Showing papers on "Cooperativity published in 1979"
TL;DR: In this article, the authors compared parameters associated with activation and desensitization of the nicotinic receptor in the BC3H-1 muscle cell line with the state transitions that result upon combination with agonist and found that the affinity increase and diminished permeability change are completely reversible and again exhibit similar kinetics for their return to the original state.
175 citations
TL;DR: The allosteric enzyme phosphofructokinase binds its substrate fructose-6-phosphate between two subunits of the tetramer, and allosteri effectors between another pair of subunits, creating ligand bridges between subunits.
Abstract: The allosteric enzyme phosphofructokinase binds its substrate fructose-6-phosphate between two subunits of the tetramer, and allosteric effectors between another pair of subunits. The effector binding site accommodates both the activator and the inhibitor. The substrate cooperativity and allosteric control are mediated by these ligand bridges between subunits.
161 citations
160 citations
TL;DR: Drugs would experience a relatively constant ionic environment when complexed to DNA even though the ionic conditions of the solvent could change considerably, according to the ion condensation theory.
Abstract: The interaction of quinacrine with calf thymus DNA was monitored at several different ionic strengths using spectrophotometric and equilibrium dialysis techniques. The binding results can be explained, assuming each base pair is a potential binding site, using a model containing two negative cooperative effects: (1) ligand exclusion at binding sites adjacent to a filled binding site and (2) ligand–ligand negative cooperativity at adjacent filled binding sites. The logarithm of the observed equilibrium constant (Kobs) determined by this model varies linearily with log[Na+], as predicted by the ion condensation theory for polyelectrolytes. When the log Kobs plot is correlated for sodium release by DNA in the intercalation conformational change, the predicted number of ion pairs between the ligand and DNA is approximately two, as expected for the quinacrine dication. Even though Kobs depends strongly on ionic strength, the ligand negative cooperativity parameter ω was found to be indpendent of ionic strength within experimental error. This finding is also in agreement with the ion condensation theory, which predicts a relatively constant amount of condensed counterion on the DNA double helix over this ionic strength range. Drugs would, therefore, experience a relatively constant ionic environment when complexed to DNA even though the ionic conditions of the solvent could change considerably.
139 citations
TL;DR: The results and other supporting data give what appears to be the most compelling evidence yet attained for alternating site catalytic cooperativity in an enzymic catalysis.
117 citations
TL;DR: The tertiary structures of all liganded hemoglobins in the R state differ in detail, and structural interpretation of this kinetic behavior indicates that the relative contributions of nonbonded ligand-globin interactions and nonbonding heme interactions to transition state free energies differ for linear and bent ligands.
Abstract: The tertiary structures of all liganded hemoglobins in the R state differ in detail. Steric hindrance arising from nonbonded ligand-globin interactions affects the binding of ligands such as CO and cyanide which preferentially form linear axial complexes to heme; these ligands bind in a strained off-axis configuration. Ligands such as O2 and NO, which preferentially form bent complexes, encounter less steric hindrance and can bind in their (preferred) unstrained configuration. Linear complexes distort the ligand pockets in the R state (and by inference, in the T state) more than bent complexes. These structural differences between linear and bent complexes are reflected in the kinetic behavior of hemoglobin. Structural interpretation of this kinetic behavior indicates that the relative contributions of nonbonded ligand-globin interactions and nonbonded heme interactions to transition state free energies differ for linear and bent ligands. The relative contributions of these interactions to the free energy of cooperativity may also differ for linear and bent ligands. Thus the detailed molecular mechanism by which the affinity of heme is regulated differs for different ligands.
89 citations
TL;DR: Raman difference spectroscopy measurements on native and chemically modified human deoxyhemoglobins stabilized in either the R or the T quaternary structure revealed frequency differences in the oxidation state marker lines that indicate that the R structure has an effective increase in the electron density of the antibonding pi* orbitals of the porphyrin rings.
