Distinct Conformational Changes Research Articles

Expression of a class II major histocompatibility complex (MHC) heterodimer in a lipid-linked form with enhanced peptide/soluble MHC complex formation at low pH.

A murine class II major histocompatibility complex (MHC) heterodimer, Ek, expressed as a glycan-phosphatidyl inositol-anchored chimera on Chinese Hamster Ovary cells, can present peptides, but not processed antigen to T cells. This chimeric MHC requires a 100-times higher peptide concentration to achieve a two- to four-times lower level of T cell stimulation. Cleavage with phosphatidylinositol-specific phospholipase C and purification result in large quantities of heterodimer in a water-soluble form. Plates coated with this material and then incubated with peptide can efficiently stimulate the appropriate T cell hybridomas. This stimulation is significantly enhanced when peptides are preincubated with the plate-bound MHC molecules in a pH range (5.0-5.5) similar to that of late endosomes. More than half of the soluble Ek molecules can form a specific complex with cytochrome c peptides in this pH range. This suggests that class II MHC molecules undergo distinct conformational changes in endosomal compartments that render them more capable of forming functional complexes with peptide antigens, irrespective of other cell components.

Interaction of rat liver glucocorticoid receptor with a newly synthesized antisteroid ZK98299

Steroid receptor antagonists are important biochemical probes for understanding the mode of steroid hormone action. We have studied the interaction between rat liver glucocorticoid receptor and a newly synthesized antisteroid ZK98299 (13-antigestagen; [11-β-(4-dimethylaminophenyl)-17a-hydroxy-17ß-(3-hydroxypropyl)-13α-methyl-4,9-gonadien-3-onel). Glucocorticoid receptor from freshly prepared hepatic cytosol bound [ 3H]ZK98299 with affinity approximately equal to that of [ 3H]triamcinolone acetonide. The binding of both steroids reached a maximum at 4 h at 0°C. Both ligands were able to compete for the steroid binding site but progesterone, estradiol and dihydrotestosterone (DHT) failed to compete for the [ 3H]ZK98299 and [ 3H]triamcinolone acetonide binding. While [ 3H]ZK98299 binding to glucocorticoid receptor could occur in the presence of iodoacetamide and N-ethylmaleimide [ 3H]triamcinolone acetonide binding capacity was completely abolished following such treatments. The [ 3H]ZK98299-receptor complexes sedimented as 9 S and 4 S molecules under control (4 °C) and receptor transforming (23 °C) conditions, and exhibited a faster rate of dissociation at 23°C when compared with [ 3H]triamcinolone acetonide-receptor complexes. These results indicate that ZK98299 interacts with hepatic glucocorticoid receptor. The differential effects of iodoacetamide and NEM on the interaction of glucocorticoid receptor with ZK98299 and triamcinolone acetonide, and the faster rate of dissociation of [ 3H]ZK98299-receptor complexes suggest that treatment with these agents (NEM and iodoacetamide) results in distinct conformational changes in glucocorticoid receptor structure with respect to triamcinolone acetonide and ZK98299 binding. Alternatively, ZK98299 may be interacting with a site which is distinct from one which accepts triamcinolone acetonide.

Endogenous cleavage of the Arg-379-Ala-380 bond in vitronectin results in a distinct conformational change which ‘buries’ Ser-378, its site of phosphorylation by protein kinase A

Activation of blood platelets by thrombin was previously shown to specifically release protein kinase A, which in human plasma singles out and phosphorylates one protein, identified as vitronectin. This protein is known to be involved in processes that follow platelet stimulation, specifically, in the binding of heparin (interfering with the heparin-mediated inhibition of thrombin and Factor Xa by antithrombin III), in the growth of endothelial cells and in fibrinolysis. This paper shows that phosphorylation of vitronectin by protein kinase A is stoichiometric (approx. 1 mol/mol), that it is targeted to one site (Ser-378) at the C-terminal edge of the heparin-binding domain, and that it distinguishes between the two physiologically occurring forms of vitronectin: the one-chain (75 kDa) form, and the nicked two-chain (65 + 10 kDa) form, held together by an interchain disulphide bridge. Protein kinase A phosphorylates the one-chain form but not the two-chain form, although Ser-378 and the complete recognition sequence of the kinase are still present in the clipped 65 kDa chain. Cleavage of the Arg-379-Ala-380 bond results therefore in a conformationally distinct form of vitronectin in which Ser-378 is 'buried'. This is demonstrated by our finding that Ser-378 is present in the 65 kDa chain of clipped vitronectin but inaccessible to phosphorylation at physiological pH. Upon binding heparin, the phosphorylation site becomes exposed and able to undergo a stoichiometric phosphorylation at physiological pH.

