基于镜像酶正交酶切的蛋白质复合物规模化精准分析新方法

蛋白质主要以复合物的形式参与各项生命活动.化学交联质谱(CXMS)技术作为近年来新兴的蛋白质复合物解析技术,不仅可实现蛋白质复合物规模化解析,而且普遍适用于任意相对分子质量和纯度的蛋白质复合物样品,因此已成为X-射线晶体衍射技术、冷冻电镜技术等蛋白质复合物解析经典技术的重要补充.目前,CXMS主要采用胰蛋白酶将交联后的...     

含磷钼酸的超分子复合材料的制备和结构研究

介绍了一类端基含羧基结构的液晶性表面活性剂CDDA通过静电相互作用与磷钼酸(HPMo)进行复合,得到表面包覆柔性烷基链和羧基端基的复合物SEP-PMo,并通过元素分析、热失重等方法确认其化学结构.该复合物表现出稳定的液晶相,DSC,PLM,SAXS和TEM等研究表明其为层状相结构.进一步将SEP-PMo复合物与P4VP混合,通过羧基与吡啶环上氮的氢键相互作用,得到稳定的PMo和聚合物的复合物,同时对比研究了HPMo与P4VP直接共混后的静电复合物结构,表明经表面活性剂修饰后的PMo可在聚合物中保持其聚集态结构.     

原位冷冻电子断层扫描的发展及在生物研究方面的应用

对生物大分子复合物的研究和结构分析对于全面了解其功能和生物学意义至关重要. 冷冻电子显微镜在提供生物大分子结构及大分子分布等方面起到重要的作用. 近年来, 冷冻电子显微镜的硬件和软件的发展进一步提高了冷冻电子显微镜的有效性, 使其对各种生物结构、 蛋白质结构的解析更加准确快捷. 但是, 对于生物系统来说, 蛋白质和大分子复合物等均处于复杂的生理环境中, 因此原位检测生物分子的三维结构对于生物体系和结构生物学具有重要意义. 冷冻电子断层扫描作为一种功能强大的技术, 可以无需标记直接通过冷冻样品的固有衬度识别生物大分子的结构, 并且可在原位生理环境中对生物分子进行纳米级分辨率的三维成像. 本文综述了与冷冻电子断层扫描相关的样品制备和数据处理技术, 并总结了冷冻电子断层扫描技术在分离的大分子复合物和整个细胞或组织中的生物学应用.     

基于可断裂三功能探针的酪氨酸磷酸化蛋白质复合物的规模化分析

在细胞的信号转导过程中,磷酸化酪氨酸（Phosphotyrosine, pTyr）信号在许多通路中起着重要的调控作用。受pTyr信号调控的蛋白质复合物是信号传递早期过程中的关键分子机器,分析该类动态蛋白质复合物具有重要的意义。Photo-pTyr-scaffold是一种结合了化学探针与pTyr识别蛋白质结构域的化学蛋白质组学分析策略,采用该策略已经实现了对表皮生长因子受体（Epidermal growth factor receptor, EGFR）通路相关的pTyr信号蛋白质复合物的规模化分析。但是,该方法无法解析所鉴定复合物的一一对应关系,增加了后续复合物解析的复杂性。本研究在Photo-pTyr-scaffold探针设计的基础上,将可断裂基团引入至其生物素富集端,设计合成了新型的可断裂三功能探针,以实现对富集产物的可控洗脱。基于pTyr信号蛋白质复合物在化学交联后的分子量差异,利用十二烷基磺酸钠-聚丙烯酰胺凝胶电泳实现了对洗脱的pTyr蛋白质复合物的分离,进一步将不同分子量区域的蛋白质进行胶内酶解和质谱分析。理论上,发生化学交联的pTyr蛋白质复合物将在高于原蛋白质分子量的区域被...     