Abstract: Raman difference spectroscopy measurements on native and chemically modified human deoxyhemoglobins stabilized in either the R or the T quaternary structure revealed frequency differences in the oxidation state marker lines. The differences indicate that the R structure has an effective increase in the electron density of the antibonding pi* orbitals of the porphyrin rings. This increase is explained by a charge transfer interaction between donor orbitals and the pi* orbitals of the porphyrins. The relative amount of charge transferred, which is inferred from the Raman difference measurements, correlates with some but not all factors that influence the energetics of the quaternary structure equilibrium. In addition, the free energy of cooperativity for a variety of ligated proteins follows the same order as that of the degree of charge depletion of the pi* orbitals upon ligation as determined from the frequency of a Raman mode. The proposed electronic interaction between the protein and heme could result in energies large enough to provide a significant contribution to the energetics of hemoglobin cooperativity.
73 citations
TL;DR: In this article, an activation energy equal to about one barrier height has been found for the second-nearest neighbor transition of a polymer chain, where the second nearest neighbor is the second closest neighbor.
Abstract: Conformational transitions of a macromolecule have been studied by computer simulation of the Brownian dynamics of a polymer chain. An activation energy equal to about one barrier height has been found. However, there is a great deal of cooperativity of transitions especially between bonds which are second nearest neighbors.
69 citations
TL;DR: The present results show that two-state allosteric models are not adequate to describe the cooperative oxygenation of hemoglobin and provide direct correlation to the ligand-induced structural changes observed to occur in the crystals of deoxy- and oxy-like hemoglobin molecules and in the solution state.
Abstract: The structural changes associated with cooperative oxygenation of human adult hemoglobin as a function of oxygen saturation in aqueous media at neutral pH and at 25-27 degrees C have been investigated by high-resolution proton nuclear magnetic resonance spectroscopy at 250 and 360 MHz. By monitoring the intensities of two hyperfine shifted proton resonances (at about -12 and -18 ppm from H(2)O) and two exchangeable proton resonances (at about -6.4 and -9.4 ppm from H(2)O) as a function of oxygenation, the amount of oxygen bound to the alpha and beta chains of a hemoglobin molecule can be determined and the relationship between tertiary and quaternary structural changes under a given set of experimental conditions can be investigated. These results suggest that: (i) in the absence of organic phosphates, there is no preferential O(2) binding to the alpha or beta chains; (ii) in the presence of organic phosphates, the alpha hemes have a higher affinity for O(2) as compared to the beta hemes; (iii) the ligand-induced structural changes in the hemoglobin molecule are not concerted; and (iv) some cooperativity must be present within the deoxy quaternary state during the oxygenation process. The variations of the exchangeable proton resonances as a function of oxygenation strongly suggest that the breaking of one or more inter- or intrasubunit linkages of a ligated subunit can affect similar linkages in unligated subunits within a tetrameric hemoglobin molecule. Thus, the present results show that two-state allosteric models are not adequate to describe the cooperative oxygenation of hemoglobin. In addition, the present results provide direct correlation to the ligand-induced structural changes (such as in the heme pockets and subunit interfaces) observed to occur in the crystals of deoxy- and oxy-like hemoglobin molecules and in the solution state.
67 citations
01 Jan 1979
TL;DR: The Pharmacon-Receptor-Effector Concept is a Basis for Understanding the Transmission of Information in Biological Systems and the Response to Acetylcholine-Like Drugs.
