Instituto de Investigaciones Químicas

KEGG (https://www.kegg.jp/) is a database resource for representation and analysis of biological systems. Pathway maps are the primary dataset in KEGG representing systemic functions of the cell and the organism in terms of molecular interaction and reaction networks. The KEGG Orthology (KO) system is a mechanism for linking genes and proteins to pathway maps and other molecular networks. Each KO is a generic gene identifier and each pathway map is created as a network of KO nodes. This architecture enables KEGG pathway mapping to uncover systemic features from KO assigned genomes and metagenomes. Additional roles of KOs include characterization of conserved genes and conserved units of genes in organism groups, which can be done by taxonomy mapping. A new tool has been developed for identifying conserved gene orders in chromosomes, in which gene orders are treated as sequences of KOs. Furthermore, a new dataset called VOG (virus ortholog group) is computationally generated from virus proteins and expanded to proteins of cellular organisms, allowing gene orders to be compared as VOG sequences as well. Together with these datasets and analysis tools, new types of pathway maps are being developed to present a global view of biological processes involving multiple organism groups.

SUMMARY: KofamKOALA is a web server to assign KEGG Orthologs (KOs) to protein sequences by homology search against a database of profile hidden Markov models (KOfam) with pre-computed adaptive score thresholds. KofamKOALA is faster than existing KO assignment tools with its accuracy being comparable to the best performing tools. Function annotation by KofamKOALA helps linking genes to KEGG resources such as the KEGG pathway maps and facilitates molecular network reconstruction. AVAILABILITY AND IMPLEMENTATION: KofamKOALA, KofamScan and KOfam are freely available from GenomeNet (https://www.genome.jp/tools/kofamkoala/). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A basic peptide derived from human immunodeficiency virus (HIV)-1 Tat protein (positions 48–60) has been reported to have the ability to translocate through the cell membranes and accumulate in the nucleus, the characteristics of which are utilized for the delivery of exogenous proteins into cells. Based on the fluorescence microscopic observations of mouse macrophage RAW264.7 cells, we found that various arginine-rich peptides have a translocation activity very similar to Tat-(48–60). These included such peptides as the d-amino acid- and arginine-substituted Tat-(48–60), the RNA-binding peptides derived from virus proteins, such as HIV-1 Rev, and flock house virus coat proteins, and the DNA binding segments of leucine zipper proteins, such as cancer-related proteins c-Fos and c-Jun, and the yeast transcription factor GCN4. These segments have no specific primary and secondary structures in common except that they have several arginine residues in the sequences. Moreover, these peptides were able to be internalized even at 4 °C. These results strongly suggested the possible existence of a common internalization mechanism ubiquitous to arginine-rich peptides, which is not explained by a typical endocytosis. Using (Arg)n (n = 4–16) peptides, we also demonstrated that there would be an optimal number of arginine residues (n ∼ 8) for the efficient translocation. A basic peptide derived from human immunodeficiency virus (HIV)-1 Tat protein (positions 48–60) has been reported to have the ability to translocate through the cell membranes and accumulate in the nucleus, the characteristics of which are utilized for the delivery of exogenous proteins into cells. Based on the fluorescence microscopic observations of mouse macrophage RAW264.7 cells, we found that various arginine-rich peptides have a translocation activity very similar to Tat-(48–60). These included such peptides as the d-amino acid- and arginine-substituted Tat-(48–60), the RNA-binding peptides derived from virus proteins, such as HIV-1 Rev, and flock house virus coat proteins, and the DNA binding segments of leucine zipper proteins, such as cancer-related proteins c-Fos and c-Jun, and the yeast transcription factor GCN4. These segments have no specific primary and secondary structures in common except that they have several arginine residues in the sequences. Moreover, these peptides were able to be internalized even at 4 °C. These results strongly suggested the possible existence of a common internalization mechanism ubiquitous to arginine-rich peptides, which is not explained by a typical endocytosis. Using (Arg)n (n = 4–16) peptides, we also demonstrated that there would be an optimal number of arginine residues (n ∼ 8) for the efficient translocation. human immunodeficiency virus human T-cell lymphotrophic virus type-II brome mosaic virus flock house virus high performance liquid chromatography phosphate-buffered saline [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide N-(6-maleimidocaproyloxy)succinimide ester nuclear localization sequence Recently, methods have been developed for the delivery of exogenous proteins into living cells with the help of membrane-permeable carrier peptides such as HIV-11 Tat-(48–60) and Antennapedia-(43–58) (1Fawell S. Seery J. Daikh Y. Moore C. Chen L.L. Pepinsky B. Barsoum J. Proc. Natl. Acad. Sci. U. S. A. 1994; 91: 664-668Crossref PubMed Scopus (1107) Google Scholar, 2Vives E. Brodin P. Lebleu B. J. Biol. Chem. 1997; 272: 16010-16017Abstract Full Text Full Text PDF PubMed Scopus (2064) Google Scholar, 3Nagahara H. Vocero-Akbani A.M. Snyder E.L. Ho A. Latham D.G. Lissy N.A. Becker-Hapak M. Ezhevsky S.A. Dowdy S.F. Nat. Med. 1998; 4: 1449-1452Crossref PubMed Scopus (886) Google Scholar, 4Schwarze S.R. Ho A. Vocero-Akbani A. Dowdy S.F. Science. 1999; 285: 1569-1572Crossref PubMed Scopus (2200) Google Scholar, 5Schwarze S.R. Dowdy S.F. Trends Pharmacol. Sci. 2000; 21: 45-48Abstract Full Text Full Text PDF PubMed Scopus (429) Google Scholar, 6Derossi D. Joliot A.H. Chassaing G. Prochiantz A. J. Biol. Chem. 1994; 269: 10444-10450Abstract Full Text PDF PubMed Google Scholar, 7Derossi D. Calvet S. Trembleau A. Brunissen A. Chassaing G. Prochiantz A. J. Biol. Chem. 1996; 271: 18188-18193Abstract Full Text Full Text PDF PubMed Scopus (966) Google Scholar, 8Derossi D. Chassaing G. Prochiantz A. Trends Cell Biol. 1998; 8: 84-87Abstract Full Text PDF PubMed Scopus (665) Google Scholar, 9Lin Y.Z. Yao S. Veach R.A. Torgerson T.R. Hawiger J. J. Biol. Chem. 1995; 270: 14255-14258Abstract Full Text Full Text PDF PubMed Scopus (854) Google Scholar, 10Rojas M. Yao S. Lin Y.Z. J. Biol. Chem. 1996; 271: 27456-27461Abstract Full Text Full Text PDF PubMed Scopus (213) Google Scholar, 11Rojas M. Donahue J.P. Tan Z. Lin Y.Z. Nat. Biotechnol. 