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A phosphoramidite building block of the T(6-4)C photoproduct was synthesized. One of the differences from T(6-4)T was formation of cytosine hydrates by UV irradiation, and the other was acylation of the amino function with the capping reagent. The capping step was omitted to improve the yield of the desired oligonucleotides. Characterization of the (6-4) photolyase using one of the oligonucleotides revealed that this enzyme restores the pyrimidines in T(6-4)C to their original structures.

Protein deamidation, the hydrolysis of side chain amido groups of protein-bound glutaminyl or asparaginyl residues to release ammonia, has received focused attention especially in food industries since protein deamidation is regarded as a promising method to improve functional properties of food proteins. Deamidation generally decreases an isoelectric point of proteins due to increase in number of negatively charged carboxyl groups and enhances protein solubility. In addition, deamidation leads to alteration of the tertiary structures of proteins with an improved amphiphilic character that is useful as an emulsifier or a foaming agent. Therefore, deamidation of food proteins have been investigated by various methods including mild acid treatment, anion-catalyzed deamidation, dry heating under mild alkaline conditions, and thermal treatment. Although deamidation by these treatments improved protein functionalities, there were undesired side-effects, such as concomitant peptide bond cleavages, that were unavoidably brought about by the chemical/ physical treatments. Therefore, enzymatic methods have advantages due to their selectivity and mild treatments. The possibilities of the use of transglutaminases, peptidoglutaminases, and proteases have been explored for this purpose. These enzymes, however, are not suitable because the primary catalytic reactions of transglutaminases and proteases are not deamidation itself, and primary substrates of peptidoglutaminases are not proteins. Protein-glutaminase (PG) is an enzyme produced from the microorganism Chryseobacterium proteolyticum strain 9670 (Yamaguchi et al. 2001). PG catalyzes only the deamidation of the side chain amido group of protein-bound glutaminyl residues to release ammonia without catalyzing the transglutamination and hydrolysis of asparaginyl residues or producing other undesirable changes in protein structures. PG is a monomeric single polypeptide with pI = 10.0 and a molecular weight of 19,860 and is synthesized as a prepro-form, containing a 21-amino-acid signal polypeptide, a 114-amino acid pro-region, and a sequence for the mature enzyme. PG with the pro-region (pro-PG) has no enzymatic activities, but when pro-PG is removed by an extracellular protease, an active enzyme is produced in C. proteolyticum. However, the amount of PG produced by C. proteolyticum is too small to be used for industrial application that limits the application of PG to deamidation of food proteins. Recently, we have constructed the high expression system of PG with Corynebacterium glutamicum, which enables us to prepare an amount of stable-isotope labeled PG for NMR experiments (Kikuchi et al. 2009). Here, we report the solution structure of mature PG determined by NMR and discuss the catalytic mechanism of PG on the structural basis.

The utility of a liquid chromatography mass spectrometry (LC-MS) method, using a pentafluorophenylpropyl (PFPP) bonded silica, was demonstrated in a metabolomics study of fermented food samples. Our LC-MS method was applied to Japanese fermented food (miso) of different stages of ripeness. The data acquired were evaluated by principal component analysis (PCA). The score plots indicated that the miso samples could be approximately classified into three groups, based on the stage of miso ripeness. The loading plots indicated that the ions responsible for group separation included not only amino acids and citric acid but also Amadori compounds. On the other hand, the miso samples were also analyzed by a conventional LC-MS method using an octadecyl (C(18)) column for comparison. The group separation of score plots from the conventional method was less clear than that from our method. The advantage of our LC-MS method is due to the different retention properties of the PFPP column and the C(18) column with hydrophilic compounds. Our LC-MS method will be useful for the metabolic profiling of fermented food samples.

