Binding domain
View article: Unraveling theMolecular Inhibition and ConformationalChanges of Hsp70 and Hsc70 Induced by VER-155008, a Competitive ATPaseInhibitor through Molecular Dynamics Simulations and Principal ComponentAnalysis
Unraveling theMolecular Inhibition and ConformationalChanges of Hsp70 and Hsc70 Induced by VER-155008, a Competitive ATPaseInhibitor through Molecular Dynamics Simulations and Principal ComponentAnalysis Open
The heat shock protein 70 kDa (Hsp70) is critical for the survival of cancer cells, playing a role in developing chemotherapy resistance, since it inhibits apoptosis of these cells and ensures their survival in stressful environments. Due …
View article: V and C domains of Netrin-1 interact with the HBS of LIPG.
V and C domains of Netrin-1 interact with the HBS of LIPG. Open
A and B: Schematic representation of the heparin/heparan sulfate-binding sites of Netrin-1 and the substituted amino acid mutations. C: Diagram of wild-type LIPG and cleaved NTD and CTD, with or without deletion of the heparin-binding moti…
View article: Yeast two-hybrid assays for detecting the binding interactions between <i>Strongyloides stercoralis</i> insulin peptides and <i>Ss</i>-DAF-2 receptor isoforms.
Yeast two-hybrid assays for detecting the binding interactions between <i>Strongyloides stercoralis</i> insulin peptides and <i>Ss</i>-DAF-2 receptor isoforms. Open
Translational fusions were generated for the Gal4 activation domain (Gal4-AD) and the endogenous insulin peptides (ILP-1–7) in S. stercoralis. The Gal4 DNA binding domain (Gal4-BD) was fused to the insulin receptor Ss-DAF-2A …
View article: Data collection and refinement statistics.
Data collection and refinement statistics. Open
Butanol dehydrogenases (BDHs) are NAD(P)H-dependent oxidoreductases that catalyze the reversible conversion of butanol to butyraldehyde. These enzymes play essential roles in microbial butanol fermentation and show significant potential f…
View article: Targeted Inhibitionof CBP/p300–NCOA3 Interactionswith an α‑Methylated Peptide
Targeted Inhibitionof CBP/p300–NCOA3 Interactionswith an α‑Methylated Peptide Open
The CREB-binding protein (CBP) and its paralogue p300 are cellular integrators of various signaling pathways involved in various physiological functions. Together with NCOA proteins, they act as coactivators of nuclear receptors. CBP/p300 …
View article: Targeted Inhibitionof CBP/p300–NCOA3 Interactionswith an α‑Methylated Peptide
Targeted Inhibitionof CBP/p300–NCOA3 Interactionswith an α‑Methylated Peptide Open
The CREB-binding protein (CBP) and its paralogue p300 are cellular integrators of various signaling pathways involved in various physiological functions. Together with NCOA proteins, they act as coactivators of nuclear receptors. CBP/p300 …
View article: EGFR colocalizes with virions and interacts with ED3 domain of envelope protein.
EGFR colocalizes with virions and interacts with ED3 domain of envelope protein. Open
(a-b) SH-SY5Y cells were incubated with 100 MOI of virus for 1 h on ice and were subsequently fixed post at 0, 10, 30, and 60 mins of virus internalization. (a) Cells were immunostained with JEV envelope (magenta) and EGFR (green) antibodi…
View article: Phosphatase SHP2 pathogenic mutations enhance activity by altering conformational sampling
Phosphatase SHP2 pathogenic mutations enhance activity by altering conformational sampling Open
SH2 domains are critical mediators of cellular signaling, although the molecular mechanisms by which they bind their phosphopeptide ligands remain incompletely understood. We investigate the atomic mechanisms underlying both healthy regula…
View article: Image 4_Targeting a distinct binding pocket in the pregnane X receptor with natural agonist TRLW-2 ameliorates murine ulcerative colitis.tif
Image 4_Targeting a distinct binding pocket in the pregnane X receptor with natural agonist TRLW-2 ameliorates murine ulcerative colitis.tif Open
Background The therapeutic development of pregnane X receptor (PXR) agonists for ulcerative colitis (UC) is hindered by the poor selectivity of the canonical ligand-binding pocket. This study aimed to identify a novel, selectivity-enhancin…
View article: Image 3_Targeting a distinct binding pocket in the pregnane X receptor with natural agonist TRLW-2 ameliorates murine ulcerative colitis.tif
Image 3_Targeting a distinct binding pocket in the pregnane X receptor with natural agonist TRLW-2 ameliorates murine ulcerative colitis.tif Open
Background The therapeutic development of pregnane X receptor (PXR) agonists for ulcerative colitis (UC) is hindered by the poor selectivity of the canonical ligand-binding pocket. This study aimed to identify a novel, selectivity-enhancin…
View article: Structural similarity search using DALI.