A neuroimmunoregulatory-like mechanism responding to stress in the marine bivalve Mytilus edulis

Mytilus edulis has been the subject of recent studies to determine whether the relationship between the immune and nervous systems seen in vertebrates also exists in invertebrates. In the present study the effects of experimentally induced “stressful” stimuli on immunoactive hemocytes were studied in this mollusc. This subpopulation of invertebrate blood cells, resembling vertebrate granulocytes, has been previously shown to produce and react to opioid peptides. Their activation, like that of vertebrate immunocytes, expresses itself in distinctive conformational changes preceding cellular mobilization. The cellular response to “stress” observed is the same as that to the administration of exogenous mammalian opioid peptides. This strongly suggests that under the conditions of stressful stimuli, the immune/defense system can be alerted by endogenous neuropeptides. The involvement of opioids in neuroimmunoregulatory phenomena appears to have a long evolutionary history.

Non-Watson-Crick structures in oligodeoxynucleotides: self-association of d(TpCpGpA) stabilized at acidic pH.

The 1H NMR spectrum of the tetradeoxynucleotide d(TpCpGpA) was examined as a function of temperature, pH, and concentration. At pH 7 and above the solution conformation for this oligodeoxynucleotide appears to be a mixture of random coil and Watson-Crick duplex. At 25 degrees C, a pH titration of d(TpCpGpA) shows that distinct conformational changes occur as the pH is lowered below 7.0. These conformational changes are reversible upon readjusting the pH to neutrality, indicating the presence of a pH-dependent set of conformational equilibria. At 25 degrees C, the various conformational states in the mixture are in rapid exchange on the NMR time scale. Examination of the titration curve shows the presence of distinct conformational states at pH greater than 7, and between pH 4 and pH 5. At pH less than 4, a third conformational state is present. When the pH titration is repeated at 5 degrees C, the conformational equilibria are in slow exchange on the NMR time scale; distinct signals from each conformational state are observable. The stable conformational state present between pH 4 and pH 5 represents an ordered conformation of d(TpCpGpA) which dissociates to a less ordered structure upon raising the temperature. This ordered conformation does not result from an intramolecular rearrangement, as is shown by by spectra obtained by varying oligodeoxynucleotide concentration at constant pH. The ordered conformation differs from the Watson-Crick helix, as is shown from nuclear Overhauser enhancement experiments, as well as chemical shift data. An ordered conformation for d(TpCpGpA) was previously reported [Reid, D. G., Salisbury, S. A., Brown, T., & Williams, D. H. (1985) Biochemistry 24, 4325-4332].(ABSTRACT TRUNCATED AT 250 WORDS)

The effects of temperature and electrolyte at acidic and alkaline pH on the electron transfer reactions of cytochrome c at In2O3 electrodes

Abstract Spectroelectrochemical and electrochemical methods were used to investigate the characteristics of heterogeneous electron transfer between cytochrome c and indium oxide electrodes. A linear temperature dependence of the formal potential of cytochrome c was observed from 5 to 75 °C in acidic media. This behavior is attributed to a linear variation in the conformation of ferricytochrome c that results in an increase in solvent exposure of the solvent-exposed heme edge. A break in the linear temperature dependence of the formal potential occurred at 40 °C in alkaline media. This reflects a distinct conformational change that accompanies the onset of thermal denaturation of ferricytochrome c. The small change in reaction center entropy, ΔS°rc, of ca. −54 J K−1 mol−1 in neutral and acidic media (5 to ⩾ 55 °C) and in alkaline media (below 40 °C) is consistent with a small shift to a more stable conformation of cytochrome c that occurs upon reduction. Adsorption of reactant and product was detected. The strength and type of adsorption were found to be temperature- and pH-dependent. The characteristics of electron transfer between cytochrome c and an electrode depend on bulk solvent properties and electrode surface characteristics.

PH dependence of individual tryptophan N-1 hydrogen exchange rates in lysozyme and its chemically modified derivatives.

