Showing papers on "Conformational change published in 1985"

pH-induced alterations in the fusogenic spike protein of Semliki Forest virus.

Abstract: The spike glycoproteins of Semliki Forest virus mediate membrane fusion between the viral envelope and cholesterol-containing target membranes under conditions of mildly acidic pH (pH less than 6.2). The fusion reaction is critical for the infectious cycle, catalyzing virus penetration from the acidic endosome compartment. To define the role of the viral spike glycoproteins in the fusion reaction, conformational changes in the spikes at acid pH were studied using protease digestion and binding assays to liposomes and nonionic detergent. A method was also developed to prepare fragments of both transmembrane subunit glycopolypeptides of the spike, E1 and E2, which lacked the hydrophobic anchor peptides. Unlike the intact spikes the fragments were monomeric and therefore useful for obtaining information on conformational changes in individual subunits. The results showed that both E1 and E2 undergo irreversible conformational changes at the pH of fusion, that the conformational change of E1 depends, in addition to acidic pH, on the presence of cholesterol, and that no major changes in the solubility properties of the spikes takes place. On the basis of these findings it was concluded that fusion involves both subunits of the spike and that E1 confers the stereo-specific sterol requirement. The results indicated, moreover, that acid-induced fusion of Semliki Forest virus differs in important respects from that of influenza virus, another well-defined model system for protein-mediated membrane fusion.

Effect of pH on the conformation of diphtheria toxin and its implications for membrane penetration.

Abstract: The pH-triggered change in diphtheria toxin conformation and the physical properties of the toxin above and below the transition pH have been examined. Exposure to low pH (less than or equal to 5 at 23 degrees C, less than or equal to 5.3 at 37 degrees C) triggers a rapid (t1/2 less than 30 s) change in toxin conformation; the transition occurs over a narrow pH range (0.2 unit). Below the transition pH, buried tryptophans become exposed, and the toxin becomes hydrophobic, binding very tightly to detergent. Aggregation is observed at low pH, probably due to this extreme hydrophobicity. Circular dichroism and fluorescence properties show that the low-pH conformation is not extensively unfolded. Therefore, the toxin "opens" at low pH without becoming a random coil. The conformation change is partly irreversible, and the degree of irreversibility parallels the degree of aggregation. Reduction of the disulfide bonds does not increase hydrophobicity at neutral pH. Furthermore, none of the structural variants of toxin (monomer or dimer, bound to ApUp or free, and nicked between subunits or intact) are hydrophobic at neutral pH or differ in transition pH markedly. Therefore, these factors do not mimic the effect of low pH. These observations are consistent with a functional role for the pH-triggered changes during penetration of the membranes of acidic organelles. The toxin may have adapted a conformational change similar to partial denaturation for a critical role in function. The possible nature of the pH-sensitive interactions and the effects of aggregation are discussed briefly.

Mechanism of inhibition of mitochondrial adenosine triphosphatase by dicyclohexylcarbodiimide and oligomycin: relationship to ATP synthesis

Abstract: Measurement of the rate of [gamma-32P]ATP binding (k1) and release (k-1) from catalytic sites on submitochondrial particles permitted calculation of the affinity constant in catalytic sites (k1 = K1/k1-1) of 10(12) M-1. This value is the same as that determined previously for the solubilized ATPase (F1) from beef heart mitochondria. Treatment of submitochondrial particles with dicyclohexylcarbodiimide or oligomycin so as to cause about 90% inhibition of ATPase activity was accompanied by a decrease in the binding of [gamma-32P]ATP in high-affinity catalytic sites. Under the conditions of the experiment, it is expected that the inhibitors reacted not with the ATPase itself but with other proteins in the oligomycin-sensitive ATPase complex (F0-F1). It is proposed that dicyclohexylcarbodiimide and oligomycin inhibit ATPase activity by causing a conformational change in the F0 portion of the complex that is transmitted to F1, resulting in an impaired binding of substrate in catalytic sites. These observations of apparent conformational interactions between F0 and F1 on the mitochondrial membrane are relevant to the mechanism of the coupling device that links the energy store to ATP formation in oxidative phosphorylation. It is proposed that a change in the state of ionization of one or more charged amino acid residues in F0 results in a conformational change in F0 which, transmitted to F1, reversibly alters the catalytic sites and facilitates the release of product ATP.

