Showing papers on "Conformational change published in 1984"

Bromination stabilizes poly(dG-dC) in the Z-DNA form under low-salt conditions.

Abstract: Using circular dichroism studies, Pohl & Jovin (1972) [Pohl, F.M., & Jovin, T.M. (1972) J. Mol. Biol. 67, 375-396] demonstrated that poly(dG-dC) undergoes a salt-dependent conformational change characterized by a spectral inversion. The low-salt form corresponds to the right-handed B form of DNA and the high-salt form to the left-handed Z-DNA helix. Modification of poly(dG-dC) by adding bromine atoms to the C8 position of guanine and the C5 position of cytosine residues stabilized this polymer in the Z-DNA form under low-salt conditions. The guanine residues were found to be twice as reactive as the cytosine residues. With a modification of 38% Br8G and 18% Br5C, the polymers formed a stable Z-DNA helix under physiological conditions. The bromination produced spectroscopic features very similar to poly(dG-dC) in 4 M NaCl. However, bromination did not freeze the Z structure as was shown by ethidium bromide intercalation studies. Addition of the dye favored an intercalated B-DNA form. The conversion of B- to Z-DNA leads to profound conformational changes which were also seen by a reduced insensitivity to various exo- and endonucleases. Comparative studies showed that the brominated polymers have a high affinity to nitrocellulose filters. In 1 M NaCl, there was virtually no binding of B-DNA, but a substantial binding of Z-DNA was found even at rather low levels of bromination.(ABSTRACT TRUNCATED AT 250 WORDS)

1H-NMR studies of calmodulin: the nature of the Ca2+-dependent conformational change

Abstract: Using assignments of resonances in the 1H-NMR spectrum of calmodulin obtained by the use of large tryptic fragments of the molecule [Dalgarno, D. C., Klevit, R. E., Levine, B. A., Williams, R. J. P., Dobrowolski, Z., and Drabikowski, W. (1984) Eur. J. Biochem. 138, 281--289], the spectral changes which occur on Ca2+ binding to calmodulin have been examined in detail. Ca2+ binding occurs in two stages: the first two Ca2+ ions bind at sites III and IV (numbered from the N terminus) and the second two Ca2+ ions bind at sites I and II. The high-affinity binding causes perturbations of residues in both halves of the molecule, whereas binding at the two N-terminal sites only affects sidechains in that half of the molecule. The effects of binding Cd2+ to the Ca2+-binding sites of calmodulin have also been studied by 1H NMR. The cation induces spectral changes which are very similar to those seen for Ca2+, but some important differences do exist.

Kinetics of the conformational alterations associated with nucleophilic modification of alpha 2-macroglobulin.

Abstract: The effect of nucleophilic modification of alpha 2-macroglobulin (alpha 2M) with methylamine on the kinetics of sulfhydryl exposure was investigated. The generated sulfhydryl groups were detected with 4,4'-dithiodipyridine. The bimolecular rate constant for sulfhydryl exposure was determined to be 11.6 +/- 0.8 M-1 s-1 at 30 degrees C and pH 8.0. Treatment of alpha 2-macroglobulin with methylamine or proteases, such as plasmin and trypsin, results in a substantial increase in the fluorescence of 6-(p-toluidino)-2-naphthalenesulfonic acid. This probe was used to monitor the kinetics of the conformational change occurring in alpha 2-macroglobulin upon treatment with methylamine. It was found that the conformational change did not occur simultaneously with the cleavage of the thiol ester bonds by the nucleophile but, rather, the conformational alterations occurred following a lag phase. The data are consistent with a mechanism requiring the random cleavage of two thiol ester bonds of a dimeric unit in the molecule prior to the unimolecular process representing the conformational change. According to this model, the two dimeric units present in alpha 2M act as independent entities. On the basis of the best fit with the model, the bimolecular rate constant, for hydrolysis of the thiol ester bonds, was determined to be 11.9 +/- 0.7 M-1 s-1, while the rate constant for the conformational change was (9.7 +/- 2.0) X 10(-3) s-1. The measured rate of conformational change is rate limited by thiol ester cleavage at lower methylamine concentrations. The conformational change, measured with this fluorescence probe, approximately parallels the loss of trypsin binding activity of alpha 2-macroglobulin, measured by resistance of the bound trypsin to soybean trypsin inhibitor. A much slower loss of plasmin binding activity was observed than was found for trypsin, suggesting that the structural requirements on alpha 2M for the interaction with plasmin are disrupted much more slowly than the structural requirements for trypsin binding upon methylamine treatment of the molecule.