Abstract: 1 Reconstitution of Membrane Transport Functions.- 1. Introduction.- 2. Reconstitution of Active and Passive Transport Systems.- 3. General Techniques of Reconstitution.- 3.1. Liposomes: Test Tubes with a Difference.- 3.1.1. Multilamellar Liposomes.- 3.1.2. Unilamellar Liposomes.- 3.2. Methods for Inserting Proteins into Liposomes.- 3.2.1. Cholate Dialysis.- 3.2.2. Sonication.- 3.2.3. Incorporation.- 3.2.4. The Use of Superstable Membrane Proteins.- 4. What We Can Learn from Reconstitution.- 4.1. Oxidative Phosphorylation.- 4.2. Ca2+-ATPase.- 4.3. (Na+ + K+)-ATPase.- 4.4. Acetylcholine Receptor.- 4.5. The Problem of Orientation.- 5. Reconstitution in Planar Bilayer Membranes.- 5.1. Sucrase-Isomaltase Complex.- 5.2. Acetylcholine Receptor in Planar Bilayers.- 5.3. Insertion of Whole Membrane Vesicles.- 5.4. Proton Pumps.- References.- 2 The Pharmacon-Receptor-Effector Concept: A Basis for Understanding the Transmission of Information in Biological Systems.- 1. Introduction.- 2. Biological Action.- 3. Receptors and Receptor Sites.- 4. Pharmacon-Receptor Interaction.- 5. Spare Receptors.- 6. Structure and Action.- 7. Accessory Receptor Sites.- 8. Steric Structure and Action.- 9. Selectivity in Action.- 10. Differentiation in Closely Related Receptor Types.- 11. Receptor Binding and Receptor Isolation.- 12. Dualism in Receptors for Agonists and Their Competitive Antagonists.- 13. The Aggregation-Segregation Concept.- 14. Dual Receptor Model.- 15. Combination of Pharmaca.- 16. The Slope of the Concentration-Effect Curves.- 17. The Allosteric Receptor Model.- 18. Binding and Displacement on Two or More Independent Classes of Receptor Sites.- 19. Two-Site Model.- 20. Reflection.- References.- 3 The Link between Drug Binding and Response: Theories and Observations.- 1. The Response to Acetylcholine-Like Drugs.- 1.1. Methods of Investigation of the Response.- 1.2. The Nature of the Response to Acetylcholine.- 1.3. The Response-Concentration Curve at Equilibrium.- 1.4. The Kinetics of the Response.- 1.4.1. Relationship between Methods of Studying Kinetics.- 1.4.2. Concentration-Jump Studies.- 1.4.3. Fluctuation Analysis.- 1.4.4. Voltage-Jump Relaxation Studies.- 1.5. Anesthetics, Local Anesthetics, and Channel Blocking.- 2. The Binding of Drugs to Acetylcholine Receptors.- 2.1. Methods for Investigation of Binding.- 2.2. Binding at Equilibrium.- 2.2.1. Cooperativity in Binding.- 2.2.2. Is There a Single Sort of Binding Site?.- 2.2.3. Binding to Junctional and Extrajunctional Receptors in Muscle.- 2.3. The Kinetics of Acetylcholine Binding.- 3. The Link between Drug Binding and Response.- 3.1. What Should a Mechanism Explain?.- 3.2. Some Mechanisms.- 3.3. The Concentration Dependence of Binding and Response at Equilibrium.- 3.4. The Nature of Efficacy, Partial Agonists, and Desensitization...- 3.5. Kinetics and Mechanism.- 3.5.1. What Does the Observation of a Single Time Constant Imply?.- 3.5.2. What Is the Rate-Limiting Step?.- 3.5.3. Concentration Dependence of Time Constants from Kinetic Studies.- 3.6. What Is the Origin of Voltage Dependence?.- 3.7. High Affinity Versus High Speed.- References.- 4 Kinetics of Cooperative Binding.- 1. Overview.- 2. General Introduction.- 3. Model I: koff as a Linear Function of Occupancy.- 3.1. Assumptions.- 3.2. Properties of the Model.- 3.2.1. Equilibrium.- 3.2.2. Association Curves.- 3.2.3. Dissociation Curves.- 3.3. Discussion.- 4. Application to the Insulin-Receptor System.- 4.1. The Controversy.- 4.2. Experimental Design.- 4.3. Simulation Results.- 4.4. Discussion.- 5. Model II: kon as a Linear Function of Occupancy.- 5.1. Introduction.- 5.2. The Model.- 5.3. Properties of the Model.- 5.3.1. Equilibrium.- 5.3.2. Association Curves.- 5.3.3. Dissociation Curves.- 5.4. Testing for Positive Cooperativity.- 6. General Discussion.- 7. A Guide to the Experimentalist.- Appendix A: Model I: Differential Equations and Solutions.- Appendix B: Addition of Fresh (Empty) Receptors.