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Schematic overview of different gene regulatory network inference approache...
Published: 25 January 2023
Figure 1. Schematic overview of different gene regulatory network inference approaches. ( A ) Classical approaches, e.g. correlation, regression or mutual information, can be applied on gene expression data to generate undirected co-expression networks. With prior knowledge about TFs the directio... More
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The biological functions of NMD in plants.  NMD contributes plant physiolog...
Published: 25 January 2023
Figure 1. The biological functions of NMD in plants. NMD contributes plant physiology and development through its canonical role (depicted in green) as a post-transcriptional gene regulator, or via non-canonical functions (shown in orange) of respective NMD factors. While degradation of EBI1/2 tr... More
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Multiscale structural analysis using cryo-EM.  ( A ) Schematic representati...
Published: 25 January 2023
Figure 1. Multiscale structural analysis using cryo-EM. ( A ) Schematic representation of different actin cytoskeleton assemblies found in cells and migratory protrusions. ( B ) Visualization of resolution ranges and applications for SPA and helical reconstruction cryo-EM, and cryo-ET and subtomo... More
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Structural insights via cryo-EM into lamellipodium initiation and maintenan...
Published: 25 January 2023
Figure 2. Structural insights via cryo-EM into lamellipodium initiation and maintenance. A schematic drawing of branched actin network turnover in the lamellipodium, visualizing the ‘Nucleation/Elongation’, ‘Treadmilling’, and ‘Depolymerization zones that are regulated by different ABPs. Surface ... More
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Macrophage cell-extrinsic sensing.  Macrophages phagocytose dying cells and...
Published: 25 January 2023
Figure 1. Macrophage cell-extrinsic sensing. Macrophages phagocytose dying cells and sense extracellular debris ( 1 ). TLR7 and TLR8 can recognise IAV ssRNA liberated from engulfed cells, while mtDNA might escape and trigger cGAS-STING signalling. Large aggregates, like PB1-F2 fibrils or ASC spec... More
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Specific PAMP and DAMP release from major PCD pathways during IAV infection...
Published: 25 January 2023
Figure 2. Specific PAMP and DAMP release from major PCD pathways during IAV infection. This figure gives a simplified overview of PCD pathways. Clockwise from upper left: Intrinsic Apoptosis, triggered by direct IAV infection or CTL or NK-cell granule exocytosis, culminates in Caspase-9 activatio... More
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Dynamic binding of the MLL1 complex on the NCP.  ( a )Top, front and back v...
Published: 25 January 2023
Figure 1. Dynamic binding of the MLL1 complex on the NCP. ( a )Top, front and back view of the cryo-EM structure of the MLL1–WRA–NCP complex (PDB: 7MBN , EMDB: 23738) [ 31 ]. RBBP5 and ASH2L interact with DNA at SHL1.5 and SHL7, respectively. RBBP5, dark green, ASH2L, orange, MLL1 SET , light pu... More
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Schematic representation of context-specific GPCR signalling at the spatial...
Published: 23 January 2023
Figure 1. Schematic representation of context-specific GPCR signalling at the spatial, temporal, and cell-specific level. ( A ) Spatial segregation of receptors can lead to compartment-specific coupling and signalling. For instance, recent work has suggested that, apart from the established cAMP ... More
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APP processing pathways.  ( A ) Non-amyloidogenic APP processing. First, AP...
Published: 23 January 2023
Figure 1. APP processing pathways. ( A ) Non-amyloidogenic APP processing. First, APP is cleaved by ADAM10 leading to the production of C83 and sAPPα. Next, C83 is cleaved γ-secretase leading to the production of AICD and p3. ( B ) Amyloidogenic processing. First, APP is cleaved by BACE1 leading ... More
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APP, APP fragments, and mitochondria.  Current knowledge and knowledge gaps...
Published: 23 January 2023
Figure 2. APP, APP fragments, and mitochondria. Current knowledge and knowledge gaps. ( A ) Full-length APP and mitochondria. It is unknown if APP translocates into the mitochondria from the ER through MAMs. It is also unknown if APP modulates MAM function. Studies suggest APP inhibits COX (compl... More
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Overview of small molecule inhibitors targeting RAS.  ( A ) Selected SII-P ...
