IPET:测定独个生物大分子三维空间结构的实验方法

蛋白质的动态特性和结构活性对于蛋白质功能的调控具有根本意义。传统的结构确定方法(包括X射线和电子显微镜单颗粒分析技术等)往往需要成千上万不同蛋白质分子的平均信号,因此难以确定蛋白质分子的动态结构。而电子显微断层成像技术是一种对独个生物个体结构从不同的观测角度照相、并计算来恢复该个体的三维结构密度图的方法。传统的冷冻电子断层成像重构方法采用整个大尺寸电镜图像进行重构计算,通常用来研究细菌、细胞切片等大尺寸生物个体在较低分辨率下的结构;由于分辨率的限制,不足以获得小尺寸的蛋白质分子的结构细节。最近,任罡研究小组提出一种独个生物颗粒的电子显微断层成像方法(individual-particle electron tomography,IPET)。该方法通过减小图像尺寸(直至所选区域只包含单个蛋白质分子)的策略,运用提出的FETR(focused electron tomography reconstruction)算法来提高独个大分子重构的分辨率。此方法不需要初始模型和大量分子的平均信号,同时能够容忍一定的测角误差。本文综述了IPET/FETR方法在确定独个分子结构过程中的具体步骤以及如何应用该方法来研究蛋白动态特性和结构变化特征。期望通过该综述和国内同行交流,分享最新的前沿研究,为赶超世界科技前沿的建设添砖加瓦。     

2‐Amino‐5‐iodopyridinium bromide hemihydrate and 2‐amino‐5‐iodopyridinium chloride monohydrate

The hydrobromide and hydrochloride salts of 2‐amino‐5‐iodopyridine were prepared from aqueous solutions. The hydrobromide salt, C₅H₆IN₂⁺·Br⁻·0.5H₂O, crystallizes as a hemihydrate, and exhibits hydrogen bonding and π‐stacking which stabilize the crystal structure. The hydrochloride salt, C₅H₆IN₂⁺·Cl⁻·H₂O·0.375HCl, crystallized as the hydrate and exhibits similar hydrogen bonding and π‐stacking in the lattice. The most interesting feature of the hydrochloride salt is the presence of an additional fractional HCl molecule which introduces disorder in the location of the water molecule. The additional proton from the fractional HCl molecule is accounted for by the presence of a partial hydronium ion on one of the water sites.     

Suzuki Cross‐coupling Method to Prepare 4,4″‐Diamino‐p‐terphenyl

The synthesis of 4,4″‐dinitro‐p‐terphenyl is accomplished by double Suzuki cross‐coupling. The product was reduced catalytically to give 4,4″‐diamino‐p‐terphenyl in 75% overall yield.     

Safer Conditions for the Curtius Rearrangement of 1,3,5‐Benzenetricarboxylic Acid

A rapid method to prepare 1,3,5‐triaminobenzene and its derivatives is the tris‐Curtius rearrangment of 1,3,5‐benzenetricarboxylic acid. The hazards associated with the acyl azide route are minimized by using 1,2‐dichloroethane as solvent. A second method that avoids acyl azide preparation uses diphenylphosphoryl azide to yield the tricarbamate in one step.     

Solvent‐Free Claisen Condensation of Isophorone and Verbenone with para‐Hydroxyethylaminobenzaldehydes

A solvent‐free Claisen condensation between isophorone or verbenone on two para‐hydroxyethylaminobenzaldehydes is described. The method provides the condensation products quickly and, in most cases, without chromatography.     

Palladium on Carbon-Catalyzed Cross-Coupling of Aryl Halides with Potassium p-Tolyltrifluoroborate in Air

Palladium supported on carbon (Pd/C) has been shown to be an effective catalyst for the cross-coupling of potassium p-tolyltrifluoroborate with a variety of aryl bromides and iodides. Yields ranging from moderate to good were obtained using Pd/C in ethanol/water mixtures with potassium carbonate as base at 50 °C under an air atmosphere.     

Cleaning requirements for silica‐coated sensors used in optical waveguide lightmode spectroscopy

Optical waveguide lightmode spectroscopy (OWLS), based on the incoupling of laser light into a waveguide sensor by an optical grating, allows for the in situ measurement of protein adsorption. Few reports have described cleaning methods for the surfaces of such sensors, and in this investigation, we compare common methods for cleaning of silica surfaces in relation to their effectiveness for cleaning silica‐coated waveguide sensors used in OWLS. For this purpose, atomic force microscopy (AFM) analysis of surface morphology and OWLS detection of protein adsorption kinetics were used to evaluate waveguide sensors before and after cleaning. While AFM line scans showed a substantial increase in average waveguide peak‐to‐valley height after RCA cleaning relative to all other methods tested, chemical etching owing to the alkaline component of the rolling circle amplification method rendered the waveguide unusable for detection of protein adsorption with OWLS. A revised method, based on replacement of the alkaline step with immersion in sodium dodecyl sulfate, was not only effective at cleaning OWLS waveguides off‐the‐shelf but also showed excellent protein adsorption reproducibility after ex situ cleaning. Moreover, the revised method showed excellent reproducibility when applied in situ, between repeated adsorption‐elution cycles. Copyright © 2013 John Wiley & Sons, Ltd.     

Dendron to Central Core S1–S1 and S2–Sn (n>1) Energy Transfers in Artificial Special Pairs Containing Dendrimers with Limited Numbers of Conformations

Two dendrimers consisting of a cofacial free‐base bisporphyrin held by a biphenylene spacer and functionalized with 4‐benzeneoxomethane (5‐(4‐benzene)tri‐10,15,20‐(4‐n‐octylbenzene)zinc(II)porphyrin) using either five or six of the six available meso‐positions, have been synthesized and characterized as models for the antenna effect in Photosystems I and II. The presence of the short linkers, ‐CH₂O‐, and long C₈H₁₇ soluble side chains substantially reduces the number of conformers (foldamers) compared with classic dendrimers built with longer flexible chains. This simplification assists in their spectroscopic and photophysical analysis, notably with respect to fluorescence resonance energy transfer (FRET). Both steady‐state and time‐resolved spectroscopic measurements indicate that the cofacial free bases and the flanking zinc(II)–porphyrin antennas act as energy acceptor and donor, respectively, following excitation in either the Q or Soret bands of the dendrimers. The rate constants for singlet electronic energy transfer (k_EET) extracted from the S₁ and S₂ fluorescence lifetimes of the donor in the presence and absence of the acceptor are ≤ (0.1–0.3)×10⁹ and ～2×10⁹ s^?1 for S₁→S₁ (range from a bi‐exponential decay model) and about 1.5×10¹² s^?1 for S₂→S_n (n>1). Comparisons of these experimental data with those calculated from Förster theory using orientation factors and donor–acceptor distances extracted from computer modeling suggest that a highly restricted number of the many foldamers facilitate energy transfer. These foldamers have the lowest energy by molecular modeling and consist of one or at most two of the flanking zinc porphyrin antennas folded so they lie near the central artificial special pair core with the remaining antennas located almost parallel to and far from it.