Hajime Mita

Roles of a short connecting disulfide bond in the stability and function of psychrophilic Shewanella violacea cytochrome c 5

Cys-59 and Cys-62, forming a disulfide bond in the four-residue loop of Shewanella violacea cytochrome c5 (SV cytc5), contribute to protein stability but not to redox function. These Cys residues were substituted with Ala in SV cytc5, and the structural and functional properties of the resulting C59A/C62A variant were determined and compared with those of the wild-type. The variant had similar features to those of the wild-type in absorption, circular dichroic, and paramagnetic 1H NMR spectra. In addition, the redox potentials of the wild-type and variant were essentially the same, indicating that removal of the disulfide bond from SV cytc5 does not affect the redox function generated in the vicinity of heme. However, calorimetric analysis of the wild-type and variant showed that the mutations caused a drastic decrease in the protein stability through enthalpy, but not entropy. Four residues are encompassed by the SV cytc5 disulfide bond, which is the shortest one that has been proved to affect protein stability. The protein stability of SV cytc5 can be controlled without changing the redox function, providing a new strategy for regulating the stability and function of cytochrome c.

Chirality Emergence in Thin Solid Films of Amino Acids by Polarized Light from Synchrotron Radiation and Free Electron Laser

One of the most attractive hypothesis for the origin of homochirality in terrestrial bioorganic compounds is that a kind of “chiral impulse” as an asymmetric excitation source induced asymmetric reactions on the surfaces of such materials such as meteorites or interstellar dusts prior to the existence of terrestrial life (Cosmic Scenario). To experimentally introduce chiral structure into racemic films of amino acids (alanine, phenylalanine, isovaline, etc.), we irradiated them with linearly polarized light (LPL) from synchrotron radiation and circularly polarized light (CPL) from a free electron laser. After the irradiation, we evaluated optical anisotropy by measuring the circular dichroism (CD) spectra and verified that new Cotton peaks appeared at almost the same peak position as those of the corresponding non-racemic amino acid films. With LPL irradiation, two-dimensional anisotropic structure expressed as linear dichroism and/or linear birefringence was introduced into the racemic films. With CPL irradiation, the signs of the Cotton peaks exhibit symmetrical structure corresponding to the direction of CPL rotation. This indicates that some kinds of chiral structure were introduced into the racemic film. The CD spectra after CPL irradiation suggest the chiral structure should be derived from not only preferential photolysis but also from photolysis-induced molecular structural change. These results suggest that circularly polarized light sources in space could be associated with the origin of terrestrial homochirality; that is, they would be effective asymmetric exciting sources introducing chiral structures into bio-organic molecules or complex organic compounds.

NMR investigation of the heme electronic structure in deoxymyoglobin possessing a fluorinated heme

The heme electronic structures of deoxymyoglobins (deoxy-Mbs) reconstituted with 13,17-bis(2-carboxylatoethyl)-3,8-diethyl-2,12,18-trimethyl-7-(trifluoromethyl)porphyrinatoiron(III) (7-PF), 13,17-bis(2-carboxylatoethyl)-3,7-difluoro-2,8,12,18-tetramethylporphyrinatoiron(III) (3,7-DF), and 13,17-bis(2-carboxylatoethyl)-3,8-diethyl-2-fluoro-7,12,18-trimethylporphyrinatoiron(III) (2-MF) have been characterized by 1H and 19F NMR. The analysis of heme methyl proton shift patterns of the hemes in their bis-cyano forms demonstrated that, owing to the substitution of a strongly electron-withdrawing perfluoromethyl group, CF3, to porphyrin, the porphyrin π-system of 7-PF is more significantly distorted from four-fold symmetry than those of the ring-fluorinated hemes, 3,7-DF and 2-MF. The presence of the heme orientation disorder resulted in the observation of the two well-resolved 19F signals in the spectra of deoxy-Mbs possessing 7-PF and 2-MF. The 19F signals of deoxy-Mb possessing 7-PF exhibited a relatively large difference in paramagnetic shift (~30xa0ppm), despite their small paramagnetic shifts (~30xa0ppm), supporting the significant contribution of a π spin delocalization mechanism in this Mb due to the d-electron configuration derived from the 5E ground state. On the other hand, 19F signals of deoxy-Mbs with 3,7-DF as well as 2-MF exhibited large paramagnetic shifts (~250xa0ppm) with a relatively small difference in the paramagnetic shift (~20xa0ppm), indicating the predominant contribution of spin delocalization, due to a d-electron configuration derived from the 5B2 ground state. These results demonstrate for the first time that the relative contributions of the orbital ground states derived from 5E and 5B2 states to the heme electronic structure in deoxy-Mb are affected by the distortion of the porphyrin π-system exerted by chemical properties of the heme peripheral side-chains.

