Probing cellular protein complexes using single-molecule pull-down

Proteins perform most cellular functions in macromolecular complexes. The same protein often participates in different complexes to exhibit diverse functionality. Current ensemble approaches of identifying cellular protein interactions cannot reveal physiological permutations of these interactions. Here we describe a single-molecule pull-down (SiMPull) assay that combines the principles of a conventional pull-down assay with single-molecule fluorescence microscopy and enables direct visualization of individual cellular protein complexes. SiMPull can reveal how many proteins and of which kinds are present in the in vivo complex, as we show using protein kinase A. We then demonstrate a wide applicability to various signalling proteins found in the cytosol, membrane and cellular organelles, and to endogenous protein complexes from animal tissue extracts. The pulled-down proteins are functional and are used, without further processing, for single-molecule biochemical studies. SiMPull should provide a rapid, sensitive and robust platform for analysing protein assemblies in biological pathways.     

Mixed search algorithm for protein folding

0　IntroductionThedeterminationofthefoldingpathwayfollowedbyaproteinintheconformationalspacefromthedenaturedstatetothenativestructureisstillanunsolvedproblem .Itsdifficultyismainlyduetotheenormousextensionoftheconformationalspaceandtoitsexponentialgrowthwhenthelengthoftheproteinchainincreases.HowaproteinsolvestheLevinthalparadox[1 ] ,i.e.,howitfoldstoitsnativestructurewithoutanexhaustivesearchintheconforma tionalspace,hasbeenlargelydebatedinRef.[2 5 ].Thenatureofthedrivingforcesinducingtheco…     

Chaperonin-mediated protein folding at the surface of groEL through a 'molten globule'-like intermediate.

Folding of two monomeric enzymes mediated by groE has been reconstituted in vitro. The groEL protein stabilizes the polypeptides in a conformation resembling the 'molten globule' state. Mg-ATP and groES then promote the acquisition of ordered tertiary structure at the surface of groEL. Folding requires the hydrolysis of about 100 ATP molecules per protein monomer. This active process of surface-mediated chain folding might represent a general mechanism for the formation of protein structure in vivo.     

预测蛋白质折叠结构的剪枝算法

为求解蛋白质折叠结构预测问题提出一种基于剪枝策略的启发式搜索算法.剪枝算法用一棵搜索树描述蛋白质构形的生长过程,通过定义权重、上下门槛制定一套有效的控制分支繁殖的规则,从而极大地提高了搜索的效率.采用国际文献公认的10个算例作为剪枝算法的实验测试集,并与目前国际上4个著名的算法进行比较,实验比较结果表明剪枝算法是一个高效的求解算法.     

Progress in measuring biophysical properties of membrane proteins with AFM single-molecule force spectroscopy

Membrane proteins are crucial in cell physiological activities and are the targets for most drugs.Thus,investigating the behaviors of membrane proteins not only provide deeper insights into cell function,but also help disease treatment and drug development.Atomic force microscopy is a unique tool for investigating the structure of membrane proteins.It can both image the morphology of single native membrane proteins with high resolution and,via single-molecule force spectroscopy(SMFS),directly measure their biophysical properties during molecular physiological activities such as ligand binding and protein unfolding.In the context of molecular biomechanics,SMFS has been successfully used to understand the structure and function of membrane proteins,complementing the static three-dimensional structures of proteins obtained by X-ray crystallography.Here,based on the authors’antigen-antibody binding force measurements in clinical tumor cells,the principle and method of SMFS is discussed,the progress in using SMFS to characterize membrane proteins is summarized,and challenges for SMFS are presented.     

求解蛋白质折叠问题的改进PERM算法

在学习PERM算法的基础上，指出了影响PERM算法效率的关键因素，进而提出了一种改进的PERM算法——IPERM(Improved PERM)．计算结果表明，IPERM的计算效率优于PERM算法，并且远高于基于蒙特卡罗的MSOE算法和基于重要性抽样的SISPER算法．     

Solving the membrane protein folding problem

One of the great challenges for molecular biologists is to learn how a protein sequence defines its three-dimensional structure. For many years, the problem was even more difficult for membrane proteins because so little was known about what they looked like. The situation has improved markedly in recent years, and we now know over 90 unique structures. Our enhanced view of the structure universe, combined with an increasingly quantitative understanding of fold determination, engenders optimism that a solution to the folding problem for membrane proteins can be achieved.     