1998; 16: 370-375Crossref PubMed Scopus (142) Google Scholar). By genetically or chemically hybridizing these carrier peptides, the efficient intracellular delivery of various oligopeptides and proteins was achieved. One of the most amazing examples is the Tat-β-galactosidase fusion protein (4Schwarze S.R. Ho A. Vocero-Akbani A. Dowdy S.F. Science. 1999; 285: 1569-1572Crossref PubMed Scopus (2200) Google Scholar), which has a molecular mass as high as 120 kDa. Intraperitoneal injection of the protein resulted in delivery of the protein with β-galactosidase activity to various tissues in mice, including the brain. The peptide-mediated approaches would allow the incorporation of peptides containing unnatural amino acids or nonpeptide molecules such as fluorescence probes. These methods would become powerful tools not only for therapeutic purposes as an alternative to gene delivery, but also for the understanding of the mechanisms behind fundamental cellular events, such as signal transduction and gene transcription. Besides the potential of Tat-(48–60) as a protein carrier, the internalization mechanism of the peptide attracted our interest. For example, Tat-(48–60) (GRKKRRQRRRPPQ) is a highly basic and hydrophilic peptide, which contains 6 arginine and 2 lysine residues in its 13 amino acid residues. However, the peptide was reported to be translocated through the cell membranes in 5 min at a concentration of 0.1 μm (2Vives E. Brodin P. Lebleu B. J. Biol. Chem. 1997; 272: 16010-16017Abstract Full Text Full Text PDF PubMed Scopus (2064) Google Scholar). Internalization of the peptide was not inhibited even at 4 °C. The peptide is less toxic to cells than other basic membrane-interacting agents. The above features suggested that the internalization mechanism of Tat-(48–60) was completely different from the typical transmembrane mechanisms reported so far. Questions arise as to whether such an efficient translocation is specific for Tat-(48–60) and Antennapedia-(43–58) peptides and what is the mechanism of the highly efficient internalization. Based on experiments using synthetic peptides, we suggest the possible presence of a very similar translocation mechanism to Tat-(48–60) present among the various arginine-rich peptides. We also suggest the possible existence of the optimum chain length of arginine peptides for the internalization. All the peptides used in this study were chemically synthesized by Fmoc (9-fluorenylmethyloxycarbonyl)-solid-phase peptide synthesis on a Rink amide resin as reported previously (12Futaki S. Ishikawa T. Niwa M. Kitagawa K. Yagami T. Bioorg. Med. Chem. 1997; 5: 1883-1891Crossref PubMed Scopus (31) Google Scholar). Fluorescent labeling of the peptides was conducted by the treatment with 1.5 eq of 5-maleimidofluorescein diacetate (Sigma) in dimethylformamide-methanol (1:2) for 3 h followed by reverse-phase HPLC purification. The fidelity of the products was ascertained by time-of-flight mass spectrometry. Carbonic anhydrase in phosphate-buffered saline (PBS) was simultaneously treated with fluorescein-5(6)-carboxamidocaproic acid N-hydroxysuccinimide ester (Sigma) andN-(6-maleimidocaproyloxy)succinimide ester (Dojin) (15 eq, each) at room temperature for 1 h to introduce the fluorescein and the maleimide function to the protein. After the removal of the unreacted reagents by gel-filtration on a Sephadex G-25 (Amersham Pharmacia Biotech) column, the cysteine of the respective arginine-rich peptides was allowed to react with the maleimide moiety on the above fluorescein-labeled protein at room temperature for 16 h, and then the unreacted peptides were removed by gel-filtration. Based on the molecular weight estimation by SDS-polyacrylamide gel electrophoresis, one or two molecules of basic peptides and fluorescein per protein were incorporated, respectively. Mouse macrophage RAW264.7 cells were maintained in RPMI 1640 medium with 10% heat-inactivated fetal bovine serum. Cells were grown on 60-mm dishes and incubated at 37 °C under 5% CO2 to ∼70% confluence. A subculture was performed every 3–4 days. For each assay, 4 × 104/ml cells were pelleted on a eight-well Lab-Tek-II chamber slide (Nalge Nunc) (250 μl/well) and cultured for 16 h. After complete adhesion, the culture medium was exchanged. The cells were incubated at 37 °C for 3 h with the fresh medium (250 μl) containing fluorescein-labeled peptides or proteins. The concentrations of the peptides and proteins were adjusted before addition to the cell based on their fluorescent intensity. Cells were washed three times with PBS, fixed with acetone-methanol (1:1) for 2 min at room temperature, washed three times with PBS again, and then mounted in fluorescent mounting medium containing 15 mmNaN3 (Dako). The distribution of fluorescein-labeled peptides was analyzed on a Zeiss Axioskop fluorescence microscope using a 100× oil immersion lens. Cells were grown, incubated with proteins, and fixed basically as described above. Cells were then treated with PBS containing 5 μm propidium iodide (200 μl) at room temperature for 30 min, washed four times with PBS, and mounted in glycerol:PBS (9:1) containing 1%p-phenylenediamine dihydrochloride. Data were obtained using a confocal scanning laser microscope MRC 1024 (Bio-Rad) equipped with a 60× oil immersion lens or LSM 510 (Zeiss) equipped with a 40× lens. The MTT assay was conducted basically in the same manner as reported previously (2Vives E. Brodin P. Lebleu B. J. Biol. Chem. 1997; 272: 16010-16017Abstract Full Text Full Text PDF PubMed Scopus (2064) Google Scholar). Cells (1 × 104/well) were cultured in 96-microtiter plates in RPMI 1640 medium with 10% heat-inactivated fetal bovine serum in the presence of peptides (HIV-1 Tat-(48–60): GRKKRRQRRRPPQ-amide; R9-Tat: GRRRRRRRRRPPQ-amide; HIV-1 Rev-(34–50): TRQARRNRRRRWRERQR-amide; FHV coat-(35–49): RRRRNRTRRNRRRVR-amide) at 10 or 100 μm. Cells were incubated at 37 °C under 5% CO2 for 24 h before addition of MTT (Sigma, 5 mg/ml in PBS) for 4 h. The precipitated MTT formazan was dissolved overnight in 0.04 n HCl in isopropanol (100 μl). The absorbance at 570 nm was then measured. Cell viability was expressed as the ratio of the A 570 of cells treated with peptide over the control samples. To obtain insight into the translocation mechanisms of the Tat-(48–60) peptide, Tat-(48–60), its d-amino acid-substituted analog (d-Tat) and arginine-substituted analog (R9-Tat), where residues corresponding to positions 49–57 were replaced with arginine, were synthesized (Fig.1 a). An extra cysteine amide was incorporated into the C terminus of each peptide for the fluorescent labeling. The peptides corresponding to nuclear localization sequences (NLS) derived from simian virus 40 (13) and nucleoplasmin (14Görlich D. Mattaj I.W. Science. 