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Signaling Recognition Events with Fluorescent Sensors and Switches.

KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース)

Arsenic round the world: a review.

Atomically precise pieces of matter of nanometer dimensions composed of noble metals are new categories of materials with many unusual properties. Over 100 molecules of this kind with formulas such as Au25(SR)18, Au38(SR)24, and Au102(SR)44 as well as Ag25(SR)18, Ag29(S2R)12, and Ag44(SR)30 (often with a few counterions to compensate charges) are known now. They can be made reproducibly with robust synthetic protocols, resulting in colored solutions, yielding powders or diffractable crystals. They are distinctly different from nanoparticles in their spectroscopic properties such as optical absorption and emission, showing well-defined features, just like molecules. They show isotopically resolved molecular ion peaks in mass spectra and provide diverse information when examined through multiple instrumental methods. Most important of these properties is luminescence, often in the visible–near-infrared window, useful in biological applications. Luminescence in the visible region, especially by clusters prot...

Atomically Precise Clusters of Noble Metals: Emerging Link between Atoms and Nanoparticles

Enhanced stability of cis Pro-Pro peptide bond in Pro-Pro-Phe sequence motif.

The amino acid Aib predisposes a peptide to be helical with context-dependent preference for either 3(10)- or alpha- or a mixed helical conformation. Short peptides also show an inherent tendency to be unfolded. To characterize helical and unfolded states adopted by water-soluble Aib-containing peptides, the conformational preference of Ac-Ala-Aib-Ala-Lys-Ala-Aib-Lys-Ala-Lys-Ala-Aib-Tyr-NH(2) was determined by CD, NMR and MD simulations as a function of temperature. Temperature-dependent CD data indicated the contribution of two major components, each an admixture of helical and extended/polyproline II structures. Both right- and left-handed helical conformations were detected from deconvolution of CD data and (13)C NMR experiments. The presence of a helical backbone, more pronounced at the N-terminal, and a temperature-induced shift in alpha-helix/3(10)-helix equilibrium, more pronounced at the C-terminal, emerged from NMR data. Starting from polyproline II, the N-terminal of the peptide folded into a helical backbone in MD simulations within 5 ns at 60 degrees C. Longer simulations showed a mixed-helical backbone to be stable over the entire peptide at 5 degrees C while at 60 degrees C the mixed-helix was either stable at the N-terminus or occurred in short stretches through out the peptide, along with a significant population of polyproline II. Our results point towards conformational heterogeneity of water-soluble Aib-based peptide helices and the associated subtleties. The problem of analyzing CD and NMR data of both left- and right-handed helices are discussed, especially the validity of the ellipticity ratio [theta](222)/[theta](207), as a reporter of alpha-/3(10)- population ratio, in right- and left-handed helical mixtures.

Conformational preferences of a short Aib/Ala-based water-soluble peptide as a function of temperature.

Metal clusters, composed of a few atoms at the core, exhibit unique properties and have potential applications. Although atomically precise clusters of noble metals have been synthesized, analogous systems of reactive metals, such as iron, have not been realized in solution due to high reactivity. Here we report the synthesis and characterization of novel iron clusters in the hemoglobin matrix that are highly luminescent (quantum yield 10% at 565 nm). The super-paramagnetic iron clusters, after successful ligand exchange from protein and phase transfer from water to chloroform using tri-octylphosphineoxide (TOPO), were detected as [Fe₁₀(TOPO)₃(H₂O)₃](+), [Fe₁₃(TOPO)₂(H₂O)](+) and [Fe₈(TOPO)(H₂O)₂](+) by mass spectrometry. This study lays the groundwork for exploiting unique properties of soluble iron clusters.

Luminescent iron clusters in solution

Quinoxaline antibiotics intercalate dsDNA and exhibit antitumor properties. However, they are difficult to synthesize and their structural complexity impedes a clear mechanistic understanding of DNA binding. Therefore design and synthesis of minimal-intercalators, using only part of the antibiotic scaffold so as to retain the key DNA-binding property, is extremely important. Reported is a unique example of a monomeric quinoxaline derivative of a 6-nitroquinoxaline-2,3-diamine scaffold which binds dsDNA by two different modes. While benzyl derivatives bound DNA in a sequential fashion, with intercalation as the second event, nonbenzyl derivatives showed only the first binding event. The benzyl intercalation switch provides important insights about molecular architecture which control specific DNA binding modes and would be useful in designing functionally important monomeric quinoxaline DNA binders and benchmarking molecular simulations.

/pdf/the-benzyl-moiety-in-a-quinoxaline-based-scaffold-acts-as-a-4v9ef6zlgf.pdf

The Benzyl Moiety in a Quinoxaline‐Based Scaffold Acts as a DNA Intercalation Switch

http://isw3.naist.jp/IS/Bio-Info-Unit/gogroup/basu/JMB2004.pdf

Gautam Basu

Papers

Enhanced stability of cis Pro-Pro peptide bond in Pro-Pro-Phe sequence motif.

Conformational preferences of a short Aib/Ala-based water-soluble peptide as a function of temperature.

Luminescent iron clusters in solution

The Benzyl Moiety in a Quinoxaline‐Based Scaffold Acts as a DNA Intercalation Switch

Electrostatic potential of nucleotide-free protein is sufficient for discrimination between adenine and guanine-specific binding sites