Graphical analysis of interactions between oxidation-reduction sites in two site oxidation-reduction proteins

Many enzymes that catalyze electron-transfer reaction contain multiple oxidation-reduction centers (sites). The oxidation-reduction potential of one site as well as the kinetics of electron transfer through this site may be altered by the state of reduction of a neighboring site. Oxidation-reduction site interactions may be mechanistically important and quantitation of site interactions would aid the interpretation of thermodynamic data and possibly kinetic data. A graphical means to detect and quantitate interactions between oxidation-reduction sites from oxidation-reduction equilibrium data (type A + B in equilibrium C + D) is described and has its roots in the Scatchard analysis of ligand binding equilibria (type A + B in equilibrium C). Oxidation-reduction sites often have distinct physical properties allowing the titration behavior of specific sites to be monitored. Equilibrium measurements on specific sites of a two site protein allow a further analysis of the data which can be combined with the oxidation-reduction Scatchard analysis to solve for all four specific site equilibrium constants. Ligand binding systems can usually measure only total site binding and simplifying assumptions of identical sites or noninteracting sites are required to solve for the site specific equilibrium constants. Thus, specific site equilibrium measurements offer a distinct advantage over total site measurements. The principles of the method are illustrated by applying the graphical analysis to the two site protein, thioredoxin reductase, which contains an oxidation-reduction active site disulfide in addition to FAD. The specific site oxidation-reduction midpoint potentials (Em) of the FAD and disulfide couples of thioredoxin reductase at pH 6.0, 12 degrees C, were found to be FAD/FADH2-enzyme-(S)2 = -0.183 V, FAD/FADH2-enzyme-(SH)2 = -0.199 V, (FAD)-enzyme-(S)2/(SH)2 = -0.202 V, and (FADH2)-enzyme-(S)2/(SH)2 = -0.218 V. Hence, at pH 6.0, the FAD and disulfide sites of thioredoxin reductase have Em values that differ by approximately 0.019 V and have a negative interaction of about 0.016 V.     

Evaluation of series of isobenzofuranone dimers as PKCalpha ligands: implication for the distance between the two ligand binding sites

Protein kinase C (PKC) is a family of enzymes, which play important roles in intracellular signal transduction. To examine the distance between the two ligand binding sites (C1A and C1B) of PKC, we designed and synthesized two series of isobenzofuranone dimers. Peak binding activities were observed for the C3-acyl chain dimers having a C10-C12 linker and for the C7 dimers having a C14-C16.     

Analysis of competition binding between soluble and membrane-bound ligands for cell surface receptors

Binding of the Fc portion of IgG coated on targets to Fcgamma receptors (e.g., CD16) expressed on leukocytes (i.e., 2D binding) is an initiating step for immune responses such as phagocytosis or antibody-dependent cellular cytotoxicity. In vivo, circulating leukocytes are exposed to plasma IgG. The competition from soluble IgG (i.e., 3D binding) may affect the 2D binding. Many cell surface receptors, CD16 included, have soluble counterparts. While their physiological significance is not clear, receptor-based competitive inhibition therapy, in which soluble receptors, ligands, and their analogs are employed to compete with surface-bound receptors and ligands to prevent unwanted adhesion, is widely used to treat various diseases. To provide a quantitative basis for design of these therapeutic approaches, we developed a mathematical model for 2D and 3D competition binding. The model relates cell-surface adhesion (in the presence and absence of dislodging forces) to the concentration of the soluble competitor, the densities of the surface-bound receptors and ligands, as well as the binding affinities of the 2D and 3D interactions. Binding of CD16-expressing cells to an IgG-coated surface in the presence of a soluble competitor (IgG or anti-CD16 antibody) was quantified by a centrifugation assay. The agreement between experiment and theory supports the validity of the model, which could be useful in predicting the efficacy of the competitor.     

A computer simulation of the binding between flexible ligands and their polymeric receptor binding sites

In this paper we present Monte Carlo simulation calculations for model systems of flexible ligands of variable size binding to an array of surface potential wells. Some of the rules governing the overall equilibrium behaviour of the systems with respect to such factors as the shape of the receptor, the strength, distribution and specificity of the ligand-receptor interactions are probed.     

