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Biomedical subjects

R Kaptein

Publications and source records attributed to R Kaptein.

At least 181 records · Page 10Linked to original sources
PubMed1983

Sequence-specific resonance assignments in the 1H nuclear-magnetic-resonance spectrum of the lac repressor DNA-binding domain 1-51 from Escherichia coli by two-dimensional spectroscopy.

The assignment of the 1H nuclear magnetic resonance (NMR) spectrum of the DNA-binding domain 1-51 of lac repressor from Escherichia coli is described and documented. The assignments are based entirely on the amino acid sequence and on two-dimensional NMR experiments at 360 MHz and 500 MHz. Individual assignments were obtained at 18 degrees C for the backbone protons of 44 out of the total of 51 amino acids residues, the exceptions being Met-1, Lys-2, Tyr-7, Arg-35, Glu-36, Lys-37 and Ile-48. Complete assignments of the non-labile hydrogen atoms of the side chain were obtained for 33 residues, and for Asn-46 and Asn-50 the delta amide protons were also identified. The chemical shifts for the assigned resonances at 18 degrees C are listed for an aqueous solution at pH 4.9 and at pH 6.8.

Amino Acid Sequence↗
PubMed1983

Investigation by photochemically-induced dynamic nuclear polarization and nuclear Overhauser enhancement 1H-NMR of the interaction between beta-endorphin and phospholipid micelles.

The photochemically-induced dynamic nuclear polarization technique has been used to investigate the access of a photoexcited flavin dye to tyrosyl and histidyl residues in [Met]enkephalin and human and camel beta-endorphins, both alone and in the presence of n-dodecylphosphorylcholine micelles. The results indicate that the mode of binding of Tyr-1, but not of residue 27, is similar in the two endorphins and differs from that of Tyr-1 in [Met]enkephalin. In human beta-endorphin, accessibility and mobility of Tyr-27 are strongly reduced in the presence of lipid at physiological pH, whereas in camel beta-endorphin His-27 becomes immobilized only at high pH. Moreover, nuclear Overhauser enhancement experiments suggest a rigidifying influence of the peptide on the polar head groups of the micelles.

Amino Acid Sequence↗
PubMed1983

NMR study of the interaction between the lac repressor and the lac operator.

Binding of the lac repressor headpiece, the N-terminal region of the lac repressor, to the lac operator of Escherichia coli was studied by 1H-NMR spectroscopy. Two DNA fragments, of 51 base pairs and 62 base pairs, containing the lac operator region, were investigated. The signals of their hydrogen-bonded imino protons were well resolved in the 500-MHz NMR spectra. The spectra of the free lac operator DNA are similar to those obtained from ring-current-shift calculations for a B-DNA structure. Complex formation with the headpiece led to small but nevertheless characteristic changes in the spectra. The fact that very few imino resonances shifted upon addition of headpiece, as well as the variety in direction and size of these chemical shifts, indicate the formation of a specific complex between the lac repressor and the lac operator. The observed changes in the resonance positions exclude the intercalation of tyrosine residues of the headpiece between adjacent base pairs of the lac operator as well as the formation of a cruciform structure. They rather reflect a small conformational transition in the DNA itself, caused for example by an alteration in the tilt of a few base pairs or a shift of the keto-enol tautomeric equilibrium of the bases towards the enolic form.

Bacterial Proteins↗
PubMed1983

Photo-CIDNP 1H-NMR studies of bovine pancreatic phospholipase A2 and its zymogen.

Bovine pancreatic phospholipase A2 and its zymogen were studied by laser photo-CIDNP 1H-NMR. Resonances of Trp3 and Tyr69 protons of the two proteins were assigned. By varying the delay between a short light pulse and the observation pulse, time dependencies of the CIDNP signals were obtained from which effective T1 values could be derived. The photo-CIDNP chemical shifts, intensities and relaxation data pointed to environmental differences for the Tyr69 residues in the two proteins, while only small differences were noted for the Trp3 residues. The more buried position of Tyr69 in the enzyme relative to the zymogen was related to the ability of the enzyme to bind to micellar aggregates, to which the zymogen is unable to bind.