Heme Is Not Required for Aquifex aeolicus Cytochrome c 555 Polypeptide Folding

In cytochrome c, it has been supposed that heme must bind to the apo polypeptide for structure formation. We constructed a C12A/C15A variant of hyperthermophilic Aquifex aeolicus cytochrome c 555 (AA c 555) in which the covalently heme-binding Cys residues were replaced by Ala, and characterized its molecular features. The apo C12A/C15A variant had almost the same helical content as holo AA c 555, and spontaneously incorporated heme in vitro with no helical content change. These results suggest that the apo AA c 555 polypeptide is intrinsically structured without heme binding, this being the first case of a cytochrome c polypeptide. This finding provides a new suggestion as to cytochrome c formation, that heme is not necessarily required for cytochrome c polypeptide folding.

Effects of axial methionine coordination on the in-plane asymmetry of the heme electronic structure of cytochrome c.

The paramagnetic susceptibility (χ) tensors of the oxidized forms of thermophile Hydrogenobacter thermophilus cytochrome c552 (Ht cyt c552) and a quintuple mutant (F7A/V13xa0M/F34Y/E43Y/V78I; qm) of mesophile Pseudomonas aeruginosa cytochrome c551 (Pa cyt c551) have been determined on the basis of the redox-dependent 1H NMR shift changes of the main-chain NH and CαH proton resonances of non-coordinated amino acid residues and the NMR structures of the reduced forms of the corresponding proteins (J. Hasegawa, T. Yoshida, T. Yamazaki, Y. Sambongi, Y. Yu, Y. Igarashi, T. Kodama, K. Yamazaki, Y. Kyogoku, Y. Kobayashi (1998) Biochemistry 37:9641–9649; J. Hasegawa, S. Uchiyama, Y. Tanimoto, M. Mizutani, Y. Kobayashi, Y. Sambongi,Y. Igarashi (2000) J Biol Chem 275:37824–37828). From the χ tensors determined, we obtained the contact shifts for heme methyl proton resonances, which provided the heme electronic structures of the oxidized forms of Ht cyt c552 and qm. We also characterized the heme electronic structure of the cyanide adducts of the proteins, where the axial Met was replaced by an exogenous cyanide ion, through the analysis of 1H NMR spectra. The results indicated that the heme electronic structures of both the proteins in their oxidized forms with axial His and Met coordination are largely different to each other, while those in their cyanide adducts are similar to each other. These results demonstrated that the orientation of the axial Met sulfur lone pair, with respect to heme, predominantly contributes to the spin delocalization into the porphyrin-π system of heme in the oxidized proteins with axial His and Met coordination.

A new pathway to aspartic acid from urea and maleic acid affected by ultraviolet light.

The photochemistry of a mixture of ureaand maleic acid, which are thought to have been widelypresent on the primitive Earth, was studied in order toexamine a possibility of the formation of amino acids. When an aqueous solution of urea and maleic acid wasirradiated with an ultraviolet light of wavelength 172 nm,urea was revealed to be rather resistant to photochemicaldecomposition. In contrast, maleic acid was completelydecomposed within 4 h, reflecting the reactivity of a C-Cdouble bond in the molecule. In the reaction mixture, 2-isoureidosuccinic acid was detected. The acid wasconsidered to be formed by addition of an isoureido radicalwhich had been produced from urea by the action of ahydroxyl radical, to a C-C double bond of maleic acid. Theisoureido group of the product was revealed to undergothermal rearrangement to afford 2-ureidosuccinic acid (N-carbamoylaspartic acid). The result suggested a novelpathway leading to the formation of aspartic acid from non-amino acid precursors, possibly effected by UV-light on theprimitive Earth. The formation of ureidocarboxylic acidsis of another significance, since they are capable ofundergoing thermal polymerization, resulting in formationof polyamino acids.

