Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: Application to the folding of a mini‐protein,chignolin

The conformational samplings are indispensible for obtaining reliable canonical ensembles, which provide statistical averages of physical quantities such as free energies. However, the samplings of vast conformational space of biomacromolecules by conventional molecular dynamics (MD) simulations might be insufficient, due to their inadequate accessible time‐scales for investigating biological functions. Therefore, the development of methodologies for enhancing the conformational sampling of biomacromolecules still remains as a challenging issue in computational biology. To tackle this problem, we newly propose an efficient conformational search method, which is referred as TaBoo SeArch (TBSA) algorithm. In TBSA, an inverse energy histogram is used to select seeds for the conformational resampling so that states with high frequencies are inhibited, while states with low frequencies are efficiently sampled to explore the unvisited conformational space. As a demonstration, TBSA was applied to the folding of a mini‐protein, chignolin, and automatically sampled the native structure (C_α root mean square deviation < 1.0 Å) with nanosecond order computational costs started from a completely extended structure, although a long‐time 1‐µs normal MD simulation failed to sample the native structure. Furthermore, a multiscale free energy landscape method based on the conformational sampling of TBSA were quantitatively evaluated through free energy calculations with both implicit and explicit solvent models, which enable us to find several metastable states on the folding landscape. © 2015 Wiley Periodicals, Inc.     

Polymerization of Acrylamide in Aqueous Solution of Poly(N‐isopropylacrylamide) at Lower Critical Solution Temperature

Acrylamide (AAm) was found to polymerize in a solution of poly(N‐isopropylacrylamide) (PNIPAAm) in water at around its lower critical solution temperature (LCST) (32°C) without any initiators. This phenomenon was specifically observed in aqueous solutions of the polymers having LCST such as PNIPAAm and poly(methylvinylether) (PMVE). AAm polymerized only when PNIPAAm and AAm were dissolved in water below LCST of PNIPAAm and then the solution was warmed up to the polymerization temperature (40°C). On the other hand, the polymerization of AAm did not proceed when AAm was added into aqueous PNIPAAm solution during and after the phase separation above 32°C. Furthermore the polymerizability of AAm was remarkably affected by the concentration and molecular weight of the PNIPAAm additives. Under the condition of lower PNIPAAm concentration (0.30 mol/L), the increase in the molecular weight of PNIPAAm considerably increased the molecular weight of the resulting PAAm but decreased the yield of PAAm. Under the condition of higher PNIPAAm concentration (0.60 mol/L) the polymerizability was not so affected by the molecular weight of PNIPAAm, while the molecular weight of PAAm formed by using higher molecular weight PNIPAAm was higher than those of PAAm formed by using lower molecular weight PNIPAAm. Moreover, the molecular weight of PAAm formed by the PNIPAAm induced polymerization of AAm was much higher than that of the polymer obtained by the radical polymerization using AIBN in THF or VA‐ 061 in water.     

原位Raman光谱揭示中性条件下硫化钼结构变化对其电催化析氢反应的促进作用（英文）

硫化钼是析氢反应(HER)有前途的电催化剂.S-或Mo物种均被认为是形成吸附氢触发HER反应的活性位,但Mo中心和S配体间相互作用的本质仍不清楚.另外,采用中性的水作为质子源用于产氢,来开发低成本的水裂解催化剂体系为研究者高度关注,但人们很少研究中性水条件下HER反应的机理.本文采用原位电化学Raman光谱对所合成的硫化钼中Mo–Mo和S–S物种在中性条件下的结构变化进行了监测.结果显示,归属于端位S–S物种的谱带随着和Mo–S振动谱带频率而同步变化,表明Mo–Mo键与端位S–S键起着协同作用,从而有利于氢气的生成.这可能是通过三核物种的内部重组而确认的.本文所揭示的HER反应中金属-配体相互作用的本质与作用表明了一个不同的反应机理,而以往的机理认为,S或Mo活性位独立起作用而促进HER反应的进行.     

Quantification of ATRP initiator density on polymer latex particles by fluorescence labeling technique using copper‐catalyzed azide‐alkyne cycloaddition

