Showing papers on "Cooperativity published in 1997"
TL;DR: Several relatively simple, physically plausible reaction schemes are shown here to produce a variety of ligand dose‐response curve phenotypes more appropriately suited to modeling ligand–receptor interactions, especially if independent information about the stochiometry of the ligand-receptor interaction is available.
Abstract: The Hill coefficient is commonly used to estimate the number of ligand molecules that are required to bind to a receptor to produce a functional effect. However, for a receptor with more than one ligand binding site, the Hill equation does not reflect a physically possible reaction scheme; only under the very specific condition of marked positive cooperativity does the Hill coefficient accurately estimate the number of binding sites. The Hill coefficient is best thought of as an "interaction" coefficient, reflecting the extent of cooperativity among multiple ligand binding sites. Several relatively simple, physically plausible reaction schemes are shown here to produce a variety of ligand dose-response curve phenotypes more appropriately suited to modeling ligand-receptor interactions, especially if independent information about the stochiometry of the ligand-receptor interaction is available.
882 citations
TL;DR: A model is presented in which binding of substrate in a particular conformation can facilitate oxygen activation to enhance catalysis and support a model in which an allosteric site is involved, although the proximity of this putative site to the catalytic site cannot be ascertained as of yet.
Abstract: Cytochrome P450 (P450) 3A4 is the most abundant human P450 and oxidizes a diversity of substrates, including various drugs, steroids, carcinogens, and macrolide natural products. In some reactions, positive cooperativity has been reported in microsomal studies. Flavonoids, e.g., 7,8-benzoflavone (α-naphthoflavone, αNF), have been shown to stimulate some reactions but not others. In systems containing purified recombinant bacterial P450 3A4, positive cooperativity was seen in oxidations of several substrates, including testosterone, 17β-estradiol, amitriptyline, and most notably aflatoxin (AF) B1. With these and other reactions, αNF typically reduced cooperativity (i.e., the n value in a Hill plot) while either stimulating or inhibiting reactions. With the substrate AFB1, αNF both stimulated 8,9-epoxidation and inhibited 3α-hydroxylation. The same patterns were seen with AFB1 in a fused P450 3A4−NADPH-P450 reductase protein. αNF did not alter patterns of activity plotted as a function of NADPH-P450 reducta...
365 citations
TL;DR: In this paper, the van der Waals glass salol confined to nanopores (2.5, 5.0, and 7.5 nm) with lubricated inner surfaces is found to be faster than in the bulk liquid.
Abstract: The molecular dynamics in the glass transition of the “quasi” ‐ van der Waals glass salol confined to nanopores (2.5, 5.0, and 7.5 nm) with lubricated inner surfaces is found to be faster ( by up to 2 orders of magnitude) than in the bulk liquid. This effect of confinement is more pronounced for smaller pores. It reflects the cooperativity of molecular motions in the glass transition and enables its length scale to be determined quantitatively. [S0031-9007(97)04009-X]
330 citations
TL;DR: It is demonstrated for the first time that the two activities are parts of one bifunctional enzyme in rat liver, UDP-GlcNAc 2-epimerase/ManNAc kinase, and highly positive cooperativity (Hill coefficient of 4.1) was found for inhibitor binding.
288 citations
TL;DR: The data provide a rationale for previous suggestions that biotin binding induces an increase in protein tightness (structural cooperativity) leading, in turn, to a higher thermostability.
234 citations
TL;DR: A further mechanism of 'respiratory control' via allosteric inhibition of cytochrome-c oxidase by ATP, which binds to the matrix domain, of subunit IV is described.
Abstract: The activity of cytochrome-c oxidase, the terminal enzyme of the mitochondrial respiratory chain, is known to be regulated by the substrate pressure, i.e. the ferro-/ferricytochrome c ratio, by the oxygen concentration, and by the electrochemical proton gradient delta muH+ across the inner mitochondrial membrane. Here we describe a further mechanism of 'respiratory control' via allosteric inhibition of cytochrome-c oxidase by ATP, which binds to the matrix domain, of subunit IV. The cooperativity between cytochrome-c-binding sites in the dimeric enzyme complex is mediated by cardiolipin, which is essential for cooperativity of the enzyme within the lipid membrane.