1996; 271: 1513-1518Crossref PubMed Scopus (1066) Google Scholar) were also synthesized as references. Treatment of the peptides with 5-maleimidofluorescein diacetate gave the corresponding fluorescein-labeled peptides. Internalization of the peptides was monitored by fluorescence microscopic observation after a 3-h incubation of the peptides with mouse macrophage RAW 264.7 cells at 37 °C. As a result, d-Tat and R9-Tat were internalized into the cell as efficiently as the Tat-(48–60) peptides, and localization into both the cytoplasm and nucleus was observed (Fig. 2). A similar internalization of the d-amino acid analog of Tat was reported by Huq et al. (15Huq I. Ping Y.-H. Tamilarasu N. Rana T.M. Biochemistry. 1999; 38: 5172-5177Crossref PubMed Scopus (44) Google Scholar) using a linear peptide corresponding to residues 37–72. These results would contradict the idea that a specific receptor may play a crucial role in the translocation of the Tat-(48–60) peptide. On the other hand, the simian virus 40-derived and nucleoplasmin-derived peptides showed a much lower degree of internalization. These NLS-derived peptides are rich in lysine. The above results suggested that arginine residues would play an important role in the translocation.Figure 2Translocation of the arginine-rich Tat-related peptides through the cell membranes. RAW264.7 cells were treated with fluorescein-labeled peptides derived from HIV-1 Tat-(48–60) (a), R9-Tat (b),d-Tat (c), and nucleoplasmin-NLS (d) (10 μm each) for 3 h.View Large Image Figure ViewerDownload Hi-res image Download (PPT) Arginine-rich basic segments are used by a variety of RNA-binding proteins to recognize specific RNA structures (16Tan R. Frankel A.D. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: 5282-5286Crossref PubMed Scopus (177) Google Scholar). If arginine in the sequence plays an important role in the translocation, peptides corresponding to these RNA-binding segments may translocate through the cell membranes. To test this hypothesis, 10 arginine-rich RNA-binding peptides bearing a C-terminal Gly-Cys-amide (Fig. 1 b) were similarly prepared, fluorescein-labeled, and applied to the macrophage cells. To our surprise, all the peptides other than the human U2AF-(142–153) peptide translocated through the cell membranes and accumulated in the cytoplasm and nucleus (Fig. 3). As judged from the fluorescent intensity, the efficiency of incorporation into the cells showed a tendency to correspond to the number of arginine residues in the sequence. Internalization activity of the HIV-1 Rev-(34–50), FHV coat-(35–49), HTLV-II Rex-(4–16), and BMV Gag-(7–25) peptides, which have more than seven arginine residues in their sequences, were comparable with that of the Tat-(48–60) peptide. Fluorescence was observed in the cells as early as 5 min after the addition of these peptides (1 μm) to the medium. Less extensive internalization was observed in the case of the λ N-(1–22), φ21 N-(12–29), and yeast PRP6-(129–144) peptides that have five arginine residues in their sequences. The fluorescent intensity in the cells treated with the former peptides (0.1 μm) was judged not to be less than that in those treated with the latter peptides (10 μm). The P22 N-(14–30) and cowpea chlorotic mottle virus Gag-(7–25) peptides that have six arginine residues showed a moderate degree of translocation. HIV-1 Tat-(48–60) is reported to translocate through the cell membranes and accumulate in the nucleus, especially the nucleolus (2Vives E. Brodin P. Lebleu B. J. Biol. Chem. 1997; 272: 16010-16017Abstract Full Text Full Text PDF PubMed Scopus (2064) Google Scholar). A similar tendency was observed with the above peptides. Not only the RNA-binding peptides but also the DNA-binding peptides corresponding to the basic leucine zipper segments derived from cancer-related proteins, c-Fos and c-Jun, and the yeast transcription factor, GCN4, which were also rich in arginine (Fig. 1 c), were internalized into the cells with almost the same efficiency as that of Tat-(48–60) (Fig.4).Figure 4Translocation of DNA-binding peptides through the cell membranes. RAW264.7 cells were treated with the fluorescein-labeled peptides derived from human c-Jun-(252–279) (a) and yeast GCN4-(231–252) (b) (1 μm each) for 3 h.View Large Image Figure ViewerDownload Hi-res image Download (PPT) HIV-1 Tat-(48–60) was reported to induce little toxicity to HeLa cells (2Vives E. Brodin P. Lebleu B. J. Biol. Chem. 1997; 272: 16010-16017Abstract Full Text Full Text PDF PubMed Scopus (2064) Google Scholar). Using R9-Tat, HIV-1 Rev-(34–50), and FHV coat-(35–49) peptides as representatives of the above arginine-rich peptides, cytotoxicity of the peptides was investigated. Determined by the MTT assay, the above peptides did not show a significant cytotoxicity to the macrophage cells during the treatment with a peptide (10 μm) for 24 h. At 100 μm, cell viability of the cells treated with R9-Tat became 70%, whereas viability of those treated with other peptides as well as HIV-1 Tat-(48–60) was still greater than 95%. These results suggested that many of the arginine-rich peptides can be of low cytotoxicity as reported for the HIV-1 Tat-(48–60) peptide. The above experiments showed that a variety of arginine-rich RNA/DNA-binding peptides were able to translocate through the cell membranes. Little homology in these sequences was observed, except that they all have 5–11 arginine residues. Moreover, thed-amino acid substituted Rev-(34–50) peptide (1 μm) was internalized as efficiently as thel-peptide in 3 h not of the HIV-1 Tat-(48–60), R9-Tat, and FHV coat-(35–49) peptides in were of their not a significant secondary