Hisayuki Morii

Tokyo Medical and Dental University, Tokyo, Tokyo-to, Japan

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Publications (26)84.1 Total impact

  • Article: Infrared study of synthetic peptide analogues of the calcium-binding site III of troponin C: The role of helix F of an EF-hand motif.
    Masayuki Nara, Hisayuki Morii, Masaru Tanokura
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    ABSTRACT: The EF-hand motif (helix-loop-helix) is a Ca(2+) -binding domain that is common among many intracellular Ca(2+) -binding proteins. We applied Fourier-transform infrared spectroscopy to study the synthetic peptide analogues of site III of rabbit skeletal muscle troponin C (helix E-loop-helix F). The 17-residue peptides corresponding to loop-helix F (DRDADGYIDAEELAEIF), where one residue is substituted by the D-type amino acid, were investigated to disturb the α-helical conformation of helix F systematically. These D-type-substituted peptides showed no band at about 1555 cm(-1) even in the Ca(2+) -loaded state although the native peptide (L-type only) showed a band at about 1555 cm(-1) in the Ca(2+) -loaded state, which is assigned to the side-chain COO(-) group of Glu at the 12th position, serving as the ligand for Ca(2+) in the bidentate coordination mode. Therefore, helix F is vital to the interaction between the Ca(2+) and the side-chain COO(-) group of Glu at the 12th position. Implications of the COO(-) antisymmetric stretch and the amide-I' of the synthetic peptide analogues of the Ca(2+) -binding sites are discussed. © 2012 Wiley Periodicals, Inc. Biopolymers 99: 342-347, 2013.
    Biopolymers 05/2013; 99(5):342-7. · 2.87 Impact Factor
  • Article: Coordination to divalent cations by calcium-binding proteins studied by FTIR spectroscopy.
    Masayuki Nara, Hisayuki Morii, Masaru Tanokura
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    ABSTRACT: We review the FTIR spectroscopy of side-chain COO(-) groups of Ca(2+)-binding proteins: parvalbumins, bovine calmodulin, akazara scallop troponin C and related calcium binding proteins and peptide analogues. The COO(-) stretching vibration modes can be used to identify the coordination modes of COO(-) groups of Ca(2+)-binding proteins to metal ions: bidentate, unidentate, and pseudo-bridging. FTIR spectroscopy demonstrates that the coordination structure of Mg(2+) is distinctly different from that of Ca(2+) in the Ca(2+)-binding site in solution. The interpretation of COO(-) stretches is ensured on the basis of the spectra of calcium-binding peptide analogues. The implication of COO(-) stretches is discussed for Ca(2+)-binding proteins.
    Biochimica et Biophysica Acta 11/2012; · 4.66 Impact Factor
  • Article: Stem-forming regions that are essential for the amyloidogenesis of prion proteins.
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    ABSTRACT: Prion diseases represent fatal neurodegenerative disorders caused by the aggregation of prion proteins. With regard to the formation of the amyloidogenic cross-β-structure, the initial mechanism in the conversion to a β-structure is critically important. To explore the core regions forming a stem of the amyloid, we designed and prepared a series of peptides comprised of two native sequences linked by a turn-inducing dipeptide moiety and examined their ability to produce amyloids. A sequence alignment of the peptides bearing the ability to form amyloid structures revealed that paired strands consisting of VNITI (residues 180-184) and VTTTT (residues 189-193) are the core regions responsible for initiating the formation of cross-β-structures and for further ordered aggregation. In addition, most of the causative mutations responsible for inherited prion diseases were found to be located in these stem-forming regions on helix H2 and their counterpart on helix H3. Moreover, the volume effect of the nonstem domain, which contains ~200 residues, was deduced to be a determinant of the nature of the association such as oligomerization, because the stem-forming domain is only a small part of a prion protein. Taken together, we conclude that the mechanism underlying the initial stage of amyloidogenesis is the exposure of a newly formed intramolecular β-sheet to a solvent through the partial transition of a native structure from an α-helix to a β-structure. Our results also demonstrate that prion diseases caused by major prion proteins except the prions of some fungi such as yeast are inherent only in mammals, as evidenced by a comparison of the corresponding sequences to the stem-forming regions among different animals.
