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Cooperative binding
About: Cooperative binding is a research topic. Over the lifetime, 2771 publications have been published within this topic receiving 118964 citations.
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TL;DR: Adenine nucleotide binding and dissociation is more favorable when RNA is bound to Rho, whereas ATP binding and Dissociation step in the absence of RNA occurs significantly slower, at a rate ∼70- and ∼40-fold slower than those observed with the Rho-RNA complex, respectively.
Abstract: Escherichia coli transcription termination factor Rho catalyzes the unwinding of RNA/DNA duplex in reactions that are coupled to ATP binding and hydrolysis. Fluorescence stopped-flow methods using ATP and the fluorescent 2’(3’)-O-(N-methylanthraniloyl) derivatives (mant-derivatives) of ATP and ADP were used to probe the kinetics of nucleotide binding to and dissociation from the Rho-RNA complex. Presteady state nucleotide binding kinetics provides evidence for the presence of negative cooperativity in nucleotide binding among the multiple nucleotide binding sites on Rho hexamer. The binding of the first nucleotide to the Rho-RNA complex occurs at a bimolecular rate of 3.6×106 M−1sec−1, whereas the second nucleotide binds at a slower rate of 4.7×105 M−1 sec−1 at 18°C. RNA complexed with Rho affects the kinetics of nucleotide interaction with the active sites through conformational changes to the Rho hexamer, allowing the incoming nucleotide to be more accessible to the sites. Adenine nucleotide binding and dissociation is more favorable when RNA is bound to Rho, whereas ATP binding and dissociation step in the absence of RNA occurs significantly slower, at a rate ∼70- and ∼40-fold slower than those observed with the Rho-RNA complex, respectively.
28 Jul 2022
01 Jan 1976
TL;DR: The interaction between ligands and specific binding structures is a general problem which is encountered at different levels in the field of cyclic nucleotide metabolism and action.
Abstract: The interaction between ligands and specific binding structures is a general problem which is encountered at different levels in the field of cyclic nucleotide metabolism and action. Some examples of ligands which interact with specific receptor sites in order to modify the activity of adenylate cyclase and other structures modulating cyclic nucleotide concentrations are listed in Table I; cyclic nucleotides exert most of their effects by interacting with specific receptor proteins : the protein kinases in eukaryotes (1) or the cAMP receptor protein in bacteria (CRP) (2).
TL;DR: Hemoglobin is a typical, highly nonadditive binding system, for which efficiency should be studied in its own right and independently of cooperativity.
Abstract: The utility function for hemoglobin is defined as the amount of oxygen transported by a single hemoglobin molecule per roundtrip from the lungs (the loading terminal) to the various tissues (the unloading terminal). Traditionally, the efficiency of transporting any ligand by a binding system has been inferred from the cooperativity of the binding process. The larger the (positive) cooperativity, the steeper the binding curve (the so-called binding isotherm), and hence the larger efficiency. This monotonic relationship between cooperativity and efficiency is indeed valid for some simple systems, such as a two-site system. It is also valid for more complicated multisubunit systems for which all cooperativities are pairwise additive. We found that when the binding process is nonadditive, efficiency does not follow straightforwardly from cooperativity. Hemoglobin is a typical, highly nonadditive binding system, for which efficiency should be studied in its own right and independently of cooperativity.
TL;DR: NMR and X-ray crystallographic data on TIF2NRID in complex with RXR/RAR reveal a cooperative binding of the three NR-boxes as well as an active role of their flanking regions in the interaction.
Abstract: Retinoic acid receptors (RARs) and retinoid X receptors (RXRs) form heterodimers that activate target gene transcription by recruiting co-activator complexes in response to ligand binding. The nuclear receptor (NR) co-activator TIF2 mediates this recruitment by interacting with the ligand-binding domain (LBD) of NRs trough the nuclear receptor interaction domain (TIF2NRID) containing three highly conserved α-helical LxxLL motifs (NR-boxes). The precise binding mode of this domain to RXR/RAR is not clear due to the disordered nature of TIF2. Here we present the structural characterization of TIF2NRID by integrating several experimental (NMR, SAXS, CD, SEC-MALS) and computational data. Collectively, the data are in agreement with a largely disordered protein with partially structured regions, including the NR-boxes and their flanking regions, which are evolutionary conserved. NMR and X-ray crystallographic data on TIF2NRID in complex with RXR/RAR reveal a cooperative binding of the three NR-boxes as well as an active role of their flanking regions in the interaction.