Rate-limiting steps in the DNA polymerase I reaction pathway.

Abstract: The initial rates of incorporation of dTTP and thymidine 5'-O-(3-thiotriphosphate) (dTTP alpha S) into poly(dA) X oligo(dT) during template-directed synthesis by the large fragment of DNA polymerase I have been measured by using a rapid-quench technique. The rates were initially equal, indicating a nonrate-limiting chemical step. However, the rate of thionucleotide incorporation steadily diminished to 10% of its initial value as the number of consecutive dTMP alpha S residues in the primer strand increased. This anomalous behavior can be attributed to the helix instability inherent in phosphorothioate-containing duplexes. Positional isotope exchange experiments employing the labeled substrate [alpha-18O2]dATP have revealed negligible alpha, beta-bridging----beta-nonbridging isotope exchange in template-directed reactions of Escherichia coli DNA polymerase I (Pol I) both in the presence and in the absence of added inorganic pyrophosphate (PPi), suggesting rapid PPi release following the chemical step. These observations are consistent with a rate-limiting step that is tentatively assigned to a conformational change of the E X DNA X dNTP complex immediately preceding the chemical step. In addition, the substrate analogue (Sp)-dATP alpha S has been employed to examine the mechanism of the PPi exchange reaction catalyzed by Pol I. The net retention of configuration at the alpha-P is interpreted in terms of two consecutive inversion reactions, namely, 3'-hydroxyl attack, followed by PPi attack on the newly formed primer terminus. Kinetic analysis has revealed that while alpha-phosphorothioate substitution has no effect upon the initial rate of polymerization, it does attenuate the PPi exchange reaction by a factor of 15-18 fold.(ABSTRACT TRUNCATED AT 250 WORDS)

Nanosecond optical spectra of iron-cobalt hybrid hemoglobins: geminate recombination, conformational changes, and intersubunit communication.

Abstract: Hybrid hemoglobins were prepared in which cobalt was substituted for the heme iron in either the alpha or beta subunits. Transient optical absorption spectra were measured at room temperature for these hybrids at time intervals between 0 and 50 ms following photodissociation of the carbon monoxide complex with 10-ns laser pulses. The cobalt porphyrins do not bind carbon monoxide, making it possible to investigate the time-resolved response of the cobalt-containing subunits to photodissociation of carbon monoxide in the iron-containing subunits. At the same time the response of the iron-containing subunits to the photolysis event can be studied, permitting an independent determination of the kinetics of ligand rebinding and conformational changes in the alpha and beta subunits of an intact tetramer. The data were analyzed by using singular-value decomposition to obtain the kinetic progress curve for ligand rebinding, the deoxyheme and cobalt porphyrin spectral changes, and the time course of these spectral changes. The geminate rebinding kinetics following photodissociation of alpha(Co)2 beta(Fe-CO)2 were very similar to those found unsubstituted hemoglobin, alpha(Fe-CO)2 beta(Fe-CO)2, indicating equivalence of the geminate kinetics for alpha and beta subunits within the R-state tetramer. The results for alpha(Fe-CO)2 beta(Co)2 were consistent with this conclusion, even though the analysis was complicated by the presence of comparable populations of R- and T-state species. Comparison of the deoxyheme spectral changes and relaxation times among the three molecules indicated that both alpha and beta subunits contribute to the deoxyheme spectral changes that signal tertiary and quaternary conformational changes in the unsubstituted tetramer. The response of the cobalt porphyrins to photodissociation was similar in the two hybrids. No structural changes were detected in the cobalt-containing subunits until the second tertiary conformational change in the iron-containing subunits observed at 1-2 microseconds. Much larger structural changes, as judged by the amplitude of the spectral changes, occurred in the cobalt-containing subunits concomitant with the R----T quaternary change at about 20 microseconds.