224 citations
TL;DR: The structures of the bacterial F 1 -ATPase α and β subunits are very similar to their counterparts in the mitochondrial enzyme, suggesting a common catalytic mechanism.
209 citations
TL;DR: CD2/ligand interactions cooperate to align membranes with nanometer precision leading to a physiologically effective two-dimensional affinity, suggesting an affinity limit for the ability of this mode of cooperativity to achieve stable cell-cell adhesion at approximately 10 mm −1.
183 citations
TL;DR: These studies demonstrate for the first time complex formation between specific human E2s and the Hect domain family of E3 proteins and suggest that selective physical interaction between E2 and E3 enzymes forms the basis of specificity for functionally distinct E2:E3 combinations.
161 citations
TL;DR: Modelling of muscle force redevelopment after release-restretch protocols adds a state of unactivated, noncycling cross-bridges and shows that cooperativity, which tends to enhance force generation at low levels of Ca2+ activation, has a counter-intuitive effect of slowing force redevelopment.
155 citations
TL;DR: A sharp, reproducible transition was only observed in competition experiments with copper, which may suggest that copper binding has some degree of cooperativity.
TL;DR: The crystal structures of complexes of phosphoinositide-specific phospholipase C-delta1 from rat with calcium, barium, and lanthanum at 2.5-2.6 A resolution are determined and it is proposed that both the S-variant and P-Variant topologies are present among other C2 domains.
Abstract: We have determined the crystal structures of complexes of phosphoinositide-specific phospholipase C-delta1 from rat with calcium, barium, and lanthanum at 2.5-2.6 A resolution. Binding of these metal ions is observed in the active site of the catalytic TIM barrel and in the calcium binding region (CBR) of the C2 domain. The C2 domain of PLC-delta1 is a circularly permuted topological variant (P-variant) of the synaptotagmin I C2A domain (S-variant). On the basis of sequence analysis, we propose that both the S-variant and P-variant topologies are present among other C2 domains. Multiple adjacent binding sites in the C2 domain were observed for calcium and the other metal/enzyme complexes. The maximum number of binding sites observed was for the calcium analogue lanthanum. This complex shows an array-like binding of three lanthanum ions (sites I-III) in a crevice on one end of the C2 beta-sandwich. Residues involved in metal binding are contained in three loops, CBR1, CBR2, and CBR3. Sites I and II are maintained in the calcium and barium complexes, whereas sites II and III coincide with a binary calcium binding site in the C2A domain of synaptotagmin I. Several conformers for CBR1 are observed. The conformation of CBR1 does not appear to be strictly dependent on metal binding; however, metal binding may stabilize certain conformers. No significant structural changes are observed for CBR2 or CBR3. The surface of this ternary binding site provides a cluster of freely accessible liganding positions for putative phospholipid ligands of the C2 domain. It may be that the ternary metal binding site is also a feature of calcium-dependent phospholipid binding in solution. A ternary metal binding site might be a conserved feature among C2 domains that contain the critical calcium ligands in their CBR's. The high cooperativity of calcium-mediated lipid binding by C2 domains described previously is explained by this novel type of calcium binding site.
TL;DR: The complete thermodynamics of the binding of CTAB to both helical and single strand DNA are evaluated with use of isothermal titration calorimetery data and analysis of UV melting transitions.
Abstract: The binding of cationic lipids to DNA induces the condensation of complexes of the lipid and polyelectrolyte. This paper presents data on the binding of the simple cationic lipid cetyltrimethylammonium bromide (CTAB) to DNA prior to the condensation process. The complete thermodynamics of the binding of CTAB to both helical and single strand DNA are evaluated with use of isothermal titration calorimetery data and analysis of UV melting transitions. The binding to the helical form involves a two-step process: first, binding to an isolated phosphate site on the DNA strand with a binding constant of 1.5 × 103 M-1, and second, a highly cooperative binding event that seems to involve hydrophobic intereactions between hydrocarbon chains of the bound CTAB. The cooperativity parameter is 56, leading to a cooperative binding constant of 8.7 × 104 M-1. The enthalpies of the two binding events on the helix sites are resolved: −20 kJ/mol for the isolated site and +3.3 kJ/mol for contiguous sites. Binding to the sin...
