Sequence-dependent contribution of distal binding domains to CAP protein-DNA binding affinity.

We report measurements of the relative binding affinity of CAP for DNA sequences which have been systematically mutated in the region flanking the consensus binding site. Our experiments focus on the locus one helical turn from the dyad axis where DNA bending toward the minor groove is induced upon C-AP binding. The binding free energy and extent of bending are moderately well correlated for the set of 56 sequences. Changes in binding affinity spanning a factor of about 50 could be accounted for by additive contributions of dinucleotides; with a few exceptions, the relative ranking of dinucleotide contributions to binding and bending are similar. We conclude that dinucleotides are the smallest independent unit required for quantitative interpretation of CAP-induced DNA bending and binding in the distal domains of the CAP consensus binding site. The imperfect correlation between binding strength and extent of bending implies that sequence changes affect protein binding strength not only by altering the DNA deformation energy required to form the complex, but also by affecting directly the free energy of interaction between protein and DNA.     

Gamma-aminobutyric acid-modulated benzodiazepine binding sites in bacteria.

Benzodiazepine binding sites, which were once considered to exist only in higher vertebrates, are here demonstrated in the bacteria E.coli. The bacterial [3H]diazepam binding sites are modulated by GABA; the modulation is dose dependent and is reduced at high concentrations. The most potent competitors of E.Coli [3H]diazepam binding are those that are active in displacing [3H]benzodiazepines from vertebrate peripheral benzodiazepine binding sites. These vertebrate sites are not modulated by GABA, in contrast to vertebrate neuronal benzodiazepine binding sites. The E.coli benzodiazepine binding sites therefore differ from both classes of vertebrate benzodiazepine binding sites; however the ligand spectrum and GABA-modulatory properties of the E.coli sites are similar to those found in insects. This intermediate type of receptor in lower species suggests a precursor for at least one class of vertebrate benzodiazepine binding sites may have existed.     

Ligand binding distributions in nucleic acids

We illustrate a new method for the determination of the complete binding polynomial for nucleic acids based on experimental titration data with respect to ligand concentration. From the binding polynomial, one can then calculate the distribution function for the number of ligands bound at any ligand concentration. The method is based on the use of a finite set of moments of the binding distribution function, which are obtained from the titration curve. Using the maximum-entropy method, the moments are then used to construct good approximations to the binding distribution function. Given the distribution functions at different ligand concentrations, one can calculate all of the coefficients in the binding polynomial no matter how many binding sites a molecule has. Knowledge of the complete binding polynomial in turn yields the thermodynamics of binding. This method gives all of the information that can be obtained from binding isotherms without the assumption of any specific molecular model for the nature of the binding. Examples are given for the binding of Mn(2+) and Mg(2+) to t-RNA and for the binding of Mg(2+) and I(6) to poly-C using literature data.     

Comparison of acetylcholine and alpha-bungarotoxin binding sites in insects and vertebrates

1. The nervous tissue of locusts contains high affinity as well as low affinity binding sites for acetylcholine which display a similar nicotinic pharmacology. 2. Hill plot analysis indicated a non-cooperative binding of acetylcholine. 3. In membrane preparations from locust ganglia and mouse brain the number of binding sites for ACh was about ten fold lower than for BGTX, whereas in membranes from electric tissue both sites occurred in similar concentrations. 4. Drug binding studies suggest that the high affinity binding sites for ACh and BGTX in preparations from insect and mouse are different; whereas in electric tissue both sites are very similar. 5. Precipitation experiments using immobilized BGTX and specific antibodies indicated that in insect nervous tissue as in electric tissue the ACh and BGTX binding sites are located on the same receptor molecule and occupy distinct partially overlapping binding sites, whereas in the vertebrate brain both sites are located on distinct binding proteins.     

Relaxation of replication control in chaperone-independent initiator mutants of plasmid P1.