Circular dichroic evidence for an ordered sequence of ligand/binding site interactions in the catalytic reaction of the cAMP-dependent protein kinase.

Abstract: A limiting requirement for substrate specificity of the cAMP-dependent protein kinase is the presence of one or two basic residues located to the N-terminal side of the target substrate serine. Furthermore, circular dichroic (CD) studies have shown that binding of protein substrate involves a series of at least two independent conformational changes in the enzyme, each of which is initiated by a recognition signal on the substrate protein. The present study attempts to elucidate further the complete sequence of enzyme/ligand interactions by using the synthetic substrate peptide Kemptide and analogues differing from it at crucial points in the sequence: the Ala-peptide, where alanine is substituted for the target serine, and D-Ser-Kemptide, where the target serine is in the D rather than the L configuration. Examination of the effects of binding of these substrates on the intrinsic UV CD of the enzyme and the induced CD in the presence of Blue Dextran has revealed a third step in the substrate/enzyme binding interaction. Although sections of the conformational change at the active site are dependent on the basic subsite and the serine hydroxyl group on the peptide, respectively, the complete conformational change requires that the substrate be bound in random coil conformation. Where this does not occur, the kinetics show that the peptide will not act either as substrate or as inhibitor of the enzyme. Further, the interaction between the serine hydroxyl group and an enzyme tyrosine residue, previously observed, appears to be dependent on the correct orientation as well as the mere presence of the target -OH group.(ABSTRACT TRUNCATED AT 250 WORDS)

Electron microscopy of the conformational changes of alpha 2-macroglobulin from human plasma.

Abstract: High resolution electron microscopy reveals that fully active alpha 2-macroglobulin (alpha2M) from fresh human plasma presents a very characteristic tetrameric structure. This native conformation of the alpha2M molecule is described here for the first time, along with its various orientations in negatively stained preparations. Although the native form is sensitive to inactivation, glutaraldehyde fixation is not necessary for its observation except when ammonium salts are used. The tetrameric structure of alpha2M undergoes a drastic conformational change when the protein is treated either with trypsin, thrombin or methylamine, as evidenced by the appearance of the typical)+(structure already described in the literature. The various aspects of this second conformation correspond to different orientations of the molecules in the stain film, and depend upon the nature of the support.

Acyl carrier protein from Escherichia coli. Structural characterization of short-chain acylated acyl carrier proteins by NMR.

Abstract: Acylated acyl carrier proteins (ACPs) with acyl chain lengths of 2, 4, 6, 8, and 10 carbons were investigated by NMR and nuclear Overhauser methods at 500 MHz. Chemical shift changes of downfield aromatic and upfield, ring-current-shifted, isoleucine proton resonances monotonically vary as a function of acyl chain length with the most prominent shifts occurring with chain lengths between four and six carbons. Chemical shifts are largest for one of the two phenylalanines; however, substantial shifts do exist for Tyr-71, His-75, and two isoleucines. Since these residues are distributed throughout the molecule, their associated resonance chemical shifts are most probably explained by an induced conformational change. Comparative NOE measurements on reduced ACP (ACP-SH) and ACP-S-C8 suggest, however, that these induced conformational changes are small except for around one of the phenylalanines. A tertiary structural model for acyl-ACP consistent with our previous model for ACP-SH [Mayo, K. H., Tyrell, P. M., & Prestegard, J. H. (1983) Biochemistry 22, 4485-4493] is presented.

Secondary structure of human plasma fibronectin: conformational change induced by calf alveolar heparan sulfates.

Abstract: The quantitative analysis of circular dichroic spectra of native human plasma fibronectin according to the method of Provencher and Glockner [Provencher, S. W., & Glockner, J. (1981) Biochemistry 20, 33-37] indicated the presence of beta-sheet (79%), beta-turn (21%), but no alpha-helix or random coil in the secondary structure. The calf alveolar heparan sulfates induced a change in the conformation of fibronectin: the magnitude of the change depended on the molecular properties of the particular heparan sulfate preparations.