whereas the HIV-1 Rev-(34–50) peptide showed a typical of an peptide. The peptide, which was only internalized into the showed a very similar to that of the FHV coat-(35–49) peptide. These results were of the of even a common secondary in the membrane-permeable peptides. the cells were incubated with a peptide (1 μm) at 4 °C for 30 min, no significant in fluorescent intensity in the cell was observed using the HIV-1 Rev-(34–50), and FHV coat-(35–49) peptides These results suggested that typical so would not play a crucial role in the translocation of these arginine-rich of temperature on HIV-1 Rev-(34–50) peptide internalization. The cells were incubated with the peptide (1 μm) for 30 min at 4 °C or at 37 °C. the former the cells were at 4 °C for 1 h before addition of the peptide. All the were also conducted at 4 °C the of the Large Image Figure ViewerDownload Hi-res image Download (PPT) We on the whether the of arginine-rich peptides into the cells is or The cells were treated with the HIV-1 Rev-(34–50) peptide (1 μm) for 3 h, then the medium was with a fresh one not containing the peptide. The fluorescence intensity from the cells 1 h was almost comparable with or only less than that of the cells before the medium However, a in the fluorescence intensity was in the cells 6 h and complete of the fluorescence was observed 24 h To the above results were to the of the peptide from the cells, the medium was analyzed by an HPLC equipped with a fluorescence was at the corresponding to the were observed that at positions with those of the peptide treated with not we that the in fluorescence intensity of the cells resulted from the of the peptides, and not from the of the peptide. The whether the peptide a on the cell was also The above HIV-1 cells were 24 h and The cell number for the cells was comparable with that for the control cells peptide the cells were judged to to with little by the peptide. would be that the peptide in each of the cells cell significant in the intensity were not observed among the cells 6 h the of the which was to be h, a of cells have the 6 h. If the peptides would in one of the cells cell a in the fluorescence intensity be observed among the cells. However, study be to this To the of the above basic peptides as protein we basic Carbonic anhydrase was as a protein. anhydrase were using N-(6-maleimidocaproyloxy)succinimide ester as a R. H. M. M. Niwa M. S. H. 1998; PubMed Scopus Google Scholar) A fluorescein moiety was into the protein using the fluorescein-5(6)-carboxamidocaproic ester simultaneously with As judged from the SDS-polyacrylamide gel of the one to two molecules of the basic peptide and fluorescein moiety were into a of respectively. Carbonic anhydrase was into the cells with the help of the HIV-1 Rev-(34–50), FHV coat-(35–49), and R9-Tat peptides as efficiently as with the HIV-1 Tat-(48–60) peptide (Fig. of the in the and nucleus was also observed by fluorescence of the cells (Fig. microscopic of these demonstrated both and nuclear localization and not to the cellular membranes (Fig. On the other hand, fluorescein-labeled protein a carrier peptide was in a of the (Fig. suggested that the protein was in the and was not able to be into the was also into the cell with the help of these carrier peptides not The above strongly suggested the of arginine residues in the internalization. The possible existence of the internalization mechanism common in these arginine-rich peptides was also We then the of the number of arginine residues in the sequences. For peptides that are of residues of arginine were (Fig.1 To their C the Gly-Cys-amide was also for the fluorescein labeling. These results are in A. was on the translocation efficiency and intracellular localization among these peptides. showed low translocation and the internalization and in the is is that the degree of internalization as the chain length For the internalization of the peptide was not The same of was in the experiments using the of anhydrase with the arginine peptides (Fig. A similar tendency was observed on the protein delivery using and as the carrier Based on the confocal laser microscopic the anhydrase was efficiently internalized into the macrophage cells and in the nucleus was observed as was in the case of the HIV-1 Rev-(34–50) the to on the cell membranes after a 3-h incubation with the but significant in the nucleus was not this we have that not only Tat-(48–60) but also various arginine-rich peptides were able to translocate through the mouse macrophage membranes. These peptides the and arginine-substituted HIV-1 Tat-(48–60) RNA-binding peptides derived from proteins, such as HIV-1 Rev, HTLV-II BMV and FHV coat proteins, and the DNA-binding segments from c-Jun, and the proteins. a common or very similar mechanism for the internalization among these peptides. The mechanism is explained by by the peptides were internalized by the cell at 4 and there little homology both in the primary and secondary structures among these membrane-permeable peptides except that they have several arginine residues in the sequences. These results strongly suggest the possible presence of the common and internalization mechanisms among the arginine-rich basic peptides. As one more the features of the we have that the number of arginine residues has a significant on the of internalization and that there to be an optimal number of arginine residues for the internalization. still such efficient translocation is possible for the arginine-rich peptides. of arginine with B. S. D. Frankel A.D. Science. PubMed Scopus Google Scholar) or with such as B. 1997; PubMed Scopus Google Scholar) may be in the during the However, as was in the case of the is not to the mechanism only by of peptides on the membranes. Tat-(48–60) has been reported to various proteins into the cells not only into cultured cells but also into the various of a living mouse (4Schwarze S.R. Ho A. Vocero-Akbani A. Dowdy S.F. Science. 1999; 285: 1569-1572Crossref PubMed Scopus (2200) Google Scholar). As the arginine-rich peptides to have a similar ability as of proteins, study of the peptides may in peptides to specific cells by or with the help of other peptides. The results obtained not only on the possible presence of of ubiquitous transmembrane mechanisms for the arginine-rich peptides, but also on the of carrier molecules for the intracellular protein We are to S. and Y. and H. for

