The Experts below are selected from a list of 216 Experts worldwide ranked by ideXlab platform
Stuart J. Edelstein - One of the best experts on this subject based on the ideXlab platform.
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A novel equation for cooperativity of the allosteric state function.
Journal of molecular biology, 2013Co-Authors: Stuart J. EdelsteinAbstract:The MWC (Monod–Wyman–Changeux) allosteric model postulates concerted conformational changes between two states: the intrinsically more stable T state with relatively weak ligand binding and the R state with relatively strong ligand binding. The model distinguishes between Y¯ (the fractional occupation of the binding sites) and R¯ (the fraction of molecules in the R state). Cooperativity (measured by the Hill Coefficient) has strikingly different properties for Y¯ and R¯. For the latter, cooperativity depends only on the relative affinities of the two states, not on their relative intrinsic stabilities, as demonstrated here with a simple new equation relating the Hill Coefficient to R¯.
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derivation of the crick wyman equation for allosteric proteins defining the difference between the number of binding sites and the Hill Coefficient
Journal of Molecular Biology, 2013Co-Authors: Frederic Poitevin, Stuart J. EdelsteinAbstract:Abstract In response to a 100-word footnote in the 1965 article by Monod, Wyman, and Changeux, a detailed manuscript signed by Francis Crick and Jeffries Wyman with 6000 words and 30 equations entitled “A Footnote on Allostery” circulated in 1965 among a limited group of scientists interested in allosteric interactions. This interesting and provocative document is published in this special issue for the first time. An intriguing equation in their text relates the difference between n (the number of ligand binding sites) and n′ (the Hill Coefficient) to the ratio of the saturation functions Y ¯ , for oligomers with n − 1 and n binding sites. A compact derivation of this equation was not provided by Crick and Wyman, but one is presented here based on a definition of Y ¯ involving the binding polynomial and its first derivative.
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Contributions of individual molecular species to the Hill Coefficient for ligand binding by an oligomeric protein.
Journal of molecular biology, 1997Co-Authors: Stuart J. Edelstein, William G. BardsleyAbstract:New insights into the Hill Coefficient (n) as a measure of cooperativity are obtained by resolving Y, the fractional ligand binding to an oligomeric protein, into a series of integral nth-order reactions. For identical sites within a single conformational state, the weighted sum of each reaction multiplied by its net order gives a Hill Coefficient at Y = 0.5 of n50 = 1.0, indicative of non-cooperative binding. However, the disappearance of unliganded oligomers (S0) reflects the higher-order reactions, with their weighted sum (for a tetramer) leading to a Hill Coefficient at S0 = 0.5 of n50* = -1.27. For an oligomer with two conformational states (such as represented by the T and R states in the Monod-Wyman-Changeux model) capable of generating highly cooperative binding, the same nth-order reactions apply, but with different weights. For oxygen binding to hemoglobin, n50 is resolved into three components with net reaction orders of n = -2, 2, and 4 (with weights of 0.067, 0.15, and 0.754 corresponding, respectively, to the contributions of singly, triply and quadruply liganded molecules) to give n50 = 3.18. However, the cooperativity of the "state" function, R' (the normalized fraction of molecules in the R state), as characterized by n50' (the Hill Coefficient at R' = 0.5) is distinct from n50. If the T-R equilibrium lies very far in favor of either state, then even when the two states differ widely in their intrinsic affinity for ligand, the lower limit of cooperativity for Y is n50 = 1.0, but the Hill Coefficient for R' cannot fall below n50' = 1.27 (for a tetramer). Hence, the lower limit of n50' is equal to the absolute value of n50* describing the disappearance of S0 for an oligomer with a single conformational state.
Kalina Hristova - One of the best experts on this subject based on the ideXlab platform.