- Appendix C: Model II: Labeled Ligand Only.- Appendix D: Model II: Labeled and Unlabeled Ligands.- Appendix E: Optimization of Testing for Model II with ? > 0.- References.- 5 Distinction of Receptor from Nonreceptor Interactions in Binding Studies.- 1. Defining a Pharmacologic Receptor.- 2. Criteria for Receptor Interactions.- 3. The Problem of Relating Binding to Biological Responsiveness.- 4. Nonspecific Binding: Definition and Examples of Complications of Binding Data Analysis.- 5. Estimating the Affinity of the Unlabeled Ligand.- 6. Examples of Receptor-Like Nonreceptor Interactions.- 7. Conclusion.- References.- 6 Incorporation of Transport Molecules into Black Lipid Membranes.- 1. Introduction.- 2. Methodology.- 2.1. Formation and Composition of BLMs.- 2.2. Electrical Properties of BLMs.- 3. Mechanisms of Ion Permeability.- 3.1. Carriers.- 3.2. Channel Formers.- 4. Models of Interactions of Proteins with BLMs.- 5. Ionophorous Properties in BLMs of Functional Transport Molecules.- 5.1. Ca2+-ATPase: Dissection of a Transport System.- 5.2. (Na+ + K+)-ATPase.- 5.3. The Acetylcholine Receptor.- 6. The BLM as a Test System for Ionophorous Function of Isolated Membrane Proteins.- 6.1. Mitochondrial Membrane Proteins.- 6.2. Red Blood Cell Membrane Proteins.- 6.3. Gastric Mucosal Membrane Proteins.- 6.4. Dopamine-?-Hydroxylase.- 6.5. Rhodopsin.- 6.6. Immune Cytotoxic Factors.- 7. Coda.- References.- 7 Visualization and Counting of Receptors at the Light and Electron Microscope Levels.- 1. Receptors at the Cell Membrane.- 1.1. Introduction.- 1.2. Information Required on the Distribution of Receptors.- 2. The Labeling of Receptors for Localization.- 2.1. Approaches.- 2.2. Methods of Labeling and Visualizing Receptors.- 2.2.1. Autoradiography.- 2.2.2. Electron-Dense Label Attachment.- 2.2.3. Enzymatic Reaction Product Markers.- 2.2.4. Fluorescent Markers.- 2.2.5. X-Ray Microanalysis.- 2.3. Ligands for Receptor Labeling.- 2.3.1. Selection of Primary Ligands.- 2.3.2. Ligands Available for Receptor Tracing.- 3. Cell and Tissue Autoradiography.- 3.1. Problems of Application of a Labeled Ligand.- 3.1.1. Mode of Application.- 3.1.2. Nonspecific Labeling.- 3.1.3. Tissue Processing for Autoradiography of Receptors.- 3.1.4. Application to a Pseudo-Irreversible Reaction at a Receptor.- 3.2. Autoradiographic Methods.- 3.2.1. Treatments in Aqueous Media.- 3.2.2. Dry-Mount Methods.- 3.3. Interpretation of EM Autoradiographic Data on Receptors.- 3.3.1. Assignment of Silver Grains in Autoradiographs to Most Probable Locations of the Labeled Receptors.- 3.3.2. Calculation of Receptor Density.- 3.3.3. Isotopes and Resolution.- 3.4. Applications to Synaptic Receptors.- 4. Counting Receptors per Cell or per Synapse.- 4.1. Light Microscope Autoradiography of Receptors.- 4.2. Absolute Enumeration of Total Receptors.- 4.3. Direct Determination of Receptor Occupancy Relations.- 5. Electron Microscope Methods for Visualization of Receptors.- 5.1. Peroxidase Cytochemistry of Receptors.- 5.1.1. Peroxidase Methods.- 5.1.2. Applications of Peroxidase Cytochemistry to Receptors.- 5.2. Tissue Preservation for Immunocytochemistry of Receptors.- 5.3. Ferritin Labeling.- 5.4. Other Labels Applicable for Transmission and Scanning EM Studies of Receptors.- 6. Fluorescence Marker Methods.- 6.1. Fluorescence Labeling.- 6.2. Application of Fluorescent Labeling to Receptors.- 7. Possibilities of Quantitation of Receptors in Immunocytochemical and Other Nonradioisotopic Techniques.- 7.1. Quantitation in Electron-Dense Marker Techniques.- 8. Conclusions.- References.- 8 Problems and Approaches in Noncatalytic Biochemistry.- 1. Introduction.- 2. Measurement.- 2.1. Histological Techniques.- 2.2. Physical Separation: General Considerations.- 2.3. Equilibrium Dialysis.- 2.4. Other Physical Separations.- 2.5. Negative Binding.- 2.6. The Magnitude of the Off-Time.- 3. Relation of in Vivo to in Vitro Properties.- 3.1. Reversibility.- 3.2. Location.- 3.3. Specificity.- 3.4. Dissociation Constants.- 3.5. Detergents.- References.