Theoretical analysis of gramicidin A transmembrane channel. II. Energetics of helical librational states of the channel

Abstract: The degrees of conformational freedom of poly L–D β-helical chain are analyzed consistent with the helical parameters of gramicidin A structure. From conformational energy calculations, “helical librations” that can be sustained by this structure are described and the energy of libration as a function of the cavity size is presented. Two different modes of conformational change are identified corresponding to librations of all L–D-peptide units or all D–L-peptide units while retaining the helical parameters. Such helical librations are considered relative to conformational perturbations due to the presence of an ion in the channel.

Conformational changes induced by binding of bivalent cations to oncomodulin, a paravalbumin-like tumour protein

Abstract: When Mg2+ was added to rat oncomodulin, a paravalbumin-like tumour protein, changes in the c.d. spectrum and tyrosine fluorescence intensity were observed. The addition of Ca2+ resulted in even greater changes in these spectra. The fluorescence excitation spectra of apo- and Mg-oncomodulin were superimposable, whereas that of Ca-oncomodulin was markedly different. The u.v.-absorption spectrum of the Ca2+ form also showed major differences from those of the other two forms. These observations indicate that Ca2+ induced a significant and specific conformational change in the protein that was not observed on binding Mg2+. In contrast, the conformational change induced by either Mg2+ or Ca2+ was identical in the homologous rat parvalbumin. This Ca2+-specific conformational change may be the basis for oncomodulin's Ca2+-dependent protein/protein interaction.

Effects of ultraviolet light on the in vitro assembly of microtubules.

Abstract: Exposure of microtubular protein to ultraviolet light inhibits its assembly into morphologically normal microtubules. This effect appeared to result primarily from damage to the tubulin dimers. The damage consisted of a conformational change, a loss of two free sulfhydryl groups, a production of higher molecular weight cross-linked species, and the formation of aggregated amorphous material upon polymerization.

Methylamine‐induced conformational change of α2‐macroglobulin and its zinc(II) binding capacity

Abstract: Methylamine induces a conformational change of alpha 2-macroglobulin which is very similar to that obtained by proteinase reaction and binding. This was shown by small-angle X-ray scattering at 21 degrees C in 0.03 M Hepes buffer of pH 8.0 containing 0.15 M NaCl and 0.3 mM EDTA. When alpha 2-macroglobulin reacts with methylamine the side maximum virtually disappears from the X-ray scattering curve and the radius of gyration decreases from 7.8 nm to 7.2 nm. The X-ray data of alpha 2-macroglobulin are consistent with an open shape model similar to that deduced via electron micrographs [Schramm, H. J. and Schramm, W. (1982) Hoppe-Seyler's Z. Physiol. Chem. 363, 803-812]; one projection of the model resembles the letter H; the four subunits are mainly represented as elliptical cylinders which are connected via a central, quite flat cylinder. Zinc(II) ions cause aggregation of alpha 2-macroglobulin even at such a low total zinc concentration as 12.5 microM; for 25 microM zinc(II) concentration, the average molecular mass indicates that the aggregation goes beyond the dimeric stage. Monomeric species of alpha 2-macroglobulin appear to have the capacity specifically to bind 8.0 zinc(II) ions per molecule, which corresponds to two zinc(II) ions per subunit.

Localized conformational changes induced in a class I major histocompatibility antigen by the binding of monoclonal antibodies.

Abstract: We describe two monoclonal antibodies, R3/47 and YR1/1, directed against different epitopes of the expressed rat class I major transplantation antigen RT1Aa, that interact with each other so that the binding of one antibody, YR1/1, is greatly enhanced by the binding of the other. The positive interaction between R3/47 and YR1/1 also occurs when using RT1Aa molecules solubilized from cell membranes in detergent. It is therefore unlikely that the molecular environment of the membrane contributes to the interaction. The ability of R3/47 to modify the YR1/1 determinant on the RT1Aa molecule is mediated without any significant loss of potency by highly purified monomeric Fab fragments. This result suggests that the binding of R3/47 to the RT1Aa molecule alters the YR1/1 determinant by initiating a propagated conformational change in the antigen.