    Biochemistry 02/2012; 51(8):1566-76. · 3.42 Impact Factor
  • Article: Effect of glycosylation on cis/trans isomerization of prolines in IgA1-hinge peptide.
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    ABSTRACT: The hinge region of human immunoglobulin A1 (IgA1), connecting the Fab and Fc regions, is mostly composed of Ser, Thr, and Pro (VPSTPPTPSPSTPPTPSPS); hinge peptide (HP). O-Glycans are naturally attached on only particular five Ser/Thr residues in this region. NMR was employed for analysis of the structural changes in HP upon the glycosylation, especially focusing on the cis/trans isomerization of Pro residues. A series of HP containing (13)C,(15)N-labeled Pro residues were chemically synthesized and enzymatically glycosylated. The signals from cis and trans forms of the labeled Pro were identified by two-dimensional NMR spectroscopy. Cis/trans ratios of the Pro residues at the C-terminal side of the glycosylated Ser/Thr were reduced from 9-10% to 2-3% by the glycosylation. Thermodynamic analyses indicated that the decrease in the cis/trans ratio was enthalpy-driven. Hydrogen-deuterium exchange experiments and NOE-based structure determination revealed that the intraresidue hydrogen bonds between the amide group of GalNAc and carbonyl oxygen of the peptide backbone of GalNAc-Thr are formed in the major trans conformers, which is consistent with the thermodynamic parameters. These hydrogen bonds largely restrict the psi angle of the peptide backbone and, thereby, should make the trans conformation of the C-terminal Pro residue more stable than the cis conformation. Namely, it is predicted that the restricted psi angle causes interresidue steric hindrance for the cis conformation. The appropriate glycosylation of HP probably contributes to the decrease in the unfavorable variety of relative orientations between Fab and Fc in IgA1, through stabilizing the conformation of HP.
    Journal of the American Chemical Society 03/2010; 132(16):5548-9. · 9.91 Impact Factor
  • Article: Visible-light photocontrol of (E)/(Z) isomerization of the 4-(dimethylamino)azobenzene pseudo-nucleotide unit incorporated into an oligonucleotide and DNA hybridization in aqueous media.
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    ABSTRACT: We demonstrate significant photoresponsivity in aqueous media to visible light of pseudo-oligonucleotides possessing 4-(dimethylamino)azobenzene (4-DMAzo) side chains. The spectrum of the 4-DMAzo moiety during 436 nm light irradiation at pH >9 was clearly different from that of the all (E)-form, indicating the presence of the (Z)-form. Thermal (Z)-to-(E) recovery isomerization was faster at pH 9 (k(Z)(-E) = approximately 10(1) s(-1)) than at pH 11; however, addition of 50% ethanol significantly slowed the thermal recovery isomerization at pH 9 (k(Z)(-E) = approximately 2 s(-1)) and increased the magnitude of the spectral changes. Significant photoregulation of DNA hybridization by visible light was demonstrated under this condition.
    Nucleosides Nucleotides &amp Nucleic Acids 02/2009; 28(1):12-28. · 0.90 Impact Factor
  • Article: The dynein stalk head, the microtubule binding-domain of dynein: NMR assignment and ligand binding.
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    ABSTRACT: Dynein is a motor ATPase, and the C-terminal two-thirds of its heavy chain form a ring structure. One of protrudings from this ring structure is a stalk whose tip, the dynein stalk head (DSH), is thought to be the microtubule-binding domain. As a first step toward elucidating the functional mechanisms of DSH, we aimed at the NMR structural analysis of an isolated DSH from mouse cytoplasmic dynein. The DSH expressed in bacteria and purified was coprecipitated with microtubules, suggesting its proper folding. Chemical shifts of the DSH were obtained from NMR measurements, and backbone assignment identified 94% of the main-chain N-H signals. Secondary structural prediction programs showed that about 60% of the residues formed alpha-helices. A region with cationic residues K58 and R61 (and possibly R66 as well), and another with R86, K88, K90, and K91, were found to form alpha-helices. Both of these regions may be important in the formation of the DSH-binding site to a microtubule that has a low pI with a number of acidic residues. Two synthetic peptides containing the sequence of the alpha-helix 12 of beta-tubulin, considered to be important in binding to DSH, were investigated. Of these two peptides, the one with higher helix-formation propensity appeared to bind to DSH, since it precipitated with DSH in a nearly stoichiometric manner. This suggested that the alpha-helicity of this region would be important in its binding to DSH.
