Showing papers on "Cooperativity published in 1974"
TL;DR: The helix, s Applequist, 1963) in which the Zimm-Bragg parameters u and s are defined respectively as the cooperativity factor for helix initiation, and the equi- librium constant for converting a coil residue to a helical helix.
Abstract: The helix, s Applequist, 1963) in which the Zimm-Bragg parameters u and s are defined respectively as the cooperativity factor for helix initiation, and the equi- librium constant for converting a coil residue to a helical ~~~~
2,112 citations
TL;DR: Thermochemical comparison of oxygenation parameters of iron- and cobalt-containing oxygen carriers indicates that the effect of the metal substitution on the oxygen affinity is primarily enthalpic, whereas theeffect of the apoprotein binding on theoxy affinity of cobaltous porphyrins is essentially entropic.
197 citations
Journal Article•
TL;DR: Glycine and strychnine appear to bind to distinct sites which interact in a cooperative fashion, while Detergents such as deoxycholate and Triton X-100 decrease receptor binding in concentrations which solubilize membrane protein.
Abstract: The saturable binding of [3H]strychnine to synaptic membrane fractions of the rat spinal cord appears to involve an interaction with the synaptic receptor sites for the neurotransmitter actions of glycine. Binding exhibits a dissociation constant for strychnine of 2.6-4 nM and an EC50 for glycine inhibition of strychnine binding of 25 µM. Association kinetics is bimolecular, with a rate constant of 1.0 x 107 M-1 sec-1, while dissociation of the strychnine-receptor complex is first-order, with a rate constant of 1.54 x 10-2 sec-1. The dissociation constant (k2/k1) of 1.54 nM is similar to that obtained from equilibrium data. Monovalent cations increase specific and decrease nonspecific strychnine binding, while divalent cations are without effect. Detergents such as deoxycholate and Triton X-100 decrease receptor binding in concentrations which solubilize membrane protein. Displacement curves of [3H]strychnine by glycine indicate cooperative interactions with a Hill coefficient of 1.7, whereas the Hill coefficient for displacement of [3H]strychnine by unlabeled strychnine is 1.0. Diazonium tetrazole and acetic anhydride preferentially inhibit displacement of [3H]strychnine binding by glycine and reduce the Hill coefficient of glycine displacement curves. Guanidine, N-ethylmaleimide, and increases in pH also lower the Hill coefficient for glycine displacement. Diazonium tetrazole slows the dissociation of [3H]strychnine elicited by excess glycine without altering dissociation produced by excess unlabeled strychnine. Glycine and strychnine appear to bind to distinct sites which interact in a cooperative fashion.
173 citations
Journal Article•
TL;DR: Fluorescence and radioactive ligand assays demonstrate that Ca++ also causes an increase of receptor affinity for cholinergic ligands, but in a manner significantly different from that observed with local anesthetics.