Animals↗
PubMed1983

Proton nuclear magnetic resonance assignments and surface accessibility of Tryptophan residues in lysozyme using photochemically induced dynamic nuclear polarization spectroscopy.

Tryptophan resonances in the 360-MHz 1H photochemically induced dynamic nuclear polarization spectrum of hen egg white lysozyme are investigated in detail. All resonances of one tryptophan and six of another are identified and assigned to their respective protons. The methods employed, all involving nuclear spin polarization, include the study of cross-relaxation effects and the use of selective radio-frequency irradiation, Gd3+ as a paramagnetic probe, and riboflavin as the chemically induced dynamic nuclear polarization generating dye. From a comparison of the experimental results with the known X-ray structure of lysozyme, second-stage assignments of the two tryptophan residues (Trp-62 and Trp-123) are proposed. A number of other resonances are characterized, among them Trp-63 C(2)H and four indirectly polarized methyl groups.

Animals↗
PubMed1983

lac Repressor headpiece binds specifically to half of the lac operator: a proton nuclear magnetic resonance study.

The complex formation of the N-terminal domain (headpiece) of the Escherichia coli lac repressor and a synthetic 14-base-pair lac operator fragment has been investigated by 1H NMR. Titration shifts in the imino-proton region of the DNA spectrum and in the aromatic region of the headpiece spectrum are examined in detail and interpreted where possible. The assignment of the resonances in the complex follows in part from the titration data and is completed by nuclear Overhauser measurements. The shift of the His-29 C-2 resonance has been used to assess the binding strength of the complex. Evidence is presented for the presence of a high-affinity site on the lac operator fragment (KD less than or equal to 2 X 10(-5) M), which shows features in common with one of the specific binding sites on the complete lac operator, and for the presence of a second, nonspecific binding site with lower affinity. The influence of this second site on the interpretation of the binding data is discussed.

Escherichia coli↗
PubMed1983

Secondary structure of the lac repressor DNA-binding domain by two-dimensional 1H nuclear magnetic resonance in solution.

A recently proposed approach for spatial structure determination in noncrystalline proteins by nuclear magnetic resonance was applied to the lac repressor DNA-binding domain. On the basis of sequence-specific 1H NMR assignments, the location of alpha-helices in the amino acid sequence was determined from nuclear Overhauser enhancement data and from amide proton exchange studies. These investigations provide detailed experimental data on the structure of a noncrystalline DNA-binding protein. The results support the hypothesis advanced by others that sequence-specific interactions between lac repressor and DNA are mediated by a particular spatial arrangement of two alpha-helices common to various different DNA-binding proteins.

Amino Acid Sequence↗
PubMed1983

In vivo 31P and 13C nuclear magnetic resonance studies of acetate metabolism in Chromatium vinosum.

31P and 13C nuclear magnetic resonance (NMR) experiments were performed on suspensions of the phototrophic bacterium Chromatium vinosum incubated anaerobically in the dark. 31P NMR spectra revealed that during prolonged dark incubation high ATP levels are maintained. This phenomenon was independent of the presence of the energy reserves polyglucose and polyphosphate. 13C NMR experiments revealed that the amino acids glutamate, aspartate, and alanine are the major products of acetate incorporation in the dark. Apart from these amino acids, poly-beta-hydroxybutyrate was also formed. Acetate metabolism was markedly stimulated by the presence of polyglucose. The specific 13C activity of glutamate C-2 was approximately 50% that of glutamate C-4. The idea is discussed that this difference is the consequence of the maintenance of redox balance during entry of acetate into cell metabolism.

Acetates↗
PubMed1982

A photo-CIDNP study of the active sites of Megasphaera elsdenii and Clostridium MP flavodoxins.