Escherichia coli chaperones DnaJ, DnaK and GrpE increase P1 plasmid initiator binding to the origin by promoting initiator folding. The binding allows initiation and also promotes pairing of origins which is believed to control initiation frequency. Chaperone-independent DNA binding mutants are often defective in replication control. We show here that these mutants have increased rates of association for DNA binding and defects in origin pairing. The increases in association rates were found to be due either to increased protein folding into active forms or to increases in the association rate constant, kon. Since the dissociation rate constants for DNA release with these mutants are not changed, it is unlikely that the DNA binding domain is affected. The pairing domain may thus control replication and modulate DNA binding. The role of the pairing domain in DNA binding can be significant in vivo as the selection for chaperone-independent binding favors pairing-defective mutants.     

Comparison of acetylcholine and α-bungarotoxin binding sites in insects and vertebrates

1. The nervous tissue of locusts contains high affinity as well as low affinity binding sites for acetylcholine which display a similar nicotinic pharmacology.2. Hill plot analysis indicated a non-cooperative binding of acetylcholine.3. In membrane preparations from locust ganglia and mouse brain the number of binding sites for ACh was about ten fold lower than for BGTX, whereas in membranes from electric tissue both sites occurred in similar concentrations.4. Drug binding studies suggest that the high affinity binding sites for ACh and BGTX in preparations from insect and mouse are different; whereas in electric tissue both sites are very similar.5. Precipitation experiments using immobilized BGTX and specific antibodies indicated that in insect nervous tissue as in electric tissue the ACh and BGTX binding sites are located on the same receptor molecule and occupy distinct partially overlapping binding sites, whereas in the vertebrate brain both sites are located on distinct binding proteins.     

A possible role of carbohydrate moieties in prostaglandin D2 and prostaglandin E2 receptor proteins from the porcine temporal cortex.

The binding activities of prostaglandins (PGs) D2 and E2 were measured after deglycosylation of P2 membranes prepared from the porcine temporal cortex in order to investigate the role of carbohydrate moieties in the receptor binding. PGD2 and PGE2 binding activities were significantly decreased by pretreatment with various exoglycosidases, such as neuraminidase for PGE2 binding, alpha-mannosidase and beta-galactosidase for PGD2 binding, and beta-N-acetylhexosaminidase for both. Further, peptide N-glycohydrolase F and endo-alpha-N-acetylgalactosaminidase, which are specific for the cleavage of N-glycan and O-glycan linkages, respectively, in glycoproteins were used. Pretreatment with either of them also reduced both PGD2 and PGE2 binding activities. The reduction was dependent on the pretreatment time and enzyme concentration. The time courses of the reduction were typically characterized by a marked increase in the nonspecific bindings. Scatchard plot analysis revealed that the reduction was caused by a decrease in the affinity rather than one in the maximal binding capacity. The specificity of the binding sites thereby shifted to be more nonspecific without affecting the order of the relative affinities among PGs for the binding sites. These results suggest that the carbohydrate moieties on PG receptor proteins of the brain are essential for the expression of their binding activities.     

Calorimetric analysis of aspartate transcarbamylase from Escherichia coli: binding of cytosine 5'-triphosphate and adenosine 5'-triphosphate.

The binding of CTP and ATP to aspartate transcarbamylase at pH 7.8 and 8.5 at 25 degrees has been investigated by equilibrium dialysis and flow microcalorimetry. The binding isotherms for CTP at both pH 7.8 and 8.5 and ATP AT PH 8.5 can be fit by a model which assumes three tight, three moderately tight, and six weak binding sites. The binding isotherms for ATP at pH 7.8 are best fit by a model which assumes six tight and six weaker sites. Both finite differenceH binding and finite differenceS binding are negative for both nucleotides at both pH values, so that the binding is enthalpy driven. For both nucleotides, finite differenceH is the same for the first two classes of binding sites, implying that the difference in the dissociation constants of these two classes of sites is the result of entropic effects. Direct pH measurements and calorimetric measurements in two buffers with very different heats of ionization (Tris and Hepes) indicate that the binding of both nucleotides is accompanied by the binding of protons. In the pH range 6.7-8.4, the number of moles of protons bound per mole of nucleotide increases as the pH decreases.     

