Hydrogen bond donors and acceptors are generally depolarized in α-helices as revealed by a molecular tailoring approach

Hydrogen-bond (H-bond) interaction energies in α-helices of short alanine peptides were systematically examined by precise density functional theory calculations, followed by a molecular tailoring approach. The contribution of each H-bond interaction in α-helices was estimated in detail from the entire conformation energies, and the results were compared with those in the minimal H-bond models, in which only H-bond donors and acceptors exist with the capping methyl groups. The former interaction energies were always significantly weaker than the latter energies, when the same geometries of the H-bond donors and acceptors were applied. The chemical origin of this phenomenon was investigated by analyzing the differences among the electronic structures of the local peptide backbones of the α-helices and those of the minimal H-bond models. Consequently, we found that the reduced H-bond energy originated from the depolarizations of both the H-bond donor and acceptor groups, due to the repulsive interactions with the neighboring polar peptide groups in the α-helix backbone. The classical force fields provide similar H-bond energies to those in the minimal H-bond models, which ignore the current depolarization effect, and thus they overestimate the actual H-bond energies in α-helices. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.     

Shimalactone Biosynthesis Involves Spontaneous Double Bicyclo-Ring Formation with 8π-6π Electrocyclization

Shimalactones A and B are neuritogenic polyketides possessing characteristic oxabicyclo[2.2.1]heptane and bicyclo[4.2.0]octadiene ring systems that are produced by the marine fungus Emericella variecolor GF10. We identified a candidate biosynthetic gene cluster and conducted heterologous expression analysis. Expression of ShmA polyketide synthase in Aspergillus oryzae resulted in the production of preshimalactone. Aspergillus oryzae and Saccharomyces cerevisiae transformants expressing ShmA and ShmB produced shimalactones A and B, thus suggesting that the double bicyclo-ring formation reactions proceed non-enzymatically from preshimalactone epoxide. DFT calculations strongly support the idea that oxabicyclo-ring formation and 8π-6π electrocyclization proceed spontaneously after opening of the preshimalactone epoxide ring through protonation. We confirmed the formation of preshimalactone epoxide in vitro, followed by its non-enzymatic conversion to shimalactones in the dark.     

Ruthenocene‐Type Complexes of N‐Fused Porphyrins

Ruthenocene‐type hybrid complexes with N‐fused porphyrinato ligands, [Ru(NFp)Cp] (NFp=N‐fused porphyrin, Cp=cyclopentadienyl), have been prepared and characterized by NMR and UV/Vis/NIR spectroscopy, cyclovoltammetry, and X‐ray crystallography. [Ru(NFp)Cp] is a common low‐spin ruthenium(II) complex and shows strong aromaticity. The Ru–Cp distance (1.833 Å) in [Ru(NFp)Cp] is comparable to that in [RuCp₂] (1.840 Å). DFT calculations on [Ru(NFp)Cp] showed the unequivocal contribution of the RuCp moiety as well as the NFp moiety to both the HOMO and LUMO, constructing a three‐dimensional d–π conjugated system. The HOMO–LUMO gaps of [Ru(NFp)Cp] are insensitive to the substituents on the NFp ligand, which is illustrated spectroscopically as well as theoretically. This is in sharp contrast to the ligand precursor, the N‐fused porphyrin, in which the HOMO–LUMO gap is affected by substituents in a similar manner to standard porphyrins and related macrocycles.     

Construction of a pH-responsive artificial membrane fusion system by using designed coiled-coil polypeptides

In many viruses, pH-responsive coiled-coil domains in the specific fusion proteins play important roles in membrane fusion and the infection of viruses into host cells. To investigate the relationship between the conformational change of the coiled coil and the fusion process, we have introduced a de novo designed polypeptide as a model system of the coiled-coil domain. This system enables the systematic study of the dynamics of pH-responsive coiled-coil polypeptide-membrane interactions. First, we designed and synthesized pH-responsive isoleucine-zipper triple-stranded coiled-coil polypeptides. Then the relationship between the pH-induced conformational change of the polypeptide and the membrane's interactive properties was studied by physicochemical methods. Structural changes in the designed polypeptides were examined by means of circular dichroism measurements. And finally, the behavior of the membrane fusion was investigated by leakage of liposomal contents, turbidity analysis, dynamic light scattering, and lipid mixing experiments. Our data show that coiled-coil formation under acidic pH conditions enhances polypeptide-induced membrane fusion. The results in this study demonstrate that an artificial membrane fusion system can be constructed on a molecular level by the use of a pH-responsive isoleucine-zipper triple-stranded coiled-coil polypeptide.     