    Journal of Biomolecular NMR 07/2008; 41(2):89-96. · 3.61 Impact Factor
  • Article: Reversible and irreversible coiled coils in the stalk domain of ncd motor protein.
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    ABSTRACT: Ncd is a microtubule minus end-directed motor protein from Drosophila, a member of the kinesin-14 family, and an essential protein in mitosis and meiosis. Full-length ncd exists as a dimer via the formation of an alpha-helical coiled coil in its central stalk domain (P192-R346), which is thought to be one of the key regions for its motility. In our previous studies, however, none of the various synthetic polypeptide fragments (up to 46 residues) from the stalk domain formed a coiled coil. Herein, we have investigated the structural properties of the full-length ncd stalk domain using recombinant polypeptides together with shorter segments. These new fragments did form coiled coils as verified by far-UV circular dichroism (CD) spectroscopy and analytical ultracentrifugation, suggesting that a certain length of polypeptide would be required for dimer formation. Moreover, deletion mapping revealed that the cooperativity among the neighboring subdomains in the stalk domain is required for formation of the coiled coil. Interestingly, the intact stalk domain segments showed three-state transition in thermal unfolding measurements with CD, indicating the presence of two regions: (i) a coiled-coil region (P227-R306) that exhibits reversible denaturation at a lower temperature (20-30 degrees C) and (ii) a more rigid coiled-coil region (T307-E334) that exhibits irreversible denaturation at a high temperature (ca. 60 degrees C). These results imply that the N-terminal region of the stalk domain might be able to adopt both a coiled-coil conformation and a dissociated one, which might be relevant to the functions of ncd.
    Biochemistry 09/2007; 46(33):9523-32. · 3.42 Impact Factor
  • Article: Fourier transform infrared spectroscopic study on the Ca2+ -bound coordination structures of synthetic peptide analogues of the calcium-binding site III of troponin C.
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    ABSTRACT: The coordination structures of Ca(2+) ion bound to synthetic peptide analogues of the calcium-binding site III of rabbit skeletal muscle troponin C (TnC) were investigated by Fourier transform infrared (FTIR) spectroscopy. The region of the COO(-) antisymmetric stretching vibration provides information about the coordination modes of a COO(-) group to a metal ion. The 34-residue peptide corresponding to the EF hand motif (helix-loop-helix) showed a band at 1552 cm(-1) in the Ca(2+)-loaded state, indicating that the side-chain COO(-) group of Glu at the 12th position serves as a ligand for Ca(2+) in the bidentate coordination mode. On the other hand, the 13-residue peptide (Ac-DRDADGYIDAEEL-NH(2)) containing the Ca(2+)-binding site III (DRDADGYIDAEE) did not show such spectral patterns in the Ca(2+)-loaded state, meaning that shorter synthetic peptide corresponding to the site III has less or no affinity for Ca(2+). It was found that the 17-residue peptide (Ac-DRDADGYIDAEELAEIF-NH(2)) is the minimum peptide necessary for the interaction of side-chain COO(-)of Glu at the 12th position with Ca(2+) in the bidentate coordination mode. We discuss the relationship between the amino acid length of synthetic peptide analogues and the formation of Ca(2+)-bound coordination structure.
    Biopolymers 08/2006; 82(4):339-43. · 2.87 Impact Factor
  • Article: Interaction-based evaluation of the propensity for amyloid formation with cross-beta structure.
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    ABSTRACT: In order to reveal the requirements for amino acid sequences prone to form amyloid fibrils, a novel prediction method based on the original structural model of amyloids was developed. As a working hypothesis, two fundamental conditions were introduced into the design of the present system for the evaluation of the propensity for amyloidogenicity. The first of these two conditions was to ensure that the hydrophobic and hydrogen-bonding interactions between residues on neighboring antiparallel beta-strands were formed along a fibril axis. The other condition was that the hydrophobic interacting residues appeared on both faces of the protofibril, which gave line-matching interactions. Most peptides with sequences exhibiting high scores, as evaluated by this method, were found to easily form amyloids with the aid of a turn-inducing structure designed as a connection of two beta-strands. On the other hand, peptides with low-scoring native sequences and those modified by an internal residue-residue exchange (the latter yielding a null score) did not lead to amyloid formation. These data demonstrated the validity of this method for the prediction of amyloid structures. Moreover, the present study provided support for the proposed model of the essential structure associated with the above working hypothesis. The predicted high-scoring regions were in good agreement with the putative amyloid core regions reported thus far.