The XPC–HR23B complex, a mammalian factor specifically involved in global genomic nucleotide excision repair (NER) has been shown to bind various forms of damaged DNA and initiate DNA repair in cell-free reactions. To characterize the binding specificity of this factor in more detail, a method based on immunoprecipitation was developed to assess the relative affinity of XPC–HR23B for defined lesions on DNA. Here we show that XPC–HR23B preferentially binds to UV-induced (6-4) photoproducts (6-4PPs) as well as to cholesterol, but not to the cyclobutane pyrimidine dimer (CPD), 8-oxoguanine (8-oxo-G), O6-methylguanine (O6-Me-G), or a single mismatch. Human whole cell extracts could efficiently excise 6-4PPs and cholesterol in an XPC–HR23B-dependent manner, but not 8-oxo-G, O6-Me-G or mismatches. Thus, there was good correlation between the binding specificity of XPC–HR23B for certain types of lesion and the ability of human cell extracts to excise these lesions, supporting the model that XPC–HR23B initiates global genomic NER. Although, XPC–HR23B does not preferentially bind to CPDs, the excision of CPDs in human whole cell extracts was found to be absolutely dependent on XPC–HR23B, in agreement with the in vivo observation that CPDs are not removed from the global genome in XP-C mutant cells. These results suggest that, in addition to the excision repair pathway initiated by XPC–HR23B, there exists another sub-pathway for the global genomic NER that still requires XPC–HR23B but is not initiated by XPC–HR23B. Possible mechanisms will be discussed.

The reaction mechanism of Xenopus (6-4) photolyase was investigated using several mutant enzymes. In the active site, which is homologous between the cis,syn-cyclobutane pyrimidine dimer and (6-4) photolyases, four amino acid residues that are specific to (6-4) photolyase, Gln(288), His(354), Leu(355), and His(358), and two conserved tryptophans, Trp(291) and Trp(398), were substituted with alanine. Only the L355A mutant had a lower affinity for the substrate, which suggested a hydrophobic interaction with the (6-4) photoproduct. Both the H354A and H358A mutations resulted in an almost complete loss of the repair activity, although the Trp(291) and Trp(398) mutants retained some activity. Taking the pH profile of the (6-4) photolyase reaction into consideration with this observation, we propose a mechanism in which these histidines catalyze the formation of the four-membered ring intermediate in the repair process of this enzyme. When deuterium oxide was used as a solvent, the repair activity was decreased. The proton transfer shown by this isotope effect supports the proposed mechanism. The substrate binding and the reaction mechanism are discussed in detail using a molecular model.

DNA recognition by the human UV-damaged DNA-binding (UV-DDB) protein was characterized. By circular permutation analyses, DNA duplexes containing the (6-4) photoproduct and the abasic site analog were found to be bent at angles of 54 degrees and 57 degrees, respectively, when they formed a complex with this protein. Although kinked NMR structures have been reported, fluorescence resonance energy transfer experiments revealed that these duplexes had no intrinsic bend. These results suggest that the UV-DDB protein binds DNA that can be bent easily at the above angle.

The early stage products of the Maillard reaction of egg white lysozyme with D-glucose were studied. Incubation with D-glucose at 50 degrees C for 20 days caused reaction on the Lys and Arg residues of lysozyme as follows: all of the six Lys residues and 10 of the 11 Arg residues in lysozyme reacted with D-glucose; Arg 61 did not react with D-glucose. The Lys residues reacted with D-glucose with 1 mol of dehydration per mole of residue, and the Arg residues reacted with 2 mol of dehydration per mole of residue. The major constituent of the Amadori product with the epsilon-amino group of the Lys residue and the D-glucose was found to be the beta-pyranose form. The structure of the early stage product of the Maillard reaction of a protein with a sugar is the same as that of an amino acid with a sugar.

A phosphoramidite building block of the T(6-4)C photoproduct was synthesized. One of the differences from T(6-4)T was formation of cytosine hydrates by UV irradiation, and the other was acylation of the amino function with the capping reagent. The capping step was omitted to improve the yield of the desired oligonucleotides. Characterization of the (6-4) photolyase using one of the oligonucleotides revealed that this enzyme restores the pyrimidines in T(6-4)C to their original structures.

In the solid-phase synthesis of oligonucleotides containing the pyrimidine(6-4)pyrimidone photoproduct using a dinucleotide building block, considerable amounts of by-products were found as the chain length increased. The by-products were the major product when a 49mer was synthesized on a 40 nmol scale. It was assumed that these by-products were formed by the coupling of phosphoramidites with the N3 imino function of the 5' component of the (6-4) photoproduct. We examined imidazolium triflate and benzimidazolium triflate to find an alternative activator for DNA synthesis. Imidazolium triflate prevented by-product formation to some extent, but the coupling yields were low. Benzimidazolium triflate was comparable to tetrazole in coupling efficiency and reduced by-product formation to a great extent, without modification of the synthesizer program. The obtained 49mer was used to detect proteins that recognize UV-damaged DNA in HeLa cell extracts. Two major protein-DNA complexes were found when a 49mer duplex was used as probe, while a 30mer duplex failed to detect one of them. This application showed the usefulness of long chain 'damaged' oligonucleotides in biochemical studies.