66 citations
TL;DR: The results of this study indicate that the inhibition of AMPase, which is a Con A receptor, is a different process from the redistribution of the bulk of the Con A receptors, possibly short range membrane interactions rather than global effects on the cell.
Abstract: Differences in cell morphology, concanavalin A-induced receptor redistributions, and the cooperativity of the inhibition of 5'-nucleotidase (AMPase) by concanavalin A (Con A) have been investigated in ascites sublines of the 13762 rat mammary adenocarcinoma cells treated with microfilament- and microtubule-perturbing drugs. By scanning electron microscopy MAT-C1 cells exhibit a highly irregular surface, covered with microvilli extending as branched structures from the cell body. MAT-A, MAT-B, and MAT-B1 cells have a more normal appearance, with unbranched microvilli, ruffles, ridges, and blebs associated closely with the cell body. MAT-C cells have an intermediate morphology. Treatment of MAT-A, MAT-B, or MAT-B1 cells with Con A causes rapid redistribution of Con A receptors. Both cytochalasins and colchicine cause alternations in the receptor redistributions. Receptors on MAT-C1 cells are highly resistant to redistribution, even in the presence of cytoskeletal perturbant drugs. The cooperativity of the inhibition of AMPase by Con A was investigated in MAT-A and MAT-C1 cells. Untreated cells exhibit no cooperativity. If either subline is treated with colchicine, cytochalasin B or D, or dibucaine, cooperativity is observed. Lumicolchicine has no effect. Theophylline or dibutyryl cyclic AMP prevents the effects of either colchicine or cytochalasin. The concentration required for half-maximal induction of cooperativity is 0.3--0.4 microM for both colchicine and cytochalasin D, which is in the appropriate range for specific microtubule and microfilament disruptions. The effectiveness of the cytochalasins (E greater than D greater than B) is consistent with their known effects on microfilaments. No direct correlation was observed between the induction of cooperativity and drug-induced changes in Con A receptor redistribution or cell morphology. The morphology of MAT-A cells is grossly altered by cytochalasins or dibucaine and somewhat less by colchicine. MAT-C1 cells exhibit more minor alterations in morphology as a result of these drug treatments. The results of this study indicate that the inhibition of AMPase, which is a Con A receptor, is a different process from the redistribution of the bulk of the Con A receptors, possibly short range membrane interactions rather than global effects on the cell.
TL;DR: Analysis of the distribution of 18O-labeled species arising from the ATP formed eliminates explanations for substrate modulation based on preexisting or induced enzyme heterogeneity, and the occurrence of alternating site catalysis cooperativity in ATP synthesis by chloroplasts appears to be reasonably well established.
Abstract: Pronounced substrate modulation of incorporation of water oxygen into ATP formed by photophosphorylation is observed, as measured by 31P NMR analysis of products formed from ADP and highly 18O-labeled Pi. A marked increase occurs in oxygen exchange per ATP formed as ADP or Pi concentration is decreased. This is explainable by the binding-change mechanism for ATP synthesis, in which the energy-linked release of ATP from one site requires the binding of ADP and Pi at an alternate site. Analysis of the distribution of 18O-labeled species arising from the ATP formed eliminates explanations for substrate modulation based on preexisting or induced enzyme heterogeneity. Furthermore, the results, together with other related findings, make participation of control sites unlikely. The occurrence of alternating site catalysis cooperativity in ATP synthesis by chloroplasts thus appears to be reasonably well established.
TL;DR: A mechanism is proposed which explains some of the kinetic and binding properties in terms of an asymmetry in the distribution of the conformational states of the four identical subunits of ADP-glucose synthase.
TL;DR: Observations do not support the proposal that the cAMP-CRP complex could stimulate transcription via some "melting" property unless its interactions be dramatically changed when it binds specifically to promoter DNA.
Abstract: The cyclic adenosine 3',5'-monophosphate receptor protein of Escherichia coli (CRP) binds cooperatively to single- and double-stranded DNA. Binding data could be fitted to the model of McGhee and von Hippel (1) and show that neither strandedness of DNA, nor the effectors cAMP and cGMP or the ionic strength (KCl) do change appreciably the cooperativity parameter omega (omega approximately or equal to 100), and site size of DNA. Instead, distinctly different slopes were observed for the linear decrease of log K omega (a measure of the overall affinity) as a function of log (K+). From these double-log plots (2), the number of cations released and the non-electrostatic contributions to the binding free energy could be determined. Binding of CRP to single-stranded DNA is slightly favored under physiological ionic conditions (0.15-0.20 M), but such a preferential binding is almost abolished in the presence of cAMP which increases the strength of the interaction of the protein with both forms of DNA. CGMP does not change the binding properties and interactions of CRP with DNA. These observations do not support the proposal that the cAMP-CRP complex could stimulate transcription via some "melting" property unless its interactions be dramatically changed when it binds specifically to promoter DNA.
