequality [Formula: see text], where [Formula: see text] is the basic reproduction number for the environmental contamination free sub-model, our finding suggests that the contaminated environment plays a detrimental role on the transmission dynamics of polio disease by increasing the endemic level and the severity of the outbreak. Therefore, it is natural to implement control strategies to reduce the severity of the disease by providing adequate hygienic living conditions, educate populations at risk to follow rigorously those basic hygienic rules in order to avoid adequate contacts with suspected contaminated objects. Further, we perform numerical simulations to support the theory.

[Breast Cancer: Immunohistochemistry And Prognosis At Gabriel Touré Teaching Hospital In Bamako-Mali]

Breast cancer is the second cancer of women in Mali. Immunohistochemistry is poorly performed in our African countries.

OBJECTIVES

To describe the immunohistochemical aspect and determine the prognosis of breast cancer.

METHODOLOGY

This is a retrospective descriptive study (March 2006-July 2016) in the General Surgery Department of Gabriel Toure University Hospital in Bamako, Mali. Immunohistochemistry was performed in all patients through a collaboration of our German partners.

RESULTS

We collected 98 patients (95 women and 3 men) with an average age of 40.04 ± 13.07 years. Twenty-two patients (22.44%) had a personal history of benign breast disease. In 16 patients (16.33%), we found a family breast cancer. The most common histological types were intra ductal carcinoma with 84 (85.72%) and invasive lobular carcinoma in 9 cases (9.18%). Immunohistochemistry found a predominance of triple negative with forty nine patients (50%) followed by Luminal A subtype with 26 cases (26.23%). According to the TNM classification, 44 patients (44.90%) were received at stage III. The median survival was 60 months in the group of patients who received hormone therapy versus 28 months for the group without hormone therapy (p = 0.007).

CONCLUSION

Immunohistochemistry is essential for the adequate management of breast cancer. Its realization has allowed us to improve the prognosis of hormone-dependent cancers.

Lipomatosis of interdigital nerves: Unusual localization

Lipomatosis of the nerve (LN) is a rare benign tumor that is characterized by proliferating fibrous fatty tissue surrounding and infiltrating the peripheral nerves. While there are numerous case reports of LN affecting the median nerve and its branches, there are few reports, to the authors' knowledge, of their occurrence in the foot and ankle. A rare case of LN involving the second and third interdigital nerve in a 41-year-old man, which was successfully treated with surgical excision, is reported.

Pi-Pi contacts are an overlooked protein feature relevant to phase separation

Protein phase separation is implicated in formation of membraneless organelles, signaling puncta and the nuclear pore. Multivalent interactions of modular binding domains and their target motifs can drive phase separation. However, forces promoting the more common phase separation of intrinsically disordered regions are less understood, with suggested roles for multivalent cation-pi, pi-pi, and charge interactions and the hydrophobic effect. Known phase-separating proteins are enriched in pi-orbital containing residues and thus we analyzed pi-interactions in folded proteins. We found that pi-pi interactions involving non-aromatic groups are widespread, underestimated by force-fields used in structure calculations and correlated with solvation and lack of regular secondary structure, properties associated with disordered regions. We present a phase separation predictive algorithm based on pi interaction frequency, highlighting proteins involved in biomaterials and RNA processing.

Chronic anterior shoulder instability with significant Hill-Sachs lesion: Arthroscopic Bankart with remplissage versus open Latarjet procedure

BACKGROUND

The objective of this study was to compare short-term shoulder stability after arthroscopic Bankart repair with remplissage versus the open Latarjet procedure in patients who had chronic anterior shoulder instability with a significant Hill-Sachs lesion.

HYPOTHESIS

The dislocation recurrence rate is higher after Bankart repair with remplissage than after open Latarjet.

PATIENTS AND METHODS

An observational non-randomised retrospective cohort study was conducted at two surgical centres in patients treated for chronic anterior shoulder instability with a significant Hill-Sachs defect between January 2009 and July 2014. The study compared 43 patients managed by arthroscopic Bankart repair and remplissage and 43 patients managed with open Latarjet. The two groups were matched on age at surgery and on follow-up duration. All patients were evaluated by independent observers based on a questionnaire including recurrences, range of motion, and functional outcomes (Shoulder Subjective Value [SSV], Walch-Duplay score, and Rowe score).