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRecent Developments in the Synthesis and Utilization of Chiral SulfoxidesInmaculada Fernández and Noureddine KhiarView Author Information Instituto de Investigaciones Químicas, C.S.I.C-Universidad de Sevilla, c/. Américo Vespucio, s/n., Isla de la Cartuja, 41092 Sevilla, Spain, and Departamento de Química Orgánica y Farmacéutica, Facultad de Farmacia, Universidad de Sevilla, 41012 Sevilla, Spain Cite this: Chem. Rev. 2003, 103, 9, 3651–3706Publication Date (Web):August 1, 2003Publication History Received8 April 2002Published online1 August 2003Published inissue 1 September 2003https://pubs.acs.org/doi/10.1021/cr990372uhttps://doi.org/10.1021/cr990372uresearch-articleACS PublicationsCopyright © 2003 American Chemical SocietyRequest reuse permissionsArticle Views9882Altmetric-Citations1063LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Alkyls,Ligands,Oxidation,Oxides,Sulfides Get e-Alerts

Partial substitution of Pb for Bi in the Bi-Sr-Ca-Cu-O system has been found to sharply increase the volume fraction of the high- T c phase when both the starting material (coprecipitated oxalate being used in the present study) and the heating process are appropriate. The sharp powder X-ray diffraction pattern obtained from well-grown particles, 5∼10 µm wide and 0.5 µm thick typically, was assigned to an orthorhombic cell with a =0.537 nm, b =2.682 nm, and c =3.726 nm. The electrical resistance dropped to zero at 107 K within the experimental limit of 10 -6 Ω. A large diamagnetic response in the ac susceptibility due to the Meissner effect was seen below 120 K. The dominance of the high- T c phase over the low- T c phase was roughly estimated at 9/1 in volume.