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Hill Coefficient ANALYSIS OF TRANSMEMBRANE HELIX DIMERIZATION
The Journal of membrane biology, 2009Co-Authors: Ricky Soong, Mikhail Merzlyakov, Kalina HristovaAbstract:Here, we employed the Hill equation, used broadly to characterize cooperativity in protein–ligand binding, to describe the dimerization of transmembrane (TM) helices in hydrophobic environments. The Hill analysis of wild-type fibroblast growth factor receptor 3 (FGFR3) TM domain dimerization gives a Hill Coefficient of ~1 for lipid bilayers but only ~0.2 for sodium dodecyl sulfate (SDS) micelles. We propose that this finding is indicative of heterogeneity in FGFR3 TM dimer structure and stability in SDS micelles. We further speculate that (1) the Hill equation can be used as a tool to assess the existence of multiple structural states of TM dimers in different hydrophobic environments and (2) the structural heterogeneity, detectable by Hill analysis, may be the underlying reason for the broad peaks and the low resolution NMR studies of peptides in detergents.
Emanuele Caglioti - One of the best experts on this subject based on the ideXlab platform.
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On the Measurement of Cooperativity and the Physico-Chemical Meaning of the Hill Coefficient.
Current protein & peptide science, 2019Co-Authors: Andrea Bellelli, Emanuele CagliotiAbstract:Cooperative ligand binding is a fundamental property of many biological macromolecules, notably transport proteins, hormone receptors, and enzymes. Positive homotropic cooperativity, the form of cooperativity that has greatest physiological relevance, causes the ligand affinity to increase as ligation proceeds, thus increasing the steepness of the ligand-binding isotherm. The measurement of the extent of cooperativity has proven difficult, and the most commonly employed marker of cooperativity, the Hill Coefficient, originates from a structural hypothesis that has long been disproved. However, a wealth of relevant biochemical data has been interpreted using the Hill Coefficient and is being used in studies on evolution and comparative physiology. Even a cursory analysis of the pertinent literature shows that several authors tried to derive more sound biochemical information from the Hill Coefficient, often unaware of each other. As a result, a perplexing array of equations interpreting the Hill Coefficient is available in the literature, each responding to specific simplifications or assumptions. In this work, we summarize and try to order these attempts, and demonstrate that the Hill Coefficient (i) provides a minimum estimate of the free energy of interaction, the other parameter used to measure cooperativity, and (ii) bears a robust statistical correlation to the population of incompletely saturated ligation intermediates. Our aim is to critically evaluate the different analyses that have been advanced to provide a physical meaning to the Hill Coefficient, and possibly to select the most reliable ones to be used in comparative studies that may make use of the extensive but elusive information available in the literature.
Grigori Y. Rychkov - One of the best experts on this subject based on the ideXlab platform.
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pH-dependent interactions of Cd2+ and a carboxylate blocker with the rat C1C-1 chloride channel and its R304E mutant in the Sf-9 insect cell line.
The Journal of physiology, 1997Co-Authors: Grigori Y. Rychkov, D. St J. Astill, Brett Bennetts, Bernard P. Hughes, A. H. Bretag, M L RobertsAbstract:1. Gating of the skeletal muscle chloride channel (ClC-1) is sensitive to extracellular pH. In this study, whole-cell recording of currents from wild-type (WT) ClC-1 and a mutant, R304E, expressed in the Sf-9 insect cell line was used to investigate further the nature of the pH-sensitive residues. 2. Extracellular Cd2+ produced a concentration-dependent block of WT ClC-1 with an IC50 of 1.0 +/- 0.1 mM and a Hill Coefficient of 2.0 +/- 0.3. This block was sensitive to external pH, reducing at low pH, with an apparent pKa of 6.8 +/- 0.1 and a Hill Coefficient for proton binding of 3.0 +/- 0.3. Anthracene-9-carboxylate (A-9-C) block of WT ClC-1 was also pH sensitive, increasing at low pH, with an apparent pKa of 6.4 +/- 0.1 and a Hill Coefficient for proton binding of 1.0 +/- 0.2. 3. Compared with WT ClC-1, R304E had a lower affinity for Cd2+ (IC50, 3.0 +/- 0.3 mM) but it had a similar Hill Coefficient for transition metal ion binding. The Hill Coefficient for proton binding to the Cd2+ binding site was reduced to 1.4 +/- 0.3. In contrast, the A-9-C binding site in R304E showed the same pH sensitivity and affinity for the blocker as that seen in WT ClC-1. 4. ClC-1 has at least two binding sites for Cd2+, each of which has at least three residues which can be protonated. Binding of A-9-C is influenced by protonation of a single residue. Arg 304 is not sufficiently close to the A-9-C binding site to affect its characteristics, but it does. alter Cd2+ binding, indicating that transition metal ions and aromatic carboxylates interact with distinct sites. 5. The block of ClC-1 by transition metal ions and the apparent pKa of this block, together with the apparent pKa for A-9-C block and gating are all compatible with the involvement of His residues in the pore and gate of ClC-1.