Insight into the interaction sites between fatty acid binding proteins and their ligands

Fatty acid binding proteins (FABPs), are evolutionarily conserved small cytoplasmic proteins that occur in many tissue-specific types. One of their primary functions is to facilitate the clearance of the cytoplasmic matrix from free fatty acids and of other detergent-like compounds. Crystallographic studies of FABP proteins have revealed a well defined binding site located deep inside their β-clam structure that is hardly exposed to the bulk solution. However, NMR measurements revealed that, when the protein is equilibrated with its ligands, residues that are clearly located on the outer surface of the protein do interact with the ligand. To clarify this apparent contradiction we applied molecular dynamics simulations to follow the initial steps associated with the FABP–fatty acid interaction using, as a model, the interaction of toad liver basic FABP, or chicken liver bile acid binding protein, with a physiological concentration of palmitate ions. The simulations (~200 ns of accumulated time) show that fatty acid molecules interact, unevenly, with various loci on the protein surface, with the favored regions being the portal and the anti-portal domains. Random encounters with palmitate at these regions led to lasting adsorption to the surface, while encounters at the outer surface of the β-clam were transient. Therefore, we suggest that the protein surface is capable of sequestering free fatty acids from solution, where brief encounters evolve into adsorbed states, which later mature by migration of the ligand into a more specific binding site.     

Kinetic analysis of a reaction model with two binding sites for acetylcholinesterase

After having suggested a kinetic model with two binding sites for acetylcholinesterase, the authors obtained the various function of [I] (1/vi; (vo/vi-1)/[I]; 1/Vi; Ki/Vi) starting from the velocity equation. An analytical study was then carried out showing the theoretical shape of such functions at different values of the kinetic parameters.     

HINT predictive analysis of binding between retinol binding protein and hydrophobic ligands

The interaction between the retinol binding protein and four ligands was evaluated using HINT, a software based on experimental LogP values of individual atoms. A satisfactory correlation was found between the HINT scores and the experimental dissociation constants of three of the ligands, fenretinide, N-ethylretinamide and all-trans retinol, despite their hydrophobic nature. A prediction is made for the binding affinity of the fourth ligand, axerophtene, not yet determined in solution.     

Sodium exchange between two sites the binding of sodium to halotolerant bacteria

The longitudinal and transverse relaxation curves of sodium undergoing exchange between two sites are presented. When the two sites are ‘bound’ and ‘free’ sodium respectively, the relaxation curves are, in general, not exponential. It is shown that in some cases only one exponential decay could be detected experimentally though the true decay curve is much more complicated. In such cases where the population of ‘free’ and ‘bound’ sodium are equal, only 40–70% of the total intensity would be detected, depending on the lifetime of sodium in the two sites. It is also shown that the fast exchange approximation, usually applied in the interpretation of sodium relaxation curves, might lead to wrong conclusions.Measurements of sodium relaxation times in halotolerant bacteria show that T₁ and T₂ are different and frequency-dependent. The intensity of the sodium signal is 40% of the tota sodium concentration. It was possible to simulate the relaxation behaviour and intensity measurements by applying the following model. There are three types of sodium: the extracellular sodium (A) which exchanges with part of the intracellular sodium (B) and a fraction (C) which is bound but does not exchange with the extracellular sodium. It was possible to estimate the physical properties of sodium at site B. The quadrupole coupling constant $\text{(e}{}^2\text{qQ/}\text{h}\text{?}\text{)}{}_{\mathrm{<mtext>B</mtext>}}\text{= 9 · 10}{}^6\text{rad/s}$, the correlation time ⊥_cB = 5.5 · 10^?7 s and the lifetime of sodium at site B, ⊥_B = 6 · 10^?4 s.     