Phthalocyanines exhibit superior photoproperties that make them a surely attractive class of photosensitisers for photodynamic therapy of cancer. Several derivatives are at various phases of clinical trials, and efforts have been put continuously to improve their photodynamic efficacy. To this end, various strategies have been applied to develop advanced phthalocyanines with optimised photoproperties, dual therapeutic actions, tumour-targeting properties and/or specific activation at tumour sites. The advantageous properties and potential of phthalocyanines as advanced photosensitisers for photodynamic therapy of cancer are highlighted in this tutorial review.

In contrast to artificial intelligence and machine learning approaches, KEGG (https://www.kegg.jp) has relied on human intelligence to develop "models" of biological systems, especially in the form of KEGG pathway maps that are manually created by capturing knowledge from published literature. The KEGG models can then be used in biological big data analysis, for example, for uncovering systemic functions of an organism hidden in its genome sequence through the simple procedure of KEGG mapping. Here we present an updated version of KEGG Mapper, a suite of KEGG mapping tools reported previously (Kanehisa and Sato, Protein Sci 2020; 29:28-35), together with the new versions of the KEGG pathway map viewer and the BRITE hierarchy viewer. Significant enhancements have been made for BRITE mapping, where the mapping result can be examined by manipulation of hierarchical trees, such as pruning and zooming. The tree manipulation feature has also been implemented in the taxonomy mapping tool for linking KO (KEGG Orthology) groups and modules to phenotypes.