Published: 23 January 2023
Figure 1. Overview of small molecule inhibitors targeting RAS. ( A ) Selected SII-P small molecule inhibitors based on the 4-piperazin-1-yl-pyrimidine scaffold (green highlights). The common acrylamide warhead of KRAS-G12C inhibitors (top row) is highlighted in blue. Adagrasib served as a startin... More
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Overview of macromolecular RAS binders.  Crystal structure of GDP-KRAS (PDB...
Published: 23 January 2023
Figure 2. Overview of macromolecular RAS binders. Crystal structure of GDP-KRAS (PDB ID 4OBE ). Effector and allosteric lobes, as well as allosteric binding sites are indicated as in Figure 1 . The names of macromolecular RAS binders are highlighted in the same colour as their binding sites, wi... More
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Timeline of notable RAS drug development events since 2007.  Arrowheads mar...
Published: 23 January 2023
Figure 3. Timeline of notable RAS drug development events since 2007. Arrowheads mark publications of binders and sites with colours corresponding to those used for binding sites in Figures 1 and 2 . More
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Mitochondrial and mycobacterial oxidative phosphorylation.  ( A ) Schematic...
Published: 20 January 2023
Figure 1. Mitochondrial and mycobacterial oxidative phosphorylation. ( A ) Schematic of mammalian mitochondrial oxidative phosphorylation. ( B ) Schematic of mycobacterial oxidative phosphorylation. ( C ) Structure and midpoint potential of ubiquinone ( top ) and ubiquinol ( bottom ). ( D ) Struc... More
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Mycobacterial NADH:quinone oxidoreductases.  ( A ) Atomic model (PDB:  8E9G...
Published: 20 January 2023
Figure 2. Mycobacterial NADH:quinone oxidoreductases. ( A ) Atomic model (PDB: 8E9G ) ( top ) and cryoEM map (EMD-27963) ( bottom ) of mycobacterial complex I. Purple rectangle represents the mycobacterial inner membrane. ( B ) The redox centers of mycobacterial complex I. ( C ) Alignment of the... More
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Mycobacterial succinate:quinone oxidoreductases.  ( A ) Schematic showing t...
Published: 20 January 2023
Figure 3. Mycobacterial succinate:quinone oxidoreductases. ( A ) Schematic showing the two roles of succinate:quinone oxidoreductases (also known as succinate dehydrogenases or complex II) in the Krebs cycle and the electron transport chain. ( B ) Schematic of the Krebs cycle. Double-headed arrow... More
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Mycobacterial quinol:O 2  oxidoreductases.  ( A ) A cryoEM map of the  M. s...
Published: 20 January 2023
Figure 4. Mycobacterial quinol:O 2 oxidoreductases. ( A ) A cryoEM map of the M. smegmatis CIII 2 CIV 2 supercomplex (EMD-24455), also known as cytochrome bcc-aa 3 . The superoxide dismutase (SodC) region of the map ( dotted line ) is shown at a lower density threshold (0.004) than the rest... More
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Major cellular pathways frequently mutated in a large spectrum of human can...
Published: 20 January 2023
Figure 1. Major cellular pathways frequently mutated in a large spectrum of human cancers and leading to stimulation of, or increases in, eIF4F activity. Elevated eIF4E stimulates translation of selective mRNAs, a proportion of which fuel the Cancer Hallmarks. More
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Biological and small molecule inhibitors of eIF4E.  ( a ) Current target si...
Published: 20 January 2023
Figure 2. Biological and small molecule inhibitors of eIF4E. ( a ) Current target sites of eIF4F and eIF4E synthesis targeted for intervention. ( b ) Structure of eIF4E small molecule inhibitors. Compounds highlighted in pink target eIF4E:cap interaction whereas those highlighted in blue target e... More
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The TFIIS N-terminal domain (TND) is a structurally conserved fold enriched...
Published: 18 January 2023
Figure 1. The TFIIS N-terminal domain (TND) is a structurally conserved fold enriched among transcription regulators. ( A ) Enrichment of diverse SLiM interaction scaffolds among transcription regulators associated with GO term GO:0006351. ( B ) Characteristic right-handed five-helix bundle (α1–α... More
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TNDs are selective binding scaffolds for disordered TND-interacting motifs ...