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pH‐Dependent Interactions of Cd2+ and a Carboxylate Blocker with the Rat ClC‐1 Chloride Channel and Its R304E Mutant in the Sf‐9 Insect Cell Line
The Journal of Physiology, 1997Co-Authors: Grigori Y. Rychkov, D. St J. Astill, Brett Bennetts, Bernard P. Hughes, A. H. Bretag, Michael RobertsAbstract:1. Gating of the skeletal muscle chloride channel (ClC-1) is sensitive to extracellular pH. In this study, whole-cell recording of currents from wild-type (WT) ClC-1 and a mutant, R304E, expressed in the Sf-9 insect cell line was used to investigate further the nature of the pH-sensitive residues. 2. Extracellular Cd2+ produced a concentration-dependent block of WT ClC-1 with an IC50 of 1.0 +/- 0.1 mM and a Hill Coefficient of 2.0 +/- 0.3. This block was sensitive to external pH, reducing at low pH, with an apparent pKa of 6.8 +/- 0.1 and a Hill Coefficient for proton binding of 3.0 +/- 0.3. Anthracene-9-carboxylate (A-9-C) block of WT ClC-1 was also pH sensitive, increasing at low pH, with an apparent pKa of 6.4 +/- 0.1 and a Hill Coefficient for proton binding of 1.0 +/- 0.2. 3. Compared with WT ClC-1, R304E had a lower affinity for Cd2+ (IC50, 3.0 +/- 0.3 mM) but it had a similar Hill Coefficient for transition metal ion binding. The Hill Coefficient for proton binding to the Cd2+ binding site was reduced to 1.4 +/- 0.3. In contrast, the A-9-C binding site in R304E showed the same pH sensitivity and affinity for the blocker as that seen in WT ClC-1. 4. ClC-1 has at least two binding sites for Cd2+, each of which has at least three residues which can be protonated. Binding of A-9-C is influenced by protonation of a single residue. Arg 304 is not sufficiently close to the A-9-C binding site to affect its characteristics, but it does. alter Cd2+ binding, indicating that transition metal ions and aromatic carboxylates interact with distinct sites. 5. The block of ClC-1 by transition metal ions and the apparent pKa of this block, together with the apparent pKa for A-9-C block and gating are all compatible with the involvement of His residues in the pore and gate of ClC-1.
Paul A. Srere - One of the best experts on this subject based on the ideXlab platform.
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Azotobacter vinelandii citrate synthase.
Biochemistry, 1995Co-Authors: Magali Rault-leonardon, Mark A. L. Atkinson, Clive A Slaughter, Carolyn R Moomaw, Paul A. SrereAbstract:We have purified the citrate synthase from Azotobacter vinelandii and have determined that the size of the subunit is 48,000 Da and the structure of the holoenzyme is a hexamer. This contrasts with earlier estimates that indicate a 58,000 Da subunit and a tetrameric structure. In addition, the enzyme is allosteric with a Hill Coefficient of 1.5 and is inhibited by NADH. The Hill Coefficient is changed to about 1 by high ionic strength and AMP. The enzyme is thus similar to the citrate synthases of many other Gram-negative, facultative, anaerobic organisms. In addition, the amino acid sequence of about 100 residues has been determined and found to be highly similar to the sequence of Pseudomonas aeruginosa citrate synthase.