Differences in G-actin containing bound ATP or ADP: the Mg2+-induced conformational change requires ATP

Abstract: The role of adenosine 5'-triphosphate (ATP) in the Mg2+-induced conformational change of rabbit skeletal muscle G-actin has been investigated by comparing actin containing bound ADP with actin containing bound ATP. As previously described [Frieden, C. (1982) J. Biol. Chem. 257, 2882-2886], N-acetyl-N'-(5-sulfo-1-naphthyl)ethylenediamine-labeled G-actin containing ATP undergoes a time-dependent Mg2+-induced fluorescence change that reflects a conformational change in the actin. Addition of Mg2+ to labeled G-actin containing ADP gives no fluorescence change, suggesting that the conformational change does not occur. The fluorescence change can be restored on the addition of ATP. Examination of the time courses of these experiments suggests that ATP must replace ADP prior to the Mg2+-induced change. The Mg2+-induced polymerization of actin containing ADP is extraordinarily slow compared to that of actin containing ATP. The lack of the Mg2+-induced conformational change, which is an essential step in the Mg2+-induced polymerization, is probably the cause for the very slow polymerization of actin containing ADP. On the other hand, at 20 degrees C, at pH 8, and in 2 mM Mg2+, the elongation rate from the slow growing end of an actin filament, measured by using the protein brevin to block growth at the fast growing end, is only 4 times slower for actin containing ADP than for actin containing ATP.

Thrombin-induced conformational changes of human alpha 2-macroglobulin: evidence for two functional domains.

Abstract: The interaction of thrombin with alpha 2-macroglobulin (alpha 2M) was characterized by monitoring conformational changes and measuring the increase of free sulfhydryl groups during the reaction. Under experimental conditions where [thrombin] greater than [alpha 2M], the conformational change, measured by increases in the fluorescence of 6-(p-toluidino)-2-naphthalenesulfonate, and thiol group appearance displayed biphasic kinetics. The initial rapid phase results in the formation of a stable complex, the appearance of two sulfhydryl groups, the cleavage of approximately half of the Mr 180 000 subunits, and a conformational change that is not as extensive as that which occurs with trypsin. The slower phase is associated with the appearance of two additional sulfhydryl groups, increased cleavage of the Mr 180 000 subunit, and additional conformational changes. The available evidence suggests that the slow phase results from hydrolysis of the Mr 180 000 subunit(s) due to proteolysis of the alpha 2M-thrombin complex by free thrombin. Experiments with 125I-thrombin document the binding of 1 mol of thrombin/mol of alpha 2M that is not dissociated upon sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the complex. At higher ratios of thrombin to alpha 2M, a second mole of thrombin will reversibly associate with the 1:1 alpha 2M-thrombin complex. Under conditions where [thrombin] less than [alpha 2M], biphasic kinetics were not observed, and the conformational change, sulfhydryl appearance, and hydrolysis of the Mr 180 000 subunit were found to follow second-order kinetics.(ABSTRACT TRUNCATED AT 250 WORDS)

Membrane protein conformational change dependent on the hydrophobic environment.

Abstract: Two conformational states of the coat protein of the filamentous bacteriophage M13 have been detected in detergent solution by using magnetic resonance techniques. When 3-fluorotyrosine is incorporated in place of the two tyrosine residues in the protein, four 19F nuclear magnetic resonance signals are observed, two for each conformer of the protein. The equilibrium between the two forms can be modulated by pH, temperature, and detergent structure. The rate of interconversion of the isomers is rapid on the minutes time scale but is slow relative to the T1 relaxation time of the fluorine resonances of approximately 50 ms. The conformational change between the conformers results in the perturbation of a basic residue in the protein such that this group has a pKa of approximately 9.5 in one state which shifts to 10.5 or more in the other conformational state. The temperature dependence of the equilibrium suggests an enthalpy difference of about 10 kcal/mol which is offset by entropy to give nearly zero free energy difference between the states at pH 8.3 in deoxycholate solution at room temperature. This suggests a substantial reorganization of the noncovalent interactions defining the two conformational states. The conformational equilibrium is strongly dependent on detergent structure and the presence of phospholipid in the detergent micelle. The results are not consistent with a strong, specific lipid binding to the protein but appear to be consistent with a more general effect of the overall micelle structure on the conformational state of the protein.