Structural similarity search using DALI. Open
The Aspartokinase-Chorismate mutase-TyrA (ACT) domain is a conserved regulatory module found in a wide range of proteins involved in diverse biological processes, including amino acid metabolism, signal transduction, and cytoskeletal orga…
View article: Image 1_Targeting a distinct binding pocket in the pregnane X receptor with natural agonist TRLW-2 ameliorates murine ulcerative colitis.tif
Image 1_Targeting a distinct binding pocket in the pregnane X receptor with natural agonist TRLW-2 ameliorates murine ulcerative colitis.tif Open
Background The therapeutic development of pregnane X receptor (PXR) agonists for ulcerative colitis (UC) is hindered by the poor selectivity of the canonical ligand-binding pocket. This study aimed to identify a novel, selectivity-enhancin…
View article: Data collection and refinement statistics.
Data collection and refinement statistics. Open
The Aspartokinase-Chorismate mutase-TyrA (ACT) domain is a conserved regulatory module found in a wide range of proteins involved in diverse biological processes, including amino acid metabolism, signal transduction, and cytoskeletal orga…
View article: Image 2_Targeting a distinct binding pocket in the pregnane X receptor with natural agonist TRLW-2 ameliorates murine ulcerative colitis.tif
Image 2_Targeting a distinct binding pocket in the pregnane X receptor with natural agonist TRLW-2 ameliorates murine ulcerative colitis.tif Open
Background The therapeutic development of pregnane X receptor (PXR) agonists for ulcerative colitis (UC) is hindered by the poor selectivity of the canonical ligand-binding pocket. This study aimed to identify a novel, selectivity-enhancin…
View article: Functional assessment of <i>P. falciparum</i> IPMK2.
Functional assessment of <i>P. falciparum</i> IPMK2. Open
(A) A surface representation showing ATP binding and (B) a cartoon representation of the predicted P. falciparum IPMK2 domain with ATP docked into its active pocket, showing residues (yellow) in the active pocket that bind to ATP. T…
View article: Effect of Substrate-BindingDomain of Fusion Proteinon Binding with Poly(3-hydroxybutyrate)-Based Nanocarrier
Effect of Substrate-BindingDomain of Fusion Proteinon Binding with Poly(3-hydroxybutyrate)-Based Nanocarrier Open
The macromolecular stability of fused proteins is usually provided by punctual structural modifications along the primary sequence of the chimera. Among these, the disulfide bond formation stands out as a key parameter for enabling the gen…
View article: Location of incorporation of p53 mutants into HEK293 cells.
Location of incorporation of p53 mutants into HEK293 cells. Open
A cartoon schematic of the functional domains of the p53 protein overlaid with the locations of the mutations being examined in this study. Note that all three mutations lie within the DNA binding domain and that both single nucleotide pol…
View article: Three Key Regionsin Hemagglutinin Determine BindingSelectivity and Stability: Insights into Antiviral Drug Design
Three Key Regionsin Hemagglutinin Determine BindingSelectivity and Stability: Insights into Antiviral Drug Design Open
The receptor binding domain of hemagglutinin (HA) of influenza viruses contains three key regions for binding its endogenous carbohydrate receptors: loop-130, helix-190, and loop-220. To effectively predict the binding of HA with endogenou…
View article: Calculated ΔG of binding and the corresponding K<sub>d</sub> values for the different VWF species and the N-terminal (H1-T266) domain of platelet GpIbα. The binding parameters were calculated by the PRODIGY program at T = 37 °C.
Calculated ΔG of binding and the corresponding K<sub>d</sub> values for the different VWF species and the N-terminal (H1-T266) domain of platelet GpIbα. The binding parameters were calculated by the PRODIGY program at T = 37 °C. Open
Calculated ΔG of binding and the corresponding Kd values for the different VWF species and the N-terminal (H1-T266) domain of platelet GpIbα. The binding parameters were calculated by the PRODIGY program at T = 37 °C.