Cross-linking between translationally equivalent sites on the two heads of myosin. Relationship to energy transfer results between the same pair of sites

Mercenaria myosin and scallop pure hybrid myosin possessing Mercenaria regulatory light chains were reacted with various concentrations of 4-4'-dimaleimidylstilbene-2-2'-disulfonic acid (DMSDS). Regulatory light chain homodimers are formed with great efficiency (20-50%). Dimers incorporating essential light chains were not formed upon reaction of DMSDS with Mercenaria myosin but some (less than 5%) essential light chain homodimers were obtained in the case of scallop hybrid myosin, probably occurring through relatively specific intermolecular associations within small myosin aggregates. Results were invariant, irrespective of the presence or absence of calcium and/or ATP. No radioactivity is incorporated into regulatory light chain homodimers upon post-labeling DMSDS-reacted myosin with 14C-labeled N-ethylmaleimide, irrespective of the original labeling ratio of DMSDS to myosin heads. This indicates the absence of free sulfhydryl groups in the regulatory light chain homodimer and suggests, therefore, that DMSDS links the two light chains together between translationally equivalent residues (Cys-50 of the Mercenaria regulatory light chain). These results imply that translationally equivalent sites on the two heads of myosin can come within 18 A of each other, the span of reacted DMSDS. Because energy transfer results between identical pairs of translationally equivalent sites on hybrid myosins indicated a low efficiency of energy transfer between these sites (Chantler, P.D., and Tao, T. (1986) J. Mol. Biol. 192, 87-99), it would appear that even though the two cysteines can come within 18 A of each other, their mean separation is much greater than this distance (greater than 50 A), a result consistent with a considerable flexibility of the two myosin heads with respect to each other.     

Internal eutrophication in peat soils through competition between chloride and sulphate with phosphate for binding sites

Inputs of surface waters high in chloride and sulphateincreased the availability of nutrients in fenpeatlands. This `internal eutrophication' wasdemonstrated with test plants (`phytometers') andthrough water and soil analysis. Three experiments arepresented in which the level of chloride and/orsulphate was increased to 3 mmol_c l^–1. Inexperiment 1 chloride levels were increased from 0.5to 3 mmol_c l^–1 as CaCl₂ or NaCl. Inexperiment 2 and 3 similar increased levels forchloride and sulphate (3 mmol_c l^–1; as NaCland Na₂SO₄) were used. The following resultswere found:(i) No differences in soil total-N and total-P werefound before and after the treatments in any of thethree experiments.(ii) Experiment 1 showed a significant increase inBio-Available P (BAP) in pots planted with Anthoxanthum odoratum as well as in bare pots for theNaCl and CaCl₂ treatments. The plants in thesetreatments had taken up much more P.(iii) Experiment 2 showed an increase in soil BAPafter treatment with chloride and sulphate in potsplanted with Anthoxanthum odoratum. The chloridetreatment had no effect on plant biomass, whereas thesulphate treatment resulted in a reduction in rootbiomass and root N and P content. The shoots showedan increase in P content in the sulphate and chloridetreatments, while N content remained the same.(iv) In experiment 3, treatments with chloride andsulphate led to significantly increased biomass and Puptake of Anthoxanthum odoratum. Again, noeffects on N uptake were found.These experiments provide evidence for distinctlyincreased availability of phosphate in peat soils whenthese come into contact with water with evenmoderately increased sulphate or chloride levels.Surface water originating from the Rhine river, whichis enriched in chloride and sulphate, is oftensupplied to fen reserves in The Netherlands, tocompensate for water losses due to agriculturaldrainage in the region. The results of this study showthat phosphate availability to the vegetation may risedrastically, with detrimental effects on the speciesdensity and the occurrence of rare species in thevegetation. Hence, supply of this water should beavoided.     

A simplified analysis of Scatchard plots for systems with two interacting binding sites

A simple graphical method for calculating stoichiometric and site binding constants for systems with two initially equivalent interacting sites is derived from a modified Scatchard equation. The binding constants can be calculated from Scatchard plots (r/[A] as a function of r) using the values of r/[A] (r is the molar ratio of bound ligands to total protein and [A] is the equilibrium concentration of free ligand) when r = 0 and r = 1 (half-saturation). The applicability of the method to the adsorption of bilirubin by peptide pendants immobilized on a polyacrylamide support is demonstrated.     

