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M Kainosho

Publications and source records attributed to M Kainosho.

At least 73 records · Page 4Linked to original sources
PubMed1995

Synthesis and NMR applications of isotopically labeled 2'-deoxynucleosides. Stereospecific deuteration of the C2' methylene in [ul-11 C/15N]deoxyadenosine.

Stereospecific deuteration of the C2' methylenes of 2'-deoxynucleosides together with 13C label has been found to open up various applications for structural studies of DNA oligomers in solution. Major problems in analyzing the structure and dynamics of larger DNA oligomers by NMR are associated with geminal proton pairs attached to the C2' and C5' of sugar moieties. We have employed, with a minor modification, existing synthetic routes to prepare stereospecific deuteration of the C2' methylene to prepare 13C/2H-doubly labeled nucleosides. For example, [ul-13C/15N] adenosine, which was prepared by microbial fermentation using [13C6]-glucose and [15N]-ammonium salt as precursors, was derived into (2'R)- and (2'S)-[ul-13C/15N;2'-2H1]-2'-deoxy-adenosines. Each of these multiply labeled nucleosides was then incorporated into a DNA dodecamer, 5'-d(CGCG AATTCGCG)-3', which was examined by various NMR techniques in order to evaluate the precision and accuracy of the NMR parameters obtained for the labeled moieties.

Base Sequence↗
PubMed1994

Preparation and heteronuclear 2D NMR spectroscopy of a DNA dodecamer containing a thymidine residue with a uniformly 13C-labeled deoxyribose ring.

[13C5]-2-Deoxy-D-ribose, synthesized from [13C6]-D-glucose (98% 13C), was coupled with thymine to give [1',2',3',4',5'-13C5]-thymidine (T) in an 18% overall yield. The thymidine was converted to the 3'-phosphoramidite derivative and was then incorporated into a dodecamer 5'-d(CGCGAATTCGCG)-3' by solid-phase DNA synthesis. Preparation of 0.24 mumole of the labeled dodecamer, which is sufficient for a single NMR sample, consumed only 25 mg of glucose. By virtue of the 13C labels, all of the 1H-1H vicinal coupling constants in the sugar moieties were accurately determined by HCCH-E.COSY.

Base Sequence↗
PubMed1993

Localisation of methionine residues in bacteriorhodopsin by carbonyl 13C-NMR with sequence-specific assignments.

High-resolution 13C-NMR experiments have been performed on bacteriorhodopsin biosynthetically labeled with carbonyl-13C amino acids and solubilized in the detergent dodecylmaltoside. 13C-NMR spectra showing good resolution were obtained in the case of labeled amino acids moderately represented in the BR sequence. For BR labeled with [13C]carbonyl methionine, several sequence-specific assignment could be performed by co-labeling with 15N amino acids or proteolysis. These assignments were used to obtain structural data on BR. Water-exposure of methionine side chains in the protein was assessed by studying, using NMR, their oxidation by hydrogen peroxide. Local secondary structure at the level of methionine residues was monitored through the effect of 1H-2H exchange on NMR spectra. It was concluded that Met32, Met68 and Met163 are peripheral while all 6 other methionine residues are deeply embedded within hydrophobic alpha-helices. These results confirm the current model of the BR folding and secondary structure.

Amino Acid Sequence↗
PubMed1993

Folding topology and DNA binding of the N-terminal fragment of Ada protein.

Three amino terminal fragments of Escherichia coli Ada protein (39 kDa) with different molecular masses (14 kDa, 16 kDa and 20 kDa) were prepared in large quantities from an E. coli strain harboring plasmids constructed for the overproduction of the truncated proteins. The three fragments can be methylated to an extent similar to that of the intact molecule. The methylated 16 kDa fragment specifically binds to the ada box on a DNA duplex. NMR analyses revealed that the 14 kDa fragment comprises two alpha-helices and a beta-sheet with parallel and anti-parallel mixed strands. A comparison of the 15N-1H HMQC spectra of the fragments has led to the conclusion that this tertiary structure within the 14 kDa fragment is retained in the larger 16 kDa and 20 kDa fragments.

Amino Acid Sequence↗
PubMed1993

Precise analyses of DNA structure by NMR.

Novel 1H NMR techniques were developed and applied to the analyses of the DNA structure. They distinguished the base proton signals of cytosine (uracil) from those of the other bases. Two dimensional experiments were also performed by using these techniques, and were found to be useful for signal assignments. Moreover, the (2'R)-[2'-2H]-labeled DNA 10-mer and 17-mer were synthesized to be used for the determination of precise structures. These stereoselective [2'-2H]-labeling made possible explicit stereospecific assignments and exact determination of the vicinal coupling constants, 3JHH, and thus the conformation of each deoxyribose ring was accurately determined.

Cytosine↗
PubMed1991

19F and 31P NMR spectroscopy of G protein alpha subunits. Mechanism of activation by Al3+ and F-.