    Biochemical and Biophysical Research Communications 06/2006; 343(4):1262-71. · 2.48 Impact Factor
  • Article: Peripheral region for core cross-beta plays important role in amyloidogenicity.
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    ABSTRACT: The role of the peripheral sequence neighboring the core cross-beta region was investigated using a peptide library constructed with all possible combinations of Lys, Glu, Ser, and Leu at three residue positions (X1-X3) forming the N-terminal region linked to the amyloid core sequence of the barnase-derived segment (A4-K22). By means of CD spectra and thioflavin T binding assay for 64 peptides, not only the composition but also the sequence in the peripheral region were found to be responsible for amyloid formation. The preferences of amino acid residues in the peripheral region of the amyloid-forming peptides were in the order of Leu approximately SerGlu>Lys. A balance of positive and negative charges was found to be essential for amyloid formation, suggesting that the electrostatic interaction at the surface of the amyloid fibrils is relevant to their stability. On the basis of the maximum fluorescence wavelength of fibril-bound thioflavin T, the highly amyloidogenic peptides were classified into two classes, which exhibited the sequence preferences of (Leu, Ser/Glu, and Leu) and (Glu, Leu, and Ser) for the peripheral sequence (X1, X2, and X3). The former class can be rationally assigned to the structural model with deep grooves along the fibril axis. Thus, the peripheral sequence regulates the manner of molecular packing in the fibrils as well as the amyloidogenicity. In addition, the chains of the peripheral sequence are most likely to form thioflavin T binding sites.
    Biochemical and Biophysical Research Communications 05/2006; 342(3):808-16. · 2.48 Impact Factor
  • Article: Coiled coil in the stalk region of ncd motor protein is nonlocally sustained.
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    ABSTRACT: The dimeric structure of kinesin superfamily proteins plays an important role in their motile functions and characteristics. In this study, the coiled-coil-forming property of the stalk region (192-346) of Drosophila ncd, a C-terminal kinesin motor protein, was investigated by synthesizing various peptide fragments. The alpha helicity of a set of 46-residue peptides spanning the stalk region appeared too low to form a coiled-coil dimer, probably because of insufficient continuity of the hydrophobic residues at (a and d) core positions in amphipathic heptad repeats. On the other hand, several peptides with leucine residues introduced at core positions or with extensional sequences with high alpha helicity had an advantage in coiled-coil formation. When we analyzed the thermal and urea-induced unfolding of these dimeric peptides, we identified four domains having a relatively high potential to form coiled coils. Among them, three domains on the C-terminal side of the stalk region, i.e., (252-272), (276-330), and (336-346), were in the same heptad frame, although these potential coiled-coil domains were not self-sustaining individually. This is in sharp contrast to the fragment of human kinesin, (332-369), which has an extremely high tendency toward coiled-coil formation. One of the possible triggers for coiled-coil formation of the ncd stalk region may be the interaction between the motor domain and the C-terminal part of the stalk as previously revealed by X-ray crystallography. The residues, S331 and R335, seem to act as a breaking point for alpha-helix continuity. This would make the region (336-346), as the head-stalk joint, more flexible such as seen with a plus-end-directed kinesin, if this region had no interaction with the motor domain. These characteristic differences between ncd and kinesin suggest that the nonlocally sustained coiled coil of ncd is one of the factors important for minus-end-directed motility.
    Biochemistry 04/2006; 45(10):3315-24. · 3.42 Impact Factor
  • Article: Stalk region of kinesin-related protein Unc104 has moderate ability to form coiled-coil dimer.