Automated identification of binding sites for phosphorylated ligands in protein structures

Phosphorylation is a crucial step in many cellular processes, ranging from metabolic reactions involved in energy transformation to signaling cascades. In many instances, protein domains specifically recognize the phosphogroup. Knowledge of the binding site provides insights into the interaction, and it can also be exploited for therapeutic purposes. Previous studies have shown that proteins interacting with phosphogroups are highly heterogeneous, and no single property can be used to reliably identify the binding site. Here we present an energy‐based computational procedure that exploits the protein three‐dimensional structure to identify binding sites involved in the recognition of phosphogroups. The procedure is validated on three datasets containing more than 200 proteins binding to ATP, phosphopeptides, and phosphosugars. A comparison against other three generic binding site identification approaches shows higher accuracy values for our method, with a correct identification rate in the 80–90% range for the top three predicted sites. Addition of conservation information further improves the performance. The method presented here can be used as a first step in functional annotation or to guide mutagenesis experiments and further studies such as molecular docking. Proteins 2012;. © 2012 Wiley Periodicals, Inc.     

gamma-Aminobutyric acid/benzodiazepine receptor protein carries binding sites for both ligands on both two major peptide subunits

Affinity column-purified GABA-benzodiazepine receptor proteins from human, cow, and rat brain were photoaffinity labeled with both [3H]flunitrazepam and [3H]muscimol and examined by gel electrophoresis in sodium dodecyl sulfate. Using high receptor protein concentrations (1 microM), the benzodiazepine ligand [3H]flunitrazepam was incorporated covalently primarily into the expected 52 kiloDalton major subunit but also significantly into a second 57 kiloDalton peptide. Likewise the GABA ligand [3H]muscimol photolabeled primarily the 57 kiloDalton peptide but also to some extent the 52 kiloDalton peptide. This cross-labeling suggests strongly that both major subunits carry binding sites for both GABA and benzodiazepine.     

Amino acid sequence homology between ligands and their receptors: potential identification of binding sites

Mice were immunized with alpha-bungarotoxin (BGT), a nearly irreversible antagonist of the acetylcholine receptor (AChR), to produce monoclonal antibodies (Mabs). One of the Mabs (JMC2.7) bound not only to BGT, but to the AChR as well. To understand the molecular basis for this novel cross-reaction, the amino acid sequences of these proteins were searched for areas of similarity which might constitute the shared epitope. A number of short segments of sequence homology were found, one of them representing the BGT-binding site of the AChR. Because a portion of BGT resembles that part of the AChR that binds toxin, the self-binding of BGT was evaluated. As shown here, BGT binds specifically to itself to form dimers. In order to extend these observations, other ligand-receptor pairs were examined for sequence homology. The sodium channel and alpha-scorpion toxins were found to have distinct areas of similarity, as do interleukin 2 (IL-2) and the IL-2 receptor. As a general principle, we propose that peptide ligands and their receptors may often share amino acid sequence homology. In fact, the sites of interaction between two proteins may largely be determined by these regions of similarity.     

Interfacial binding sites for cholesterol on GABAA receptors and competition with neurosteroids

γ-Aminobutyric acid type A (GABA_A) receptors in the brain are located in the outer membranes of brain cells where the concentration of cholesterol is high. Of the 25 available high-resolution structures available for GABA_A receptors, none were determined in the presence of cholesterol, but four include resolved molecules of cholesterol hemisuccinate (CHS). Here, a molecular docking procedure is used to sweep the transmembrane (TM) surfaces of the receptors for cholesterol binding sites. Cholesterol docking poses determined in this way match 89% of the resolved CHS when CHS molecules deemed unlikely to represent typical bound cholesterols are excluded. The receptors are pentameric, and their TM surfaces consist of a set of five facets, each including pairs of TM helices from two adjacent subunits. Each facet contains hydrophobic hollows running from one side of the membrane to the other, within which are six potential binding sites for cholesterol, three on each side of the membrane. High-resolution structures of GABA_A receptors with bound neurosteroids show that neurosteroids bind in these cholesterol binding sites, so the binding of neurosteroids and cholesterol will be competitive.