We developed a novel fluorescence labeling technique for quantification of surface densities of atom transfer radical polymerization (ATRP) initiators on polymer particles. The cationic P(St‐CPEM‐C₄DMAEMA) and anionic P(St‐CPEM) polymer latex particles carrying ATRP‐initiating chlorine groups were prepared by emulsifier‐free emulsion polymerization of styrene (St), 2‐(2‐chloropropionyloxy)ethyl methacrylate (CPEM), and N‐n‐butyl‐N,N‐dimethyl‐N‐(2‐methacryloyloxy)ethylammonium bromide (C₄DMAEMA). ATRP initiators on the surface of polymer particles were converted into azide groups by sodium azide, followed by fluorescent labeling with 5‐(N,N‐dimethylamino)‐N′‐(prop‐2‐yn‐1‐yl)naphthalene‐1‐sulfonamide (Dansyl‐alkyne) by copper‐catalyzed azide‐alkyne cycloaddition (CuAAC). The reaction time required for both azidation of ATRP‐initiating groups and successive fluorescence labeling of azide groups with Dansyl‐alkyne by CuAAC were investigated in detail by FTIR and fluorescence spectral measurement, respectively. The ATRP initiator densities on the cationic P(St‐CPEM‐C₄DMAEMA) and anionic P(St‐CPEM) particle surfaces were estimated to be 0.21 and 0.15 molecules nm^?2, respectively, which gave close agreement with values previously determined by a conductometric titration method. The fluorescence labeling through click chemistry proposed herein is a versatile technique to quantify the surface ATRP initiator density both on anionic and cationic polymer particles. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013 , 51, 4042–4051     

Organocatalytic Enantioselective Aza‐Friedel–Crafts Reaction of Cyclic Ketimines with Pyrroles using Imidazolinephosphoric Acid Catalysts

Organocatalytic enantioselective aza‐Friedel–Crafts reactions of cyclic ketimines with pyrroles or indoles were catalyzed by imidazoline/phosphoric acid catalysts. The reaction was applied to various 3H‐indol‐3‐ones to afford products in excellent yields and enantioselectivities. The chiral catalysts can be recovered by a single separation step using column chromatography and are reusable without further purification. Based on the experimental investigations, a possible transition state has been proposed to explain the origin of the asymmetric induction.     

Leveraging Material Properties in Fluorescence Anion Sensor Arrays: A General Approach

As the demand for probes suitable for sensor development increases, investigation of approaches that utilize known successful receptors gains in general importance. This study describes a two‐prong approach that can be used as a guide to developing sensors from known receptors. First, the conversion of a simple receptor, calix[4]pyrrole, into a fluorescent probe to establish a ratiometric signal is described. Secondly, the sensors that employ an output from a single ratiometric calix[4]pyrrole probe are fabricated by using poly(ether‐urethane) hydrogel copolymers. These hydrogels are designed to absorb, internalize and transport aqueous electrolytes. A sensor array of ten different poly(ether‐urethane) matrices with varying comonomer proportions were doped with a single probe and were exposed to eight different anions: acetate, benzoate, fluoride, chloride, phosphate, pyrophosphate, hydrogen sulfide, and cyanide, eight urine samples and anti‐inflammatory drugs (NSAIDs). The poly(ether‐urethane) matrices comprise different proportions of anion‐binding urethane moieties and different hydrophilicity given by the ratio between ethylene glycol ether and butylene glycol ether. This diversity in the hydration behavior provides different environment polarity, in which the recognition and self‐assembly processes display enough diverse behavior to allow for unique response of the probe to the analytes. Furthermore, a single probe is shown to recognize eight different aqueous anions and eight urine samples when embedded in ten different polyurethanes in an array that displays 100 % classification accuracy. To demonstrate the potential of the concept for quantitative studies, an estimation of non‐steroidal anti‐inflammatory drugs ibuprofen and diclofenac in water and in saliva was performed. A limit of detection of 0.1 ppm and a dynamic range of 0.1–0.6 and 0.05–60 ppm was observed, respectively. Given the general difficulty of chemosensors to recognize aqueous anions, the fact that one probe recognizes eight different analytes attests to an enormous effect of the polymer environment on the recognition process. This method could be used to generate a variety of sensor arrays for various analyses including species that are difficult to recognize, such as small‐molecule‐ and inorganic anions.     

One-pot hydrothermal synthesis of an assembly of magnetite nanoneedles on a scaffold of cyclic-diphenylalanine nanorods

The assembly of metal oxide nanoparticles (NPs) on a biomolecular template by a one-pot hydrothermal synthesis method is achieved for the first time. Magnetite (Fe₃O₄) nanoneedles (length: ~100 nm; width: ~10 nm) were assembled on cyclic-diphenylalanine (cFF) nanorods (length: 2–10 μm; width: 200 nm). The Fe₃O₄ nanoneedles and cFF nanorods were simultaneously synthesized from FeSO₄ and l-phenylalanine by hydrothermal synthesis (220 °C and 22 MPa), respectively. The samples were analyzed by powder X-ray diffraction (XRD), Fourier transform infrared spectroscopy (IR), transmission electron microscopy (TEM), and superconducting quantum interference device (SQUID) magnetometry. Experimental results indicate that Fe₃O₄ nanoneedles were assembled on cFF nanorods during the hydrothermal reaction. The composite contained 3.3 wt% Fe₃O₄ nanoneedles without any loss of the original magnetic properties of Fe₃O₄.