Abstract: Studies are presented of the interaction in a physiological ionic environment of aromatic amine local anesthetics (prilocaine, lidocaine, and dimethisoquin) and Ca++ with receptor-rich membrane fragments isolated from Torpedo electric organ. The environmentaly sensitive fluorophore 1-(5-dimethylaminonaphthalene-1-sulfonamido)ethane 2-trimethylammonium iodide (DNS-chol)interacts with two classes of sites in the membrane fragments: the cholinergic receptor site and secondary sites characterized by probe emission properties (λmax) sensitive to the pharmacological nature (agonist or antagonist) of the cholinergic ligand bound to the receptor site. Fluorescence studies show that the local anesthetics cause an increase of affinity of the membrane-bound receptor for DNS-chol and for cholinergic ligands, both agonists and antagonists. The increase of affinity is not associated with a change of DNS-chol emission properties. At the same concentrations at which the anesthetics control receptor affinity, they also affect the fluorescence of DNS-chol bound to the secondary sites: the presence of local anesthetic causes a loss of the DNS-chol spectral properties characteristic of the binding of agonists to the receptor site. Local anesthetics also control the binding of [3H]acetylcholine to the membrane-bound receptor. In the absence of prilocaine the acetylcholine binding curve is slightly sigmoid (Hill coefficient, nH = 1.4, half-saturation at 10 nM free acetylcholine). In the presence of 3 mM prilocaine there is a decrease of cooperativity and an increase of affinity (nH = 1.0, half-saturation at 6 mM free acetylcholine). The concentrations at which the local anesthetics act on the membrane fragments are those at which they block the permeability response of Electrophorus electroplax upon addition to the bath of the agonist carbamylcholine. Fluorescence and radioactive ligand assays demonstrate that Ca++ also causes an increase of receptor affinity for cholinergic ligands, but in a manner significantly different from that observed with local anesthetics. Solubilization of membrane fragments by detergent leads to changes in the binding properties of the receptor protein. On the membrane fragments the binding data for each agonist can be analyzed in terms of a homogeneous population of sites, while after solubilization heterogeneity of the binding constants appears. Prilocaine or Ca+ no longer affects the binding of acetylcholine to the solubilized receptor protein. The observed effects of local anesthetics and Ca++ on the affinity of the cholinergic receptor are related to the phenomenon of receptor desensitization.
112 citations
TL;DR: The kinetics of oxygen combination and dissociation for the various hemocyanin preparations show that variations in the rate of oxygen dissociation are primarily responsible for the observed differences in oxygen affinity.
Abstract: Hemocyanin in the hemolymph of the horseshoe crab, Limulus polyphemus L., is a high-molecular-weight copper protein which binds oxygen cooperatively and shows a higher oxygen affinity at pH 7 than at pH 9. Treatment with EDTA (ethylenediaminetetra-acetate) disaggregates the hemocyanin molecules and abolishes both the reverse Bohr effect and cooperative oxygen binding. Chloride ions interact with the EDTA-treated material and, in the presence of saturating amounts of NaCl, a reverse Bohr effect is restored, but cooperativity is not. The EDTA-treated hemocyanin contains at least five electrophoretically distinct hemocyanins. These hemocyanins have similar molecular weights (about 66,000) but are functionally dissimilar. They have different oxygen affinities and different responses to chloride ions. The effect of chloride ions on unfractionated hemocyanin is due to pH-dependent chloride interactions with only two of the five hemocyanin components. The functional differences between the hemocyanin components may provide Limulus with a valuable respiratory flexibility in its interaction with the environment. The kinetics of oxygen combination and dissociation for the various hemocyanin preparations show that variations in the rate of oxygen dissociation are primarily responsible for the observed differences in oxygen affinity. The rate of oxygen dissociation varies 20-fold under conditions where the apparent rate of oxygen combination shows less than a 2-fold variation. Cooperative interactions in the untreated hemocyanin are most obvious in the “off” reaction, which increases in rate as successive oxygen molecules are released.
110 citations
TL;DR: It is argued that the co-operative sites arise from the tRNA tertiary structure, and is further strengthened by the observation that cooperativity is present in a tRNAPhe molecule which has been split in the anticodon loop, but it is absent in oneWhich has beensplit in the extra loop.
92 citations
TL;DR: In the 30S ribosomal subunit of Escherichia coli, two pairs of cross-linked proteins have been identified by several independent techniques; these are S7-S9 and S13-S19 as mentioned in this paper.
Abstract: Diimidoesters have been used to cross-link neighboring proteins in the 30S ribosomal subunit of Escherichia coli. Two pairs of cross-linked proteins have been identified by several independent techniques; these are S7-S9 and S13-S19. Since it has been shown earlier that these four proteins cooperate during ribosome assembly in vitro (Green and Kurland, 1973), their identification as near neighbors in the ribosome is quite suggestive. Thus, the data indicate that a cluster of proteins which interact with each other during assembly would be, in general, found in close proximity in the functional ribosome. A more detailed discussion of the arrangement of the proteins in the 30S subunit is presented.
