The interaction of histone H3 with histone H4 and with other histones studied by 19F nuclear magnetic resonance.

The behaviour, upon variations in ionic strength, pH and temperature of 19F nuclear nuclear magnetic resonance signals of the trifluoroacetonylated derivative of histone H3 is compared with those of the H3-H4 complex and of the Hv fraction (an equimolar mixture of H2A, H2B, H3 and h4). The line width of the 19F-labelled histone H3 signals increases with ionic strength or pH, an effect consistent with aggregation of the protein. In the case of H3-H4 complex or Hv the line width decreases at intermediate ionic strengths (0.1-0.25 M NaCl). This effect is interpreted as the consequence of the formation of a well defined structure with ionic strength. At high salt concentrations the line width increases as a consequence of the final rigid quaternary structure or of the formation of higher aggregates.     

Conformation of 1- and 3-deazaadenosines in solution as studied by 1H nuclear magnetic resonance spectroscopy.

¹H nuclear magnetic resonance spectra of 1 - (II) and 3-deazaadenosines (III) together with adenosine (I) in dimethylsulfoxide have been examined. Features of coupling constants indicate that the furanose rings of I, II, and III have similar conformational preferences and that conformations about the 4′-C–5′-C bond are preferentially $\text{gauche-gauche}$. Nuclear Overhauser effect and spin-lattice relaxation-time measurements demonstrate that II predominantly adopts the $\text{syn}$-conformation similar to that of I, whereas that of III has a greater $\text{anti}$ (freely rotating) component. The results suggest that the $\text{syn}$-conformation in II as well as I is stabilized presumably through a hydrogen bond between the 3-N and 5′-hydroxyl group.     

Lecithin translational diffusion studied by pulsed nuclear magnetic resonance.

The translational diffusion coefficient of egg yolk and dilauroyl lecithin in optically isotropic phases containing sodium cholate has been measured using the pulsed NMR magnetic field gradient method. After a correction for geometrical factors the measured diffusion coefficient is found to agree well with previous determinations in phospholipid systems. The experimental data imply that the cubic mesophase of the lecithin-sodium cholate-water system contains continuous lipid aggregates. A possible model of the arrangement of the different amphiphile molecules in the cubic phase is discussed.     

The aromatic residues of bovine pancreatic ribonuclease studied by 1H nuclear magnetic resonance.

1. The aromatic proton resonances in the 360-MHz 1H nuclear magnetic resonance (NMR) spectrum of bovine pancreatic ribonuclease were divided into histidine, tyrosine and phenylalanine resonances by means of pH titrations and double resonance experiments. 2. Photochemically induced dynamic nuclear polarization spectra showed that one histidine (His-119) and two tyrosines are accessibly to photo-excited flavin. This permitted the identification of the C-4 proton resonance of His-119. 3. The resonances of the ring protons of Tyr-25, Tyr-76 and Tyr-115 and the C-4 proton of His-12 were identified by comparison with subtilisin-modified and nitrated ribonucleases. Other resonances were assigned tentatively to Tyr-73, Tyr-92 and Phe-46. 4. On addition of active-site inhibitors, all phenylalanine resonances broadened or disappeared. The resonance that was most affected was assigned tentatively to Phe-120. 5. Four of the six tyrosines of bovine RNase, identified as Tyr-76, Tyr-115 and, tentatively, Tyr-73 and Tyr-92, are titratable above pH 9. The rings of Tyr-73 and Tyr-115 are rapidly rotating or flipping by 180 degrees about their C beta--C gamma bond and are accessible to flavin in photochemically induced dynamic nuclear polarization experiments. Tyr-25 is involved in a pH-dependent conformational transition, together with Asp-14 and His-48. A scheme for this transition is proposed. 6. Binding of active-site inhibitors to bovine RNase only influences the active site and its immediate surroundings. These conformational changes are probably not connected with the pH-dependent transition in the region of Asp-14, Tyr-25 and His-48. 7. In NMR spectra of RNase A at elevated temperatures, no local unfolding below the temperature of the thermal denaturation was observed. NMR spectra of thermally unfolded RNase A indicated that the deviations from a random coil are small and might be caused by interactions between neighbouring residues.     

Influence of Ca2+ binding on the structure and stability of bovine alpha-lactalbumin studied by circular dichroism and nuclear magnetic resonance spectra

Both the Ca2+-bound and Ca2+-free forms of alpha-lactalbumin can assume essentially the same folded conformation as evidenced by similarity in their CD and proton n.m.r. spectra. Thermal unfolding followed by the aromatic CD has shown that the stability of the folded state is markedly enhanced by Ca2+ and that the stabilization is almost entirely entropic; addition of 0.1 mM Ca2+ shifts the transition temperature from 40 degrees to 62 degrees in 0.1M Na+ at pH 7.0. The enthalpy change of the unfolding, coincident between the two forms, is, however, significantly smaller than that known for lysozyme. The n.m.r. spectrum under the condition that both the forms of the protein are in the folded state reflects minor environmental changes of certain protons upon Ca2+ binding, and these changes are shown to afford useful probes for assessment of the location of the binding site. From the pH dependence and temperature dependence of the spectrum and also by using spin decoupling in the aromatic region (6.4-8.7 p.p.m.), it is shown that none of histidyl residues are affected and that at least two tryptophanyl ring protons experience environmental changes upon Ca2+ binding to the folded apo-protein. Effect of free excess Ca2+ on the spectrum has also shown that in native alpha-lactalbumin there is only one Ca2+-binding site that is detectable by the present method.     