Nuclear magnetic resonance analyses have been made of the individual hydrogen-deuterium exchange rates of tryptophan indole N-1 hydrogens in native lysozyme and its chemically modified derivatives including lysozyme with an ester cross-linkage between Glu-35 and Trp-108, lysozyme with an internal amide cross-linking between the epsilon-amino group of Lys-13 and the alpha-carboxyl group of Leu-129, and lysozyme with the beta-aspartyl sequence at Asp-101. The pH dependence curves of the exchange rates for Trp-63 and Trp-108 are different from those expected for tryptophan. The pH dependence curve for Trp-108 exchange exhibits the effects from molecular aggregation at pH above 5 and from a transition between the two conformational fluctuations at around pH 4. The exchange rates for tryptophan residues in native lysozyme and modified derivatives are not correlated with the thermodynamic or kinetic parameters in protein denaturation, suggesting that the fluctuations responsible for the exchange are not global ones. The exchange rates for tryptophan residues remote from the modification site are perturbed. Such tryptophan residues are found to be involved in a small but distinct conformational change due to the modification. Therefore, the perturbations of the N-1 hydrogen exchange rates are related to the minor change in local conformation or in conformational strain induced by the chemical modification.

Calcium release from calmodulin and its C-terminal or N-terminal halves in the presence of the calmodulin antagonists phenoxybenzamine and melittin measured by stopped-flow fluorescence with Quin 2 and intrinsic tyrosine. Inhibition of calmodulin-dependent protein kinase of cardiac sarcoplasmic reticulum.

Calcium dissociation from the C-terminal and N-terminal halves of calmodulin, intact bovine brain calmodulin and the respective phenoxybenzamine complexes or melittin complexes was measured directly by stopped-flow fluorescence with the calcium chelator Quin 2 and, when possible, also by protein fluorescence using endogenous tyrosine fluorescence by mixing with EGTA. Calcium dissociation from the C-terminal half of calmodulin, which contains only the two high-affinity calcium-binding sites, and from intact calmodulin was monophasic, with good correlation of the rates of calcium dissociation obtained by the two methods. The apparent rates with Quin 2 and endogenous tyrosine fluorescence were 13.4 s-1 and 12.8 s-1, respectively, in the C-terminal half and 10.5 s-1 and 10.8 s-1, respectively, in intact calmodulin (pH 7.0, 25 degrees C, 100 mM KCl). Alkylation of the C-terminal half resulted in a biphasic calcium dissociation (Quin 2: kobs 1.90 s-1 and 0.73 s-1 respectively; tyrosine: kobs 1.65 s-1 and 0.61 s-1 respectively). Alkylation of intact calmodulin resulted in a four-phase calcium dissociation measured with Quin 2 (kobs 85.3 s-1, 11.1 s-1, 1.92 s-1 and 0.59 s-1); the latter two phases are assumed to represent calcium release from high-affinity sites since they correspond to the biphasic tyrosine fluorescence change in intact alkylated calmodulin (kobs 2.04 s-1 and 0.53 s-1 respectively) and the rate parameters determined in the C-terminal half. Evidently perturbation of the calcium-binding sites by alkylation reduces the rate of calcium dissociation and allows a distinction to be made between dissociation from each of the two high-affinity sites as well as the distinct conformational change on dissociation of each calcium. Alkylation of the N-terminal half resulted in biphasic calcium release with rates (kobs 153 s-1 and 10.9 s-1 respectively) similar to those observed in intact alkylated calmodulin. The rates of calcium dissociation from calmodulin-melittin or fragment-melittin complexes, measured with Quin 2, were slower and monophasic in the C-terminal half (kobs 1.12 s-1), biphasic in the N-terminal half (kobs 140 s-1 and 26.8 s-1 respectively) and triphasic in intact calmodulin (kobs 126 s-1, 12.1 s-1 and 1.38 s-1). Calmodulin antagonists thus increase the apparent calcium affinity of high and low-affinity sites mainly due to a reduced calcium 'off rate', presumably because of conformation restrictions.(ABSTRACT TRUNCATED AT 400 WORDS)