The direct borylation of hydrocarbons via C-H activation has reached an impressive level of sophistication and efficiency, emerging as a fundamental tool in synthesis because of the versatility offered by organoboron compounds. As a remarkable particularity, the catalytic systems originally developed for these reactions are relatively insensitive to directing effects, and the regioselectivity of the borylations is typically governed by steric factors. Likely stimulated by the great synthetic potential of the expected functionalised organoboranes, however, many groups have recently focused on the development of complementary strategies for directed, site-selective borylation reactions where a directing group controls the course of the reaction. In this tutorial review, the different strategies and findings related to the development of these directed borylation reactions via C(sp(2))-H or C(sp(3))-H activation will be summarized and discussed.

Multivalency plays a major role in biological processes and particularly in the relationship between pathogenic microorganisms and their host that involves protein-glycan recognition. These interactions occur during the first steps of infection, for specific recognition between host and bacteria, but also at different stages of the immune response. The search for high-affinity ligands for studying such interactions involves the combination of carbohydrate head groups with different scaffolds and linkers generating multivalent glycocompounds with controlled spatial and topology parameters. By interfering with pathogen adhesion, such glycocompounds including glycopolymers, glycoclusters, glycodendrimers and glyconanoparticles have the potential to improve or replace antibiotic treatments that are now subverted by resistance. Multivalent glycoconjugates have also been used for stimulating the innate and adaptive immune systems, for example with carbohydrate-based vaccines. Bacteria present on their surfaces natural multivalent glycoconjugates such as lipopolysaccharides and S-layers that can also be exploited or targeted in anti-infectious strategies.

A study is made on the dispersions of resistivity and dielectric constant of α-Fe 2 O 3 , γ-Fe 2 O 3 , Fe 3 O 4 , Zn ferrite, Mn ferrite, and MnZn ferrite fine particles over the frequency range of 10 Hz to 1 MHz in the temperature range from 77°K to 300°K. The Maxwell-Wagner interfacial polarization arising from the heterogeneity of oxidation is observed in the fine particles of the oxides, except α-Fe 3 O 3 , which are prepared from aqueous solutions of divalent metal salts as well as in the powders of ferrites containing ferrous ions which are prepared by the calcination at high temperatures. The structures of heterogeneity in the fine particles are explained by the model that there are high resistivity shells with poor ferrous ions on the surfaces of the particles.

The folding types of 135 proteins, the three-dimensional structures of which are known, were analyzed in terms of the amino acid composition. The amino acid composition of a protein was expressed as a point in a multidimensional space spanned with 20 axes, on which the corresponding contents of 20 amino acids in the protein were represented. The distribution pattern of proteins in this composition space was examined in relation to five folding types, alpha, beta, alpha/beta, alpha + beta, and irregular type. The results show that amino acid compositions of the alpha, beta, and alpha/beta types are located in different regions in the composition space, thus allowing distinct separation of proteins depending on the folding types. The points representing proteins of the alpha + beta and irregular types, however, are widely scattered in the space, and the existing regions overlap with those of the other folding types. A simple method of utilizing the "distance" in the space was found to be convenient for classification of proteins into the five folding types. The assignment of the folding type with this method gave an accuracy of 70% in the coincidence with the experimental data.

This tutorial review provides a systematic overview of the available methodologies for the atroposelective transformation of (heterobiaryl)biaryl precursors toward the synthesis of enantiomerically enriched products and the conceptual aspects associated to each type of transformation. Depending on the presence or absence of symmetry in the starting material and the participation of racemization or dynamization events along the process, several strategies have been developed, including desymmetrization, classical kinetic resolution (KR), dynamic kinetic resolution (DKR) and dynamic kinetic asymmetric transformation (DYKAT). Seminal contributions and a handful of selected examples are discussed to illustrate the potential of these synthetic tools.

Cyclodextrin (CD) history has been largely dominated by their unique ability to form inclusion complexes with guests fitting in their hydrophobic cavity. Chemical funcionalization was soon recognized as a powerful mean for improving CD applications in a wide range of fields, including drug delivery, sensing or enzyme mimicking. However, 100 years after their discovery, CDs are still perceived as novel nanoobjects of undeveloped potential. This critical review provides an overview of different strategies to promote interactions between CD conjugates and genetic material by fully exploiting the inside-outside/upper-lower face anisotropy of the CD nanometric platform. Covalent modification, self-assembling and supramolecular ligation can be put forward with the ultimate goal to build artificial viruses for programmed and efficient gene therapy (222 references).

Glycosphingolipid clustering and interactions at the cell membrane can be modeled by gold glyconanoparticles prepared with biologically significant oligosaccharides. Such water-soluble gold glyconanoparticles with highly polyvalent carbohydrate displays (see picture, gray hemisphere: gold nanoparticle) have been obtained by a simple and versatile strategy.