64 citations
TL;DR: The method of sequence generating functions not only permits the prediction of binding isotherms for systems like those described above, but also provides statistical distributions for any type of binding event to which a statistical weight can be attached.
Abstract: The method of sequence generating functions is applied to the binding of substrates to a linear array of binding sites such as is encountered in DNA. Cooperativity parameters are introduced for contact between bound ligands and for the extension of interaction over one or two empty binding units. By allowing these parameters to have values less than or greater than one, a large variety of anticooperative and cooperative situations can be developed. These and other parameters are systematically built into the sequence generating function as markers which are useful for statistical averages even in the absence of cooperativity. The resulting equations are applied to a system of highly cooperative binding, resulting in predicted behavior that simulates many features of the binding of T4 gene 32 protein to DNA. A model for the intercalation of dyes in DNA is also proposed which is based on two anticooperativity parameters: one for intercalating dyes in adjacent sites, the other for dyes separated by one empty site. The method of sequence generating functions not only permits the prediction of binding isotherms for systems like those described above, but also provides statistical distributions for any type of binding event to which a statistical weight can be attached. The only limitation is that the chains must be sufficiently long that end effects are negligible.
61 citations
TL;DR: The addition of organic phosphates or orthophosphate to fully liganded human hemoglobin produces ultraviolet and visible spectroscopic changes which are very similar to those observed when isolated unliganded alpha and beta subunits combine to form hemoglobin.
60 citations
TL;DR: Results indicate that the two vinyl groups at positions 2 and 4 of the porphyrin ring are functionally nonequivalent, which indicates that oxygen affinities of hemoglobins can be correlated to the electron-withdrawing effects of heme substituents when these protein factors are normalized.
57 citations
Book•
10 Jun 1974
TL;DR: The Huckel Method with Self-Consistent Charge and the Jahn-Teller Effect and Cooperativity in Hemoglobin are studied, which provide insights into the determinants of Cooperativity and Amino Acids, Peptides and Proteins.
Abstract: I Amino Acids, Peptides and Proteins.- 1.1 Amino Acids.- 1.2 Peptides.- 1.3 Proteins.- II Hemoglobin.- 2.1 Primary Structure.- 2.2 Spin States.- 2.3 Heme.- 2.4 Secondary and Tertiary Structure.- 2.5 Quaternary Structure.- 2.6 Dissociated Hemoglobin.- III Oxygenation Characteristics.- 3.1 Equilibrium Curves.- 3.2 Quantitative Description.- 3.3 The Bohr Effect.- 3.4 Thermodynamic and Kinetic Properties.- IV Approaches to Cooperativity.- 4.1 The Monod-Wyman-Changeux (MWC) Model.- 4.2 The Koshland-Nemethy-Filmer (KNF) Model.- 4.3 Stereochemical Theory.- 4.4 Magnetic Resonance.- 4.5 Discussion.- V Electronic States of Iron.- 5.1 Free Ions.- 5.2 Cubic Symmetry.- 5.2.1 Symmetry Elements.- 5.2.2 Basis Functions.- 5.2.3 Coupling Coefficients.- 5.2.4 Crystal Field Potential.- 5.3 Tetragonal and Rhombic Symmetries.- 5.4 One-Electron Energies.- 5.5 Multielectron Configurations.- 5.6 Kramers Theorem.- 5.7 The Jahn-Teller Effect.- 5.8 Molecular Orbitals.- VI Magnetic Properties.- 6.1 General Features.- 6.1.1 Electron Spin Resonance.- 6.1.2 Paramagnetic Susceptibility.- 6.2 Electron Spin Resonance of Low-Spin Ferrihemoglobin.- 6.3 Electron Spin Resonance of High-Spin Ferrihemoglobin.