Evaluation of single-base substitution rate in DNA by affinity capillary electrophoresis

Capillary electrophoretic separation of 60 mer single-stranded DNA (ssDNA) and a single-base-substituted ssDNA was demonstrated using a size- and composition-controlled poly(ethylene glycol)-oligodeoxyribonucleotide block copolymer (PEG-b-ODN) as an affinity ligand. Under appropriate conditions, PEG-b-ODN and ssDNA with a complementary sequence formed a reversible complex via hybridization during the electrophoresis, while the copolymer did not interact with the single-base-substituted ssDNA. The copolymer's PEG length determined the electrophoretic mobility of the ssDNA; upon formation of the complex, the electrically neutral PEG added hydrodynamic friction to ssDNA. Simultaneously using two types of PEG-b-ODN copolymers whose PEG segments were of different lengths, we achieved the complete separation of the 60 mer ssDNA, its single-base-substituted ssDNA, and impurities. This method was sensitive enough to quantify a slight amount (approximately 1%) of the single-base-substituted ssDNA. The present results suggest that our approach is applicable to quantitative detection of minor genotypes.     

Anion recognition by a disiloxane-1,3-diol in organic solvents

To explore the anion recognition ability of silanol derivatives, ESI-MS and ¹H NMR titrations of a 1,3-disiloxanediol 1 with anions were studied in CDCl₃ and MeCN-d₃. The results indicate that 1 showed strong binding to anions such as AcO⁻ and halides.     

Determination of total cholesterol in serum by high-performance liquid chromatography with electrochemical detection

A simple and sensitive HPLC method that does not require derivatization for determining cholesterol has been developed. Investigation of voltammetric behavior of cholesterol showed that cholesterol could be oxidized on a glassy carbon electrode in non-aqueous solvents. This was applied to the development of a method by HPLC with electrochemical detection (HPLC-ED). The HPLC-ED was optimized using the separation of cholesterol and oxysterols including 26-hydroxycholesterol and 24S-hydroxycholesterol. The separation was carried out with a Develosil C30-UG-3 column; acetonitrile-2-propanol (9:1, v/v) containing 50mM LiClO(4) as a mobile phase; and an applied potential at 1.9V versus Ag/AgCl. The current peak height was linearly related to the amount of cholesterol injected from 0.5-100 microM (r>0.999). The detection limit (S/N=3) of cholesterol was 0.36 microM (1.8 pmol). Cholesterol at 100 microM was directly detected with a relative standard deviation (RSD) of less than 1.0% (n=8). Total cholesterol and free cholesterol in control human serum were determined by the present method with the recovery of more than 90% and the RSD (n=6) of less than 3.0%.     

Label-free detection of protein-protein interactions at the GaAs/water interface through surface infrared spectroscopy: discrimination between specific and nonspecific interactions by using secondary structure analysis