Ca2+ interaction with phospholipid bilayers studied by multifrequency phase fluorometry

Calcium interaction with phospholipid membranes containing phosphatidic acid is studied by multifrequency phase fluorometry, using DPH as fluorescent molecule. DPH decay is analysed by a continuous distribution of lifetimes. The results suggest an increase of membrane heterogeneity at low calcium concentrations, without changes in the polarity of the environment surrounding the probe.     

3-Hydroxy-3-methylglutaryl-CoA lyase deficiency studied using 2-dimensional proton nuclear magnetic resonance spectroscopy

1H-NMR spectroscopy has been applied to identify components in the urine of subjects with a deficiency of the enzyme 3-hydroxy-3-methylglutaryl-CoA lyase. One-dimensional spectra of samples from a pair of non-identical twins with this disorder were very similar and are probably diagnostic. The most intense signals were from singlets. Complete assignment of these major components was made possible by the use of 2-dimensional chemical shift correlated spectroscopy since several long-range couplings were detected. 2-dimensional spectroscopic techniques may therefore be of value in the identification of singlets in multicomponent systems.     

Study of specific interaction between nucleotides and dye support by nuclear magnetic resonance

The binding between four matrices (beaded cellulose, cellulose acetate, cellulose triacetate and Sepharose CL-6B) and beaded cellulose derivatized with a thiacarbocyanine dye with 5'-mononucleotides is investigated by Saturation Transfer Difference Nuclear Magnetic Resonance (STD-NMR) technique. This procedure intends to identify unspecific interactions between 5'-mononucleotides and matrices commonly used in affinity chromatography systems and also clarify the contribution of a thiacarbocyanine dye immobilized onto cellulose beads in a biorecognition process. The differences between non-derivatized and derivatized beaded cellulose evidence the contribution of thiacarbocyanine dye in the observed interaction. STD-NMR experiments show that Sepharose CL- 6B interact less with the 5'-mononucleotides comparatively with beaded cellulose. Indeed, beaded cellulose shows nonspecific interactions with almost all 5'-mononucleotides that compromises the specificity of the interaction between the thiacarbocyanine dye immobilized with the 5'-mononucleotides. The cellulose matrices where the hydroxyl groups are replaced by acetate and triacetate groups do not exhibit binding response to the 5'- mononucleotides, whereas the thiacarbocyanine dye contribution is evidenced by the reinforcement of the interactions with the sugar moiety of 5'-GMP and 5'-UMP and with base of 5'-AMP, 5'-CMP and 5'-TMP. This screening of the nucleotide atoms involved in the binding to the supports can be very useful in chromatography evaluations in which dye-affinity chromatography supports may be used, such as purification of nucleic acids.     

Chiral recognition of dextran sulfate with D- and L-cystine studied by multiwavelength surface plasmon resonance

A multiwavelength surface plasmon resonance (mwSPR) approach has been developed to study the chiral discrimination between D- and L-cystine (Cys). A monolayer of the two enantiomers was separately assembled on a pair of gold films of about 50 nm in thickness and their resonance wavelength shifts, Deltalambda, were measured under a continuous flow of an identical chiral probe solution. Dextran sulfate (DS) was found to be an excellent chiral probe because it has rich chiral centers and is large enough to produce sensitive mwSPR response. The chiral discrimination was investigated either by Deltalambda(max), the maximum resonance wavelength shift in recognition equilibrium, or by recognition kinetics (Deltalambda vs time). The equilibrium data showed that D-Cys yielded always the smaller Deltalambda(max) as compared to L-Cys at pH 5.0 or above. This differentiation was enlarged by raising the probe content and became naught at pH <4.5. The kinetic results showed that, as pH increased from 5.0 to 7.5, the non-equilibrium Deltalambda for D-Cys rose above the level for L-Cys at the first 30s of recognition but came back gradually to its equilibrium position after about 150 s, with crossing at 50--150 s depending on DS concentration. This phenomenon was thought to be the result of molecular orientation adjustment after DS binding to D-Cys. Both kinetic and thermodynamic mechanisms were thus considered to be deeply involved in the investigated chiral recognition system.     