- 6.3.1 Spin-Orbit Coupling.- 6.3.2 Spin Hamiltonian.- 6.3.3 Interaction with a Magnetic Field.- 6.4 Paramagnetic Susceptibility.- 6.4.1 Low-Spin Ferrihemoglobin.- 6.4.2 High-Spin Ferrihemoglobin.- 6.4.3 Ferrohemoglobin.- 6.5 Discussion.- VII Molecular Orbitals and Optical Spectra.- 7.1 Computational Method.- 7.1.1 Extended Huckel Method with Self-Consistent Charge (EH-SCC).- 7.1.2 Symmetry Considerations.- 7.2 Results of Molecular Orbital Calculations.- 7.3 Optical Spectra.- VIII Mossbauer Spectroscopy.- 8.1 General Features.- 8.1.1 Isomer Shift.- 8.1.2 Quadrupole Splitting.- 8.1.3 Magnetic Hyperfine Interactions.- 8.2 Mossbauer Spectra of Hemoglobin.- 8.3 Theoretical Interpretation and Discussion.- 8.3.1 Quadrupole Splitting.- 8.3.2 Magnetic Hyperfine Interaction.- IX Further Aspects.- 9.1 Diamagnetism of Oxyhemoglobin.- 9.2 The Jahn-Teller Effect and Cooperativity in Hemoglobin.- References.
TL;DR: Comparative studies show that the exaggerated chain differences and low oxygen affinity of stripped Lemur hemoglobin are closely paralleled by the behavior of human hemoglobin in the presence of saturating amounts of inositol hexaphosphate.
TL;DR: Results are consistent with the hypothesis that the small planar anion is acting as an analog of a planar phosphoryl group, thus mimicking the transition state of the enzyme-substrate complex, and suggest that two of the distinguishing features of this transition-state complex are a substantial interaction between the two protomeric subunits and the formation of a ligand from the protein to the divalent metal ion.
TL;DR: Results support the general conclusion that p-mercuribenzoate reactivity is a probe of over-all quaternary conformation and its functional abnormalities can be explained by a shift in the conformational equilibrium toward the R state.
TL;DR: The reduced pyridoxal-5'-P-AMP deaminase derivative prepared in the presence of GTP is still sensitive to inhibition by nucleoside triphosphates, but is no longer sensitive to GTP, ATP, and high salt concentration inhibitions.
TL;DR: The binding of phytochrome to a particulate fraction from maize coleoptiles has been examined as a function of the level of Pfr1 offeredin vivo and it is indicated that the response is the product of both the steady-statePfr concentration and the light dose and is determined therefore ultimately by the cycling rate.
Abstract: The binding of phytochrome to a particulate fraction from maize coleoptiles has been examined as a function of the level ofP
fr
1 offeredin vivo. Further evidence is provided that the degree of binding is a function of both the form of the phytochrome and the state of the binding sites; and thatP
fr
induces a change in the state of the binding sites such that the subsequent affinity forP
r
is enhanced. Increasing the steady-state level ofP
fr
offeredin vivo results in a subsequent binding curve forP
r
that is suggestive of cooperativity. However, increasing both time and irradiance parameters of the light dose while holding the steady-stateP
fr
level constant results in increased binding ofP
r
up to a saturation level. This indicates that the response is the product of both the steady-stateP
fr
concentration and the light dose and is determined therefore ultimately by the cycling rate. The system appears to respond therefore to the total number ofP
fr
molecules integrated over time rather than simply to the steady-state concentration ofP
fr
.
TL;DR: Results not only show for the first time that contacts between the porphyrin and amino acid side chains change upon oxygenation, but they are also consistent with the Hoard-Perutz hypothesis on the nature of the stereochemical trigger.