RESULTS

Mean follow-up was 47.3 months (range, 24-67 months). The recurrence rate at last follow-up was not significantly different between the two groups (9.3% versus 11.2%; P=0.67). The Bankart group had significantly greater loss of external rotation and a significantly higher proportion of patients with residual pain (21% versus 9%, P=0.023). The SSV, Walch-Duplay score, and Rowe score values were similar between groups.

DISCUSSION

In patients who had chronic anterior shoulder instability with a significant Hill-Sachs lesion, arthroscopic Bankart repair with remplissage and open Latarjet were reliable and safe procedures associated with low and similar recurrence rates. However, loss of external rotation and residual pain were significantly more common with the combined Bankart-remplissage procedure.

LEVEL OF EVIDENCE

III; comparative retrospective study.

[Bilio-Digestives Derivative In The Palliative Surgery Of Pancreatic Head Cancer At The CHU Gabriel TOURE]

OBJECTIVES

Our objective was to determine the frequency of bilio-digestive bypass in palliative surgery in pancreatic head cancers, to determine the clinical and para-clinical aspects and to analyze the results of the treatment.

METHODS

This was a-15 year retrospective study from 1999 to 2014 including any patient with confirmed pancreatic cancer in the anatomo-pathology treated by palliative surgery in the department.

RESULTS

In 15 years, we operated152 cases of cancer of the head of the pancreas. The bilio-digestive derivation was performed in 78 patients, or 51.32%. The average age was 58.61 years ± 11.22 years with the extremes of 34 and 79 years old, the sex ratio was 1.44. The disease duration was 4.88 months on average with a standard deviation of 4.28 months and extremes of 1 and 24 months. Courvoisier-Terrier's disease was observed in 76 cases with lesions of the cases. The average pancreatic tumor size was 62.98 mm, and standard deviation = 8.68 with the extremes of45 and 121 mm. We performed a choledoco-duodenal anastomosis and a gastro-entero-anastomosis (GEA) in 85.90% of cases (n = 67), a choledocojejunal anastomosis and a GEA in 7 cases and a choledoco-duodenal anastomosis without GEA in 4 cases. The morbidity and the mortality rates were15.4% and 6.41%, respectively. At six (6) months postsurgery, a complete disappearance the majority of the functional signs was observed.

CONCLUSION

Pancreatic cancer is a slowly developing tumor. Therefore its diagnosis is late; the derivation makes it possible to improve the quality of life of the patients.

Structural and hydrodynamic properties of an intrinsically disordered region of a germ cell-specific protein on phase separation

Membrane encapsulation is frequently used by the cell to sequester biomolecules and compartmentalize their function. Cells also concentrate molecules into phase-separated protein or protein/nucleic acid "membraneless organelles" that regulate a host of biochemical processes. Here, we use solution NMR spectroscopy to study phase-separated droplets formed from the intrinsically disordered N-terminal 236 residues of the germ-granule protein Ddx4. We show that the protein within the concentrated phase of phase-separated Ddx4, [Formula: see text], diffuses as a particle of 600-nm hydrodynamic radius dissolved in water. However, NMR spectra reveal sharp resonances with chemical shifts showing [Formula: see text] to be intrinsically disordered. Spin relaxation measurements indicate that the backbone amides of [Formula: see text] have significant mobility, explaining why high-resolution spectra are observed, but motion is reduced compared with an equivalently concentrated nonphase-separating control. Observation of a network of interchain interactions, as established by NOE spectroscopy, shows the importance of Phe and Arg interactions in driving the phase separation of Ddx4, while the salt dependence of both low- and high-concentration regions of phase diagrams establishes an important role for electrostatic interactions. The diffusion of a series of small probes and the compact but disordered 4E binding protein 2 (4E-BP2) protein in [Formula: see text] are explained by an excluded volume effect, similar to that found for globular protein solvents. No changes in structural propensities of 4E-BP2 dissolved in [Formula: see text] are observed, while changes to DNA and RNA molecules have been reported, highlighting the diverse roles that proteinaceous solvents play in dictating the properties of dissolved solutes.

An evolutionary switch in ND2 enables Src kinase regulation of NMDA receptors

The non-receptor tyrosine kinase Src is a key signalling hub for upregulating the function of N-methyl D-aspartate receptors (NMDARs). Src is anchored within the NMDAR complex via NADH dehydrogenase subunit 2 (ND2), a mitochondrially encoded adaptor protein. The interacting regions between Src and ND2 have been broadly identified, but the interaction between ND2 and the NMDAR has remained elusive. Here we generate a homology model of ND2 and dock it onto the NMDAR via the transmembrane domain of GluN1. This interaction is enabled by the evolutionary loss of three helices in bilaterian ND2 proteins compared to their ancestral homologues. We experimentally validate our model and demonstrate that blocking this interaction with an ND2 fragment identified in our experimental studies prevents Src-mediated upregulation of NMDAR currents in neurons. Our findings establish the mode of interaction between an NMDAR accessory protein with one of the core subunits of the receptor.