19F and 31P NMR spectroscopy was used to study the mechanism of activation of the alpha subunits of guanine nucleotide-binding regulatory proteins (G proteins) by Al3+, Mg2+, and F-. 19F NMR spectra of solutions containing Al3+, Mg2+, and F- showed a characteristic F- peak at -10 ppm. Addition of the GDP-bound form of either of two G protein alpha subunits (G alpha) resulted in the appearance of an additional peak at -29 or -30 ppm. This peak was not observed with guanosine 5'-3-O-(thio)triphosphate-G alpha or with GDP alone. Titration of Al3+, Mg2+, and F- indicated that each molecule of G alpha binds 3-5 molecules of F- (Kd = 0.47 mM), a single molecule of Al3+ (Kd much less than 0.1 mM), and a single Mg2+ ion (Kd about 0.1 mM). Replacement of Mg2+ with Mn2+ caused a dramatic broadening of the NMR signal, indicating that the metal ion binds in proximity to the protein-bound F- (less than 1 nm). 31P NMR of GDP-G alpha showed peaks at -2 and -8.6 ppm, corresponding to the beta- and alpha-phosphoryl groups of GDP, respectively. Binding of Al3+, Mg2+, and F- caused an upfield shift of 6 ppm for the beta-phosphoryl signal with no change in the alpha-phosphoryl signal. These observations indicate that Mg2+.GDP.AlF3-5 mimics Mg2+.GTP in its capacity to activate G protein alpha subunits.

Aluminum↗
PubMed1991

Reductive cleavage and regeneration of the disulfide bonds in Streptomyces subtilisin inhibitor (SSI) as studied by the carbonyl 13C NMR resonances of cysteinyl residues.

Four enhanced carbonyl carbon resonances were observed when Streptomyces subtilisin inhibitor (SSI) was labeled by incorporating specifically labeled [1-13C]Cys. The 13C signals were assigned by the 15N, 13C double-labeling method along with site-specific mutagenesis. Changes in the spectrum of the labeled protein ([C]SSI) were induced by reducing the disulfide bonds with various amounts of dithiothreitol (DTT). The results indicate that, in the absence of denaturant, the Cys71-Cys101 disulfide bond of each SSI subunit can be reduced selectively. This disulfide bond, which is in the vicinity of the reactive site scissile bond Met73-Val74, is more accessible to solvent than the other disulfide bond, Cys35-Cys50, which is embedded in the interior of SSI. This half-reduced SSI had 65% of the inhibitory activity of native SSI and maintained a conformation similar to that of the fully oxidized SSI. Reoxidation of the half reduced-folded SSI by air regenerates fully active SSI which is indistinguishable with intact SSI by NMR. In the presence of 3 M guanidine hydrochloride (GuHCl), however, both disulfide bonds of each SSI subunit were readily reduced by DTT. The fully reduced-unfolded SSI spontaneously refolded into a native-like structure (fully reduced-folded state), as evidenced by the Cys carbonyl carbon chemical shifts, upon removing GuHCl and DTT from the reaction mixture. The time course of disulfide bond regeneration from this state by air oxidation was monitored by following the NMR spectral changes and the results indicated that the disulfide bond between Cys71 and Cys101 regenerates at a much faster rate than that between Cys35 and Cys50.

Bacterial Proteins↗
PubMed1989

Application of 13C nuclear magnetic resonance spectroscopy to molecular structural analyses of antibody molecules.

A 13C nuclear magnetic resonance study of a mouse anti-dansyl monoclonal antibody is reported. The antibody molecule was specifically labeled with [1-13C]methionine by growing hybridoma cells in serum-free medium. It was possible to observe all the carbonyl carbon resonances of the antibody. Fab and Fc fragments have been obtained from the antibody and used successfully for the assignment of each of the carbonyl resonances to either the Fab or Fc region. It has been shown that the spectrum of the intact antibody is simply those of Fab and Fc superimposed. It has also been shown that site specific assignments of carbonyl resonances can be made by means of a double labeling technique developed by Kainosho and coworkers.

Amino Acids↗
PubMed1988

Internal motion of a tryptophan residue in Streptomyces subtilisin inhibitor: deuterium nuclear magnetic resonance in solution.

Deuterium NMR spectroscopy was used to study internal motions of a deuterium-labeled single tryptophan (Trp) residue (per subunit) of Streptomyces subtilisin inhibitor (SSI) in solution. The free inhibitor with the five ring protons of the Trp replaced with deuterons showed a narrow resonance component (56 Hz) of about one-quarter of the total intensity, in addition to the broad resonance component (about 600 Hz) at 25 degrees C, showing that it exits in an equilibrium mixture of two conformers, in one of which the tryptophan side chain is highly mobile. In analogy to the two structures of SSI found in the crystal, these two conformers were attributed to the one in which the contact between the alpha-lobe and the beta-lobe of the subunit is tight and the other in which the same contact is loose. When SSI forms a complex with subtilisin BPN', the broad component becomes invisibly broad, but the narrow component increases with even further narrowing, suggesting that the binding to the enzyme favors the "loose" conformer over the "tight" conformer.