TL;DR: It is concluded that multiple Ca2+-binding sites are localized on the InsP3R-1 and that at least four different Ca2-interaction sites may be involved in the complex feedback regulation of the release by Ca2+.
TL;DR: It is concluded that fully metalated mammalian APs are noncooperative allosteric enzymes but that the stability and catalytic properties of each monomer are controlled by the conformation of the second AP subunit.
TL;DR: In this article, the authors describe purification of CcpA from Bacillus subtilis and Bacillus megaterium and its interaction with regulatory sequences from the xyl operon.
TL;DR: In this article, the T state of hemoglobin in silica gels was determined to have a reduced affinity compared with solution, with no Bohr effect and with no influence of other allosteric effectors.
TL;DR: This work characterized the binding of HMG I(Y) to the model beta-interferon enhancer and characterized the function of each basic repeat, showing that only the central repeat accounts for specific DNA binding and that the presence of a second repeat bound to an adjacent AT-rich region results in intramolecular cooperativity in binding.
Abstract: The mammalian high-mobility-group protein I(Y) [HMG I(Y)], while not a typical transcriptional activator, is required for the expression of many eukaryotic genes. HMG I(Y) appears to recruit and stabilize complexes of transcriptional activators through protein-DNA and protein-protein interactions. The protein binds to the minor groove of DNA via three short basic repeats, preferring tracts of adenines and thymines arranged on the same face of the DNA helix. However, the mode by which these three basic repeats function together to recognize HMG I(Y) binding sites has remained unclear. Here, using deletion mutants of HMG I(Y), DNase I footprinting, methylation interference, and in vivo transcriptional assays, we have characterized the binding of HMG I(Y) to the model beta-interferon enhancer. We show that two molecules of HMG I(Y) bind to the enhancer in a highly cooperative fashion, each molecule using a distinct pair of basic repeats to recognize the tandem AT-rich regions of the binding sites. We have also characterized the function of each basic repeat, showing that only the central repeat accounts for specific DNA binding and that the presence of a second repeat bound to an adjacent AT-rich region results in intramolecular cooperativity in binding. Surprisingly, the carboxyl-terminal acidic tail of HMG I(Y) is also important for specific binding in the context of the full-length protein. Our results present a detailed examination of HMG I(Y) binding in an important biological context, which can be extended not only to HMG I(Y) binding in other systems but also to the binding mode of many other proteins containing homologous basic repeats, which have been conserved from bacteria to humans.
TL;DR: In this article, a precise analysis of the dynamic mechanical data in terms of activation energies and entropies, the extent of the β transition strongly depends on the role played by the crosslinks.
TL;DR: The regulation of PGHS1 activity by substrate-dependent cooperative activation is reported, which results in a dramatic difference in PGHS2/PGHS1 selectivity at different arachidonic acid concentrations.
TL;DR: The results show that the two heads of HMM can induce structural changes in F-actin that are not observed with the single head of S1, and support the notion that the binding of myosin to F-Actin induces a conformational change in subdomain-2 of actin, and that under certain conditions this conformationalchange can be cooperatively propagated through an actin filament.
TL;DR: A model is presented wherein the receptor interconverts spontaneously between two or more states differing in their cooperative properties, and the effects of GMP-PNP can be rationalized as a shift in the equilibrium between the different states.
Abstract: Cooperativity has been investigated as the mechanistic basis for effects observed with cardiac muscarinic receptors in washed membranes from Syrian hamsters. Specifically, N-[3H]methylscopolamine l...
TL;DR: The inhibitory effect of Mg2+ on the formation of complexes between CaM and its targets may contribute to the specificity of CaM in target activation in response to cellular Ca2+ concentration fluctuations.
