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323 results for “Binding specificity”
Phase separation of hnRNP A1 upon specific RNA-binding observed by magnetic resonance
<p>Experimental data, <a href="https://mmmx.info">MMMx</a> restraint and ensemble analysis files (.mcx), restraint data, raw ensembles, and ensemble lists with populations (.ens) pertaining to the manuscript "Phase separation of hnRNP A1 upon specific RNA-binding observed by magnetic resonance" <a href="https://www.biorxiv.org/content/10.1101/2022.03.21.485092v1">available at bioRxiv</a> and submitted to a peer-reviewed journal.</p>
Elucidating molecular mechanisms of protoxin-2 state-specific binding to the human NaV1.7 channel
<p>Human voltage-gated sodium (hNaV) channels are responsible for initiating and propagating action potentials in excitable cells and mutations have been associated with numerous cardiac and neurological disorders. hNaV1.7 channels are expressed in peripheral neurons and are promising targets for pain therapy. The tarantula venom peptide protoxin-2 (PTx2) has high selectivity for hNaV1.7 and is a valuable scaffold for designing novel therapeutics to treat pain. Here, we used computational modeling to study the molecular mechanisms of the state-dependent binding of PTx2 to hNaV1.7 voltage-sensing domains (VSDs). Using Rosetta structural modeling methods, we constructed atomistic models of the hNaV1.7 VSD II and IV in the activated and deactivated states with docked PTx2. We then performed microsecond-long all-atom molecular dynamics (MD) simulations of the systems in hydrated lipid bilayers. Our simulations revealed that PTx2 binds most favorably to the deactivated VSD II and activated VSD IV. These state-specific interactions are mediated primarily by PTx2's residues R22, K26, K27, K28, and W30 with VSD and the surrounding membrane lipids. Our work revealed important protein-protein and protein-lipid contacts that contribute to high-affinity state-dependent toxin interaction with the channel. The workflow presented will prove useful for designing novel peptides with improved selectivity and potency for more effective and safe treatment of pain.</p>
Data from: Residues neighboring an SH3-binding motif participate in determining affinity and specificity in vivo
<p>In signaling networks, many protein-protein interactions are mediated by modular domains that bind short linear motifs. The motifs' sequences modulate many factors, among them affinity and specificity, or the ability to bind strongly and to bind the appropriate partners. Previous studies have proposed a trade-off between affinity and specificity, suggesting that motifs with high affinity are less capable of differentiating between domains with similar sequences and structures. Using Deep Mutational Scanning to create a mutant library of a well characterized binding motif, and protein complementation assays to measure protein-protein interactions, we tested this trade-off in vivo for the first time. We measured the binding strength and specificity of a library of mutants of a binding motif on the MAP kinase kinase Pbs2, which binds the SH3 domain of the osmosensor protein Sho1 in Saccharomyces cerevisiae. We find that many mutations in the region surrounding the binding motif modify binding strength, but that few mutations have a strong impact on specificity. Moreover, we find no systematic relationship between affinity and specificity as measured in vivo. Interestingly, all Pbs2 mutations which increase affinity or specificity are situated outside of the Pbs2 residues that interact with the canonical SH3-binding pocket, suggesting that other surfaces on Sho1 contribute to binding. We use predicted structures to propose a model of binding which involves residues neighboring the core Pbs2 motif binding outside of the canonical SH3-binding pocket, allowing affinity and specificity to be determined by a broader range of sequences than what has previously been considered.</p>
Elucidating molecular mechanisms of protoxin-2 state-specific binding to the human NaV1.7 channel
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ROS-specific Huntingtin Interactions: In vitro poly-ADP ribose binding assays
<p>Poly-ADP ribose overlay assay with purified huntingtin protein to test ability of full-length and fragment huntingtin to bind poly-ADP ribose.</p>
ROS-Specific Huntingtin Interactions: Summary of PAR binding for different huntingtin protein preps
<p>PAR overlay assay with different preparations of huntingtin has yielded variable results. These results are summarized.</p>