N-methyl D-aspartate receptor (NMDAR) activity is modulated by Src tyrosine kinase via the mitochondrial protein NADH dehydrogenase subunit 2 (ND2). Here the authors show that ND2 interacts with the transmembrane region of NMDAR GluN1 subunit, a process that is crucial for Src regulation of NMDAR activity.

Parameter and state estimation in a Neisseria meningitidis model: A study case of Niger

Neisseria meningitidis (Nm) is a major cause of bacterial meningitidis outbreaks in Africa and the Middle East. The availability of yearly reported meningitis cases in the African meningitis belt offers the opportunity to analyze the transmission dynamics and the impact of control strategies. In this paper, we propose a method for the estimation of state variables that are not accessible to measurements and an unknown parameter in a Nm model. We suppose that the yearly number of Nm induced mortality and the total population are known inputs, which can be obtained from data, and the yearly number of new Nm cases is the model output. We also suppose that the Nm transmission rate is an unknown parameter. We first show how the recruitment rate into the population can be estimated using real data of the total population and Nm induced mortality. Then, we use an auxiliary system called observer whose solutions converge exponentially to those of the original model. This observer does not use the unknown infection transmission rate but only uses the known inputs and the model output. This allows us to estimate unmeasured state variables such as the number of carriers that play an important role in the transmission of the infection and the total number of infected individuals within a human community. Finally, we also provide a simple method to estimate the unknown Nm transmission rate. In order to validate the estimation results, numerical simulations are conducted using real data of Niger.

Anemia Offers Stronger Protection Than Sickle Cell Trait Against the Erythrocytic Stage of Falciparum Malaria and This Protection Is Reversed by Iron Supplementation

Background

Iron deficiency causes long-term adverse consequences for children and is the most common nutritional deficiency worldwide. Observational studies suggest that iron deficiency anemia protects against Plasmodium falciparum malaria and several intervention trials have indicated that iron supplementation increases malaria risk through unknown mechanism(s). This poses a major challenge for health policy. We investigated how anemia inhibits blood stage malaria infection and how iron supplementation abrogates this protection.

Methods

This observational cohort study occurred in a malaria-endemic region where sickle-cell trait is also common. We studied fresh RBCs from anemic children (135 children; age 6–24 months; hemoglobin < 11 g/dl) participating in an iron supplementation trial (ISRCTN registry, number ISRCTN07210906) in which they received iron (12 mg/day) as part of a micronutrient powder for 84 days. Children donated RBCs at baseline, Day 49, and Day 84 for use in flow cytometry-based in vitro growth and invasion assays with P. falciparum laboratory and field strains. In vitro parasite growth in subject RBCs was the primary endpoint.

Findings

Anemia substantially reduced the invasion and growth of both laboratory and field strains of P. falciparum in vitro (~ 10% growth reduction per standard deviation shift in hemoglobin). The population level impact against erythrocytic stage malaria was 15.9% from anemia compared to 3.5% for sickle-cell trait. Parasite growth was 2.4 fold higher after 49 days of iron supplementation relative to baseline (p < 0.001), paralleling increases in erythropoiesis.

Interpretation

These results confirm and quantify a plausible mechanism by which anemia protects African children against falciparum malaria, an effect that is substantially greater than the protection offered by sickle-cell trait. Iron supplementation completely reversed the observed protection and hence should be accompanied by malaria prophylaxis. Lower hemoglobin levels typically seen in populations of African descent may reflect past genetic selection by malaria.

Funding

National Institute of Child Health and Development, Bill and Melinda Gates Foundation, UK Medical Research Council (MRC) and Department for International Development (DFID) under the MRC/DFID Concordat.

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P. falciparum laboratory and field strains invade and grow less efficiently in RBCs from anemic children.

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Deficits in invasion and growth for erythrocytic stage P. falciparum are reversed when RBCs are used from anemic children receiving iron supplementation for 49 and 84 days.

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The population level impact of protection against malaria from anemia was greater than that for sickle-cell trait.