Vascular Smooth Muscle

In strip preparations from the rabbit main pulmonary artery, it was not possible to differentiate convincingly between alpha 1- and alpha 2-adrenoceptors, when selective agonists such as methoxamine, St 587, B-HT 920, and clonidine, as well as selective antagonists such as prazosin and yohimbine were used for receptor characterization. Measurements of the membrane potential of the vascular smooth-muscle cells with intracellular glass micropipettes showed similar depolarizations in response to the alpha 1-selective methoxamine and the alpha 2-selective B-HT 920. These observations suggest the occurrence of a uniform alpha-adrenoceptor population in the rabbit main pulmonary artery. However, in contrast to alpha 1-agonists, contractile responses to alpha 2-agonists differed considerably in their dependence on external Ca, as revealed in Ca withdrawal experiments, as well as by the use of Ca antagonists. Furthermore, inactivation of the guanine nucleotide-binding inhibitory protein (Ni protein) by pertussis toxin impaired vasoconstriction, in response to alpha 2-agonists, but left that to alpha 1-agonists unaffected. It is suggested that alpha 1- and alpha 2-agonists induce two distinct conformational changes in an otherwise uniform alpha-adrenoceptor of the rabbit main pulmonary artery. By the mediation of Ni protein, alpha 2-agonists appear to allow influx of Ca into the vascular muscle cells through a type of Ca channel that is unlikely to be controlled by voltage.

Characterization of transducin from bovine retinal rod outer segments. II. Evidence for distinct binding sites and conformational changes revealed by limited proteolysis with trypsin.

The first stage of amplification in the cyclic GMP cascade in bovine retinal rod is carried out by transducin, a guanine nucleotide regulatory protein consisting of two functional subunits, T alpha (Mr approximately 39,000) and T beta gamma (Mr approximately 36,000 and approximately 10,000). Limited trypsin digestion of the T beta gamma subunit converted the beta polypeptide to two stable fragments (Mr approximately 26,000 and approximately 14,000). The GTPase and Gpp(NH)p binding activities were not significantly affected by the cleavage. Trypsin digestion of the T alpha subunit initially removed a small segment from the polypeptide terminus and resulted in the formation of a single 38,000-Da fragment. When this fragment was recombined with the intact T beta gamma subunit in the presence of membranes containing photolyzed rhodopsin, the reconstituted transducin exhibited greatly reduced GTPase and Gpp(NH)p binding activities. The loss in activities was due to the inability of the cleaved T alpha to bind to the photolyzed rhodopsin. Prolonged digestion converted the 38,000-Da fragment to a transient 32,000-Da fragment and then to two stable 23,000-Da and 12,000-Da fragments. The cleavage of the 32,000-Da fragment, however, can be blocked by bound Gpp(NH)p. The 32,000-Da fragment contains the Gpp(NH)p binding site and retains the ability to activate phosphodiesterase. These results indicate that the guanine nucleotide binding and rhodopsin binding sites are located in topologically distinct regions of the T alpha subunit and proved evidence that a large conformational transition of the molecule occurs upon the conversion of the bound GDP to GTP.

Distinct conformational changes in the catalytic subunit of cAMP-dependent protein kinase around physiological conditions. Do these changes reflect an ability to assume different specificities?

The free catalytic subunit of cAMP-dependent protein kinase readily undergoes a pronounced, salt-induced conformational change at neutral pH and around physiological values of ionic strength. This change, which is fully reversible, can be monitored directly by the relative chemical reactivity of two SH groups in the enzyme. Upon increasing the ionic strength of the medium from 0.03 to 0.22, one sulfhydryl becomes more reactive towards 5,5′-dithiobis[2-nitrobenzoic acid] while the other sulfhydryl becomes less reactive towards the same reagent. In parallel, the enzyme undergoes a salt-induced inactivation when histone H2b is used as a substrate. Though not reflected in the V max, this conformational change considerably increases the K m of the enzyme for histone H2b as well as for MgATP. This intrinsic malleability of the enzyme can account for the well-known salt inhibition of the enzyme for certain substrates and ion-dependent activation towards other substrates. It is suggested that this malleability might constitute the molecular basis for modulating the specificity of the enzyme and channeling its activity from one substrate to another in response to intracellular specifier signals.

Thyrotropin-ganglioside interactions and their relationship to the structure and function of thyrotropin receptors.

