Overlap Of Binding Sites Research Articles

A Roadmap for the Computational Prediction and Experimental Validation of Competitive Endogenous RNAs.

MicroRNAs (miRNAs) are fine-tuners of gene expression and contribute to the regulation of most, if not all, biological processes in eukaryotes by targeting both coding and noncoding RNAs. Typically, miRNAs repress numerous target transcripts and most target RNAs harbor binding sites for multiple miRNA families. It was recently proposed that transcripts sequester miRNAs and thereby regulate the abundance of other transcripts with which they have miRNA binding sites in common. Since competition for shared miRNAs is the mechanistic basis for this cross-regulation, such transcripts were termed competitive endogenous RNAs (ceRNAs). In this chapter, I discuss considerations for the computational prediction of ceRNAs based on miRNA binding site overlap. Moreover, I provide a framework for the experimental validation of miRNA-dependent reciprocal regulation of putative ceRNAs.

Facilitated dissociation of transcription factors from single DNA binding sites

The binding of transcription factors (TFs) to DNA controls most aspects of cellular function, making the understanding of their binding kinetics imperative. The standard description of bimolecular interactions posits that TF off rates are independent of TF concentration in solution. However, recent observations have revealed that proteins in solution can accelerate the dissociation of DNA-bound proteins. To study the molecular basis of facilitated dissociation (FD), we have used single-molecule imaging to measure dissociation kinetics of Fis, a key Escherichia coli TF and major bacterial nucleoid protein, from single dsDNA binding sites. We observe a strong FD effect characterized by an exchange rate [Formula: see text], establishing that FD of Fis occurs at the single-binding site level, and we find that the off rate saturates at large Fis concentrations in solution. Although spontaneous (i.e., competitor-free) dissociation shows a strong salt dependence, we find that FD depends only weakly on salt. These results are quantitatively explained by a model in which partially dissociated bound proteins are susceptible to invasion by competitor proteins in solution. We also report FD of NHP6A, a yeast TF with structure that differs significantly from Fis. We further perform molecular dynamics simulations, which indicate that FD can occur for molecules that interact far more weakly than those that we have studied. Taken together, our results indicate that FD is a general mechanism assisting in the local removal of TFs from their binding sites and does not necessarily require cooperativity, clustering, or binding site overlap.

Klotho Coreceptors Inhibit Signaling by Paracrine Fibroblast Growth Factor 8 Subfamily Ligands

It has been recently established that Klotho coreceptors associate with fibroblast growth factor (FGF) receptor tyrosine kinases (FGFRs) to enable signaling by endocrine-acting FGFs. However, the molecular interactions leading to FGF-FGFR-Klotho ternary complex formation remain incompletely understood. Here, we show that in contrast to αKlotho, βKlotho binds its cognate endocrine FGF ligand (FGF19 or FGF21) and FGFR independently through two distinct binding sites. FGF19 and FGF21 use their respective C-terminal tails to bind to a common binding site on βKlotho. Importantly, we also show that Klotho coreceptors engage a conserved hydrophobic groove in the immunoglobulin-like domain III (D3) of the "c" splice isoform of FGFR. Intriguingly, this hydrophobic groove is also used by ligands of the paracrine-acting FGF8 subfamily for receptor binding. Based on this binding site overlap, we conclude that while Klotho coreceptors enhance binding affinity of FGFR for endocrine FGFs, they actively suppress binding of FGF8 subfamily ligands to FGFR.

Opioid Binding Sites in Human Serum Albumin

Human serum albumin (HSA) is an important carrier for opioids. However, the locations of the binding sites remain unclear. In the present study, we have characterized opioid-HSA interactions using multiple biochemical and biophysical techniques to reveal: (a) the location of the binding site(s); (b) whether naloxone shares the binding site with morphine; and (c) whether opioid agonists share their binding site(s) with general anesthetics. Elution chromatography to determine the global interactions and tryptophan intrinsic fluorescence to determine the localized interactions of opioids with HSA were used. Competition studies using isothermal titration calorimetry were used to determine the overlap of binding site(s) among opioid agonists, antagonists, and general anesthetics. An automatic docking calculation was used to predict the possible binding sites and to assess findings of the solution studies. For elution chromatography with immobilized HSA, the retention times of naloxone, morphine, and fentanyl were prolonged but shorter than that of propofol. The inhibition of tryptophan fluorescence by naloxone was not affected by morphine or fentanyl. The calorimetric heat profiles of propofol and halothane interaction with HSA were changed significantly, but not equally by morphine, naloxone, or fentanyl. Consistent with direct binding studies, docking results demonstrated that opioids share sites with general anesthetics; a distinct binding site for naloxone was revealed near the sole tryptophan in HSA that is not shared with morphine. The interaction of opioids with HSA is weak in comparison with propofol. Naloxone has a distinct binding site in HSA not shared with opioid agonists. Opioids share binding sites with general anesthetics in HSA.

The stoichiometry of trimeric SIV glycoprotein interaction with CD4 differs from that of anti-envelope antibody Fab fragments.