Scyllatoxin, a blocker of Ca(2+)-activated K+ channels: structure-function relationships and brain localization of the binding sites.

Chemical modifications of scyllatoxin (leiurustoxin I) have shown that two arginines in the sequence, Arg6 and Arg13, are essential both for binding to the Ca(2+)-activated K+ channel protein and for the functional effect of the toxin. His31 is important both for the binding activity of the toxin and for the induction of contractions on taenia coli. However, although its iodination drastically decreases the toxin activity, it does not abolish it. Chemical modification of lysine residues or of Glu27 does not significantly alter toxin binding, but it drastically decreases potency with respect to contraction of taenia coli. The same observation has been made after chemical modification of the lysine residues. The brain distribution of scyllatoxin binding sites has been analyzed by quantitative autoradiographic analysis. It indicates that apamin (a bee venom toxin) binding sites are colocalized with scyllatoxin binding sites. The results are consonant with the presence of apamin/scyllatoxin binding sites associated with Ca(2+)-activated K+ channels. High-affinity binding sites for apamin can be associated with very-high-affinity (less than 70 pM), high-affinity (approximately 100-500 pM), or moderate-affinity (greater than 800 pM) binding sites for scyllatoxin.     

The binding of atractylate and carboxy-atractylate to mitochondria.

35S-labelled atractylate and carboxy-atractylate are produced biosynthetically and used for studying the binding of these specific ligands to the ADP, ATP carrier in beef heart mitochondria. The following results are obtained. 1. Inhibition of translocation activity goes parallel to the increase of binding by [35S]atractylate. No additional binding is observed after full inhibition of translocation is reached giving evidence that atractylate binds exclusively to the carrier. 2. The maximum number of binding sites of both atractylates is about 1.6 mumol/g protein in beef heart mitochondria and decreases on treatment of the membrane by Pi, freezing, ageing, etc. The dissociation constants of the binding are approximately for atractylate Kd = 5-10(-8) M and for carboxy-atractylate Kd = 10(-8) M. The mass action plots of the concentration dependence for the binding are nonlinear-convex in particular with carboxy-atractylate and more linear with atractylate. Nonlinearity appears to be caused by some retardation of equilibration in the case of very high affinity binding. 3. The binding of atractylate and carboxy-atractylate is relatively fast in intact mitochondria and slower in aged membranes. There is a slower and a faster binding portion. 4. The atractylates remove ADP in a nearly 1:1 stoichiometry from untreated mitochondria. In aged and Pi-treated membranes the ratio deltaADP/deltaatractylate approaches 0. Obviously binding of carrier sites to ADP is more sensitive to alterations than that of the atractylates. The assumption is maintained that the binding site for atractylate is identical with that for ADP and ATP. 5. Bongkrekate prevents binding of both atractylates. However, when added after, it only removes atractylate but not the carboxy compound because of its different tight binding. The removal of atractylate depends on the synergistic effect of bongkrekate with ADP. 6. The binding studies with [35S]atractylate and in particular the interaction with bongkrekate support the reorienting carrier model in which atractylate as an impermeable ligand fixes the binding site of the carrier outside while with bongkrekate the carrier site is turned to the inside.     

Moment invariants as shape recognition technique for comparing protein binding sites

MOTIVATION: An approach for identifying similarities of protein-protein binding sites is presented. The geometric shape of a binding site is described by computing a feature vector based on moment invariants. In order to search for similarities, feature vectors of binding sites are compared. Similar feature vectors indicate binding sites with similar shapes. RESULTS: The approach is validated on a representative set of protein-protein binding sites, extracted from the SCOPPI database. When querying binding sites from a representative set, we search for known similarities among 2819 binding sites. A median area under the ROC curve of 0.98 is observed. For half of the queries, a similar binding site is identified among the first two of 2819 when sorting all binding sites according the proposed similarity measure. Typical examples identified by this method are analyzed and discussed. The nitrogenase iron protein-like SCOP family is clustered hierarchically according to the proposed similarity measure as a case study. AVAILABILITY: Python code is available on request from the authors.     

