球状蛋白质分子中氨基酸紧密接触对性质的研究

采用CSU软件 (Contactsofstructuralunits) ,对 61种球状蛋白质分子中氨基酸紧密接触对 (Residue residuecontact)进行了研究 .重点研究了不同氨基酸在形成远程紧密接触对 (Long rangecontact)和近程紧密接触对 (Short rangecontact)时的不同能力 .发现氨基酸Leu,Val,Ile,Met,Phe,Tyr,Cys,Trp(疏性氨基酸 ,H)比较容易形成远程紧密接触对 ,氨基酸Glu,Gln ,Asp ,Asn,Lys,Ser,Arg,Pro(亲水氨基酸 ,P)比较难形成远程紧密接触对 ,而氨基酸Ala,Gly,Thr,His(中性氨基酸 ,N)在形成远程紧密接触对时能力一般 .它们平均每个氨基酸可形成 6 0 3 ,3 64和 4 43个远程紧密接触对 .同时它们在形成近程紧密接触对时能力非常接近 ,平均每个氨基酸可形成的近程紧密接触对数目在 2 3 4～ 2 85变化 ,差别非常小 .亲水氨基酸 (P) ,中性氨基酸 (N)和疏水性氨基酸 (H)在蛋白质分子结构稳定性上起着不同的作用     

What crystals of small analogs are trying to tell us about cellulose structure

The molecular geometries from crystal structures of 23 small molecules such as cellobiose were reviewed and extrapolated to give model cellulose chains. Within a given model, all monosaccharide units and their linkages are identical so the models are regular helices. Despite fairly large ranges for the glycosidic linkage torsion angles and , 29° and 57°, respectively, there is little variation in the n and h parameters of the model helices. They are extended, with h values (the advance per residue along the helix axis) of 5.04–5.27 Å. Some models were slightly right-handed, with n values up to 2.12 residues per helix turn. Left-handed models were in the majority, and their n values were as large as –2.91. These results are consistent with known structures of cellulose and its derivatives. An exception comes from a heavily derivatized cellobiose molecule. It yields right-handed helices with n 4.5 and h 3 Å. Because one half turn of this helix reverses the direction of the chain in a compact region, the linkage geometry is a model for chain-folding. Other derivatives that are unable to form the O3O5 hydrogen bond gave left-handed helices. The puckering of the glucose rings was also surveyed. A number of rings in small molecule structures are puckered to a degree that is similar to the puckering determined for methyl cellotrioside, cellotetraose, cellulose I and cellulose II.     

Adaptive Constrained Control of Unknown Strict Feedback Nonlinear Systems With Dead Zone Input北大核心CSCD

研究了具有死区输入的预设约束未知高阶严格反馈非线性系统的控制问题,提出了一种基于免疫函数的自抗扰预设漏斗约束自适应控制策略。首先,针对系统内部的未知问题,采用免疫函数与扩张状态观测器结合对系统内部未知项进行观测;其次,通过Lyapunov方法与漏斗控制相结合设计控制器,使得跟踪误差能够维持在预先设定的漏斗约束范围内;同时,利用双曲正切函数速率变化快这一特性设计自适应控制律,引入指令滤波器避免反步法中重复求导问题,分析证明了闭环系统所有信号的有界性。仿真实例表明了控制方法的有效性。     

Variable low-mass filtering using an electrodynamic ion funnel

An adjustable low-mass filter has been developed for an electrospray ionization (ESI) source to block ions associated with unwanted background species from entering the mass spectrometer. The low-mass filter is made by using an adjustable potential energy barrier from the conductance-limiting plate of an electrodynamic ion funnel, which prohibits species with higher ion mobilities from exiting the ESI source. We show that this arrangement provides a linear voltage adjustment for low-mass filtering from m/z 0 to 500. Mass filtering above m/z 500 is also performed; however, higher-mass species are attenuated. The mass filter was tested with a liquid chromatography/mass spectrometry (LC/MS) analysis of a bovine serum albumin (BSA) tryptic digest and resulted in the ability to block low-mass, background species, which accounted for 40-70% of the total ion current immediately behind the ESI source during peak elution and detection.     

A Water Molecule Triggers Guest Exchange at a Mono-Zinc Centre Confined in a Biomimetic Calixarene Pocket: a Model for Understanding Ligand Stability in Zn Proteins

In this study, the ligand exchange mechanism at a biomimetic Zn^II centre, embedded in a pocket mimicking the possible constrains induced by a proteic structure, is explored. The residence time of different guest ligands (dimethylformamide, acetonitrile and ethanol) inside the cavity of a calix[6]arene-based tris(imidazole) tetrahedral zinc complex was probed using 1D EXchange SpectroscopY NMR experiments. A strong dependence of residence time on water content was observed with no exchange occurring under anhydrous conditions, even in the presence of a large excess of guest ligand. These results advocate for an associative exchange mechanism involving the transient exo-coordination of a water molecule, giving rise to 5-coordinate Zn^II intermediates, and inversion of the pyramid at the Zn^II centre. Theoretical modelling by DFT confirmed that the associative mechanism is at stake. These results are particularly relevant in the context of the understanding of kinetic stability/lability in Zn proteins and highlight the key role that a single water molecule can play in catalysing ligand exchange and controlling the lability of Zn^II in proteins.     