ROS-Specific Huntingtin Interactions: Competition of huntingtin PAR binding by PBM3 peptide
<p>Attempts to use the PBM3 peptide in a competition assay to measure the on-off rates of huntingtin PAR binding.</p>
Supplemental information and raw data: Developmental and caste-specific expression patterns of ATP-Binding Cassette (ABC) transporters in honey bees (Apis mellifera)
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Divalent cations bind to phosphoinositides to induce ion and isomer specific propensities for nano-cluster initiation in bilayer membranes
<p>We report all-atom molecular dynamics simulations of physiologically composed asymmetric bilayers containing phosphoinositides in the presence of monovalent and divalent cations. We have characterized the molecular mechanism by which these divalent cations interact with phosphoinositides. Calcium desolvates more readily, consistent with single-molecule calculations, and forms a network of ionic-like bonds that serve as a "molecular glue'' that allows a single ion to coordinate with up to three phosphatidylinositol-(4,5)-bisphosphate lipids. The phosphatidylinositol-(3,5)-bisphosphate isomer shows no such effect and neither does PI(4,5)P2 in the presence of Mg. The resulting network of Ca-mediated lipid-lipid bonds grows to span the entire simulation space and therefore has implications for the lateral distribution of phosophoinositides in the bilayer. We observe context-specific differences in lipid diffusion rates, lipid surface densities, and bilayer structure. The molecular-scale delineation of ion-lipid arrangements reported here provides insight into similar nanocluster formation induced by peripheral proteins to regulate the formation of functional signaling complexes on the membrane.</p>
Figure 2. Rubicon and Pacer RH domain have inverted pRAB7A binding specificity [FINAL]
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Single-molecule analysis of specificity and multivalency in binding of short linear substrate motifs to the APC/C
<p>Robust regulatory signals in the cell often depend on interactions between short linear motifs (SLiMs) and globular proteins. Many of these interactions are poorly characterized because the binding proteins cannot be produced in the amounts needed for traditional methods. To address this problem, we developed a single-molecule off-rate (SMOR) assay based on microscopy of fluorescent ligand binding to immobilized protein partners. We used it to characterize substrate binding to the Anaphase-Promoting Complex/Cyclosome (APC/C), a ubiquitin ligase that triggers chromosome segregation. We find that SLiMs in APC/C substrates (the D box and KEN box) display distinct affinities and specificities for the substrate-binding subunits of the APC/C, and we show that multiple SLiMs in a substrate generate a high-affinity multivalent interaction. The remarkably adaptable substrate-binding mechanisms of the APC/C have the potential to govern the order of substrate destruction in mitosis.</p>
Sex-specific maternal programming of corticosteroid binding globulin by predator odour
<p>Predation is a key organizing force in ecosystems. The threat of predation may act to program the endocrine hypothalamic-pituitary-adrenal axis during development to prepare offspring for the environment they are likely to encounter. Such effects are typically investigated through measurement of corticosteroids (Cort). Corticosteroid-binding globulin (CBG) plays a key role in regulating the bioavailability of Cort, with only free unbound Cort being biologically active. We investigated the effects of prenatal predator odour exposure (POE) in mice on offspring CBG and its impact on Cort dynamics before, during, and after restraint stress in adulthood. POE males, but not females, had significantly higher serum CBG at baseline and during restraint and lower circulating levels of Free Cort. Restraint stress was associated with reduced liver transcript abundance of <i>SerpinA6 </i>(CBG-encoding gene) only in control males. POE did not affect <i>SerpinA6</i> promoter DNA methylation. Our results indicate that prenatal exposure to a natural stressor led to increased CBG levels, decreased percent of Free Cort relative to total, and inhibited restraint stress-induced downregulation of CBG transcription.<i> </i>These changes suggest an adaptive response to a high predator risk environment in males but not females, that could buffer male offspring from chronic Cort exposure.</p>