View article: Evaluation of Approved Drugs' Prion Protein Binding Profiles Using a Drug Repurposing Approach
Evaluation of Approved Drugs' Prion Protein Binding Profiles Using a Drug Repurposing Approach Open
Objective: Prion diseases are a critical neurodegenerative group with rapid progression, high mortality, and a lack of disease-modifying treatments. The conversion of PrP^C to the infectious PrP^Sc isoform is central to pathogenesis, and c…
View article: Ligand Binding tothe Membrane-Distal Domain of theMet Receptor Induces Dimerization at the Membrane-Proximal Domain
Ligand Binding tothe Membrane-Distal Domain of theMet Receptor Induces Dimerization at the Membrane-Proximal Domain Open
Activation of cytokine and growth factor receptors by ligands triggers crucial cellular responses in various physiological processes. However, our understanding of their structural basis remains incomplete due to the limited information on…
View article: Structural details of helix-mediated multimerization of the conserved region of TDP-43 C-terminal domain
Structural details of helix-mediated multimerization of the conserved region of TDP-43 C-terminal domain Open
Pathological inclusions of the C-terminal domain (CTD) of TAR DNA binding protein-43 (TDP-43) are neurodegenerative hallmarks in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia, yet CTD’s aggregation propensity complicates …
View article: Ligand Binding tothe Membrane-Distal Domain of theMet Receptor Induces Dimerization at the Membrane-Proximal Domain
Ligand Binding tothe Membrane-Distal Domain of theMet Receptor Induces Dimerization at the Membrane-Proximal Domain Open
Activation of cytokine and growth factor receptors by ligands triggers crucial cellular responses in various physiological processes. However, our understanding of their structural basis remains incomplete due to the limited information on…
View article: Ligand Binding tothe Membrane-Distal Domain of theMet Receptor Induces Dimerization at the Membrane-Proximal Domain
Ligand Binding tothe Membrane-Distal Domain of theMet Receptor Induces Dimerization at the Membrane-Proximal Domain Open
Activation of cytokine and growth factor receptors by ligands triggers crucial cellular responses in various physiological processes. However, our understanding of their structural basis remains incomplete due to the limited information on…
View article: Ligand Binding tothe Membrane-Distal Domain of theMet Receptor Induces Dimerization at the Membrane-Proximal Domain
Ligand Binding tothe Membrane-Distal Domain of theMet Receptor Induces Dimerization at the Membrane-Proximal Domain Open
Activation of cytokine and growth factor receptors by ligands triggers crucial cellular responses in various physiological processes. However, our understanding of their structural basis remains incomplete due to the limited information on…
View article: Ligand Binding tothe Membrane-Distal Domain of theMet Receptor Induces Dimerization at the Membrane-Proximal Domain
Ligand Binding tothe Membrane-Distal Domain of theMet Receptor Induces Dimerization at the Membrane-Proximal Domain Open
Activation of cytokine and growth factor receptors by ligands triggers crucial cellular responses in various physiological processes. However, our understanding of their structural basis remains incomplete due to the limited information on…
View article: Ligand Binding tothe Membrane-Distal Domain of theMet Receptor Induces Dimerization at the Membrane-Proximal Domain
Ligand Binding tothe Membrane-Distal Domain of theMet Receptor Induces Dimerization at the Membrane-Proximal Domain Open
Activation of cytokine and growth factor receptors by ligands triggers crucial cellular responses in various physiological processes. However, our understanding of their structural basis remains incomplete due to the limited information on…
View article: Molecular basis for occlusion of the jeilongvirus receptor-binding site by the elongated C-terminus
Molecular basis for occlusion of the jeilongvirus receptor-binding site by the elongated C-terminus Open
Paramyxoviral transmission between hosts may be, in part, attributed to the ability of the viral envelope-displayed receptor-binding protein (RBP) to bind to cell surface receptors of different host species. We sought to elucidate the arch…
View article: Human Elastin Binding Protein (EBP) Full Homology Model
Human Elastin Binding Protein (EBP) Full Homology Model Open
Elastin-derived peptides (EDPs) interact with elastin-binding protein (EBP), a key component of the elastin receptor complex, modulating cellular processes such as protease activation, apoptosis, and chemotaxis via regulation of NEU-1 sial…
View article: Human Elastin Binding Protein (EBP) Full Homology Model
Human Elastin Binding Protein (EBP) Full Homology Model Open
Elastin-derived peptides (EDPs) interact with elastin-binding protein (EBP), a key component of the elastin receptor complex, modulating cellular processes such as protease activation, apoptosis, and chemotaxis via regulation of NEU-1 sial…