Statistical mechanics applied to cooperative ligand binding to proteins

By using the lattice statistical argument, we have shown that for a protein whose subunits have the same number of neighbors, the three parameters (K(AB), K(BB), and K(S)K(t)) in the sequential theory formulated by Koshland, Nemethy, and Filmer [Biochemistry (1966) 5, 365] can be reduced to two parameters. One of the parameters, Z, measures the strength of the subunit interactions and is related to the apparent free energy of interaction (DeltaF degrees I) by Z = exp (-DeltaF degrees I/2mkT), where m is the number of neighbors in a subunit and kT has the usual meaning. In addition, we relate Wyman's allosteric binding potential [Advan. Protein Chem. (1964) 19, 223] to the canonical partition function of the McMillan-Mayer theory [J. Chem. Phys. (1945) 13, 276]. An explicit form relating the apparent free energy of interaction and the Hill coefficient is given for an allosteric protein that has nonequivalent and independent ligand-binding sites. The present formulation can be used to account for a number of recent experimental results on hemoglobins.     

Competitive inhibition of colchicine binding to tubulin by microtubule-associated proteins.

Microtubule-associated proteins (MAPs) promote tubulin polymerization, whereas colchicine inhibits this process. In this paper, MAPs have been shown to inhibit colchicine binding to tubulin in a competitive manner. Attempts were made to identify which of the MAPs fraction(s) was responsible; both tau protein (a thermostable molecule with a molecular weight of approximately 70,000) and a high molecular weight fraction (HMW) were able to compete with colchicine. In contrast, Mg2+, which also induces microtubule assembly in vitro, had no effect on colchicine binding to tubulin.     

Frequency-dependent action of antiarrhythmic drugs: The useful concept of periodical ligand binding

Summary The action of most antiarrhythmic drugs which block cardiac ionic channels depends on heart rate, which is established as use- or frequency-dependence. This property is consistent with periodical drug (ligand) binding to channel binding sites which are transiently available during the excitation sequence of cardiac tissue. Antiarrhythmic drugs differ with respect to their binding and unbinding kinetics, i.e., with respect to their blocking and unblocking kinetics. This gives rise to different block-frequency relations and onset-kinetics of frequency-dependent ion channel blockade. Antiarrhythmic drugs have never been systematically compared with regard to their block-frequency relations. However, both the onset-kinetics as well as the block-frequency relation are essential in characterizing the frequency-dependent drug action, since both may be predictors of the anti- and proarrhythmic potential of antiarrhythmic drugs.     

Voltage-dependent gating and single-channel conductance of adult mammalian atrial gap junctions.

In the heart, the rapid propagation and synchronization of action potentials necessary for a normal heart rhythm and an effective cardiac output are mediated by specialized ionic channels that link adjacent cells and are known collectively as gap junctions. Cardiac gap junctions are gated by various physiological and pharmacological agents, but the role of voltage in their gating is unclear. Whereas embryonic or neonatal ventricular cells have voltage-gated gap junctions, adult cells are reported to have only voltage-independent gap junctions. We studied the voltage dependence of adult rat atrial gap junctions by individually voltage clamping each cell of a connected cell pair and controlling the transjunctional voltage (Vj), measuring transjunctional current (Ij), and calculating junctional conductance (gj). Two distinct populations of cell pairs were observed: highly coupled pairs with the peak gjs ranging from 3.4 to 40 nS and weakly coupled pairs with the peak gjs ranging from 0.3 to 2.0 nS. gj was dependent on Vj, and Ij decayed exponentially, with the time constants being voltage dependent. Voltage dependence was most apparent when cells were poorly coupled. The gj did not decrease to zero. The normalized conductance--Vj plot was fit with a two-state Boltzmann model as a first approximation, resulting in a half-inactivation potential and gating charge of 42.5 mV and 1.14 eV, respectively, for the weakly coupled cell pairs. For highly coupled cell pairs, the half-inactivation potential shifted to 53.3 mV. Single gap junctional channels had a gj of 36.2 +/- 7.6 pS (range, 27-49 pS), which was Vj independent.(ABSTRACT TRUNCATED AT 250 WORDS)     

Central action of dendrotoxin: selective reduction of a transient K conductance in hippocampus and binding to localized acceptors.