Secondary structure of heart sarcolemmal proteins during interaction with metallic cofactors of (Na+ + K+)-ATPase.

Abstract: he secondary structure of membrane proteins was studied in rat heart sarcolemma by circular dichroism under conditions of interaction with metallic cofactors of (Na+ + K+)-ATPase at their optimal concentrations and under metal free conditions. Approximately 80 per cent of polypeptide chains in the membrane were organized in alpha-helical structure. Upon stabilizing the E1. Na conformation state of (Na+ + K+)-ATPase by Mg2+ and Na+ ions, only a slight increase in the protein alpha-helix content (to 83 per cent) was observed. On the other hand, simultaneous addition of Mg2+ and K+ ions resulting in the establishment of the E2 . K conformational state of the enzyme, was followed by a significant decrease in the membrane protein helicity (to 72 per cent). The presence of all three metallic cofactors of (Na+ + K+)-ATPase did not induce any further conformational change in sarcolemmal proteins as compared to the state induced by the interaction with Mg2+ and Na+ ions. In contrast to results obtained with Mg2+ ions, the interaction of Na+ with the sarcolemmal membranes led to a considerable decrease and that of K+ to a significant increase in alpha-helicity of the membrane polypeptides. These findings have confirmed the regulatory role of magnesium in transition of the conformational state from E1 to E2 in the reaction sequence of (Na+ + K+)-ATPase. Specific modulation by Na+ and K+ of the helicity of sarcolemmal proteins in the presence of Mg2+ and in the absence of ATP might be considered as a preprint of conformational changes which will occur in the presence of ATP.

Magnesium binding and conformational change of DNA in chromatin

Abstract: The structure of chromatin in the presence of Mg2+ ions was examined by circular dichroism and equilibrium dialysis. Circular dichroism (CD) shows that above 260 nm the intensity of the spectrum of DNA in nucleoproteins decreases as the Mg2+ concentration increases. This change is an intrinsic characteristic of DNA since it is also observed in protein-free DNA and has been attributed to a change in the winding angle of base pairs around the DNA axis. Some structural elements of the DNA in the nucleosome core, therefore, are as movable as those of protein-free DNA. The basic organization of H1-depleted chromatin, 146 base pairs (bp) of DNA wound around core histones and a residual 49 bp in the linker region in the repeating unit, is maintained both in the presence and in the absence of Mg2+ ions, as shown by the fact that the CD spectrum of H1-depleted chromatin has the same type of linear combination between the spectrum of protein-free DNA and that of the nucleosome core in 0.2 mM MgCl2-10 mM triethanolamine (pH 7.8) as it has in 1 mM ethylenediaminetetraacetic acid-10 mM tris(hydroxymethyl) aminomethane (pH 7.8). The ellipticity of chromatin shows a smaller decrease relative to the other nucleoproteins and protein-free DNA upon the addition of Mg2+ ions. Therefore, some structural elements of chromatin are apparently somewhat protected against the conformational change induced by these ions. The spectrum of chromatin becomes almost indistinguishable from that of H1-depleted chromatin in 0.2 mM MgCl2.(ABSTRACT TRUNCATED AT 250 WORDS)

Effect of template conversion from the B to the Z conformation on RNA polymerase activity.

Abstract: Transition from the right-handed B to the left-handed Z conformation of DNA was studied by circular dichroism in parallel with the ability of the DNA to support RNA synthesis with Escherichia coli RNA polymerase. Since the B to Z transition is generally induced by a chemical agent, a definitive demonstration that a change in activity is due to the conformational change, and not to the agent itself or to other factors, requires the clear-cut correlation of template activity and conformation under a variety of conditions that result in conformational change. Such correlation was achieved by following the [Co(NH3)6]3+-induced transition of poly(dG-dC) X poly(dG-dC) and poly(dG-dm5C) X poly(dG-dm5C) and the Mg2+-induced transition of poly(dG-dm5C) X poly(dG-dm5C). In addition, conditions were chosen to minimize possible aggregation. In each of these three systems, the B to Z conformational transition was accompanied by a substantial decrease in transcription activity. While the conversion from B to Z of poly(dG-dm5C) X poly(dG-dm5C) is induced by a 25-fold lower concentration of [Co(NH3)6]3+ than that required for the conversion of unmethylated polymer, in both cases the RNA polymerase activity is decreased at the same cation concentration as that producing the conformational transition. Neither [Co(NH3)6]3+ nor Mg2+ inhibits RNA synthesis with control templates that are not converted to Z under the same conditions, such as poly(dA-dT) X poly(dA-dT) or calf thymus DNA with [Co(NH3)6]3+ or poly(dG-dC) X poly(dG-dC) with Mg2+.(ABSTRACT TRUNCATED AT 250 WORDS)