Abstract: The binding of Mg2+ to calmodulin (CaM) and the effect of Mg2+ on the binding of Ca2+-CaM to target peptides were examined using two-dimensional nuclear magnetic resonance and fluorescence spectroscopic techniques. We found that Mg2+ preferentially binds to Ca2+-binding sites I and IV of CaM in the absence of Ca2+ and that Ca2+-binding site III displays the lowest affinity for Mg2+. In contrast to the marked structural transitions induced by Ca2+ binding, Mg2+ binding causes only localized conformational changes within the four Ca2+-binding loops of CaM. Therefore, Mg2+ does not seem to be able to cause significant structural effects required for the interaction of CaM with target proteins. The presence of excess Mg2+ (up to 10 mM) does not change the order and cooperativity of Ca2+ binding to CaM, and as expected, the structure of Ca2+-saturated CaM is not affected by the presence of Mg2+. However, we found that the binding of Ca2+-saturated CaM to target peptides is affected by Mg2+ with the binding affinity decreasing as the Mg2+ concentration increases. Three different peptides, corresponding to the CaM binding domain of skeletal muscle myosin light-chain kinase (MLCK), CaM-dependent cyclic nucleotide phosphodiesterase (PDE), and smooth muscle caldesmon (CaD), were examined and show different reductions in their affinities toward CaM. The CaM-binding affinity of the MLCK peptide in the presence of 50 mM Mg2+ is approximately 40-fold lower than that seen in the absence of Mg2+, and a similar response was observed for the PDE peptide. The affinity of the CaD peptide for CaM also shows a Mg2+ dependence, though to a much lower magnitude. The Mg2+-dependent decrease in the affinities between CaM and its target peptides is an intrinsic property of Mg2+ rather than a nonspecific ionic effect, as other metal ions such as Na+ do not completely replicate the effect of Mg2+. The inhibitory effect of Mg2+ on the formation of complexes between CaM and its targets may contribute to the specificity of CaM in target activation in response to cellular Ca2+ concentration fluctuations.
TL;DR: The introduction of favourable local interactions by mutational redesign can be used to increase the folding speed of certain proteins, showing that not all proteins in nature have been optimized for rapid folding, contrary to what has been theoretically indicated.
TL;DR: In this paper, a series of polyintercalating compounds, including the first known tetraintercalator based on the 1,4,5,8-naphthalenetetetracarboxylic diimide chromophore, were synthesized by peptide linkers.
Abstract: We have synthesized a series of polyintercalating compounds, including the first known tetraintercalator, based on the 1,4,5,8-naphthalenetetracarboxylic diimide chromophore. The chromophores are attached in a head-to-tail arrangement by peptide linkers and are synthesized by standard solid phase peptide synthesis methods. We report evidence, based on UV−visible spectroscopy and viscometry, that the compounds are fully intercalated upon binding to double-stranded DNA. Using DNAse I footprinting experiments, the bisintercalator 2 was found to bind to DNA in a cooperative manner. The footprinting results as well as association and dissociation kinetics data reveal that the compounds exhibit a tremendous preference for GC over AT sequences. A mode of binding is proposed in which the compounds intercalate completely from the major groove, and not in a threading manner as may be suggested by their structures. A kinetic scheme is proposed that takes into account the observed cooperativity and fits the data for ...
TL;DR: It is concluded that PC12 BgtRs and α7/5HT3 homomers contain at least three distinguishable agonist binding sites and thus are different from other nicotinic receptors.
Abstract: We have characterized the alpha-bungarotoxin receptors (BgtRs) found on the cell surface of undifferentiated pheochromocytoma (PC12) cells. The PC12 cells express a homogeneous population of alpha7-containing receptors that bind alpha-Bgt with high affinity (Kd = 94 pM). The BgtRs mediate most of the response elicited by nicotine, because the BgtR-specific antagonists methyllycaconitine and alpha-Bgt block approximately 90% of the whole-cell current. The binding of nicotinic agonists to cell-surface BgtRs was highly cooperative with four different agonists showing Hill coefficients in the range of 2.3-2.4. A similar agonist binding cooperativity was observed for BgtR homomers formed from chimeric alpha7/5HT3 subunits expressed in tsA 201 cells. Two classes of agonist binding sites, in the ratio of 4:1 for PC12 cell BgtRs and 3:1 for alpha7/5HT3 BgtRs, were revealed by bromoacetylcholine alkylation of the reduced sites on both PC12 BgtRs and alpha7/5HT3 BgtRs. We conclude from this data that PC12 BgtRs and alpha7/5HT3 homomers contain at least three distinguishable agonist binding sites and thus are different from other nicotinic receptors.