Dendrotoxin, a small single-chain protein from the venom of Dendroaspis angusticeps, is highly toxic following intracerebroventricular injection into rats. Voltage-clamp analysis of CA1 neurons in hippocampal slices, treated with tetrodotoxin, revealed that nanomolar concentrations of dendrotoxin reduce selectively a transient, voltage-dependent K conductance. Epileptiform activity known to be induced by dendrotoxin can be attributed to such an action. Membrane currents not affected directly by the toxin include (i) Ca-activated K conductance; (ii) noninactivating voltage-dependent K conductance; (iii) inactivating and noninactivating Ca conductances; (iv) persistent inward (anomalous) rectifier current. Persistence of the effects of the toxin when Cd was included to suppress spontaneous transmitter release indicates a direct action on the neuronal membrane. Using biologically active, 125I-labeled dendrotoxin, protein acceptor sites of high affinity were detected on cerebrocortical synaptosomal membranes and sections of rat brain. In hippocampus, toxin binding was shown autoradiographically to reside in synapse-rich and white matter regions, with lower levels in cell body layers. This acceptor is implicated in the action of toxin because its affinities for dendrotoxin congeners are proportional to their central neurotoxicities and potencies in reducing the transient, voltage-dependent K conductance.     

Plasma binding proteins as mediators of corticosteroid action in vertebrates

Stressors elicit a complex but variable suite of endocrine events. Comparative studies of the stress response have focused primarily on the adrenocortical response to stress, in particular the measurement of plasma levels of glucocorticoids. However, a number of other factors contribute to and modify cellular and organismal responses to glucocorticoids. Notably, plasma corticosteroid binding globulins (CBGs) can regulate the general availability of steroid to tissues, and/or direct the delivery of hormones to specific sites. In this paper, we discuss possible functions of CBG and mechanisms of CBG action, review CBG characteristics among vertebrates, and discuss our recent studies indicating that CBG may indeed modulate responses to stressors. For example, in house sparrows, we found that basal and stress-induced concentrations of total corticosteroid (cortisol or corticosterone) (CORT) vary seasonally, but CBG concentrations change proportionally, so that free CORT concentrations appear static year-round. In contrast, in white-crowned sparrows and tree lizards, CBG concentrations change under conditions when total CORT levels do not, resulting in significant changes in circulating free CORT. These differences in free CORT are masked if CBG is not accounted for. We have also found that the binding properties of CBG vary considerably between species and need to be determined empirically. Such studies led to the observation that CBG in several species may also serve as a functional androgen binding protein; this is especially important for birds, because previous studies had concluded that birds lack androgen binding globulins. We propose that consideration of CBG is paramount to understanding the role of glucocorticoids in mediating behavioral and physiological responses to stress.     

Three-dimensional modeling of and ligand docking to vitamin D receptor ligand binding domain

The ligand binding domain of the human vitamin D receptor (VDR) was modeled based on the crystal structure of the retinoic acid receptor. The ligand binding pocket of our VDR model is spacious at the helix 11 site and confined at the beta-turn site. The ligand 1alpha, 25-dihydroxyvitamin D(3) was assumed to be anchored in the ligand binding pocket with its side chain heading to helix 11 (site 2) and the A-ring toward the beta-turn (site 1). Three residues forming hydrogen bonds with the functionally important 1alpha- and 25-hydroxyl groups of 1alpha,25-dihydroxyvitamin D(3) were identified and confirmed by mutational analysis: the 1alpha-hydroxyl group is forming pincer-type hydrogen bonds with S237 and R274 and the 25-hydroxyl group is interacting with H397. Docking potential for various ligands to the VDR model was examined, and the results are in good agreement with our previous three-dimensional structure-function theory.     

Mucosal iron binding proteins and the inhibition of iron absorption by endotoxin

Summary The uptake of iron from a tied off jejunal segment into the body after the injection of a ⁵⁹Fe labeled test dose was decreased after the administration of endotoxin by about 80% in both normal and iron deficient animals. — In the iron deficient group the distribution of ⁵⁹Fe in the cytosol fraction of jejunal mucosa between transferrin and ferritin was determined chromatographically; the amount of ⁵⁹Fe in the ferritin fraction increased remarkably after the endotoxin treatment and the ratio of both was changed in favor of ferritin. — It is hypothesized that the association of the diversion of iron to the mucosal ferritin with the decrease of the transport of iron into the blood caused by endotoxin might be the consequence of abnormal oxidations in the mucosa measured by others in liver tissue.     