Megasphaera elsdenii and Clostridium MP flavodoxins have been investigated by photo-CIDNP techniques. Using time-resolved spectroscopy and external dyes carrying different charges it was possible to assign unambiguously the resonance lines in the NMR-spectra to tyrosine, tryptophan and methionine residues in the two proteins. The results show that Trp-91 in M.elsdenii and Trp-90 in Cl.MP flavodoxin are strongly immobilized and placed directly above the benzene subnucleus of the prosthetic group. The data further indicate that the active sites of the two flavodoxins are extremely similar.

Binding Sites↗
PubMed1982

Carbon-13 nuclear magnetic resonance studies of acetate metabolism in intact cells of rhodopseudomonas sphaeroides.

13C-nuclear magnetic resonance was used to study the metabolism of [2-(13)C]acetate in suspensions of Rhodopseudomonas sphaeroides. In the dark, in logarithmic-phase cells the 13C label appeared first in butyrate C-2 and C-4 and subsequently in glutamate C-4 and succinate C-2 and C-3. In the light, synthesis of poly(beta-hydroxybutyrate) (PHB) takes place. Butyrate synthesis seems to be independent of PHB synthesis or degradation activity. Starved, logarithmic-phase cells also show massive synthesis of PHB in the dark. Stationary-phase cells incorporate 13C predominantly into glutamate and succinate. No significant butyrate biosynthesis can be detected in the dark or during illumination. The incorporation of label in PHB is very slow in these cells and most probably originates from exchange of 12C for 13C into PHB. This might indicate slow turnover without net synthesis of the polymer occurring under these conditions. The results are discussed in relation to the redox state and the availability of metabolic energy for biosynthetic reactions in the dark and during illumination of cell suspensions of Rps. sphaeroides.

Acetates↗
PubMed1981

Limited trypsinolysis of porcine and equine colipases. Spectroscopic and kinetic studies.

Porcine and equine colipases have been submitted to mild tryptic digestion. Proteolysis occurs at the Arg5-Gly6 bond with the loss of the N-terminal pentapeptide. Studies of native and trypsin-treated colipases by circular dichroism and laser chemically induced dynamic nuclear polarization indicate that proteolysis induces conformational changes in the region of the tyrosine cluster. Experiments in the presence of phospholipid provide further evidence showing that these residues are in or close to the region of the protein interacting with aggregated lipids. Kinetic studies of the reaction of bile salt-inhibited lipase with emulsified triolein in the absence and in the presence of lecithin show that tryptic hydrolysis of the protein cofactor increases its affinity for the enzyme in the presence of lipid substrate. In both cases, it was found that the apparent dissociation constant of the lipase-colipase complex is decreased by one order of magnitude. Our results confirm that the biological activity of the lipase cofactor is enhanced by specific tryptic cleavage in the amino terminal region of the polypeptide and support the suggestion by Borgström et al. (Borgström, B., Wieloch, T., Erlanson-Albertsson (1981) FEBS. Lett. 108, 407-410) that the secreted form of colipase is a precursor.

Animals↗
PubMed1981

1H NMR studies of lac-operator DNA fragments.

The hydrogen-bonded imino protons of a 14 base pair double-stranded DNA fragment comprising one half of the lac operator of E. coli were investigated by 360 MHz H NMR. From combined melting studies of this synthetic 14 b.p. fragment and its two constituent 7 b.p. fragments a nearly complete assignment for the low-field proton resonances was obtained. The experimental spectra are compared with calculated spectra and with the spectrum of a 51 b.p. DNA restriction fragment from E. coli containing the complete lac operator. Structural information on these oligonucleotides is presented. This study is a prerequisite for future 1H NMR investigations of the interaction of the lac operator with the lac repressor.

DNA, Bacterial↗
PubMed1981

Nuclear magnetic resonance characterization of aromatic residues of alpha-lactalbumins. Laser photo chemically induced dynamic nuclear polarization nuclear magnetic resonance studies of surface exposure.