TL;DR: In this article, a double-reciprocal plot was used to measure the effect of hydrogen bonding in the α-helix and β-sheet of polypeptides.
Abstract: Hydrogen bonding in the α-helix and β-sheet has been studied by ab initio molecular orbital calculations carried out on complexes of formamide. Hydrogen-bond geometries were taken from x-ray crystallography of polypeptides. Positive cooperativity is found in all cases. The limiting value for infinite chains is obtained by use of a double-reciprocal plot and indicates an increase in the effective bond strength of 25% over that of a single isolated bond. Parallel calculations based on a classical electrostatic model yield qualitatively similar trends but underestimate the cooperativity by half. Charge redistribution accompanying cooperativity is characterized by a new type of charge-density difference plot, the cooperativity map. The magnitude and distance over which cooperativity acts suggest several significant biological consequences. Thus the average of α-helices and the number of β-sheet strands found in protein may be influenced by cooperativity. Cooperativity in the interpeptide hydrogen bond may also be partly responsible for the rapid formation of secondary structure in renaturing proteins and help stabilize secondary structure relative to the random-coil conformation.
TL;DR: This work investigates single-shell dimyristoyl-lecithin vesicles of different diameters by calorimetry and 90” light-scattering techniques and finds that the steepness of the lipid phase transition is predominantly determined by the transition enthalpy rather than by the cooperativity.
TL;DR: The proton nuclear magnetic resonance spectrum of human adult deoxyhemoglobin in D2O in the region from 6 to 20 ppm downfield from the proton resonance of residual water shows a number of hyperfine shifted proton resonances that are due to groups on or near the alpha and beta hemes, suggesting that some cooperativity must exist in the deoxy quaternary structure of the hemoglobin molecule during the oxygenation process.
Abstract: The proton nuclear magnetic resonance spectrum of human adult deoxyhemoglobin in D2O in the region from 6 to 20 ppm downfield from the proton resonance of residual water shows a number of hyperfine shifted proton resonances that are due to groups on or near the alpha and beta hemes. The sensitivity of these resonances to the ligation of the heme groups and the assignment of these resonances to the alpha and beta chains provide an opportunity to investigate the cooperative oxygenation of an intact hemoglobin molecule in solution. By use of the nuclear magnetic resonance correlation spectroscopy technique, at least two resonances, one at approximately 18 ppm downfield from HDO due to the beta chain and the other at approximately 12 ppm due to the alpha chain, can be used to study the binding of oxygen to the alpha and beta chains of hemoglobin. The present results using approximately 12% hemoglobin concentration in 0.1 M Bistris buffer at pD 7 and 27 degrees C with and without organic phosphate show that there is no significant line broadening on oxygenation (from 0 to 50% saturation) to affect the determination of the intensities or areas of these resonances. It is found that the ratio of the intensity of the alpha-heme resonance at 12 ppm to that of the beta-heme resonance at 18 ppm is constant on oxygenation in the absence of organic phosphate but decreases in the presence of 2,3-diphosphoglycerate or inositol hexaphosphate, with the effect of the latter being the stronger. On oxygenation, the intensities of the alpha-heme resonance at 12 ppm and of the beta-heme resonance at 18 ppm decreases more than the total number of deoxy chains available as measured by the degree of O2 saturation of hemoglobin. This shows the sensitivity of these resonances to structural changes which are believed to occur in the unligated subunits upon the ligation of their neighbors in an intact tetrameric hemoglobin molecule. A comparison of the nuclear magnetic resonance data with the populations of the partially saturated hemoglobin tetramers (i.e., hemoglobin with one, two, or three oxygen molecules bound) leads to the conclusion that in the presence of organic phosphate the hemoglobin molecule with one oxygen bound maintains the beta-heme resonance at 18 ppm but not the alpha-heme resonance at 12 ppm. These resluts suggest that some cooperativity must exist in the deoxy quaternary structure of the hemoglobin molecule during the oxygenation process. Hence, these results are not consistent with the requirements of two-state concerted models for the oxygenation of hemoglobin. In addition, we have investigated the effect of D2O on the oxygenation of hemoglobin by measuring the oxygen dissociation curves of normal adult hemoglobin as a function of pH in D2O andH2O media. We have found that (1) the pH dependence of the oxygen equilibrium of hemoglobin (the Bohr effect) in higher pH in comparison to that in H2O medium and (2) the Hill coefficients are essentially the same in D2O and H2O media over the pH range from 6.0 to 8.2...