Protein interactions and ligand binding: From protein subfamilies to functional specificity

The divergence accumulated during the evolution of protein families translates into their internal organization as subfamilies, and it is directly reflected in the characteristic patterns of differentially conserved residues. These specifically conserved positions in protein subfamilies are known as “specificity determining positions” (SDPs). Previous studies have limited their analysis to the study of the relationship between these positions and ligand-binding specificity, demonstrating significant yet limited predictive capacity. We have systematically extended this observation to include the role of differential protein interactions in the segregation of protein subfamilies and explored in detail the structural distribution of SDPs at protein interfaces. Our results show the extensive influence of protein interactions in the evolution of protein families and the widespread association of SDPs with protein interfaces. The combined analysis of SDPs in interfaces and ligand-binding sites provides a more complete picture of the organization of protein families, constituting the necessary framework for a large scale analysis of the evolution of protein function.     

Extrapancreatic action of sulfonylureas: hypoglycemic effects are not dependent on altered insulin binding or inhibition of transglutaminase

It has been proposed by others that sulfonylureas exert their extrapancreatic hypoglycemic effects by increasing insulin binding through inhibition of receptor-mediated hormone internalization. In this study, we examined the possibility that the drugs act by inhibiting transglutaminase, an enzyme thought important in the internalization process. For ten days, male rats were fed pulverized chow containing either no drug, glipizide (5 mg/kg initial body wt/d), or tolazamide (75 mg/kg initial body wt/d). Prior to sacrifice, the six-hour fasting level of serum glucose was significantly reduced from 96 mg/100 ml in the control rats to 81 and 42 mg/100 ml in the glipizide- and tolazamide-treated rats, respectively. In contrast, the serum level of insulin was similar for all groups. The activity of transglutaminase in the postnuclear fraction of liver homogenate also was the same for all experimental groups. The specific binding of labeled insulin to purified liver plasma membranes was examined over a broad range of insulin concentrations; once again, there was no difference between experimental groups. Thus, the hypoglycemia caused by sulfonylurea administration could not be attributed to increases in insulin binding, inhibition of transglutaminase activity, or enhanced insulin levels. These data support our previous suggestion, based on in vitro studies, that sulfonylureas act predominately on processes beyond the binding portion of the insulin receptor.     

Mechanism of action of EDRF on pressurized arteries: effect on K+ conductance

Experiments were performed to study the cellular mechanism of endothelium-derived relaxing factor (EDRF) on vascular smooth muscle. Rat femoral arteries were cannulated and pressurized to 100 mm Hg. Vascular smooth muscle membrane potential (Em) and diameter responses to perfusion with 5 x 10(-6) M acetylcholine (ACh) were measured in vessels precontracted with 5 x 10(-6) M norepinephrine (NE). Hyperpolarization (-35 +/- 1.2 to -66 +/- 2.0 mV) and dilation were observed during ACh administration. Both responses were abolished on removal of the endothelium with collagenase. A bioassay was developed in which two vessel segments from the same artery were connected in series. The downstream vessel was deendothelialized while the endothelium of the upstream vessel remained intact. The protocol used was the same as in the first set of measurements. Hyperpolarization and dilation were observed in both vessels during ACh perfusion. However, when the direction of the perfusate flow in the bioassay system was reversed so that the deendothelialized vessel was upstream, only the "endothelium-intact" vessel demonstrated vascular smooth muscle hyperpolarization. To examine the ionic mechanism underlying the hyperpolarization presumably by released EDRF, the Em was measured as a function of increasing extracellular potassium ([K+]o). In the presence of ACh (but not NE) the maximum depolarization produced by a decade increase of [K+]o (10-100 mM) was 50 mV. In the deendothelialized vessel, this depolarization was decreased significantly to 39 mV. Addition to the superfusate of 10 mM tetraethylammonium, a K+ channel blocker, significantly reduced the hyperpolarization caused by ACh-induced EDRF release.(ABSTRACT TRUNCATED AT 250 WORDS)     

Two polyclonal antisera to rat luteal LH/CG receptor with different ligand binding inhibition and immunohistochemical receptor detection capabilities