Dataset I related to publication: Beyond KRAS(G12C): biochemical and computational characterization of sotorasib and adagrasib binding specificity and the critical role of H95 and Y96
<p>MD simulation data (sotorasib and adagrasib in complex with NRAS(WT) and KRAS(WT)) related to publication: "Beyond KRAS(G12C): biochemical and computational characterization of sotorasib and adagrasib binding specificity and the critical role of H95 and Y96". </p> <p>ACS Chem. Biol. 2024, XXXX, XXX, XXX-XXX</p> <p>https://pubs.acs.org/doi/10.1021/acschembio.4c00315</p> <ul> <li>The .zip files contain raw Desmond simulation trajectories of KRAS(WT) or NRAS(WT) in complex with adagrasib or sotorasib [5 replicas; each 5 us] <ul> <li>(-out.cms files and trajectories).</li> </ul> </li> </ul> <p>Related datasets: 10.5281/zenodo.10781452</p>
Dataset II related to publication: Beyond KRAS(G12C): biochemical and computational characterization of sotorasib and adagrasib binding specificity and the critical role of H95 and Y96
<p>MD simulation data (KRAS(G12C) and KRAS(G12C/Y96D)) related to publication: "Beyond KRAS(G12C): biochemical and computational characterization of sotorasib and adagrasib binding specificity and the critical role of H95 and Y96". </p> <p>ACS Chem. Biol. 2024, XXXX, XXX, XXX-XXX</p> <p>https://pubs.acs.org/doi/10.1021/acschembio.4c00315</p> <ul> <li>The .zip files contain raw Desmond simulation trajectories of KRAS(G12C) and KRAS(G12C/Y96D) with apo SII-P or in complex with sotorasib [5 replicas; each 4 us] <ul> <li>(-out.cms files and trajectories).</li> </ul> </li> </ul> <p>Related datasets: 10.5281/zenodo.10812233 </p>
Data of Le Crom and Boily 2024: Adsorption of ciprofloxacin on goethite: I. Approach and non-specific binding
<p><span><span><span>Simulation input files, data and scripts that were used for the article Le Crom and Boily 2024: Molecular-level insight into the adsorption of ciprofloxacin on goethite: I. Approach and non-specific binding</span></span></span></p>
Characterizing the consensus residue specificity and surface of Bcl-2 binding to BH3 ligands using the knob-socket model
<p><span>Cancer cells bypass cell death by changing the expression of the BCL-2 family of proteins, which are apoptotic pathway regulators. Upregulation of pro-survival BCL-2 proteins or downregulation of cell death effectors BAX and BAK interferes with the initiation of the intrinsic apoptotic pathway. In normal cells, apoptosis can occur through pro-apoptotic BH3-only proteins interacting and inhibiting pro-survival BCL-2 proteins. When cancer cells over-express pro-survival BCL-2 proteins, a potential remedy is the sequestration of these pro-survival proteins through a class of anti-cancer drugs called BH3 mimetics that bind in the hydrophobic groove of pro-survival BCL-2 proteins. To improve the design of these BH3 mimetics, the packing interface between BH3 domain ligands and pro-survival BCL-2 proteins was analyzed using the Knob-Socket model to identify the amino acid residues responsible for interaction affinity and specificity. A Knob-Socket analysis organizes all the residues in a binding interface into simple 4 residue units: 3-residue sockets defining surfaces on a protein that pack a 4th residue knob from the other protein. In this way, the position and composition of the knobs packing into sockets across the BH3/BCL-2 interface can be classified. A Knob-Socket analysis of 19 BCL-2 protein and BH3 helix co-crystals reveal multiple conserved binding patterns across protein paralogs. Conserved knob residues such as a Gly, Leu, Ala and Glu most likely define binding specificity in the BH3/BCL-2 interface, whereas other residues such as Asp, Asn, and Val are important for forming surface sockets that bind these knobs. These findings can be used to inform the design of BH3 mimetics that are specific to pro-survival BCL-2 proteins for cancer therapeutics.</span></p>
Assessment of the Effect of Sertaline on the Specific Binding of 123-I MZINT in Healthy Subjects
ClinicalTrials.gov study NCT00470925. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Characterizing the consensus residue specificity and surface of Bcl-2 binding to BH3 ligands using the knob-socket model
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Divalent cations bind to phosphoinositides to induce ion and isomer specific propensities for nano-cluster initiation in bilayer membranes
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Sex-specific maternal programming of corticosteroid binding globulin by predator odour
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