Flexible docking using tabu search and an empirical estimate of binding affinity

This article describes the implementation of a new docking approach. The method uses a Tabu search methodology to dock flexibly ligand molecules into rigid receptor structures. It uses an empirical objective function with a small number of physically based terms derived from fitting experimental binding affinities for crystallographic complexes. This means that docking energies produced by the searching algorithm provide direct estimates of the binding affinities of the ligands. The method has been tested on 50 ligand-receptor complexes for which the experimental binding affinity and binding geometry are known. All water molecules are removed from the structures and ligand molecules are minimized in vacuo before docking. The lowest energy geometry produced by the docking protocol is within 1.5 Å root-mean square of the experimental binding mode for 86% of the complexes. The lowest energies produced by the docking are in fair agreement with the known free energies of binding for the ligands. Proteins 33:367–382, 1998. © 1998 Wiley-Liss, Inc.     

Functional studies of the Mycobacterium tuberculosis iron-dependent regulator

The iron-dependent regulator (IdeR) protein in Mycobacterium tuberculosis, and its better characterized homologue, the diphtheria toxin repressor (DtxR) from Corynebacterium diphtheriae, are iron-dependent regulatory proteins that control gene expression in response to iron availability in bacteria. IdeR regulates several genes required for iron uptake and storage including those involved in the synthesis of transition metal chelators called siderophores that are linked to the M. tuberculosis virulence. In this study, the metal ion and binding affinities for IdeR binding to an fxbA operator duplex DNA were estimated using fluorescence assays. The Fe(2+), Co(2+), and Ni(2+) affinities of the two metal ion binding sites in IdeR that are involved in the activation of the regulator DNA binding process in vitro were independently estimated. Binding to the two metal ion binding sites is apparently cooperative and the two affinities differ significantly. Occupation of the first metal ion binding site causes dimerization of IdeR, and the metal ion affinity is about 4 microM for Ni(2+) and much less for Fe(2+) and Co(2+). Binding of the second metal ion fully activates IdeR for binding to the fxbA operator. The equilibrium metal ion dissociation constants for IdeR-fxbA operator binding are approximately 9 microM for Fe(2+), 13 microM for Ni(2+), and 23 microM for Co(2+). Interestingly, the natural IdeR cofactor, Fe(2+), shows high affinities toward both binding sites. These results provide insight into the possible roles for each metal binding site in IdeR activation.     

Role of Escherichia coli IHF protein in lambda site-specific recombination. A mutational analysis of binding sites

The phage lambda attachment site, attP, contains three binding sites for an Escherichia coli protein, IHF, that is needed for efficient integrative recombination. We have used synthetic oligodeoxyribonucleotides to direct multiple base changes at each of these three sites. Alteration by two base-pairs of the consensus sequence for the leftmost binding site specifically interferes with IHF binding to that site and modestly depresses recombination in vitro. For each of the three binding sites, alteration of the consensus sequence by four base-pairs strongly depresses recombination in vitro, indicating that all three sites are important for attP function. The mutated attP sites are also depressed for recombination in vivo but some of the mutants are less affected than they are in vitro. The disparity between effects in vivo and in vitro for some mutants but not others suggests that the three binding sites are not functionally equivalent and that at some sites additional E. coli factors may replace or assist IHF. The non-equivalence of the three IHF sites is also indicated by the behavior of prophage attachment sites carrying mutations in the binding sites.     