The long-term consequences of anemia are severe, and it is easily treatable. However, concerns remain about the safety of iron supplements, particularly for children in malaria-endemic countries lacking adequate access to health services. We used RBCs from Gambian children before, during, and after 12 weeks of daily iron supplementation for in vitro P. falciparum assays. P. falciparum invasion and growth was decreased in anemic RBCs and increased after 49 days of iron supplementation relative to baseline (p < 0.001), paralleling increases in young RBCs, which the parasite prefers. The parasite growth protection from anemia was substantial, providing greater population level impact than sickle-cell trait.

Modulation of Intrinsically Disordered Protein Function by Post-translational Modifications

Post-translational modifications (PTMs) produce significant changes in the structural properties of intrinsically disordered proteins (IDPs) by affecting their energy landscapes. PTMs can induce a range of effects, from local stabilization or destabilization of transient secondary structure to global disorder-to-order transitions, potentially driving complete state changes between intrinsically disordered and folded states or dispersed monomeric and phase-separated states. Here, we discuss diverse biological processes that are dependent on PTM regulation of IDPs. We also present recent tools for generating homogenously modified IDPs for studies of PTM-mediated IDP regulatory mechanisms.

Folding of an intrinsically disordered protein by phosphorylation as a regulatory switch

Intrinsically disordered proteins play important roles in cell signalling, transcription, translation and cell cycle regulation. Although they lack stable tertiary structure, many intrinsically disordered proteins undergo disorder-to-order transitions upon binding to partners. Similarly, several folded proteins use regulated order-to-disorder transitions to mediate biological function. In principle, the function of intrinsically disordered proteins may be controlled by post-translational modifications that lead to structural changes such as folding, although this has not been observed. Here we show that multisite phosphorylation induces folding of the intrinsically disordered 4E-BP2, the major neural isoform of the family of three mammalian proteins that bind eIF4E and suppress cap-dependent translation initiation. In its non-phosphorylated state, 4E-BP2 interacts tightly with eIF4E using both a canonical YXXXXLΦ motif (starting at Y54) that undergoes a disorder-to-helix transition upon binding and a dynamic secondary binding site. We demonstrate that phosphorylation at T37 and T46 induces folding of residues P18-R62 of 4E-BP2 into a four-stranded β-domain that sequesters the helical YXXXXLΦ motif into a partly buried β-strand, blocking its accessibility to eIF4E. The folded state of pT37pT46 4E-BP2 is weakly stable, decreasing affinity by 100-fold and leading to an order-to-disorder transition upon binding to eIF4E, whereas fully phosphorylated 4E-BP2 is more stable, decreasing affinity by a factor of approximately 4,000. These results highlight stabilization of a phosphorylation-induced fold as the essential mechanism for phospho-regulation of the 4E-BP:eIF4E interaction and exemplify a new mode of biological regulation mediated by intrinsically disordered proteins.

Evaluation of bovine (Bos indicus) ovarian potential for in vitro embryo production in the Adamawa plateau (Cameroon)

An abattoir study was conducted to evaluate the ovarian potential of 201 local zebu cattle from Ngaoundere, Adamawa region (Cameroon) for in vitro embryo production (IVEP). The ovaries were excised, submerged in normal saline solution (0.9%) and transported to the laboratory for a detailed evaluation. Follicles on each ovary were counted, their diameters (F) measured and were grouped into 3 categories: small (F < 3 mm), medium (3 = F = 8 mm) and large (F > 8 mm). Each ovary was then sliced into a petri dish; the oocytes were recovered in Dulbecco’s phosphate buffered saline, examined under a stereoscope (x10) and graded into four groups based on the morphology of cumulus oophorus cells and cytoplasmic changes of the oocytes. Grade I (GI): oocytes with more than 4 layers of bunch of compact cumulus cells mass with evenly granulated cytoplasm; grade II (GII): oocyte with at least 2–4 layers of compact cumulus cell mass with evenly granulated cytoplasm; grade III (GIII): oocyte with at least one layer of compact cumulus cell mass with evenly granulated cytoplasm; grade IV (GIV): denuded oocyte with no cumulus cells or incomplete layer of cumulus cell or expanded cells and having dark or unevenly granulated cytoplasm. The effects of both ovarian (ovarian localization, corpus luteum, size and weight of ovary) and non-ovarian factors (breed, age, body condition score (BCS) and pregnancy status of cow) on the follicular population and oocyte recovery rate were determined. There were an average of 16.75±0.83 follicles per ovary. The small, medium and large follicles were 8.39±0.60, 8.14±0.43 and 0.21±0.02 respectively. Oocyte recovery was 10.97±0.43 per ovary (65%). Oocytes graded I, II, III and IV were 3.53±0.19 (32.21%), 2.72±0.15 (24.82%), 2.24±0.15 (20.43%) and 2.47±0.20 (22.54%) respectively. The oocyte quality index was 2.26. Younger non pregnant cows having BCS of 3 and large ovaries presented higher number of follicles and oocyte quality (P < 0.05) compared with other animals. Oocytes with quality (grade I and II) acceptable for IVEP constituted 57.15% of the harvest. This study indicated that factors such as age, pregnancy status, BCS and ovarian size must be taken into account to increase the potential of the ovary for IVEP.