Polyclonal antisera to a SDS-denatured and partially renatured rat luteal 90 K LH/CG receptor were raised in rabbits, characterized, and their applicability for immunohistochemical location of the receptor examined. The LH/CG receptor was purified by hCG-affinity chromatography and subjected either to a preparative SDS-PAGE or Western blotting. Gel slices containing the SDS-denatured or nitrocellulose strips containing the renatured 90 K LH/CG receptor were used for immunization. The antisera, termed ARS-2 and ARS-3, respectively, possessed similar antibody titres. Both antisera were able to recognize the native, SDS-denatured, and SDS-denatured and reduced forms of the LH/CG receptor on dot blots, but only ARS-3 contained antibodies to the hormone binding site or a region near to it, as it was able to inhibit the hCG binding to the membrane-bound LH/CG receptor in a dilution-dependent manner. Both antisera recognized the receptor-hCG complex, but ARS-2 stained the complex with about 50% less intensity than the free receptor. ARS-3 located the LH/CG receptor distinctly on the luteal cell surfaces in immunohistochemical staining with peroxidase antiperoxidase complex method, but ARS-2, although it possessed similar antibody titre, revealed negligible staining. Thus, the antisera readily recognize the native receptor, but differ in their capability for inhibiting hormone binding. Only ARS-3, produced against the renatured receptor, contains sufficient amounts of antibodies capable of recognizing free and occupied receptors in immunohistochemistry.     

Structural determinants of ligand binding to the mineralocorticoid receptor

The first and critical step in the mechanism of aldosterone action is its binding to the mineralocorticoid receptor (MR), a member of the nuclear receptor superfamily. Over the last 40 years, numerous studies have attempted to determine the structural determinants of ligand-binding to MR. An initial set of data showed that hsp90 is bound to the receptor via specific regions and maintains it in a ligand-binding competent state. Site-directed mutagenesis and functional studies guided by a 3D model of the MR ligand-binding domain (LBD) made it possible to identify the residues responsible for the high affinity and selectivity for aldosterone, and to characterize the mechanisms of MR activation and inactivation. The recent determination of the X-ray crystal structures of the LBD of the wild-type MR and MR_S810L, which is responsible for a familial form of hypertension, has made it possible to elucidate the peculiar mechanism of activation of MR_S810L and established a clear structure/activity relationship for steroidal and non-steroidal MR antagonists.     

Structural factors controlling ligand binding to myoglobin: A kinetic hole-burning study

Using temperature-derivative spectroscopy in the temperature range below 100 K, we have studied the dependence of the Soret band on the recombination barrier in sperm whale carbonmonoxy myoglobin (MbCO) after photodissociation at 12 K. The spectra were separated into contributions from the photodissociated species, Mb*CO, and CO-bound myoglobin. The line shapes of the Soret bands of both photolyzed and liganded myoglobin were analyzed with a model that takes into account the homogeneous bandwidth, coupling of the electronic transition to vibrational modes, and static conformational heterogeneity. The analysis yields correlations between the activation enthalpy for rebinding and the model parameters that characterize the homogeneous subensembles within the conformationally heterogeneous ensemble. Such couplings between spectral and functional parameters arise when they both originate from a common structural coordinate. This effect is frequently denoted as “kinetic hole burning.” The study of these correlations gives direct insights into the structure–function relationship in proteins. On the basis of earlier work that assigned spectral parameters to geometric properties of the heme, the connections with the heme geometry are discussed. We show that two separate structural coordinates influence the Soret line shape, but only one of the two is coupled to the enthalpy barrier for rebinding. We give evidence that this coordinate, contrary to widespread belief, is not the iron displacement from the mean heme plane.     

Insulin binding and action on bovine adipocytes

The present study was undertaken to determine whether bovine adipocytes could bind and respond to insulin. Adipose tissue from young bulls showed little response to physiological and higher concentrations of insulin over a 3-h incubation. In contrast, insulin did stimulate glucose uptake during prolonged incubations and also increased the activity of pyruvate kinase; in each case, half-maximum stimulation was observed with concentrations of about 0.5 ng/ml. Specific binding of [125I] iodoinsulin to bovine adipocytes was observed; the binding capacity was greater than that of young female rats determined under the same conditions. Bovine adipocytes internalized insulin. Incubation of bovine adipocytes with insulin resulted in a concentration-dependent loss of insulin receptors from the adipocyte surface. In summary, bovine adipocytes possess the capacity to both bind and respond to insulin; these findings are discussed in relation to a recent report to the contrary.     