TL;DR: The binding of polymyxin-B to charged dipalmitoyl phosphatidic acid membranes has been studied as function of the external pH and of the ionic strength of the buffer solution to find the cooperativity of the binding process increases with increasing Ionic strength and reaches a constant value at I greater than 0.2 mol/l.
TL;DR: The predicted temperature dependence of the Hill coefficient for the MWC and Adair models is identical at low and intermediate temperatures, but, interestingly, would show a strong divergence at high temperatures where negative cooperativity is suggested for the Adair case and positive cooperativity for theMWC case.
TL;DR: The purple membrane of Halobacterium halobium contains a single protein to which a retinal is bound via a protonated Schiff base, bacteriorhodopsin, and the structure and the organization of this retinal-protein complex was investigated by X-ray diffraction and electron microscopy.
TL;DR: A comparison between the metal-binding properties of SCP’s and troponin C’'s from invertebrate muscle reveals that the former are much more complex than the latter, which contrasts sharply with the situation prevailing in vertebrate skeletal muscle, where complexity is found in myofibrillar tropon in C and not in sarcoplasmic parvalbumin.
TL;DR: Mylossoma hemoglobins resemble those of Hoplosternum, trout, salmon, sucker, eel and loach in the degree of their functional differentiation and may represent evolutionary specializations designed to serve diverse physiological functions.
TL;DR: This study suggests a new strategy for delineating the molecular mechanism responsible for cooperative ligand binding from binding isotherms, and demonstrates that the cooperativity of ligandbinding can be modulated when a competitive ligand is present in the protein-ligand binding mixture.
Abstract: A few molecular models have been developed in recent years to explain the mechanism of cooperative ligand binding. The concerted model of Monod, Wyman and Changeux and the sequential model of Koshland, Nemethy and Filmer were formulated to account for positively cooperative binding. The pre-existent asymmetry model and the sequential model can account for negatively cooperative ligand binding. In most cases, however, it is virtually impossible to deduce the molecular mechanism of ligand binding solely from the shape of the binding isotherm. In the present study we suggest a new strategy for delineating the molecular mechanism responsible for cooperative ligand binding from binding isotherms. In this approach one examines the effect of one ligand on the cooperativity observed in the binding of another ligand, where the two ligands compete for the same set of binding sites. It is demonstrated that the cooperativity of ligand binding can be modulated when a competitive ligdnd is present in the protein-ligand binding mixture. A general mathematical formulation of this modulation is presented in thermodynamic terms, using model- independent parameters. The relation between the Hill coefficient at 50% ligand saturation with respect to ligand X in the absence, h(x), and in the presence of a competing ligand Z, h(x,z), is expressed in terms of the thermodynamic parameters characterizing the binding of the two ligands. Then the relationship between h(x) and h(x,z), in terms of the molecular parameters of the different allosteric models, is explored. This analysis reveals that the different allosteric models predict different relationships between h(x,z) and h(x). These differences are especially focused when Z binds non-cooperatively. Thus, it becomes possible, on the basis of ligand binding experiments alone, to decide which of the allosteric models best fits a set of experimental data.
TL;DR: In this article, the binding isotherms for acridine orange (AO) and heparin systems can be evaluated solely on the basis of quantitative fluorescence spectroscopic measurements.