Interaction of the eukaryotic initiation factor 4E with 4E-BP2 at a dynamic bipartite interface

Cap-dependent translation initiation is regulated by the interaction of eukaryotic initiation factor 4E (eIF4E) with eIF4E binding proteins (4E-BPs). Whereas the binding of 4E-BP peptides containing the eIF4E-binding ⁵⁴YXXXXLΦ⁶⁰ motif has been studied, atomic-level characterization of the interaction of eIF4E with full-length 4E-BPs has been lacking. Here, we use isothermal titration calorimetry and nuclear magnetic resonance spectroscopy to characterize the dynamic, structural and binding properties of 4E-BP2. Although disordered, 4E-BP2 contains significant fluctuating secondary structure and binds eIF4E at an extensive bipartite interface including the canonical ⁵⁴YXXXXLΦ⁶⁰ and ⁷⁸IPGVT⁸² sites. Each of the two binding elements individually has submicromolar affinity and exchange on and off of the eIF4E surface within the context of the overall nanomolar complex. This dynamic interaction facilitates exposure of regulatory phosphorylation sites within the complex. The 4E-BP2 interface on eIF4E overlaps yet is more extensive than the eIF4G:eIF4E interface, suggesting that these key interactions may be differentially targeted for therapeutics.

Solution structure of a minor and transiently formed state of a T4 lysozyme mutant

Proteins are inherently plastic molecules, whose function often critically depends on excursions between different molecular conformations (conformers). However, a rigorous understanding of the relation between a protein's structure, dynamics and function remains elusive. This is because many of the conformers on its energy landscape are only transiently formed and marginally populated (less than a few per cent of the total number of molecules), so that they cannot be individually characterized by most biophysical tools. Here we study a lysozyme mutant from phage T4 that binds hydrophobic molecules and populates an excited state transiently (about 1 ms) to about 3% at 25 °C (ref. 5). We show that such binding occurs only via the ground state, and present the atomic-level model of the 'invisible', excited state obtained using a combined strategy of relaxation-dispersion NMR (ref. 6) and CS-Rosetta model building that rationalizes this observation. The model was tested using structure-based design calculations identifying point mutants predicted to stabilize the excited state relative to the ground state. In this way a pair of mutations were introduced, inverting the relative populations of the ground and excited states and altering function. Our results suggest a mechanism for the evolution of a protein's function by changing the delicate balance between the states on its energy landscape. More generally, they show that our approach can generate and validate models of excited protein states.

Rigidification of the autolysis loop enhances Na(+) binding to thrombin

Binding of Na(+) to thrombin ensures high activity toward physiological substrates and optimizes the procoagulant and prothrombotic roles of the enzyme in vivo. Under physiological conditions of pH and temperature, the binding affinity of Na(+) is weak due to large heat capacity and enthalpy changes associated with binding, and the K(d)=80 mM ensures only 64% saturation of the site at the concentration of Na(+) in the blood (140 mM). Residues controlling Na(+) binding and activation have been identified. Yet, attempts to improve the interaction of Na(+) with thrombin and possibly increase catalytic activity under physiological conditions have so far been unsuccessful. Here we report how replacement of the flexible autolysis loop of human thrombin with the homologous rigid domain of the murine enzyme results in a drastic (up to 10-fold) increase in Na(+) affinity and a significant improvement in the catalytic activity of the enzyme. Rigidification of the autolysis loop abolishes the heat capacity change associated with Na(+) binding observed in the wild-type and also increases the stability of thrombin. These findings have general relevance to protein engineering studies of clotting proteases and trypsin-like enzymes.