Abstract: THERE is considerable X-ray evidence that the haem stereochemistry is different in oxy- and deoxyhaemoglobin1–3. This structural change is an important part of the oxygenation process, because it is believed to induce conformational changes in the surrounding protein that are responsible for cooperativity. We have investigated conformational changes in the haem region by measuring polarised absorption spectra on single crystals. Using this technique we have detected changes in porphyrin plane orientation associated with an alteration of the ligand, spin, and oxidation state of the haem iron, factors which influence haem stereochemistry. Our results not only show for the first time that contacts between the porphyrin and amino acid side chains change upon oxygenation, but they are also consistent with the Hoard-Perutz hypothesis on the nature of the stereochemical trigger1–3.
TL;DR: The pyruvate dehydrogenase complex from Escherichia coli is subject to an allosteric control as discussed by the authors, which exhibits positive cooperativity in steady-state measurements.
Abstract: The pyruvate dehydrogenase complex from Escherichia coli is subject to an allosteric control. Pyruvate shows a homotropic cooperative effect. The extent of the cooperativity increases with decreasing concentrations of thiamine pyrophosphate. This cofactor itself exhibits positive cooperativity in steady-state measurements. The saturation curves both of pyruvate and of thiamine pyrophosphate have a very unusual asymmetric shape. The sigmoidal range is limited to low ligand concentrations and changes to a hyperbolic form far below half saturation. It was demonstraed that allosteric systems with more than eight interacting protomers, which obeys the allosteric model of Monod, J., Wyman, J., and Changeux, J.-P. [J. Mol. Biol. 12 (1965) 88–117], behave in this manner.
In the absence of substrate and thiamine pyrophosphate, the pyruvate dehydrogenase exists in an inactive form. At low thiamine pyrophosphate concentrations addition of pyruvate leads, after a lag phase of several minutes, to a partial activation. Within less than one second, complete activation occurs when saturating amounts of thaiamine pyrophosphate are added, irrespective of the presence or absence of pyruvate. The lag period increases with decreasing degree of enzyme dilution. This phenomenon is not due to a dissociation and reassociation of subunits.
TL;DR: The sequence would appear to be that the binding of ATP and UTP as well as thebinding of guanosine triphosphate induces a conformational change into the formation of glutamyl enzyme and liberating nascent ammonia.
Abstract: Publisher Summary This chapter discusses the structure and chemistry of cytidine triphosphate (CTP) synthetase CTP synthetase is an enzyme of four identical subunits, which is elegantly tailored for its particular needs It utilizes glutamine as a nitrogen source and apparently has an active site in which the consecutive steps occur in a rapid, if not essentially concerted, manner It would appear that the binding properties allow the simultaneous presence of glutamine, uridine triphosphate (UTP), and adenosine triphosphate (ATP) on the surface of the enzyme This results in a rapid zipperlike effect in which a combination of conformational changes and nascent reactive compound's lead to high reactivity The sequence would appear to be that the binding of ATP and UTP as well as the binding of guanosine triphosphate induces a conformational change into the formation of glutamyl enzyme and liberating nascent ammonia Nascent ammonia then immediately attacks UTP before equilibrating with the medium leading to a UTP adduct This, however, is highly reactive and reacts instantaneously with the adjacent ATP to form a phosphorylated intermediate, which then eliminates inorganic phosphate to form CTP The conformational changes induced in the process are highly focused The protein is designed to enhance the cooperativity pattern for the particular needs of the cell
TL;DR: It is concluded from these experiments that histone F1 binds preferentially and cooperatively to AT rich regions of λ-DNA, implying that «premelting phenomena may be due to the true melting of AT rich areas».
TL;DR: Ulacentrifuge experiments indicate that the tetramer-dimer subunit dissociation constants of the liganded forms of types I and II of cat hemoglobin are pH-dependent and liganded cat hemoglobins dissociates about 10 times more readily than any other mammalian hemoglobin investigated.
TL;DR: Comparison of these spectra to those of hemoglobin, methemoglobin, cytochrome c, and model cobalt porphyrin complexes suggests that they support Perutz's trigger mechanism for cooperativity, consistent with Hopfield's distributed energy model.