Here, we propose a label-free detection of protein-protein interactions that enables simultaneous qualitative analysis of target proteins by using Fourier transform infrared (FTIR) absorption spectroscopy in multiple internal reflection geometry (MIR-FTIR). Using this method, the target proteins were detected based on the peak height of the amide I and amide II bands, while discrimination of specific and nonspecific signals is made based on the secondary structure of the analytes, which is determined through second-derivative analysis of the amide I band. As a model system, an antigen peptide was immobilized on the surface of GaAs, which was transparent to mid-infrared light, and the interaction with its antibody was examined in aqueous media. We demonstrated that the binding of the antibody to the antigen immobilized on a GaAs surface selectively gave rise to beta-sheet amide I vibrations (1639 and 1690 cm-1), while no structurally related signals were induced by nonspecifically adsorbed proteins. The peak height of the beta-peak (1639 cm-1) in the amide I band linearly increased with the antiserum concentration as well as that of the amide II band. The detection limit (S/N = 3) was a 1:36 000 dilution for the amide I signal. In addition, through the use of surface-sensitive MIR-FTIR, the present sensor selectively detected the antigen-antibody interactions at the surfaces without being affected by the presence of bulk species, enabling rapid and wash-free detection. Our method provides not only rapid label-free detection of protein-protein interactions but a more accurate discrimination between specific and nonspecific interactions through the use of the secondary structure of the target proteins as a measure for the specific signals.     

Phosphatidylcholine vesicle-mediated decomposition of hydrogen peroxide

The decomposition of hydrogen peroxide (H2O2) was examined in aqueous solution (50 mM Tris-HCl buffer, pH 7.4, containing 100 mM NaCl) at 25 degrees C in pure buffer or in the presence of either vesicles or micelles formed from various phosphatidylcholines (PCs). In the absence of PCs, more than 90% of the initially added H2O2 (1.0 mM) remained intact after incubation for 120 h. The effect of the PCs on the decomposition of H2O2 was studied by using different PCs that varied in terms of number of carbon atoms in the two acyl chains n as well as in terms of the degree of unsaturation. PCs with short hydrocarbon chains (n = 4, 6-8) were dissolved in the buffer solution in the form of nonassociated monomers or as micelles in equilibrium with monomers at a fixed PC concentration of 10 mM. The presence of these short-chain PCs slightly enhanced the H2O2 decomposition rate. Micelles formed by non-lipid detergents (sodium cholate, Triton X-100, and sodium dodecylsulfate) had a similar effect. In marked contrast, PCs with long hydrocarbon chains (n > or = 10) dispersed in buffer solution as vesicles (liposomes) significantly enhanced the rate of H2O2 decomposition, with the most effective PC being 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) at 25 degrees C. This indicates that the packing density of the PC molecules influences the reactivity, presumably through the direct interaction of the PC assemblies with H2O2 molecules. Furthermore, in the case of vesicles formed from PCs with unsaturated acyl chains (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, POPC; 1,2-dioleoyl-sn-glycero-3-phosphocholine, DOPC), carbon-carbon double bond oxidation did not occur extensively under the conditions used. This indicates that the observed effect of PCs on the decomposition of H2O2 is indeed related to the assembly structure (vesicle vs micelles vs monomers) and is clearly not related to the presence of unsaturated hydrocarbon chains. Fluorescence polarization measurements of two fluorescent probes embedded either in the acyl chain region of the vesicles (DPH, 1,6-diphenyl-1,3,5-hexatriene) or on the surface of the vesicles (TMA-DPH, 1-(4-trimethylammoniumphenyl)-6-phenyl-1,3,5-hexatriene iodide) show that the presence of H2O2 leads to a decrease in the fluidity of the lipid-water surface and not to a change in the fluidity of the hydrophobic region of the vesicle bilayer. This indicates that the decomposition of H2O2 is triggered through interactions between H2O2 and the polar head group area of PC vesicles.     

The unprecedented role of a CuII cryptand in the luminescence properties of a EuIII cryptate complex

Abstract  

A Eu^III cryptate complex constructed from a Cu^II cryptand with an L ^tBu ligand, [Eu^IIICu₂^II(L ^tBu)₂(NO₃)₃(MeOH)], and the corresponding Ca^II and Na^I cryptates, [Ca^IICu₂^II(L ^tBu)₂(NO₃)₂(MeOH)₂] and [Na^ICu₂^II(L ^tBu)₂(Me₂CO)](BPh₄), have been synthesized and characterized in order to shed light on the essential role of Cu^II in the luminescence of a Eu^III cryptate. The unprecedented role of a Cu^II cryptand makes it possible to produce lanthanide luminescence in a Eu^III cryptate complex and is successfully elucidated by comparison with the corresponding Ca^II and Na^I cryptates.