Monellin, an intensely sweet protein and a non-sweet analog in which the AspB7 in monellin has been replaced with AbuB7 were studied by NMR. The results of our investigations show that the 3-dimensional structure of these two proteins are very similar indicating that the lack of the β-carboxyl group in the AbuB7 analog is responsible for the loss of sweet potency. Selectively labeled monellin was prepared by solid-phase peptide synthesis by incorporating 15N-labeled amino acids into 10 key positions including AspB7. The internal mobility of these 10 key residues in monellin was estimated by the method of model-free analyses and our NMR studies show that AspB7 is the most flexible of these 10 residues. The flexibility of the AspB7 side chain may be important for receptor binding.

MALDI imaging mass spectrometry (IMS) provides information about the spatial distribution of metabolites within thin slices of tissue, and has been used to elucidate complex phenotypes under various physiological conditions. Previously, our group reported distinct spatial distribution of a variety of metabolites in experimental model of hepatic micrometastasis of the solid tumor. However the metabolic properties in tumor and host tissues are not fully characterized, because of difficulty in visualizing most amino acids, due to their lower ionization efficiency. Here, by using of p-N,N,N-trimethylammonioanily N’-hydroxysuccinimidyl carbamate iodide (TAHS) as a derivatizing reagent, we have successfully developed the method for the detection of various amino acids simultaneously by MALDI-MS on tissue section. We prepared liver section from hepatic metastasis model of human colon cancer, and then performed MALDI-IMS. To compare the signal intensities of amino acids among the different sections, we normalized the MALDI-IMS data with the quantified value of each amino acid obtained from capillary electrophoresis-mass spectrometry. The result indicated the amount of glycine, phenylalanine, leucine, glutamate, and glutamine were significantly elevated in metastatic foci compared to liver parenchyma. Other metabolites such as ATP and glutathione also accumulated in metastatic foci, and these results suggested that increased amino acid pool were required to maintain ATP and GSH levels in tumor. In conclusion, we have demonstrated that novel imaging technique by using of IMS combined with on-tissue TAHS derivatization enables the visualization of amino acid distribution in tissue. The current method could be powerful tool to elucidate the mechanism for metabolic changes of cancer disease in vivo. Citation Format: Sakino Toue, Yuki Sugiura, Akiko Kubo, Mitsuyo Ohmura, Sachise Karakawa, Toshimi Mizukoshi, Junya Yoneda, Hiroshi Miyano, Yasushi Noguchi, Tsuyoshi Kobayashi, Yasuaki Kabe, Makoto Suematsu. Accumulation of amino acids in metastatic foci of human colon cancer xenografts revealed by newly developed method for imaging mass spectrometry of amino acids. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 719. doi:10.1158/1538-7445.AM2013-719

Nine analogues of methyl acarviosin (1), the core structure of acarbose and its homologues, the 6-hydroxy-(2), 6-azido-(3), 6-amino- (4), 6-acetamido-(5), 6-methoxy-(6), 6-hydroxy-2-O-methyl-(8), and 6-hydroxy-3-O-methyl derivatives (9), including the 5-methoxycarbonyl analogue (7) and 3,6-anhydro derivative (10) of 2, were synthesized by chemical modification of the sugar part of 2 derived by condensation of methyl 3,4-anhydro-alpha-D-galactopyranoside (17) and 4,7:5,6-di-O-isopropylidenevalienamine (26) or by direct coupling between 26 and the 6-substituted methyl 3,4-anhydro-alpha-D-galactopyranoside derivatives. Compounds 2 and 8 show notable inhibitory activity against yeast alpha-D-glucosidase almost comparable to that of 1. Introduction of a polar substituent at C-6 of 1 decreases the inhibitory activity. Interestingly, inversion of the conformation of the sugar part of 1 by introduction of the 3,6-anhydro bridge elicits almost no effect on the inhibitory activity.

In addition to the synthesis of 2′-deoxy[5′-13C]ribonucleosides (6) via the D-[5-13C]ribose derivative (4), the construction of the corresponding dodecanucleotide with the Dickerson's sequence and its HMQC-NOESY NMR analysis are described.

Compound 3a has been shown to possess stronger inhibitory activity against α-glucosidase than methyl acarviosin 1.