Published: 18 January 2023
Figure 2. TNDs are selective binding scaffolds for disordered TND-interacting motifs (TIMs). ( A ) Comparison of human TNDs and interaction interfaces that each TND utilizes for TIM recognition. Residues forming the hydrophobic pockets (dark gray) and residues forming the positively charged basic... More
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TND-mediated interactions govern many transcriptional and co-transcriptiona...
Published: 18 January 2023
Figure 3. TND-mediated interactions govern many transcriptional and co-transcriptional processes. TND-containing proteins and mechanisms by which their TNDs contribute to transcription. More
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MHC-I antigen processing pathway.  Antigen Processing Pathway for MHC-I. Pr...
Published: 16 January 2023
Figure 1. MHC-I antigen processing pathway. Antigen Processing Pathway for MHC-I. Proteins are recycled into shorter peptides via the proteasome and further trimmed by cytosolic aminopeptidases. TAP1/2 transports peptides of optimal length and sequence preference into the ER, where they either di... More
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Proposed mechanisms of peptide editing and tapasin dependency.  Conformatio...
Published: 16 January 2023
Figure 2. Proposed mechanisms of peptide editing and tapasin dependency. Conformational and dynamic features observed to correlate with peptide editing. ( a ) Cartoon representations of peptide-free MHC-I heavy chain (blue) complexed with β2-microglobulin (purple) and tapasin (orange), visualised... More
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Overview of chain initiating and chain elongating E2 enzymes.  ( A ) E2 enz...
Published: 16 January 2023
Figure 1. Overview of chain initiating and chain elongating E2 enzymes. ( A ) E2 enzymes are charged with ubiquitin by a ubiquitin activating E1 enzyme. The resulting E2∼Ub conjugate is usually activated by interacting with an E3 ligase (indicated as RING) that promotes ubiquitin transfer. For in... More
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Structure of Ube2s, Ube2k, and Ube2r.  ( A ) Domain structure of the E2 enz...
Published: 16 January 2023
Figure 2. Structure of Ube2s, Ube2k, and Ube2r. ( A ) Domain structure of the E2 enzymes where flexible regions of the E2 enzymes are indicated with lines and domains are shown as coloured boxes. The numbers indicate the number of amino acids in the E2 enzymes. ( B ) Representative chain-building... More
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Regulation of Ube2s.  ( A ) In the absence of recruitment by the APC/C E3 l...
Published: 16 January 2023
Figure 3. Regulation of Ube2s. ( A ) In the absence of recruitment by the APC/C E3 ligase, Ube2s can form a dimer that prevents the conjugated ubiquitin from binding Ube2s in the catalytically active closed conformation. The dimerisation blocks interaction with the E1 enzyme and Ube2s-catalysed u... More
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Ube2k generates Lys48-linked ubiquitin chains.  ( A ) A second interface on...
Published: 16 January 2023
Figure 4. Ube2k generates Lys48-linked ubiquitin chains. ( A ) A second interface on the UBA domain of Ube2k helps position the acceptor ubiquitin (orange) on its active site (interactions highlighted in red) so it is oriented to produce Lys48-linked ubiquitin chains. ( B ) The UBA domain of Ube2... More
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Ube2r2 positions the donor ubiquitin and regulates its activity.  ( A ) The...
Published: 16 January 2023
Figure 5. Ube2r2 positions the donor ubiquitin and regulates its activity. ( A ) The acidic loop and C-terminal domain (both in red ribbons, interactions indicated by dotted lines) of Ube2r2 can help position ubiquitin in the closed conformation (PDB 6NYO ). ( B ) The helix-loop-helix motif (HLH... More
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Quantification of tyrosine hydroxylase (TH)+ cells in control and experimen...
Published: 16 January 2023
Figure 1. Quantification of tyrosine hydroxylase (TH)+ cells in control and experimental groups (treated with 100 µM of 6-hydroxydopamine, 6-OHDA). ( A ) comparison of control with experimental groups (1, 3, and 5 days of exposure to 6-OHDA). The results showed reduction in TH+ cells in all exper... More
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Effect of rotenone on the ascidian  Styela plicata  as evaluated by the sip...
Published: 16 January 2023
Figure 2. Effect of rotenone on the ascidian Styela plicata as evaluated by the siphon test. After systemic injection with 3 mg/kg of rotenone, the time of closure of the oral siphon after mechanical stimulation was evaluated from days 0 to 10 after injection. (*) animals injected with rotenone... More
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