蛋白质表面模块划分及其在结合位点预测中的应用

蛋白质-蛋白质复合物的结合位点预测是计算分子生物学的一个难题. 本文对蛋白质-蛋白质复合物数据集Benchmark 3.0 中的双链蛋白质复合物进行了研究, 计算了单体的残基溶剂可接近表面积和残基间的接触面积, 并据此提出了蛋白质表面模块划分方法. 发现模块的溶剂可接近表面积与其内部接触面积的乘积(PSAIA)值能够提供结合位点的信息. 在78 个双链蛋白质复合物中, 有74 个体系其受体或配体上具有最大或次大PSAIA值的模块是界面模块. 将该方法获得的结合位点信息应用在CAPRI竞赛Target 39 的复合物结构预测中取得了较好的结果. 本文提出的基于模块的蛋白质结合位点预测方法不同于以残基为基础且仅考虑表面残基的传统预测方法, 为蛋白质-蛋白质复合物结合位点预测提供了新思路.     

应用全内反射单分子荧光成像研究蛋白复合物亚基组成

细胞的生化过程大都是由蛋白复合物完成的,研究蛋白复合物亚基的组成对于了解蛋白质的结构和生物学功能具有重要的意义,然而如何准确确定蛋白复合物中蛋白质亚基的数量（stoichiometry）仍然是一个挑战.近年来,活细胞体系单分子荧光成像技术的不断发展为原位实时动态地研究蛋白质的结构和性质提供了新的手段.本文主要介绍了应用活细胞全内反射单分子荧光成像技术表征细胞膜区蛋白复合物组成的3种方法,包括单分子漂白步数分析、荧光强度统计分布以及蛋白运动分析,并结合其基本原理介绍了这几种方法在活细胞体系膜蛋白研究中的应用.     

用于寡糖链分析的HPLC柱前衍生化方法研究进展

糖复合物中的糖链具有广泛的生理和病理作用. 在研究糖复合物中糖链的功能时, 需要解析其化学结构, 以便进一步研究结构与功能的关系. 糖链的释放常采用化学法或酶法, 如何纯化释放的糖链对结构解析至关重要, 目前常用的方法是高效液相色谱法(HPLC), 为提高检测的灵敏度, 往往需要对糖链衍生化. 对糖链的HPLC柱前衍生化方法进行综述和评价.     

Hg^2＋ -牛血清白蛋白复合体系中蛋白质微观结构的研究

研究了Hg2+在生物体内与牛血清白蛋白相互作用的毒性机理以及蛋白质的微观结构变化.测定了Hg2+与牛血清白蛋白(BSA)复合体系的红外光谱(FT-IR)和圆二色谱(CD),并对图谱进行拟合解析处理.红外光谱实验数据表明Hg2+与BSA发生作用的结合位点可能包括-SH、-OH和-NH基团,采用红外拟合技术对BSA二级结构的变化进行了研究,结果表明蛋白质α-螺旋结构含量降低,β-折叠结构含量升高.圆二色谱图也表明由于一定浓度的Hg2+与BSA结合,从而导致蛋白质的二级结构被破坏,这与拟合红外光谱得到的蛋白质二级结构数据相吻合.Hg2+与牛血清蛋白作用致使蛋白质的构象改变,形成金属离子与蛋白质作用的复合物,因而蛋白质失去活性导致生物体发生病变.     

氢氘交换质谱技术在蛋白质和蛋白复合物结构研究中的应用进展

蛋白质是生命功能的执行者,其功能的发挥受自身结构动态变化、与其他生物分子的相互作用及修饰等因素的调节。因此,对蛋白质及蛋白复合物结构的研究有助于揭示重要生命过程中的分子机理与机制。氢氘交换质谱(Hydrogen deuterium exchange mass spectrometry,HDX-MS)是研究蛋白质结构、动态变化和相互作用的强有力工具,也是传统生物物理手段的重要补充。该文综述了HDX-MS的基本原理、机制、实验方法和研究最新进展,并从蛋白质自身动态变化、蛋白质-小分子相互作用、蛋白质-蛋白质相互作用3个方面介绍了近年来HDX-MS在蛋白及蛋白复合物研究中的应用进展。     

BSA-羟基磷灰石可溶性复合物的FTIR光谱

利用富立叶变换红外光谱对水溶性牛血清白蛋白(BSA)羟基磷灰石复合物的组成及结构进行了研究.结果表明,其组成具有非化学计量的性质,且复合物中BSA与羟基磷灰石间存在相互作用.从而增加了羟基磷灰石在水中的溶解度.正是由于羟基磷灰石与蛋白质形成了水溶性的复合物,使羟基磷灰石在蛋白质结构的基质上成核和自组装成为可能,从而引起和促进了生物矿化过程.     