TL;DR: In this article, the authors reported the discovery of potent, nonpeptide inhibitors of the matrix metalloproteinase stromelysin that were prepared by linking two ligands which bind weakly to adj...
Abstract: In the preceding paper,1 we reported on the discovery of potent, nonpeptide inhibitors of the matrix metalloproteinase stromelysin that were prepared by linking two ligands which bind weakly to adj...
TL;DR: Comparisons of Tm-actin-S1 ATPase with values of n using GTm, RSTm, and 5aTm, a 1/7 shorter nonmuscle Tm from rat fibroblast cells are reported, indicating a correlation between ATPase activation and n value.
Abstract: Tropomyosin (Tm) bound to actin induces cooperative activation of actomyosin subfragment 1 (actin-S1) ATPase, observed as a sigmoid ATPase vs [S1] dependence. The activation is much steeper for gizzard muscle Tm (GTm) than for rabbit skeletal Tm (RSTm). To investigate if this greater cooperativity is due to increased communication between GTms along the thin filament, we studied effects of S1 binding on the state of actin-Tm using the fluorescence of pyrene-labeled Tm. Kinetic and equilibrium studies provided values for n, the apparent cooperative unit size [Geeves, M. A., and Lehrer, S. S. (1994) Biophys. J. 67, 273]. We report comparative studies of Tm-actin-S1 ATPase with values of n using GTm, RSTm, and 5aTm, a 1/7 shorter nonmuscle Tm from rat fibroblast cells [Pittenger, M. F., et al. (1994) Curr. Opin. Cell Biol., 6, 96]. 5aTm and GTm produce similar cooperative activation of actin-S1 ATPase and have similar n values that are 2-fold greater than RSTm, indicating a correlation between ATPase activation and n value. This appears to be due to the similarity of the C-terminal amino acid sequences of 5a and GTm which produce strong end-to-end interactions. The results are discussed in terms of a continuous flexible Tm strand on the actin filament.
TL;DR: The alpha mRNA conformational switch is similar in its slow kinetics, large activation energy, and Mg2+ dependence of the equilibrium constant to slow steps in the folding of tRNA, group I introns, and RNase P RNA tertiary structures, though it differs from these in the association of a single Mg1+ with the rate-limiting step.
TL;DR: A general mechanism for hexameric helicases, an F1-ATPase-like rotational movement around the single-stranded DNA, which is bound through the central hole of the hexamer, is proposed to lead to unidirectional translocation along single-strate DNA and duplex DNA unwinding.
Abstract: Bacteriophage T7 DNA helicase is a ring-shaped hexamer that catalyzes duplex DNA unwinding using dTTP hydrolysis as an energy source. Of the six potential nucleotide binding sites on the hexamer, we have found that three are noncatalytic sites and three are catalytic sites. The noncatalytic sites bind nucleotides with a high affinity, but dTTPs bound to these sites do not dissociate or hydrolyze through many dTTPase turnovers at the catalytic sites. The catalytic sites show strong cooperativity which leads to sequential binding and hydrolysis of dTTP. The elucidated dTTPase mechanism of the catalytic sites of T7 helicase is remarkably similar to the binding change mechanism of the ATP synthase. Based on the similarity, a general mechanism for hexameric helicases is proposed. In this mechanism, an F1-ATPase-like rotational movement around the single-stranded DNA, which is bound through the central hole of the hexamer, is proposed to lead to unidirectional translocation along single-stranded DNA and duplex DNA unwinding.