Human and simian immunodeficiency viruses infect host lymphoid cells by binding CD4 molecules via their gp160 envelope glycoproteins. Biochemical studies on recombinant SIVmac32H (pJ5) envelope ectodomain gp140 precursor protein show that the envelope is a trimer. Using size exclusion chromatography, quantitative amino acid analysis, analytical ultracentrifugation, and CD4-based competition assay, we demonstrate that the stoichiometry of CD4 receptor-oligomeric envelope interaction is 1:1. By contrast, Fab fragments of both neutralizing and non-neutralizing monoclonal antibodies bind at a 3:1 ratio. Thus, despite displaying equivalent CD4 binding sites on each of the three gp140 protomers within an uncleaved trimer, only one site binds the soluble 4-domain human CD4 extracellular segment. The anti-cooperativity and the faster k(off) of gp140 trimer:CD4 versus gp120 monomer:CD4 interaction suggest that CD4-induced conformational change is impeded in the intact envelope. The implications of these findings for immunity against human immunodeficiency virus and simian immunodeficiency virus are discussed.

Electron Shuttle between Membrane-Bound Cytochrome P450 3A4 andb5Rules Uncoupling Mechanisms

Contradictory mechanisms involving conformational or redox effects have been proposed for the enhancement of cytochrome P450 activities by cytochrome b5 in reconstituted systems. These mechanisms were reinvestigated for human liver P450 3A4 bound to recombinant yeast membranes including human P450 reductase and various levels of human b5. Species conversions were calculated on the basis of substrate, oxygen, and electronic balances in six different substrate conditions. Electron flow from P450 reductase to ferric 3A4 was highly dependent on the nature of substrate but not on the presence of b5. P450 uncoupling by hydrogen peroxide formation was decreased by b5, leading to a corresponding increase in the rate of ferryl-oxo complex formation. Nevertheless, the major b5 effects mainly relied on an increased partition of ferryl-oxo complex to substrate oxidation compared to reduction to water, which could support a conformation change based mechanism. However, further steady-state investigations evidenced that electron carrier properties of b5 were strictly required for this modulation and that redox state of b5 was ruled by the nature and concentration of 3A4 substrates. Moreover, rapid kinetic analysis of b5 reduction following NADPH addition suggested that b5 was reduced by the 3A4 ferrous-dioxygen complex and reoxidized by subsequent P450 oxygenated intermediates. A kinetic model involving a 3A4-b5 electron shuttle within a single productive P450 cycle was designed and adjusted. This model semiquantitatively simulated all presented experimental data and can be made compatible with the effect of the redox-inactive b5 analogue previously reported in reconstituted systems. In this model, synchronization of the b5 and 3A4 redox cycles, binding site overlap between b5 and reductase, and dynamics of the b5-3A4 complex were critical features. This model opened the way for designing complementary experiments for unification of b5 action mechanisms on P450s.

Effects of i.v. anaesthetic agents and halothane on [3H]tetracaine binding to rat cerebrocortical membranes

In an attempt to determine if there is any overlap in local and general anaesthetic binding sites, we have examined the effects of thiopental, phenobarbital, pentobarbital, propofol, ketamine (racemic and R(+)/S(-)), alfaxalone, etomidate and halothane on [3H]tetracaine binding to rat cerebrocortical membranes. Membranes were prepared in Tris HCI 50 mmol litre-1, pH 7.4, by homogenization and centrifugation. Binding assays were performed in 1-ml volumes of Tris HCI buffer at room temperature or 37 degrees C for halothane. Binding of [3H]tetracaine was displaced dose-dependently by unlabelled tetracaine with a mean pIC50 value of 6.91 (SEM 0.07) (123 nmol litre-1). With the exception of propofol (at high concentrations), all i.v. anaesthetic agents failed to displace the binding of [3H]tetracaine. In contrast, halothane produced a dose-dependent and statistically significant reduction in total [3H]tetracaine binding at clinically achievable concentrations (0.289, 0.885 and 1.484 mmol litre-1 equivalent to 1.0, 3.1 and 5.1 rat MAC) without markedly affecting the pIC50. Collectively these data may suggest some overlap in the binding sites for [3H]tetracaine and volatile but not i.v. general anaesthetic agents.

Use of binding site neighbor-effect parameters to evaluate the interactions between adjacent ligands on a linear lattice: Effects on ligand-lattice association

A method using binding site “neighbor-effect” parameters (NEPs) is introduced to evaluate the effects of interaction between adjacent ligands on their binding to an infinite linear lattice. Binding site overlap is also taken into account. This enables the conditional probability approach of McGhee & von Hippel to be extended to more complex situations. The general equation for the isotherm is ν L F = S F K F , where ν is the ratio of bound ligands to lattice residues, L F is the free ligand concentration, S F is the fraction of binding sites that are free, and K̄ F is the average association constant of a free site. Solutions are derived for three cases: symmetric ligands, and asymmetric ligands on isotropic or anisotropic lattices. For symmetric ligands there is one NEP, E, which is the ratio of the average binding affinity of a free site if the status of the lattice residue neighboring one end of the site is unspecified (left to chance) to the affinity when this residue is free (holding the other neighbor constant). Thus K̄ F is KE 2, where K is the affinity of an isolated site. If a site is n residues long, S F is f ff n−1 , where f = 1 − nv is the fraction of residues that are free and ff is the conditional probability that a free residue is bordered on a given side by another free residue. The expression for ff is 1 (1+x/E) , where x is ν f , E is (1 − x +[(1−x) 2 + 4xω)] 1 2 )/2 , and ω is the co-operativity parameter. The binding of asymmetric ligands to an isotropic lattice is described by two NEPs; the last case involves four NEPs and a bound ligand orientation parameter. For each case, the expected length distribution of clusters of bound ligands can be calculated as a function of ν. When Scatchard plots with the same intercepts and initial slope are compared, it is found that ligand asymmetry lowers the isotherm (relative to the corresponding symmetric ligand isotherm), whereas lattice anisotropy raises it.