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    ABSTRACT: Unc104/KIF1A, a kinesin family member, is reported to be monomeric in solution, though its polypeptide has regions that potentially form coiled coils. For a better understanding of the mechanism underlying Unc104/KIF1A's motility, it is important to evaluate the dimerization ability of this protein. The CD measurement of relevant segments of Caenorhabditis elegans Unc104 indicated that peptides having a common region (N358-K379) showed spectra characteristic to an alpha-helix. Dimerization by coiled-coil formation was confirmed by analytical ultracentrifugation. By analyzing the concentration dependence of the CD spectra, the monomer-dimer dissociation constant, Kd, of (N354-E388) was estimated to be about 5 microM, which is considerably larger than that of the corresponding segment of human kinesin (62 nM). Though its dimerization ability is rather moderate, Unc104/KIF1A could nonetheless dimerize and therefore could move by the same mechanism as human kinesin when the concentration of Unc104 is high due to, e.g., local crowding. This suggests that the motility could be controlled by the concentration of the motor protein.
    Biochemical and Biophysical Research Communications 12/2005; 337(3):868-74. · 2.48 Impact Factor
  • Article: Orientation of dye molecules in DNA-based films with chain alignment and judgment of their DNA-binding modes.
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    ABSTRACT: Novel composite films of chain-oriented DNA, which contain the DNA-binding dyes aligned in specific orientation, were successfully prepared by drying the solution under a horizontal magnetic field. Most of the dye-DNA composite films showed linear dichroism, as revealed by polarized ultraviolet-visible (UV-vis) spectroscopy. The intercalators, ethidium bromide and acridine orange, were fixed in chain-oriented DNA films in a similar binding manner as in solutions. Also, Hoechst 33258 and 4',6-diamidino-2-phenylindole were found to be aligned along the minor groove, even in the solid films. Thus, our new method of preparing dye-DNA composite films with chain orientation is useful for aligning small molecules, and it will provide views of the novel anisotropic materials expected in various application fields. We used this method to prepare composite DNA films with newly designed original compounds. Seven of nine dyes were judged to bind obviously to DNA as intercalators by polarized UV-vis spectroscopy. The DNA-binding manners were further analyzed by fluorescence anisotropy measurements. On the basis of the curves for the rotational angle dependence of the anisotropy, we were able to estimate the angles between the transition-dipole moments of dyes and the aligned chain axis of DNA. Interestingly, two original compounds were found to be in the tilted forms with regard to the plane of base pairs. We emphasize here that the method using aligned dye-DNA films is very convenient for identifying the binding modes of the compounds for double-stranded DNA.
    The Journal of Physical Chemistry B 09/2005; 109(32):15636-44. · 3.70 Impact Factor
  • Article: Removal of tightly bound ADP induces distinct structural changes of the two tryptophan-containing regions of the ncd motor domain.
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    ABSTRACT: ncd is a molecular motor belonging to the kinesin superfamily. In solution, it is a homo-dimer of a 700 amino acid polypeptide. The C-terminus of each polypeptide forms a globular domain of about 40 kDa, the motor domain with ATPase activity. The ATPase site of the motor domain of kinesin family members, including ncd, binds ADP tightly, the release of which is facilitated by microtubules during the mechanochemical ATPase cycle. Previously, we studied the spectroscopic characteristics of the ncd motor domain, focusing on interactions of the transition-moment-dipoles between ADP and aromatic amino acid side chains using circular dichroism (CD) spectroscopy. In the present study, we generated several ncd motor domain mutants. In each, a tryptophanyl or specific tyrosyl residue was mutated. We found that Trp370 and Tyr442, the latter of which stacks directly with the adenine moiety of bound ADP, caused the bound ADP to exhibit peculiar CD signals. In addition, fluorescence measurements revealed that Trp370, but not Trp473, was responsible for the emission intensity change depending on the presence or absence of bound ADP. This fluorescence result implies that the structural change induced at the ADP-binding site (on the release of the ADP) is transmitted to the region that includes Trp370, which is relatively close to the ADP-binding site but not in direct contact with the ADP-binding region. In contrast, Trp473 in the region that is in contact with the alpha-helical coiled coil stalk did not experience the structural changes caused on removal of ADP. The distinct behavior of these two tryptophanyl residues suggests that the ncd motor domain has a bifacial architecture made up of a relatively deformable side including the nucleotide binding site and a more rigid one.