Correlation between the Stability and Redox Potential of Three Homologous Cytochromes c from Two Thermophiles and One Mesophile

The stability of the oxidized and reduced forms of three homologous cytochromes c from two thermophiles and one mesophile was systematically monitored by means of Soret absorption measurements in the presence of various concentrations of a denaturant, guanidine thiocyanate, at pH 7.0 at 25 °C. Thermophilic Hydrogenobacter thermophilus cytochrome c 552 was the most stable in both redox states, followed by moderately thermophilic Hydrogenophilus thermoluteolus cytochrome c 552, and then mesophilic Pseudomonas aeruginosa cytochrome c 551. Further stability and electrochemical analysis of the three proteins and the reciprocal variants, which exhibited a different hydrophobic interaction with the heme, showed that the one with the higher stability in both redox states had the lower redox potential. Consequently, these cytochromes c probably adapted to the cellular environments of the original bacteria with correlated stability and redox potential constraints, which are in part regulated by the hydrophobicity around the heme.

α-Aminoisobutyric Acid and Isovaline in Tokyo Bay Sediments

Abstract Two nonprotein amino acids, 2-amino-2-methylpropionic acid (α-aminoisobutyric acid, αAiBA) and 2-amino-2-methylbutanoic acid (isovaline, iVal) were found in modern Tokyo bay sediments together with several protein amino acids. Concentrations of the two nonprotein amino acids were approximately 1 nmol per g of dry sediment, and the protein amino acids were several hundred to slightly over one thousand nmol per g. iVal was found to be nearly racemic, whereas the protein amino acids were predominantly in the l -form. We do not consider the two nonprotein amino acids to be of extraterrestrial origin as suggested by the study of the Cretaceous/Tertiary (K/T) boundary sediments at Stevns Klint ( Zhao and Bada 1989 ) and propose a terrestrial origin. The source of the two nonprotein amino acids is not biological because the iVal is racemic. They may come from industrial waste water containing C-5 substituted hydantoins which then hydrolyzed to give αAiBA and racemic iVal.

Characterization of dicarboxylic acids in the Cretaceous/Tertiary boundary sediments at Kawaruppu, Hokkaido, Japan, and comparison with those of carbonaceous chondrites

Abstract Twenty-seven C 2 to C 9 dicarboxylic acids were identified in the Cretaceous/Tertiary (K/T) boundary sediments at Kawaruppu, Hokkaido, Japan. These dicarboxylic acids included normal, branched, and unsaturated forms. Their concentrations were lowest (17, 0.40, and 0.71 nmol g −1 for normal, branched, and unsaturated, respectively) at the lowest horizon (0–0.8 cm) of the boundary claystone, reflecting the minimal biomass production due to the massive extinction of organisms at the boundary. However, the concentrations were higher at the other horizons (0.8–13.7 cm) within the boundary claystone than above (40–495 cm) or below (−395–0 cm) it. In general, the normal dicarboxylic acids showed a roughly logarithmic decrease in concentration with increasing carbon number. Only methylsuccinic acid among the branched dicarboxylic acids could be shown to be racemic, because only in this case was enough material present in the sediments for analysis. Unsaturated dicarboxylic acids showed an apparent cis -form predominance over trans with C 4 and C 5 isomers. The logarithmic decrease, the presence of racemic methyl succinic acid, and the cis -form predominance can be explained as a result of the 65-million-year diagenesis of the sediments. These characteristics were compared with those found in the Murchison and Yamato-791198 carbonaceous chondrites (Shimoyama and Shigematsu, 1994) in order to seek evidence for a contribution of dicarboxylic acid(s) of extraterrestrial origin to the K/T boundary sediments at Kawaruppu; however, the observed dicarboxylic acids in the sediments could not be attributed to an extraterrestrial origin.

2-Ethyl-3-methylmaleimide in Tokyo Bay Sediments Providing the First Evidence for its Formation from Chlorophylls in the Present Photic and Oxygenic Zone

Tokyo Bay bottom sediments were analyzed for 2-ethyl-3-methylmaleimide, a degradation product of chlorophylls, which has been detected in ancient sediments. It was found in all sediments examined in concentrations of about 1 to 15 nmol/g- of dried sediment, and it was shown to be preserved for 100 years in the sediments. Its depth distribution agreed with that of the reported total organic carbon content of the sediments, reflecting a change in primary productivity. We concluded that this maleimide was produced under photic and oxygenic conditions in nature before the incorporation of photosynthesizing organisms into sediments.