The alpha-lactalbumins are involved as modifier proteins in lactose biosynthesis. Lactalbumins from different mammalian species are cross-reactive with the galactosyltransferases from others because of their homologous primary and tertiary structure. We have studied the surface exposure of several alpha-lactalbumins (bovine, goat, human, guinea pig, and rabbit) by the laser photo-CIDNP technique, an NMR method which measures the access of a photoexcited flavin dye to surface exposed Tyr, Trp, and His residues. An exposed histidine-68 residue exists in the bovine and goat species but is missing in other species and is replaced with a His-10 in the guinea pig species. The only exposed tryptophan residue was Trp-104, which cross-relaxed to nearby Trp-60. Cross-polarization to the latter residue was proven by taking free induction decays after extremely short light pulses (0.1 s). Furthermore, this cross-polarized Trp-60 resonance was absent in the guinea pig species, which has a substitution at position 60. The chemical shifts of these Trp residues were extremely similar in all species but rabbit, which has substituted His for a Tyr at position 103, situated close to both Trp-104 and -60. Three of the four tyrosines in bovine, goat, human, and guinea pig alpha-lactalbumin were exposed (the latter species has an extra Tyr in its sequence which was apparently not accessible). The rabbit species contains only two Tyr residues, the one which was not accessible (Tyr-50) being common to all species.

Animals↗
PubMed1981

Exposure of aromatic residues of Streptomyces subtilisin inhibitor. A photo-CIDNP study.

Exposure of aromatic residues, Tyr 7, Tyr 75, Tyr 93, His 43, His 106, and Trp 8, was studied by laser-induced photo-CIDNP in the 1H NMR spectrum of Streptomyces subtilisin inhibitor at 360 MHz. Only Tyr 7 and Tyr 75 gave strong CIDNP signals, whereas the rest of the aromatic residues gave no detectable signals in the temperature range 25-55 degrees C. From the temperature dependence data, it is concluded that Tyr 7 is well exposed at all temperatures, whereas the exposure of Tyr 75 increases with temperature, in agreement with the conclusion obtained by other methods. Agreements and discrepancies between the conclusions derived from the CIDNP data and the results so far obtained by other methods are compared for all the aforementioned aromatic residues.

Bacterial Proteins↗
PubMed1981

31P nuclear magnetic resonance studies of energy transduction in Rhodopseudomonas sphaeroides.

31P nuclear magnetic resonance spectra of th phototrophic bacterium Rhodopseudomonas sphaeroides reveal the presence of inorganic phosphate, sugar phosphates and two non-identified P,P1-diesterified pyrophosphate compounds. Due to the presence of paramagnetic cations the resonances of these compounds can only be detected after repeated washing of the bacterial cells with a buffer, containing EDTA plus excess Mg2+. Washing with Mg2+-free EDTA buffer deteriorates the structural integrity of the membranes of Rps. sphaeroides. This is indicated by the appearance of an extra resonance peak in the spectra of these cells in a region where the phospholipids absorb and by a fivefold increase in proton permeability of the cytoplasmic membrane of Rps. sphaeroides under these conditions. Upon illumination of the cell suspension in the NMR tube the generation of a transmembrane pH gradient can be inferred from the shift in the resonances of extracellular and intracellular inorganic phosphate. Intracellular inorganic phosphate shows one homogeneous resonance peak upon illumination. This demonstrates that the mixing system, which has been developed for this application, functions efficiently. The magnitude of the light-dependent pH difference is 0.8 at the external pH 6. The width at half height of the internal inorganic phosphate peak is essentially independent of internal pH from pH 5--8, remains unchanged upon addition of uncoupler and is inversely proportional to the number of EDTA washings applied. These observations indicate that the inorganic phosphate NMR peak width is predominantly determined by the presence of a residual amount of paramagnetic cations, rather than by a broad distribution of internal pH values over the cells. Ionophores have an effect on the light-dependent pH-gradient in accordance with the chemiosmotic theory: valinomycin increases, and carbonylcyanide p-trifluoromethoxyphenylhydrazone decreases, the magnitude of this gradient.

Adenosine Triphosphate↗