    Journal of Biochemistry 08/2005; 138(1):95-104. · 2.37 Impact Factor
  • Article: Higher-order molecular packing in amyloid-like fibrils constructed with linear arrangements of hydrophobic and hydrogen-bonding side-chains.
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    ABSTRACT: Various mutants of the protein fragment, barnase module-1 (1-24) were investigated in order to reveal the structural principle of amyloid-like fibrils. By means of circular dichroism spectroscopy, X-ray diffraction, electron microscopy, and thioflavin T binding assay, we found that the molecules containing two beta-strands and an intervening turn structure are assembled to form a cross-beta structure. Stabilization by both the hydrophobic interactions and hydrogen bonding between the respective paired side-chains on the coupled beta-strands was essential for fibril formation. These two types of interaction can also arrange the corresponding residues in lines on both sheet surfaces of protofilaments with a cross-beta structure. This leads to the most probable fibril structure constructed with the line-matching interactions between protofilaments. Consideration of the geometrical symmetry resulted in our finding that a limited number of essential models for molecular packing in fibril structure are stable, which would rationally explain the occurrence of two or three morphologies from an identical molecular species. The ribbon-like fibrils exhibited striped texture along the axis, which was assigned to a stacked two-sheet repeat as a structural unit. The comprehensively proposed structural model, that is, the sheet-sheet interaction between left-handed cross-beta structures, results in a slightly right-handed twist of beta-sheet stacking, which reasonably elucidates the intrinsic sizes of the fibril width and its helical period along the fibril axis, as the bias in the orientation of the hydrogen-bonded beta-strand pair at the lateral edge is larger than that at the central protofilament.
    Journal of Molecular Biology 06/2005; 348(4):983-98. · 4.00 Impact Factor
  • Article: Annular self-assembly of DNA molecular chains occurring in natural dry process of diluted solutions.
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    ABSTRACT: The molecular orientation of DNA membranes, which were prepared by subjecting diluted solution of salmon sperm DNA to a natural drying process, was examined. X-ray diffraction and polarization microscopy revealed that the dried membranes have zonal structures. Each zone shows different features in molecular orientation. In the outer zones formed at the early stage in drying, DNA molecular chains were found to be aligned along the annular curve of the peripheral edge. Both the uneven thickness and disproportional molecular weight distribution in a membrane suggested that the radial flow transported DNA molecules to the edge and that they formed the accumulated phase. Above the critical concentration for the formation of liquid crystalline, the DNA chains would be aligned onto the preformed solid--liquid interface. The membranes with the highest birefringence were obtained from DNA samples with the relatively high molecular weight of around 29 kbp. In the innermost zone, on the other hand, the DNA molecules were radially oriented. This alignment can be attributed to the hydrodynamic effect caused by the rapid translation of the edge interface, which overcomes the Brownian motion of the chain segments. A transitive balance of physical effects was revealed in the dry process, which provided quite orthogonal molecular orientations in a single droplet.
    Biopolymers 03/2005; 77(3):163-72. · 2.87 Impact Factor
  • Article: Conformational changes in the antibody constant domains upon hapten-binding.
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    ABSTRACT: Bacterial proteins A and G (SpA and SpG) are immunoglobulin receptors that can be used as probes for monitoring change in the conformation of heavy chain constant (C(H)) domains. Interaction of anti-(4-hydroxy-3-nitrophenyl)acetyl (NP) antibody (Ab) with SpA and SpG were measured by isothermal titration calorimetry and surface plasmon resonance in order to address the question of whether hapten-binding induces a conformational change in the C(H) domain. The interactions of IgG2a or its enzymatic fragments with SpA were measured in the presence or absence of the hapten. Although binding of Fab and F(ab')2 fragments were not observed to free SpA, they did bind to immobilized SpA. In addition, the association constant (K(a)) for interaction of IgG2a with immobilized SpA was approximately 20-fold higher than that with free SpA. This was explained in terms of high avidity resulting from multivalent interaction between IgG2a and immobilized SpA on the chip. Interestingly, the hapten-binding weakened the interaction between the F(ab')2 fragment and SpA. Furthermore, approximately half of the IgG2a was incapable of binding to immobilized SpA in the presence of hapten. These results were explained using a model which assumed the formation of two kinds of SpA/IgG complexes; one through sites on F(ab')2 arms and the other through sites on the Fc region. The former type dissociated as a result of hapten-binding, as did the F(ab')2 fragment and suggested that a conformational change had occurred around the Fab arms, while the latter type did not dissociate because of the higher avidity of the Fc region. However, using a mutant SpA with a lower K(a) value for the interaction with IgG2a, it was shown that hapten-binding induced long range conformational changes in the Fc region of IgG2a. Similar evidence of conformational change upon hapten-binding was also obtained using SpG as a probe.