Abstract: The resonance Raman spectra of oxy and deoxy cobalt-substituted hemoglobin (CoHb) are reported. Comparison of these spectra to those of hemoglobin, methemoglobin, cytochrome c, and model cobalt porphyrin complexes suggests that the displacement of the cobalt atom upon oxygenation of CoHb is no greater than the out-of-plane distance in five-coordinate Co(II) porphyrins, 0.15 A. Combining this distance with the expected contraction of the cobalt-histidine bond, Ibers has estimated a maximum displacement of 0.37 A for the proximal histidine with respect to the heme plane upon oxygenation, about one-third the corresponding distance estimated for iron hemoglobin. The free energy of cooperativity for cobalt hemoglobin is also estimated to be one-third that of iron hemoglobin. These results are therefore consistent with Hopfield's distributed energy model, which predicts proportionality between proximal histidine displacement and the free energy of cooperativity. By implication they support Perutz's trigger mechanism for cooperativity.
TL;DR: The values of N 3 − binding constants calculated from inhibition experiments, which are higher than those obtained in the titration experiments, can be explained by the reduction of the protein during catalytic turnover.
TL;DR: The high cooperativity between glycerol binding sites on the enzyme, in glycine buffer, can be abolished by the addition of phosphate, which seems to act as an allosteric activator.
TL;DR: Human platelet 6-phosphofructokinase was partially purified and SO42− activated the enzyme activity especially at low Fru-6-P concentrations, andSO42− diminished the allosteric inhibition by ATP.
TL;DR: Hemoglobin Leiden shows a decreased response to inorganic phosphate, chloride, 2,3-diphosphoglycerate, and inositol hexaphosphate, both in equilibria and kinetics of ligand binding.
TL;DR: New data shows that cooperativity prevents resolution of successive heats of reaction and only average heats are currently accessible, which form a consistent thermodynamic cycle.
TL;DR: Results strongly indicate that Pt(CN)42- is bound at a site within the protein region occupied by the phosphate groups of the coenzyme, and it is suggested that arginine-47 in the enzymatic amino-acid sequence is part of a common binding site for negative charges on the cofenzyme and coen enzyme competitive anions such as Pt( CN)42-, Au(CN2-, chloride and iodoacetate.
Abstract: Single and multiple-inhibition experiments provide evidence that the complex anion Pt(CN)42- is bound at a single site per subunit of liver alcohol dehydrogenase in strict competition with coenzyme, ADP-ribose, AMP and (less than 100 mM) chloride ion, but independently of 1,10-phenanthroline. Binding of adenosine decreases the stability constant for the enzyme · Pt(CN)42- complex from 16 mM-1 to 4 mM-1.
Au(CN)2- is bound at two sites per subunit of the enzyme. Both interactions are competitive with coenzyme, ADP-ribose and AMP, but independent of 1,10-phenanthroline. Only one site is available for interaction with Au(CN)2- in the binary enzyme complexes formed with Pt(CN)42-, chloride ion, or adenosine. Estimation of the corresponding binding constants for Au(CN)2- gave evidence for cooperativity between the two Au(CN)2- binding sites.
These results strongly indicate that Pt(CN)42- is bound at a site within the protein region occupied by the phosphate groups of the coenzyme, and it is suggested that arginine-47 in the enzymatic amino-acid sequence is part of a common binding site for negative charges on the coenzyme and coenzyme competitive anions such as Pt(CN)42-, Au(CN)2-, chloride and iodoacetate. The second binding site for Au(CN)2- appears to be situated within the protein region occupied by the adenosine part of the coenzyme.
TL;DR: The sequence of the first 15 residues of the β chain indicates that it is homologous with the β chains of other fish and vertebrate hemoglobins, and the oxygen affinity of Latimeria hemoglobin is unusually high.