Fluorescent probes as a measure of conformational alterations induced by nucleophilic modification and proteolysis of bovine alpha 2-macroglobulin.

Abstract: Conformational alterations occurring in bovine alpha 2-macroglobulin (alpha 2M) resulting from proteolysis and nucleophilic modification have been monitored by UV difference spectra, circular dichroism, and changes in the fluorescence of 6-(p-toluidino)-2-naphthalenesulfonate (TNS) and bis(8-anilino-1-naphthalenesulfonate) (Bis-ANS). The results of this study indicate that these two dyes appear capable of differentiating between conformational changes induced by proteolysis and those induced by methylamine treatment. It appears that TNS is a sensitive probe for monitoring protease-induced but not methylamine-induced conformational changes in bovine alpha 2M. Bis-ANS, on the other hand, appears suitable for monitoring conformational changes induced by methylamine treatment or proteolysis of the molecule and was used as a probe to monitor the kinetics of the conformational change induced by methylamine treatment. It was found that the conformational change did not occur simultaneously with cleavage of the thiol ester bonds by the nucleophile, measured by titration of free sulfhydryl groups with 5,5'-dithiobis(2-nitrobenzoate). The data are consistent with a model in which initial nucleophilic attack results in exposure of sulfhydryl groups, resulting in a conformational change measured by an increase in fluorescence. This event is followed by a unimolecular step representing a conformational change in the protein that results in a further increase in the fluorescence signal. The second-order rate constant for hydrolysis of the thiol ester bonds was determined to be 3.4 +/- 1.0 M-1 s-1, while the rate constant for the conformational change was (4.4 +/- 0.8) X 10(-4) s-1.

Conformational change of Ca2+,Mg2+-adenosine triphosphatase of sarcoplasmic reticulum upon binding of Ca2+ and adenyl-5'-yl-imidodiphosphate as detected by trypsin sensitivity analysis.

Abstract: Ca2+-Mg2+-ATPase of sarcoplasmic reticulum was subjected to trypic digestion under various conditions and the cleavage patterns were compared. The first tryptic cleavage to yield the NH2-terminal A-fragment (Mr approximately equal to 55,000) and COOH-terminal B-fragment (Mr approximately equal to 45,000) [Thorley-Lawson, D.A. & Green, N.M. (1977) Biochem. J. 167, 739-748] was little affected by adding ligands such as Ca2+ and AMP-P(NH)P. On the other hand, subsequent splitting of A-fragment into A1 (Mr approximately equal to 30,000) and A2 (Mr approximately equal to 20,000), and further cleavages giving rise to three smaller fragments of Mr approximately equal to 27,000-28,000 (A1a, A1b, and C) [Saito, K., et al. (1984) J. Biochem. 95, 1297] were profoundly affected by these ligands. A difference in cleavage sites was noted depending on Ca2+ ion concentration; thus, A1b and C were the major components remaining after digestion in the presence and absence of Ca2+, respectively. AMP-P(NH)P markedly stabilized both A1 and A2 fragments, but the effect was much more prominent when Ca2+ was simultaneously present on the transport site. These findings suggest that conformational changes of the ATPase molecule upon binding of Ca2+, AMP-P(NH)P, or both are accompanied by corresponding changes in the susceptibility to tryptic digestion. Fragments A1 and A2 were both quite stable and fragmentation did not proceed beyond A1, when sarcoplasmic reticulum membranes were treated with trypsin at 0 degrees C. Significant further fragmentation of A1 was observed only above 20 degrees C, suggesting a conformational transition of the ATPase protein around that temperature.