    Molecular Immunology 02/2005; 42(1):9-18. · 2.90 Impact Factor
  • Article: Judgment for DNA-binding modes of dye molecules by novel chain-aligned film method.
    [show abstract] [hide abstract]
    ABSTRACT: We have succeeded in preparation of novel composite films composed of chain-oriented DNA and the DNA-binding dyes aligned in specific orientation by drying the solution under a horizontal magnetic field. The dye-DNA composite films mostly showed linear dichroism, as revealed by polarized ultraviolet-visible spectroscopy (UV-VIS) and fluorescence anisotropy measurement. The intercalators such as ethidium bromide was fixed in chain-oriented DNA films in a similar binding manner as in solutions. Also, Hoechst 33258 was found to be aligned along the minor groove even in the solid films. In addition, by means of this film method, we could estimate the DNA-binding modes of newly designed original compounds. Here, we emphasize that the method using aligned dye-DNA films is very convenient for identifying the binding modes for double-stranded DNA.
    Nucleic Acids Symposium Series 02/2005;
  • Article: 10 residue folded peptide designed by segment statistics.
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    ABSTRACT: We have designed a peptide termed chignolin, consisting of only 10 amino acid residues (GYDPETGTWG), on the basis of statistics derived from more than 10,000 protein segments. The peptide folds into a unique structure in water and shows a cooperative thermal transition, both of which may be hallmarks of a protein. Also, the experimentally determined beta-hairpin structure was very close to what we had targeted. The performance of the short peptide not only implies that the methodology employed here can contribute toward development of novel techniques for protein design, but it also yields insights into the raison d'etre of an autonomous element involved in a natural protein. This is of interest for the pursuit of folding mechanisms and evolutionary processes of proteins.
    Structure 09/2004; 12(8):1507-18. · 6.35 Impact Factor
  • Source
    Article: Secondary structure analyses of protein films on gold surfaces by circular dichroism.
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    ABSTRACT: In order to analyze the secondary structures of protein molecules adsorbed on gold surfaces, circular dichroism (CD) spectra were measured and the secondary structure contents of protein ultra-thin films were estimated quantitatively. A disulfide group was introduced to cytochrome b(562) (cyt.b562), which is a water-soluble b-type heme protein. The cyt.b562 molecules self-assembled to form an ultra-thin protein film both on a gold substrate modified with 2,2(')-dithiodiacetic acid and on a bare gold surface. CD measurements were carried out both in solution and in air, and these results were compared. The protein denaturation was partially prevented, not only in solution but also in air, by both the modification of the substrate and the introduction of the anchor group to the protein molecule. The secondary structure contents of ultra-thin protein films on flat gold surfaces were observed for the first time both in solution and in air by CD spectra.
    Biochemical and Biophysical Research Communications 11/2003; 310(2):606-11. · 2.48 Impact Factor

Institutions

  • 2006–2013
    • Tokyo Medical and Dental University
      • • Department of Chemistry
      • • College of Liberal Arts and Sciences
      Tokyo, Tokyo-to, Japan
  • 2012
    • Kinki University
      Ōsaka-shi, Osaka-fu, Japan
  • 2005–2008
    • The University of Tokyo
      • • Faculty & Graduate School of Agriculture and Life Sceince
      • • Department of Applied Biological Chemistry
      Tokyo, Tokyo-to, Japan
    • National Institute for Materials Science
      Tsukuba, Ibaraki-ken, Japan
    • Tokyo University of Science
      • Department of Fire Science and Technology
      Tokyo, Tokyo-to, Japan
  • 2003–2006
    • National Institute of Advanced Industrial Science and Technology
      Ibaraki, Osaka-fu, Japan