Gangliosides inhibit 125I-labeled thyrotropin binding to the thyrotropin receptors on bovine thyroid plasma membranes, on guinea pig retro-orbital tissue plasma membranes, and on human adipocyte membranes. This inhibition by gangliosides is critically altered by the number and location of the sialic acid residues within the ganglioside structure, the efficacy of inhibition having the following order: GD1b greater than GT1 greater than GM1 greater than GM2 = GM3 greater than GD1a. The inhibition results from the interaction of thyrotropin and gangliosides, rather than the interaction of membrane and gangliosides. Fluorescence studies show that the inhibition is associated with a distinct conformational change of the thyrotropin molecule and that the progression from a "noninhibitory conformation" to an "inhibitory conformation" parallels exactly the order of effectiveness in inhibiting 125I-labeled thyrotropin binding. The ganglioside inhibition of 125I-labeled thyrotropin binding appears to be hormonally specific in that it is not affected by albumin, glucagon, insulin, prolactin, follicle-stimulating hormone, growth hormone, or corticotropin. The possibility that a ganglioside or ganglioside-like structure is a component of the thyrotropin receptor is suggested by the finding that gangliosides more complex than N-acetylneuraminylgalactosylglucosylceramide are present in bovine thyroid membranes in much higher quantities than have been previously found in extraneural tissue. The finding that the B component of cholera toxin, which also interacts with gangliosides, has a peptide sequence in common with the beta subunit of thyrotropin, suggests that thyrotropin and cholera toxin may be analogous in their mode of action on the membrane.

Correlations between photophosphorylation and light-induced conformational changes of chloroplasts in whole cells of the halophilic green alga Dunaliella parva

Summary In whole cells of the extremely halophilic unicellular green alga Dunaliella parva slow changes in apparent absorbance, peaking at 535 nm, can be separated from the well-known fast 515 nm shift. It is concluded that this 535 nm change is caused by light scattering and indicates conformational changes (shrinkage) of the chloroplasts. Properties of the 535 nm change are compared with those of the light-induced increase of the endogenous ATP-level in vivo. From similar responses of both reactions to electron transport inhibitors and uncouplers it is concluded that the 535 nm change is correlated to light-induced ATP-formation and can be taken as a useful indicator for photophosphorylation in whole cells. In far-red light, exciting predominantly photosystem I, neither distinct conformational changes of chloroplasts nor an increase of the ATP-level could be observed. In red light, exciting both photosystem II and I, both the 535 nm change and ATP-formation are strongly suppressed by DCMU. These results suggest that in the presence of O2 cyclic photophosphorylation plays a minor role in Dunaliella. DBMIB, which inhibits photosynthetic electron transport between plastoquinone and cytochrome f, inhibits both ATP-formation and the 535 nm change. However, both reactions could be reactivated in vivo 1) by the addition of the Hill-reagent benzoquinone, which restored O2-evolution and 2) by the addition of the electron donor DAD, which caused O2-uptake. The former system was sensitive, the latter one insensitive to DCMU. FCCP inhibited ATP-formation and the 535 nm change in both systems. Photosynthetic control (stimulation of electron transport by FCCP) was observed only in the DBMIB/benzoquinone-system. These results seem to indicate two different ATP-sites in Dunaliella. One is located between the site of water oxidation and photosystem II. The second one is located after the DBMIB-inhibition site in the region of photosystem I.

Conformational change of the [formula omitted] repressor induced with the inducer

The repressor of the lac operon in Escherichia , coli undergoes a distinct conformational change upon addition of a specific inducer isopropyl-β-D-thiogalactoside (IPTG), which is evidenced by changes in ultraviolet absorption spectrum, sedimentation coefficient and in circular dichroism spectrum. The significance of the conformational change reported here is discussed in relation to the allosteric properties of the repressor.

Fluorescence studies of the molecular conformation of α-lactalbumin

The ultraviolet fluorescence of α-lactalbumin was shown to be markedly altered during the 2 distinct conformational changes which this protein undergoes. The more subtle of these, which occurs at pH 6 as the temperature is lowered from 25° to 1°, involves contraction of the “crevices” housing the 2 ‘exposed’ tryptophan groups and is accompanied by a short-wavelength shift of about 10 mμ of the emission spectrum. The more drastic process, denaturation below pH 4, results in a long-wavelength shift of 10–18 mμ and an increase in the apparent quantum yield of about 40%. The molecular origins of these spectral shifts have been interpreted in terms of a model derived from a recent theory which explains shifts in the emission spectrum of tryptophan in terms of an excited state complex. According to this model, the thermal transition which occurs at pH 6 for α-lactalbumin produces a short-wavelength shift due to inhibition of complex formation resulting from hindered rotation of tryptophans in the contracted “crevice”. The low pH denaturation of α-lactalbumin, which we have shown earlier to involve molecular swelling but no enhanced exposure of tryptophans, produces a long-wavelength shift of the emission spectrum due to enhanced complex formation resulting from increased freedom of rotation of the 3 “buried” tryptophans.