Glycosphingolipid clustering and interactions at the cell membrane can be modeled by gold glyconanoparticles prepared with biologically significant oligosaccharides. Such water-soluble gold glyconanoparticles with highly polyvalent carbohydrate displays (see picture, gray hemisphere: gold nanoparticle) have been obtained by a simple and versatile strategy.

By means of the activated reactive evaporation, YBa 2 Cu 3 O 7- x single-crystal thin films with the c axis perpendicular to the substrate plane have been directly and epitaxially grown on the (100) surface of SrTiO 3 . The substrate temperature was kept below 600°C and the oxidation treatment was performed at below 500°C. The ac-resistive measurement for a film with 2000 Å thickness gave a sharp superconducting transition, where the endpoint was 90.2 K and Δ T c (10–90%)=1.7 K. From the complex susceptibility measurement we confirmed the Meissner effect as well as the structural uniformity of the specimen.

The imidazo[1,5-a]pyridine skeleton provides a versatile platform for the generation of new types of stable N-heterocyclic carbenes. Rh(I) mono- (6) and biscarbenes (7) from imidazo[1,5-a]pyridin-3-ylidenes (ImPy) and derivatives such as 13 from a mesoionic carbene were synthesized and characterized.

Abstract Approximately 8% to 19% of patients with acute myeloid leukemia (AML) have isocitrate dehydrogenase-2 (IDH2) mutations, which occur at active site arginine residues R140 and R172. IDH2 mutations produce an oncometabolite, 2-hydroxyglutarate (2-HG), which leads to DNA and histone hypermethylation and impaired hematopoietic differentiation. Enasidenib is an oral inhibitor of mutant-IDH2 proteins. This first-in-human phase 1/2 study evaluated enasidenib doses of 50 to 650 mg/d, administered in continuous 28-day cycles, in patients with mutant-IDH2 hematologic malignancies. Overall, 214 of 345 patients (62%) with relapsed or refractory (R/R) AML received enasidenib, 100 mg/d. Median age was 68 years. Forty-two patients (19.6%) attained complete remission (CR), 19 patients (10.3%) proceeded to an allogeneic bone marrow transplant, and the overall response rate was 38.8% (95% confidence interval [CI], 32.2-45.7). Median overall survival was 8.8 months (95% CI, 7.7-9.6). Response and survival were comparable among patients with IDH2-R140 or IDH2-R172 mutations. Response rates were similar among patients who, at study entry, were in relapse (37.7%) or were refractory to intensive (37.5%) or nonintensive (43.2%) therapies. Sixty-six (43.1%) red blood cell transfusion–dependent and 53 (40.2%) platelet transfusion–dependent patients achieved transfusion independence. The magnitude of 2-HG reduction on study was associated with CR in IDH2-R172 patients. Clearance of mutant-IDH2 clones was also associated with achievement of CR. Among all 345 patients, the most common grade 3 or 4 treatment-related adverse events were hyperbilirubinemia (10%), thrombocytopenia (7%), and IDH differentiation syndrome (6%). Enasidenib was well tolerated and induced molecular remissions and hematologic responses in patients with AML for whom prior treatments had failed. The study is registered at www.clinicaltrials.gov as #NCT01915498.

Carboxylesterases hydrolyze numerous endogenous and exogenous ester-containing compounds. They play a role in the detoxification of many agrochemicals including pyrethroids, organophosphates, and carbamates. Research on these enzymes is still developing and there are several topics that should be addressed to further investigations in this area. This paper focuses on a number of these issues including enzyme nomenclature, catalytic mechanism, substrate specificity, agrochemical metabolism, role in insecticide resistance and environmental significance. It is expected that carboxylesterase research will increase with specific emphasis on isozyme and substrate identification. Future research directions are discussed and the current state of the field is evaluated. © Pesticide Science Society of Japan

Dense and uniform layers of a biologically active carbonate‐containing hydroxyapatite can be formed on various kinds of organic polymers by the following biomimetic method. First, a substrate is set in contact with particles of CaO–SiO 2 ‐based glass soaked in a simulated body fluid (SBF) with ion concentrations nearly equal to those of human blood plasma for forming the apatite nuclei on the substrate. Second, the substrate is soaked in another solution highly supersaturated with respect to the apatite, e.g, with ion concentrations 1.5 times those of SBF (1.5SBF) for making the apatite nuclei grow on the substrate in situ. The induction period for the apatite nucleation, which is defined as the time of the first treatment required for forming enough of the apatite nuclei to make the continuous layer after the second treatment, was almost 24 h for most of the examined polymers. The adhesive strength of the formed apatite layer to the polymers was as high as 3 to 4 M Pa for poly(ethylene terephthalate), poly‐ether sulfone, and poly (vinyl alcohol) hydrogel. This type of apatite–organic polymer composite is expected to be useful for repairing not only living hard tissues but also soft ones.