Abstract: Binding isotherms for acridine orange (AO)–heparin systems can be evaluated solely on the basis of quantitative fluorescence spectroscopic measurements. The evaluation of thermodynamic parameters indicates that the interactions of AO with heparins from several animal sources are similar to each other in magnitude. Binding is highly exothermic (ΔH = −6 kcal mol−1) and is stabilized by dye–polymer and dye–dye (coopertive) interactions, as well as by entropic factors (ΔS = +7 e.u.). The predominant stabilizing factor appears to be the electrostatic attraction between the AO cation and the heparin polyanion, although the other factors are important as well. At 24°C the value of the cooperative binding constants for the various heparins range from 8.8 to 11.3 × 105M−1, corresponding to a free energy of −8 kcal mol−1. The degree of cooperativity, which is a direct measure of dye–dye interaction, varies with polymer:dye ratio; the theoretical basis for this variation remains to be elucidated. Electrophoretic data indicate that each heparin sample consists of a mixture of species, each with its own charge density. This precludes definitive interpretation of observed small differences in the values of the thermodynamic parameters among the various samples until each sample can be resolved into its components.
TL;DR: In this paper, a simpler way of attacking cooperativity problems and demonstrating its utility by applying it to several situations of increasing complexity is presented, and applied to several scenarios of varying complexity.
Abstract: Provides a simpler way of attacking cooperativity problems and demonstrates its utility by applying it to several situations of increasing complexity.
TL;DR: In this article, the authors present a survey of the properties of the B-A transition of DNA in solution: the degree of cooperativity and influence of sequence, and its possible role in genes activation.
Abstract: This survey covers the following topics: (1) Theoretical calculation of the total multitude of the energetically permitted regular DNA helices. (2) Theoretical study of flexibility of the double helix with emphasis on nucleosome structure. (3) Experimental data on the properties of the B to A transition of DNA in solution: the degree of cooperativity and influence of sequence. (4) The B-A transition and its possible role in genes activation.
TL;DR: Kinetic studies suggest two preferred enzyme conformations in the presence of low concentrations of the cosubstrates: a higher affinity form manifesting hyperbolic substrate kinetics, induced by submicromolar activity, and a lower affinity form exaggerating cooperativity with respect to substrate.
Abstract: Tryptophan hydroxylase from rat midbrain, EGTA-pretreated and dialyzed, manifested allosteric properties with respect to its substrate tryptophan, cofactor tetrahydrobiopterin, and the calcium ion. Kinetic studies suggest two preferred enzyme conformations in the presence of low concentrations of the cosubstrates: a higher affinity form manifesting hyperbolic substrate kinetics, induced by submicromolar (0.4--0.8 microM) calcium in vitro and cocaine in vivo, and a lower affinity form exaggerating cooperativity with respect to substrate, induced by submicromolar (0.4 to 0.8 microM) lithium in vitro and lithium in vivo. Lithium's effect on serotonin biosynthesis may be due to its antagonism of the positive effector influence of calcium on tryptophan hydroxylase, either as a negative effector or by blocking the calcium site.
Journal Article•
TL;DR: It is verified from studies of a streaming system reconstituted from rabbit skeletal F-actin and HMM that one life phenomenon, active streaming, is caused by the 'order-from-order' mechanism, and dynamic cooperativity is the key mechanism for life phenomena caused by this mechanism at the subcellular level.
TL;DR: The cluster model ofprotein folding is further investigated for the thermodynamic and kinetic properties of protein folding–unfolding transitions and the qualitative aspects of the folding dynamics are as follows.
Abstract: The cluster model of protein folding [Kanehisa, M I & Tsong, T Y (1978) J Mol Biol124, 177–194] is further investigated for the thermodynamic and kinetic properties of protein folding–unfolding transitions A cluster is a locally formed ordered region in the polypeptide chain due to cooperative interactions among residues In the cluster model a cooperative term is assigned as proportional to the surface area of a globular cluster This assignment is compared with that for the helix–coil transition of homopolypeptides, where the cooperative term is proportional to the two ends of a linear helical sequence The dynamics of the cluster model exhibit a slow phase, which is well-separated from other faster phases, because of the cooperative interaction of the macrosystem This slow phase not only appears within the transition region, but can also persist well below the transition region if the cooperativity depends on the external condition The amplitudes of certain kinetic phases can vary depending on the choice of physical parameters monitoring the reaction Thus the same reaction may display different time courses The qualitative aspects of the folding dynamics are as follows In one case the rate-limiting formation of a critical-size cluster is followed by its rapid growth, while in the other the rate-limiting step appears in a later stage, where preformed smaller clusters merge into larger ones The former case is similar to the dynamics of the helix–coil transition, and the latter represents a stepwise mechanism of protein structure formation