Relationships between Ca2+ release, Ca2+ cycling, and Ca2+-mediated permeability changes in mitochondria

Ruthenium red and/or EGTA prevent cyclic uptake and release of Ca2+ in mitochondria. These compounds inhibit but do not prevent the swelling of liver mitochondria induced by Ca2+ plus t-butyl hydroperoxide or Ca2+ plus N-ethylmaleimide. Ruthenium red and/or EGTA have complex effects on the release rate of Ca2+ and other cations induced by t-butyl hydroperoxide or N-ethylmaleimide. To determine the relationship between permeability changes and Ca2+ release in the absence of Ca2+ cycling, a novel method of data collection and analysis is developed which allows the relative time courses of Ca2+ release and Mg2+ release or swelling to be accurately and quantitatively compared. This method eliminates errors in time course comparisons which arise from the aging of mitochondrial preparations and allows data from different preparations to be directly contrasted. Using the method, it is shown that permeability changes caused by Ca2+-releasing agents are not secondary effects arising from Ca2+ cycling between uptake and release carriers. In the absence of Ca2+-cycling inhibitors, Ca2+ release induced by t-butyl hydroperoxide or N-ethylmaleimide is, in part, carrier-mediated. In the presence of EGTA and ruthenium red, Ca2+ release induced by either agent is mediated solely by the permeability pathway. No differences are apparent in the solute selectivity of the inner membrane permeability defect induced by Ca2+ plus t-butyl hydroperoxide or Ca2+ plus N-ethylmaleimide. A novel type of Ca2+ release from energized liver mitochondria is reported. This release is induced by EGTA, occurs in the absence of other releasing agents or nonspecific permeability changes, and is rapid (greater than or equal to 50 nmol/min/mg protein).     

Ca(2+)-mediated interaction between negatively charged and neutral liposomes.

In the present work it is shown that large unilamellar lecithin/cholesterol liposomes are able to sequester small negatively charged liposomes in the presence of divalent cations. Evidence is presented suggesting that the sequestration occurs via the formation of membrane invaginations transformed further into intraliposomal vesicles.     

Interaction between calcium-free calmodulin and IQ motif of neurogranin studied by nuclear magnetic resonance spectroscopy

The interaction of Ca(2+)-free calmodulin (apoCaM) with the IQ motif corresponding to the calmodulin-binding domain of neurogranin has been studied by nuclear magnetic resonance (NMR) methods. The NMR spectra of uncomplexed apoCaM and apoCaM in complex with the IQ motif recorded at 750 MHz were studied and the backbone assignments of the protein in both forms were obtained by triple-resonance multidimensional NMR experiments. Chemical shift perturbations were used to map the binding surfaces. Only a single set of resonances was observed throughout the titration, indicating that the binding interaction is under fast exchange. Analysis of chemical shift changes indicates that (a) the main interaction and conformational changes occur in the C-terminal domain of calmodulin and (b) linker-1 (residues 40-44) between EF-1 and EF-2, linker-3 (residues 112-117) between EF-3 and EF-4, and the end of the alpha-helix H (residues 145-148) may be involved in the binding process. The dissociation constant (K(d)), estimated by fitting the chemical shift changes against the IQ peptide concentration, ranged from about 1.2 x 10(-5) to 8.8 x 10(-5) M. This result demonstrates that the interaction falls into the weak binding regime.     

Metabolism of lactic acid bacteria studied by nuclear magnetic resonance

The complexity of metabolic and regulatory networks presents a great scientific challenge to an integrated view of how individual components contribute to the overall function. Nuclear magnetic resonance (NMR) spectroscopy is undoubtedly a suitable technique for global investigations of microbial metabolism, since it allows a view into living cells without disturbing the cellular organisation. Therefore, metabolic processes can be monitored in real time under physiological conditions. In the present paper, examples of the application of NMR to study the metabolism of lactic acid bacteria will be given. These include the analysis of labelling patterns in end-products using ¹³C as a tracer, thereby establishing metabolic pathways, the detection and quantification of intermediates in the pathway of exopolysaccharide biosynthesis, and on line monitoring of glycolytic kinetics to assess the effect of metabolic engineering strategies.     

Molecular interaction between HIV-1 major envelope glycoprotein and dextran sulfate.

We investigated at the molecular level the interaction between, HIV-1 recombinant gp160 (rgp160) and low-molecular-weight dextran sulfate. We demonstrate the occurrence of a specific interaction between rgp160 and sulfated dextran beads, which is saturable, pH-dependent and inhibitable by soluble dextran sulfate but not by soluble dextran. This specific interaction has a low affinity, with an estimated Kd in the 10(-4) M range. In addition, the binding of rgp160 to soluble recombinant CD4 (sT4) can only be inhibited by the preincubation of rgp160, but not of sT4, with dextran sulfate. Taken together, these results demonstrate the occurrence of a low affinity, but specific interaction between dextran sulfate and rgp160. This may account, at least in part, for the anti-HIV-1 activity of dextran sulfate.     

Specific aggregations of alanine tetrapeptide derivatives as studied by nuclear magnetic resonance.

By use of high resolution nuclear magnetic resonance and infrared spectroscopy, we have found evidence for specific folded forms for the methoxyethoxyethoxyacetyl-blocked alanine tetramer ethyl ester. It appears that this tetrapeptide derivative exists in a folded form which is in rapid equilibrium with an extended structure (i.e., below 1% w/v). At high concentrations (i.e., above 1% w/v in chloroform) the folded form is stabilized by an association of the alanine tetrapeptide derivative into a side-by-side dimer which contains specific hydrogen bonds between the amine terminal regions of the two folded structures.