Bacterial Proteins↗
PubMed1987

Local structural features around the C-terminal segment of Streptomyces subtilisin inhibitor studied by carbonyl carbon nuclear magnetic resonances three phenylalanyl residues.

The carbonyl carbon NMR signals of the Phe residues in Streptomyces subtilisin inhibitor (SSI) were selectively observed for [F]SSI, in which all phenylalanines were uniformly labeled with [1-13C]Phe. The three enhanced resonances in the spectrum of [F]SSI were unambiguously assigned to the specific sites in the amino acid sequence by means of 15N,13C double-labeling techniques. Namely, the resonances at 174.9 and 172.6 ppm (in D2O, pH 7.3, 50 degrees C) showed the satellite peaks due to 13C-15N spin coupling in the spectra of [F,GS]SSI and [F,A]SSI, in which Ser/Gly and Ala residues were labeled with [15N]Gly/Ser and [15N]Ala, respectively, together with [1-13C]Phe. The carbonyl groups of Phe-97 and Phe-111 are involved in peptide bonds with the amino nitrogens of Ser-98 and Ala-112, respectively. These results clearly indicate that the signals at 174.5 and 172.6 ppm are due to Phe-97 and Phe-111, respectively. The signal at the lowest field (177.1 ppm) was thus assigned to the carboxyl carbon of the C-terminal Phe-113. The lifetimes of the amide hydrogens of the three Phe residues and their C-terminal-side neighbors (Ser-98 and Ala-112) were investigated by using the effect of deuterium-hydrogen exchange of amide on the line shapes (DEALS) for the Phe carbonyl carbon resonances. In this method, the NMR spectra of [F]SSI dissolved in 50% D2O (pH 7.3) were measured at various temperatures, and the line shape changes caused by deuteriation isotope shifts were analyzed.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1983

NMR studies on the new cluster complexes between 5'-nucleotides and uranyl ions. Structure and dynamic equilibria in alkaline aqueous solution.

Structures of the equimolar uranyl complexes of various 5'-nucleotides, such as AMP, GMP, UMP, and CMP, were extensively studied by high-field proton NMR spectroscopy. The unambiguous assignment of the proton resonances was established by correlating with the C-13 NMR spectrum of the complex from [N-15]AMP, which showed a doublet for the C-1' carbon signal due to the spin coupling with N-15 (N-9). Uranyl-nucleotide complexes were found to be the mixture of several oligomeric species having a common structural unit. The primary coordination sites of the uranyl ion were phosphate and 3'-hydroxyl oxygens, but no interaction was observed for the bases. The major oligomer at a high pH (above 11) was a cage-like octamer, and two isomeric cyclic tetramers predominated at a lower pH (below 10).

Hydrogen-Ion Concentration↗
PubMed1982

A 15N-NMR study on ribonuclease T1-guanylic acid complex.

Ribonuclease T1 is highly specific for the guanylic acid residue in polyribonucleotides. To clarify the origin of the substrate specificity, the interaction sites of guanylic acid with ribonuclease T1 were investigated by the use of 15N-NMR. 95% 15N-enriched guanosine-3'-phosphate was prepared and mixed with purified ribonuclease T1. 15N-NMR spectra of the mixtures at different concentrations were obtained and compared with that of the 15N-enriched substrate alone. Upon complex formation, a 15N signal assigned to the amino group nitrogen at position 2 of guanine shifted and was significantly broadened, suggesting a strong interaction with the enzyme through the amino group. This observation is consistent with the results of studies on the substrate specificity of chemical modification. Nuclear Overhauser effects of signals assigned to N-7 and N-3 were also changed, but not shift was observed. The observations do not support the occurrence of protonation at N-7 upon complex formation, which was previously proposed.

Guanine Nucleotides↗
PubMed1982

NMR studies of base-pairing in 15N-labeled ribotetranucleotide GGCUp.

95% N-15 enriched ribotetranucleotide GGCUp was prepared. Its aqueous solution gives three imino-proton resonances at 10.6, 12.0 and 13.6 ppm. The peak at 10.6 ppm split by N-15 into a doublet with coupling constant 90 Hz. On the preirradiation at this peak, the intensity of the 12.0 ppm peak decreased and the peak at 13.6 ppm remained unchanged. Therefore the 10.6 ppm peak was unambiguously assigned to the G imino proton and the 12.0 ppm peak to the U imino proton in the G:U base pair. By raising temperature the former two peaks coalesced at around 25 degrees C, while the signal of the G imino proton in the G:C pair was observed up to 35 degrees C. The G:U base pair seems to be disrupted first, then the break of the G:C pair is followed. Temperature dependences of the CH proton, N-15 and P-31 nuclei resonances were also measured.

Kinetics↗