Structural variety of membrane permeable peptides

Peptide-mediated protein delivery into living cells has been attracting our attention. Among the peptides that have been reported to have carrier activity, the one from the human immunodeficient virus (HIV)-1 Tat has been most often used for the introduction of exogenous macromolecules into cells. We have shown that not only the Tat peptide, but also various arginine-rich peptides showed very similar characteristics in translocation, and the possible presence of ubiquitous internalization mechanisms among the arginine-rich peptides has also been suggested. These arginine-rich peptides includes ones derived from HIV-1 Rev and flock house virus coat proteins. The linear- and branched-chain peptides containing approximately 8 residues of arginine also show a similar ability. In this review, we present the structural variety of membrane permeable peptides and provide a survey of the findings on the translocation of these peptides through the cell membranes.     

DNA-bleomycin interaction: Nucleotide sequence-specific binding and cleavage of DNA by bleomycin

Biosynthetic intermediates and synthetic analogues of bleomycin (BLM) have been investigated for their metal binding, dioxygen activation, and DNA cleavage. Molecular O₂ was activated by the Fe(II) complex of a synthetic model ligand. Nucleotide sequence specificities in DNA cleavage by the BLM-Fe(II) and deglyco-BLM-Fe(II) complexes were almost identical. It has been shown that (1) the β-aminoalanine-pyrimidine-β-hydroxyhistidine portion of BLM is essential for the metal binding and dioxygen activation and (2) the bithiazole moiety contributes to the specific binding to guanine base of DNA.     

Construction of a chiral quaternary carbon center by indium-catalyzed asymmetric alpha-alkenylation of beta-ketoesters

Construction of a nonracemic all-carbon quaternary stereocenter at the alpha-position of beta-ketoesters was achieved by way of an indium(III)-catalyzed diastereoselective alpha-alkenylation reaction of chiral enamines with 1-alkynes. The enamine bearing a chiral auxiliary derived from l-isoleucine was added to the alkyne to give an alpha-alkenylated product in excellent yield and with a stereoselectivity better than 90% ee. One can ascribe the high selectivity to a chelate intermediate involving the auxiliary and the metal atom and the high yield to efficient interactions between the indium(III) atom and the alkyne. The selectivity increased as the reaction temperature was raised to 120 degrees C and decreased at higher temperatures.     

Contribution of individual zinc ligands to metal binding and peptide folding of zinc finger peptides

Little is known about the contribution of individual zinc-ligating amino acid residues for coupling between zinc binding and protein folding in zinc finger domains. To understand such roles of each zinc ligand, four zinc finger mutant peptides corresponding to the second zinc finger domain of Sp1 were synthesized. In the mutant peptides, glycine was substituted for one of four zinc ligands. Their metal binding and folding properties were spectroscopically characterized and compared to those of the native zinc finger peptide. In particular, the electronic charge-transfer and d-d bands of the Co(II)-substituted peptide complexes were used to examine the metal coordination number and geometry. Fluorescence emission studies revealed that the mutant peptides are capable of binding zinc despite removing one ligand. Circular dichroism results clearly showed the induction of an alpha-helix by zinc binding. In addition, the structures of certain mutant zinc finger peptides were simulated by molecular dynamics calculation. The information indicates that His23 and the hydrophobic core formed between the alpha-helix and the beta-sheet play an essential role in alpha-helix induction. This report demonstrates that each ligand does not contribute equally to alpha-helix formation and coordination geometry in the zinc finger peptide.     

ESTIMATION OF AN INDEX OF HYDROPHOBICITY OF DNA INTERIOR USING 5-METHOXYPSORALEN AS A FLUORESCENT PROBE

The index of hydrophobicity of DNA interior was estimated by measuring fluorescence spectra of psoralen derivatives associated with DNA. The environment around 5-MOP associated with DNA was as hydrophobic (D_k = 34) as methanol, suggesting that the molecules reside at the space between the base-pairs in B-form DNA. This is also true for 8-MOP. Thus, planar and aromatic molecules of 5- and 8-MOP are more stable in the interior of DNA than in aqueous medium due to hydrophobic affinity.     

Gas chromatography of manganese(II) and manganese(III) trifluoroacetylacetonates by the ligand vapour technique

The thermal properties and gas Chromatographie behaviour of manganese(II) and manganese(III) trifluoroacetylacetonates (TFA) were investigated by using the ligand vapour technique. The two chelates, Mn(TFA); and Mn(TFA)₃, can be quantitatively eluted on a mixed-liquid phase (1.9% OV-17 ÷ 0.1% PEG-20M) at column temperatures above 210°C and 130–150°C, respectively; Mn(TFA)₃ is completely converted to Mn(TFA)₂ by thermal dissociation at column temperatures above 180°C and completely eluted as Mn(TFA)₂ above 210°C. The chelates can be determined separately within errors of about 1% after a preliminary extraction.     

Cypridina bioluminescence—IX: Tautomeric structures of 2-methyl-3,7-dihydroimidazo[1,2-a]-pyrazin-3-one, 2-methyl-3-aminoimidazo[1,2-a]pyrazine and their derivatives in neutral and acidic media

Tautomeric structures of the title compounds in neutral and acidic media are discussed. In neutral solutions 3 and 4 exist as structure A and E, respectively. In weakly acidic methanol 3 exists as monocation H, whereas in aqueous solution as monocation G. In both strongly acidic aqueous and methanolic solutions 3 exists as dication K. On the other hand, 4 exists in weakly acidic and strongly acidic media as monocation L and dication M, respectively. The above conclusion can be extended to the 6-phenyl and 6-(3′-indolyl) derivatives of 3 as well as Cypridina luceferin (1) in aqueous and methanolic solutions.     