蛋白质、凝胶电泳及其分析应用

蛋白质是重要的生物高分子，具有催化、传输、运动、防御和调节等重要生理功能，其分离、纯化和表征对理解和利用它们在生命过程中的作用具有重大理论意义和实际价值。凝胶电泳是蛋白质测定中应用最广泛和最强有力的工具。本文讨论凝胶电泳方法及其在蛋白质分析方面的新进展。首先介绍蛋白质的性质和功能，然后讨论蛋白质试样制备方法，最后评述各种凝胶电泳分离技术及其在蛋白质分离、纯化和表征等方面的应用。     

Activity-Directed Synthesis of Inhibitors of the p53/hDM2 Protein–Protein Interaction

Protein–protein interactions (PPIs) provide a rich source of potential targets for drug discovery and biomedical science research. However, the identification of structural-diverse starting points for discovery of PPI inhibitors remains a significant challenge. Activity-directed synthesis (ADS), a function-driven discovery approach, was harnessed in the discovery of the p53/hDM2 PPI. Over two rounds of ADS, 346 microscale reactions were performed, with prioritisation on the basis of the activity of the resulting product mixtures. Four distinct and novel series of PPI inhibitors were discovered that, through biophysical characterisation, were shown to have promising ligand efficiencies. It was thus shown that ADS can facilitate ligand discovery for a target that does not have a defined small-molecule binding site, and can provide distinctive starting points for the discovery of PPI inhibitors.     

Radiation Damage and Racemic Protein Crystallography Reveal the Unique Structure of the GASA/Snakin Protein Superfamily

Proteins from the GASA/snakin superfamily are common in plant proteomes and have diverse functions, including hormonal crosstalk, development, and defense. One 63‐residue member of this family, snakin‐1, an antimicrobial protein from potatoes, has previously been chemically synthesized in a fully active form. Herein the 1.5 Å structure of snakin‐1, determined by a novel combination of racemic protein crystallization and radiation‐damage‐induced phasing (RIP), is reported. Racemic crystals of snakin‐1 and quasi‐racemic crystals incorporating an unnatural 4‐iodophenylalanine residue were prepared from chemically synthesized d ‐ and l ‐proteins. Breakage of the C?I bonds in the quasi‐racemic crystals facilitated structure determination by RIP. The crystal structure reveals a unique protein fold with six disulfide crosslinks, presenting a distinct electrostatic surface that may target the protein to microbial cell surfaces.     

Protein Ligation of the Photosynthetic Oxygen-Evolving Center

Photosynthetic water oxidation is catalyzed by a unique Mn(4)Ca cluster in Photosystem II. The ligation environment of the Mn(4)Ca cluster optimizes the cluster's reactivity at each step in the catalytic cycle and minimizes the release of toxic, partly oxidized intermediates. However, our understanding of the cluster's ligation environment remains incomplete. Although the recent X-ray crystallographic structural models have provided great insight and are consistent with most conclusions of earlier site-directed mutagenesis studies, the ligation environments of the Mn(4)Ca cluster in the two available structural models differ in important respects. Furthermore, while these structural models and the earlier mutagenesis studies agree on the identity of most of the Mn(4)Ca cluster's amino acid ligands, they disagree on the identity of others. This review describes mutant characterizations that have been undertaken to probe the ligation environment of the Mn(4)Ca cluster, some of which have been inspired by the recent X-ray crystallographic structural models. Many of these characterizations have involved Fourier Transform Infrared (FTIR) difference spectroscopy because of the extreme sensitivity of this form of spectroscopy to the dynamic structural changes that occur during an enzyme's catalytic cycle.     