Studies on cytosol thyroid hormone binding proteins in the rat liver: Part I. Stability and binding characteristics of thyroid hormone binding proteins

Many studies demonstrated the presence of cytosolic thyroid hormone binding proteins (CTHBPs) in various tissues, but the physiologic significance of these CTHBPs is not clear, partially because of the lack of information about the physicochemical properties of CTHBPs as purified forms. Since the difficulty in isolating these CTHBPs is considered to be due to instability during the various procedures for their isolation, studies on the stability of CTHBPs of rat liver were performed using a charcoal binding method to separate bound and free hormones. Binding characteristics of CTHBPs of rat liver were also determined. Specific triiodothyronine (T3) binding sites of cytosolic T3 binding protein (CT3BP) of rat liver were destroyed as the time progressed in homogenate at 0 degrees C, and Aprotinin (500 U/ml) had little effect in protecting these binding sites. T3 binding sites were stable in the form of cytosol at -20 degrees C up to 10 weeks. Dithiothreitol (DTT) had no effect on T3 binding to cytosol. T3 binding to CT3BP was pH-dependent with maximum specific binding at pH 7.4. T3 binding to CT3BP was stable at 4 degrees C overnight but was destroyed rapidly at 37 degrees C. Interestingly, specific T3 binding sites of CT3BP were completely abolished by dialysis, and Ca2+ or Mg2+ had no effect on retaining the specific binding sites. Thus, CT3BP was supposed to require some dialysable small molecule(s) to maintain specific T3 binding sites. Scatchard plot of T3 binding to crude cytosol revealed a high affinity, limited capacity T3 binding site with affinity constant (Ka) of 5.9 X 10(7) M-1 and maximum binding capacity (MBC) of 118 ng/g. liver. Relative affinities of T3 analogues for CT3BP were determined by comparing the molar concentrations of T3 analogues required for 50% inhibition of tracer 125I-T3 binding. If the affinity of L-T3 was assigned 100, D-T3 would have a value of 66.1; L-T4, 22.3; D-T4, 16.5; Triac, 6.2; and both Tetrac and reverse T3 were less than 1. Thus, the binding characteristics of CT3BP were fundamentally different from those of nuclear T3 receptor. Cytosolic thyroxine (T4) binding protein (CT4BP) of rat liver was relatively stable compared with CT3BP in homogenate at 0 degrees C. CT4BP was also stable in the form of cytosol at -20 degrees C for 10 weeks. CT4BP was pH-dependent with maximum specific binding at pH 7.4. It was stable at 4 degrees C overnight but destroyed rapidly at 37 degrees C. Specific T4 binding was decreased by dialysis but not abolished completely.(ABSTRACT TRUNCATED AT 400 WORDS)     

Diethylpyrocarbonate inhibition of estradiol receptor binding to oligonucleotides

Exposure of calf uterine estradiol-receptor complexes to diethylpyrocarbonate (ethoxyformic anhydride) at pH 6.3–6.5 results in a decrease in the ability of the receptor to bind to oligodeoxyribonucleotides. The inhibition of binding to oligodeoxypyrimidines is greater than the inhibition of binding to oligodeoxyguanylate. The inhibition by 6.6 mM diethylpyrocarbonate is complete within 10 min at 4°C. Addition of equimolar quantities of histidine or imidazole prior to exposure to diethylpyrocarbonate prevents subsequent inhibition of oligodeoxyribonucleotide binding. In comparison to histidine, other amino acids tested were deficient in this ability. Diethylpyrocarbonate modification of the receptor causes complete loss of oligodeoxyribonucleotide binding activity at times when there is a loss of less than 20% of bound steroid. Pyridoxal 5'-phosphate treatment of receptor does not prevent subsequent modification by diethylpyrocarbonate, suggesting that the site of reaction is not an essential lysine of the DNA-binding domain. Treatment of the ethoxyformylated receptor with 0.45 M hydroxylamine results in recovery of 70% of the receptor's oligonucleotide-binding ability. The time course of the reaction of diethylpyrocarbonate with the estradiol receptor and the demonstration of hydroxylamine reversal of inhibition suggest that histidine is involved in the binding of estradiol receptor to oligodeoxyribonucleotides.     

Structural basis for ligand and heparin binding to neuropilin B domains

Neuropilin (Nrp) is a cell surface receptor with essential roles in angiogenesis and axon guidance. Interactions between Nrp and the positively charged C termini of its ligands, VEGF and semaphorin, are mediated by Nrp domains b1 and b2, which share homology to coagulation factor domains. We report here the crystal structure of the tandem b1 and b2 domains of Nrp-1 (N1b1b2) and show that they form a single structural unit. Cocrystallization of N1b1b2 with Tuftsin, a peptide mimic of the VEGF C terminus, reveals the site of interaction with the basic tail of VEGF on the b1 domain. We also show that heparin promotes N1b1b2 dimerization and map the heparin binding site on N1b1b2. These results provide a detailed picture of interactions at the core of the Nrp signaling complex and establish a molecular basis for the synergistic effects of heparin on Nrp-mediated signaling.