Linear NiII-MnIII2-NiII tetramers: an oligomeric component of the MnIII2NiII single-chain magnets

Heterometallic linear tetramers [Mn(5-R-saltmen)Ni(pao)(bpy)(2)](2)(ClO(4))(4) (5-R-saltmen(2-) = N,N'-1,1,2,2-tetramethylethylene bis(5-R-salicylideneiminate); pao(-) = pyridine-2-aldoximate; bpy = 2,2'-bipyridine, R = H, 1; Cl, 2; Br, 3; MeO, 4) have been synthesized and structurally characterized. These compounds exhibit a [Ni(II)-NO-Mn(III)-(O)(2)-Mn(III)-ON-Ni(II)] skeleton where -ON- is an oximate bridge between Mn(III) and Ni(II) ions and -(O)(2)- is a bi-phenolate bridge between Mn(III) ions. These tetramers can be seen as oligomeric units of the heterometallic Mn(III)(2)-Ni(II) chain observed in a family of single-chain magnets (Clérac, R.; Miyasaka, H.; Yamashita, M.; Coulon, C. J. Am. Chem. Soc. 2002, 124, 12837. Miyasaka, H.; Clérac, R.; Mizushima, K.; Sugiura, K.; Yamashita, M.; Wernsdorfer, W.; Coulon, C. Inorg. Chem. 2003, 42, 8203.). Magnetic measurements on these tetramers confirm the nature of the magnetic interactions reported for the Mn(III)(2)-Ni(II) chains: a strong antiferromagnetic Mn(III)/Ni(II) coupling via the oximate bridge (J(Ni-Mn) ranges from -23.7 to -26.1 K) and a weak ferromagnetic Mn(III)/Mn(III) coupling through the bi-phenolate bridge (J(Mn-Mn) ranges from +0.4 to +0.9 K). These magnetic interactions lead to tetramers with an S = 2 ground state.     

Two-dimensional networks based on Mn4 complex linked by dicyanamide anion: from single-molecule magnet to classical magnet behavior

Three two-dimensional (2D) network compounds based on Mn(III)/Mn(II) tetranuclear single-molecule magnets (SMMs) connected by dicyanamide (dcn-) linkers have been synthesized: [Mn4(hmp)4(Hpdm)2(dcn)2](ClO4)2 x 2 H2O x 2 MeCN (2), [Mn4(hmp)4Br2(OMe)2(dcn)2] x 0.5 H2O x 2 THF (3), [Mn4(hmp)6(dcn)2](ClO4)2 (4), where Hhmp and H2pdm are 2-hydroxymethylpyridine and pyridine-2,6-dimethanol, respectively. The [Mn4]/dcn- system appears very versatile, but enables its chemistry to be rationalized by a fine-tune of the synthetic conditions. The double cuboidal [Mn4] unit is preserved in the whole family of compounds, despite strong modifications of its Mn(II) coordination sphere. The chemical control of the coordination number of dcn- on the Mn(II) sites has been the key to obtain the following series of compounds: a discrete cluster, [Mn4(hmp)6(NO3)2(dcn)2] x 2 MeCN (1), 2D networks (2, 3, and 4), and the previously reported 3D compound, [Mn4(hmp)4(mu3-OH)2][Mn(II)(dcn)6] x 2 MeCN x THF. Direct current magnetic measurements show that both Mn2+-Mn3+ and Mn3+-Mn3+ intra-[Mn4] magnetic interactions are ferromagnetic leading to an S(T) = 9 ground state for the [Mn4] unit. Despite the very similar 2D lattices in 2-4, the two kinds of orientation of the [Mn4] unit (i.e., angle variations between the two easy axes) lead to different magnetic properties ranging from SMM behavior for 2 and 1 to a long-range canted antiferromagnetic order for 4. Compound 3 is more complicated as the magnetic measurements strongly suggest the presence of a canted antiferromagnetic order below 2.1 K, although the magnetization slow relaxation is simultaneously observed. Heat capacity measurements confirm the long-range magnetic order in 4, while in 3, the critical behavior is frozen by the slow relaxation of the anisotropic [Mn4] units.     

A straightforward approach to antibodies recognising cancer specific glycopeptidic neoepitopes

Aberrantly truncated immature O-glycosylation in proteins occurs in essentially all types of epithelial cancer cells, which was demonstrated to be a common feature of most adenocarcinomas and strongly associated with cancer proliferation and metastasis. Although extensive efforts have been made toward the development of anticancer antibodies targeting MUC1, one of the most studied mucins having cancer-relevant immature O-glycans, no anti-MUC1 antibody recognises carbohydrates and the proximal MUC1 peptide region, concurrently. Here we present a general strategy that allows for the creation of antibodies interacting specifically with glycopeptidic neoepitopes by using homogeneous synthetic MUC1 glycopeptides designed for the streamlined process of immunization, antibody screening, three-dimensional structure analysis, epitope mapping and biochemical analysis. The X-ray crystal structure of the anti-MUC1 monoclonal antibody SN-101 complexed with the antigenic glycopeptide provides for the first time evidence that SN-101 recognises specifically the essential epitope by forming multiple hydrogen bonds both with the proximal peptide and GalNAc linked to the threonine residue, concurrently. Remarkably, the structure of the MUC1 glycopeptide in complex with SN-101 is identical to its solution NMR structure, an extended conformation induced by site-specific glycosylation. We demonstrate that this method accelerates dramatically the development of a new class of designated antibodies targeting a variety of “dynamic neoepitopes” elaborated by disease-specific O-glycosylation in the immunodominant mucin domains and mucin-like sequences found in intrinsically disordered regions of many proteins.

We developed new class of designated antibodies targeting of “dynamic neoepitopes” elaborated by disease-specific O-glycosylation at the immunodominant mucin domains.