Protein profile of the HeLa cell line

HeLa cells are widely used for all kinds of in vitro studies in biochemistry, biology and medicine. Knowledge on protein expression is limited and no comprehensive study on the proteome of this cell type has been reported so far. We applied proteomics technologies to analyze the proteins of the HeLa cell line. The proteins were analyzed by two-dimensional (2D) gel electrophoresis and identified by matrix-assisted laser desorption ionization mass spectrometry (MS) on the basis of peptide mass fingerprinting, following in-gel digestion with trypsin. Approximately 3000 spots, excised from six two-dimensional gels, were analyzed. The analysis resulted in the identification of about 1200 proteins that were the products of 297 different genes. The HeLa cell database includes proteins with important functions and unknown functions, representing today one of the largest two-dimensional databases for eukaryotic proteomes and forming the basis for future expressional studies at the protein level.     

Folding of the Tau Protein on Microtubules

Microtubules are regulated by microtubule‐associated proteins. However, little is known about the structure of microtubule‐associated proteins in complex with microtubules. Herein we show that the microtubule‐associated protein Tau, which is intrinsically disordered in solution, locally folds into a stable structure upon binding to microtubules. While Tau is highly flexible in solution and adopts a β‐sheet structure in amyloid fibrils, in complex with microtubules the conserved hexapeptides at the beginning of the Tau repeats two and three convert into a hairpin conformation. Thus, binding to microtubules stabilizes a unique conformation in Tau.     

Revisiting the Rate-Limiting Step of the ANS–Protein Binding at the Protein Surface and Inside the Hydrophobic Cavity

8-Anilino-1-naphthalenesulfonic acid (ANS) is used as a hydrophobic fluorescence probe due to its high intensity in hydrophobic environments, and also as a microenvironment probe because of its unique ability to exhibit peak shift and intensity change depending on the surrounding solvent environment. The difference in fluorescence can not only be caused by the microenvironment but can also be affected by the binding affinity, which is represented by the binding constant (K). However, the overall binding process considering the binding constant is not fully understood, which requires the ANS fluorescence binding mechanism to be examined. In this study, to reveal the rate-limiting step of the ANS–protein binding process, protein concentration-dependent measurements of the ANS fluorescence of lysozyme and bovine serum albumin were performed, and the binding constants were analyzed. The results suggest that the main factor of the binding process is the microenvironment at the binding site, which restricts the attached ANS molecule, rather than the attractive diffusion-limited association. The molecular mechanism of ANS–protein binding will help us to interpret the molecular motions of ANS molecules at the binding site in detail, especially with respect to an equilibrium perspective.     

Protein structure along the order-disorder continuum

Thermal fluctuations cause proteins to adopt an ensemble of conformations wherein the relative stability of the different ensemble members is determined by the topography of the underlying energy landscape. "Folded" proteins have relatively homogeneous ensembles, while "unfolded" proteins have heterogeneous ensembles. Hence, the labels "folded" and "unfolded" represent attempts to provide a qualitative characterization of the extent of structural heterogeneity within the underlying ensemble. In this work, we introduce an information-theoretic order parameter to quantify this conformational heterogeneity. We demonstrate that this order parameter can be estimated in a straightforward manner from an ensemble and is applicable to both unfolded and folded proteins. In addition, a simple formula for approximating the order parameter directly from crystallographic B factors is presented. By applying these metrics to a large sample of proteins, we show that proteins span the full range of the order-disorder axis.     

Radiation Chemical Studies of Protein Reactions: Effect of Post-irradiation on the Breaking of Secondary Bonding in Protein

When protein was irradiated by prays from a ⁶⁰Co source, a post-irradiation effect of the breaking of secondary bonding in protein was caused. An empirical equation for the reactivity decay was obtained, and the phenomena were explained on the basis of molecular mechanism.