Research Progress and Application of Ion Funnel Technique

Ion funnel is a new-style ion guider which can reduce spatial divergence and energy dispersity of the transmission ions by using radio frequency (RF) electric field to confine the ions radially and the direct current (DC) axial electric field to move the ions toward the exit, and thus it can greatly increase the ion transmission efficiency and improve the sensitivity of the mass spectrometry. Since ion funnel was invented in 1997, it has attracted a close attention of mass spectrometry scientists all over the world. Ion funnel has been used in various kinds of mass spectrometry, and built a bridge with high efficiency ion transmission between low vacuum ionization source and high vacuum mass analyzer. In this paper, the principle, technology development, and application progress of ion funnel are reviewed, and the future prospects are prospected.     

Sensitive detection of drug vapors using an ion funnel interface for secondary electrospray ionization mass spectrometry

In this study, we use an ion funnel (IF) at ambient pressure to enhance the sensitivity of secondary electrospray ionization (SESI). Atenolol, salbutamol and cocaine as test compounds are delivered to the SESI interface in the gas phase and are charged with three nano electrosprays. In our experiments, we show that the compounds can be detected at concentrations in the low pptv range, which is an increase of two orders of magnitude compared with the results without the IF. With a standard SESI interface, the compounds could not be detected at all. With the use of the SESI IF interface for the headspace analysis of bananas and limes, we can detect many more compounds and at higher intensities than with a standard SESI interface. Copyright © 2012 John Wiley & Sons, Ltd.     

Macrocycles consisting of flexible and rigid segments: enforced folding and host-guest inclusion exciplex formation

Macrocycles consisting of two tris(phenylene ethynylene) (or tri-PE) units connected via two flexible linkers adopt an ‘unfolded’ conformation that is converted into a folded conformation upon introducing intramolecular hydrogen bonding interaction. These foldable macrocycles are capable of forming inclusion charge transfer (CT) complex with electron-deficient small aromatics.     

模型多肽Trp-Cage折叠形成机制的研究进展

蛋白质折叠是目前结构生物学领域的核心问题之一, 理解蛋白质结构折叠机制及其与生物功能之间的相互关系一直是生命科学家非常重要的研究内容, 并且该研究受到越来越多不同学科领域研究工作者的高度重视. 蛋白质大多数在数十毫秒、微秒或几秒内完成自我折叠过程, 但其折叠过程中所发生的分子结构精细转变却在纳秒甚至更短时间尺度内完成. 由于其折叠时间分辨率的限制, 目前无论是从常规实验还是理论计算角度对其研究都存在一定的难度. 本文首先概述了蛋白质折叠研究在实验和理论模拟方面存在的一些问题,然后以结构典型且可快速折叠的人工设计多肽Trp-cage为例,主要对其折叠过渡温度、折叠形成模型及其肽链上关键氨基酸残基在折叠过程中的作用三个方面进行了详细讨论, 综述了模型多肽Trp-cage的折叠动力学行为分别在实验和理论模拟方面的研究进展. 最后就如何有效化解蛋白质残基间相互作用网络进而降低其折叠机制的复杂性提出了一些新的建议, 不仅有助于阐明该迷你蛋白Trp-cage快速折叠、稳定形成的驱动力成因, 而且也能为蛋白质折叠机制研究和多肽设计提供有益参考.     

Prediction of entrance length and mass suction rate for a cylindrical sucking funnel

Conservation equations for mass, momentum and energy have been solved numerically for a cylindrical funnel with louvers (lateral openings on the side wall of the cylindrical funnel through which air can come into it) to compute the suction rate of air into the funnel. The nozzle placed centrally at the bottom of the cylinder ejects high‐velocity hot gaseous products so that atmospheric air gets sucked into the funnel. The objective of the work is to compute the ratio of the rate of mass suction to that of the mass ejected by the nozzle for different operating conditions and geometrical size of the funnel. From the computation it has been found that there exists optimum funnel diameter and optimum funnel height for which the mass suction is the highest. The protruding length of the nozzle into the funnel has almost no effect on the mass suction rate after a certain funnel height. The louvers opening area has a very high impact on the mass suction rate. The entrance length for such a sucking funnel is strikingly much lower compared with a simple cylindrical pipe having uniform flow at the inlet at same Reynolds number. A new correlation has been developed to propose the entrance length for a sucking pipe, the rate of mass suction into it and the exhaust plume temperature over a wide range of operating parameters that are normally encountered in a general funnel operations of naval or merchant ship. Copyright © 2009 John Wiley & Sons, Ltd.