Conformational changes in Newcastle disease virus fusion glycoprotein during intracellular transport.

Abstract: The migration on polyacrylamide gels of nascent (pulse-labeled) and more processed (pulse-labeled and then chased) forms of nonreduced Newcastle disease virus fusion glycoprotein were compared. Results are presented which demonstrate that pulse-labeled fusion protein, which has an apparent molecular weight of 66,000 under reducing conditions (Collins et al., J. Virol. 28: 324-336), migrated with an apparent molecular weight of 57,000 under nonreducing conditions. This form of the Newcastle disease virus fusion protein has not been previously detected. This result suggests that the nascent fusion protein has extensive intramolecular disulfide bonds which, if intact, significantly alter the migration of the protein on gels. Furthermore, upon a nonradioactive chase, the migration of the fusion protein in polyacrylamide gels changed from the 57,000-molecular-weight species to the previously characterized nonreduced form of the fusion protein (molecular weight, 64,000). Evidence is presented that this change in migration on polyacrylamide gels is due to a conformational change in the molecule which is likely due to the disruption of some intramolecular disulfide bonds: Cleveland peptide analysis of the pulse-labeled nonreduced fusion protein (molecular weight, 57,000) yielded a pattern of polypeptides quite different from that obtained from the more processed form of the fusion protein (molecular weight, 64,000). However, the pattern of polypeptides obtained from the nonreduced 64,000-molecular-weight species was quite similar to that obtained from the fully reduced nascent protein (molecular weight, 66,000). This conformational change occurred before cleavage of the molecule. To determine the cell compartment in which the conformational change occurs, use was made of inhibitors which block glycoprotein migration at specific points. Monensin allowed the appearance of the 64,000-molecular-weight form of the fusion protein, whereas carboxyl cyanide m-chlorophenylhydrazine blocked the appearance of the 64,000-molecular-weight form of the fusion protein. Thus, the fusion protein undergoes a conformational change as it moves between the rough endoplasmic reticulum and the medial Golgi membranes.

Changes of the proteinase binding properties and conformation of bovine alpha 2-macroglobulin on cleavage of the thio ester bonds by methylamine.

Abstract: Cleavage of the thio ester bonds of human alpha2-macroglobulin (alpha 2M) by methylamine leads to an extensive conformational change and to inactivation of the inhibitor. In contrast, cleavage of these bonds in bovine alpha 2M only minimally perturbs the hydrodynamic volume of the protein [Dangott, L. J., & Cunningham, L. W. (1982) Biochem. Biophys. Res. Commun. 107, 1243-1251], as well as its spectroscopic properties, as analyzed by ultraviolet difference spectroscopy, circular dichroism, and fluorescence in this work. A conformational change analogous to that undergone by human alpha 2M thus does not occur in the bovine inhibitor. However, changes of several functional properties of bovine alpha 2M are induced by the amine. The apparent stoichiometry of inhibition of trypsin thus is reduced from about 1.2 to about 0.7 mol of enzyme/mol of inhibitor. In spite of this decrease, the interaction with the proteinase induces similar conformational changes in methylamine-treated alpha 2M as in intact alpha 2M, as revealed by spectroscopic analyses, indicating that the mode of binding of the proteinase to the inhibitor is essentially unperturbed by thio ester bond cleavage. The reaction with methylamine also greatly increases the sensitivity of bovine alpha 2M to proteolysis by trypsin at sites other than the "bait" region. Moreover, the second-order rate constant for the reaction with thrombin is reduced by about 10-fold. These results indicate that the thio ester bonds of bovine alpha 2M, although not required per se for the binding of proteinases, nevertheless are responsible for maintaining certain structural features of the inhibitor that are of importance for full activity.