Cofilin binding to muscle and non-muscle actin filaments: isoform-dependent cooperative interactions

I have monitored equilibrium binding of human cofilin to rabbit skeletal muscle (alpha) and human non-muscle (85% beta, 15% gamma) actin filaments from the quenching of pyrene actin fluorescence. Filament binding is cooperative and stoichiometric (i.e. one cofilin molecule per actin subunit) for both actin isoforms. The Hill coefficient for binding to betagamma-actin filaments (n(H)=3.5) is greater than for muscle actin (n(H)=2.3). Analysis of equilibrium binding using a nearest-neighbor cooperativity model indicates that the intrinsic affinities for binding to an isolated site are comparable (10-14 microM) for both filament isoforms but the cooperative free energy is greater for binding betagamma-actin filaments. The predicted cofilin cluster sizes and filament binding densities are small at concentrations of cofilin where efficient filament severing is observed, indicating that a few bound cofilin molecules are sufficient to destabilize the filament lattice and promote fragmentation. The analysis used in this study provides a framework for evaluating proton and ion linkage and effects of regulatory proteins on cofilin binding and severing of actin filaments.     

A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes

Many cellular functions rely on interactions between protein pairs and higher oligomers. We have recently shown that binding mechanisms are robust and owing to the minimal frustration principle, just as for protein folding, are governed primarily by the protein's native topology, which is characterized by the network of non-covalent residue-residue interactions. The detailed binding mechanisms of nine dimers, a trimer, and a tetramer, each involving different degrees of flexibility and plasticity during assembly, are surveyed here using a model that is based solely on the protein topology, having a perfectly funneled energy landscape. The importance of flexibility in binding reactions is manifested by the fly-casting effect, which is diminished in magnitude when protein flexibility is removed. Many of the grosser and finer structural aspects of the various binding mechanisms (including binding of pre-folded monomers, binding of intrinsically unfolded monomers, and binding by domain-swapping) predicted by the native topology based landscape model are consistent with the mechanisms found in the laboratory. An asymmetric binding mechanism is often observed for the formation of the symmetric homodimers where one monomer is more structured at the binding transition state and serves as a template for the folding of the other monomer. Phi values were calculated to show how the structure of the binding transition state ensemble would be manifested in protein engineering studies. For most systems, the simulated Phi values are reasonably correlated with the available experimental values. This agreement suggests that the overall binding mechanism and the nature of the binding transition state ensemble can be understood from the network of interactions that stabilize the native fold. The Phi values for the formation of an antibody-antigen complex indicate a possible role for solvation of the interface in biomolecular association of large rigid proteins.     

Models for binding cooperativities of inhibitors with transthyretin

Here, molecular dynamics (MD) simulations are performed to study the differences of binding channel shapes of TTR with two inhibitors, flufenamic acid (FLU) and one kind of N-phenyl phenoxazine (BPD). The asymmetries of global structure including the central binding channel are found to be intrinsic. Moreover, the conformational changes of the binding channel are responsible for negative cooperativity (NC) or independent cooperativity (IC) of ligands. The results suggested a possible binding mechanism addressing NC of FLU and IC of BPD. For FLU, when the first ligand binds with TTR, it leads to expansion of the second binding site which may weaken the interaction of the second FLU with TTR. But for BPD, the first ligand's binding changes the second site's shape slightly, the second ligand has similar binding ability with TTR in the second site like the first binding event.     

Localization and characterization of prostaglandin E1 receptors in rat small intestine

While prostaglandins of the E series are known to affect several small intestinal functions, their cellular mechanisms are poorly understood. The purposes of our study were to determine whether receptors for PGE are present in rat small intestine and to locate and characterize the receptor binding in the subcellular fractions. Small intestinal binding of prostaglandin E1 was significantly higher than that of prostaglandin E2. Highest receptor binding for prostaglandin E1 was found in the plasma membrane fraction of isolated small intestinal enterocytes. Curvilinearity of prostaglandin E1 binding in plasma membranes upon Scatchard analysis indicated two receptor binding sites in rat small intestine. Competitive binding studies demonstrated that receptor binding was highest for prostaglandins of the E series. These studies are the first to demonstrate specific prostaglandin E1 receptors in different subcellular fractions of rat small intestine. We suggest that receptor binding of prostaglandin E may be an important initial step in the mechanism of prostaglandin-E-induced responses in the small intestine.