Personification algorithm for protein folding problem：Improvements in PERM

PERM is the most efficient approach for solving protein folding problem based on simple lattice model. In this article a personification explanation of PERM is proposed. A new version of PERM, population control algorithm with two main improvements is presented: one is that it is able to redefine the weight and its predicted value in PERM,and the other is that it is able to unify the calculation of weight when choosing possible branches. The improved PERM is more efficient than the previous version; specifically it can find the known lowest energy states for the four well-known difficult instances and is generally several to hundreds times faster than PERM. It is noteworthy that with the improved PERM we found new lowest energy configurations of three of the four difficult problems missed in previous papers.     

Mapping the transition state and pathway of protein folding by protein engineering

In the transition state for unfolding of barnase, the hydrophobic core between the major alpha-helix and beta-sheet is somewhat weakened, the C terminus of the major helix is largely intact but its N terminus is exposed and a major loop has been invaded by solvent.     

Efficient and reproducible folding simulations of the Trp-cage protein with multiscale molecular dynamics

Folding simulations are often time-consuming or highly sensitive to the initial conformation of the simulation even for mini protein like the Trp-cage. Here, we present a multiscale molecular dynamics method which appears to be both efficient and insensitive to the starting conformation based on the testing results from the Trp-cage protein. In this method the simulated system is simultaneously mod- eled on atoms and coarse-grained particles with incremental coarsening levels. The dynamics of coarse-grained particles are adapted to the recent trajectories of finer-grained particles instead of fixed and parameterized energy functions as used in previous coarse-grained models. In addition, the compositions of coarse-grained particles are allowed to be updated automatically based on the coherence during its history. Starting from the fully extended conformation and other several different conformations of the Trp-cage protein, our method successfully finds out the native-like conformations of the Trp-cage protein in the largest cluster of the trajectories in all of the eight performed simulations within at most 10 ns simulation time. The results show that approaches based on multiscale modeling are promising for ab initio protein structure prediction.     

Implications of thermodynamics of protein folding for evolution of primary sequences

Natural proteins exhibit essentially two-state thermodynamics, with one stable fold that dominates thermodynamically over a vast number of possible folds, a number that increases exponentially with the size of the protein. Here we address the question of whether this feature of proteins is a rare property selected by evolution or whether it is in fact true of a significant proportion of all possible protein sequences. Using statistical procedures developed to study spin glasses, we show that, given certain assumptions, the probability that a randomly synthesized protein chain will have a dominant fold (which is the global minimum of free energy) is a function of temperature, and that below a critical temperature the probability rapidly increases as the temperature decreases. Our results suggest that a significant proportion of all possible protein sequences could have a thermodynamically dominant fold.     

药物与蛋白质相互作用的荧光光谱法研究概述

结合1972年以来的内容、研究方法和进展.     

荧光光谱法研究六噻吩与富勒烯的相互作用

文章采用荧光光谱法研究在六嚷吩(6T)/富勒烯(C60,C70和C84)混合液中由电子转移所引起的荧光猝灭现象,并由Stern-Volmer方程分别确定了6T/C60、6T/C70和6T/C84混合液中的双分子猝灭速率常数.结果表明,双分子猝灭速率常数与富勒烯的电子亲和力相关,对6T/C60、6T/C70和6T/C84...     

荧光分析法研究抗氧化剂与单重态氧的反应能力

本文以二苯基苯并呋喃为发荧光的单重态氧(~1O_2)接受体,并作为与抗氧化剂(X)竞争反应中的标准物质。根据它在反应时引起的荧光强度变化,利用类似的Stern-Volmer方程式作图,从中求得各X的β值(~1O_2自行失活为基态氧的速度常数和~1O_2与X反应的速度常数kx的比值)和kx值。在选用的五类X中,以色满类的kx为最大(kx=3.78×10~8m~(-1)s~(-1));双螺色满类次之(9—10×10~7m~(-1)s~(-1));再次为对苯二酚类(6—7×10~7m~(-1)s~(-1))和双酚类(2—3×10~7m~(-1)s~(-1));苯酚类最小(5×10~6m~(-1)s~(-1))。将上述各X加入彩色相纸的品红层乳剂中进行光退色试验时,所得结果亦相一致。即kx愈大,染料影像的密度变化愈小。     

高盐条件下溶菌酶在疏水表面的折叠吸附

采用摇床法测定不同硫酸铵浓度时天然溶菌酶（Lys）在疏水作用色谱填料PEG-600上的吸附等温线,运用计量置换理论（SDT）计算出不同盐浓度条件下蛋白在吸附过程中的吸附自由能.得出在高盐浓度时（大于1.5mol/L）,总的置换吸附自由能为负值,推断出吸附是自发进行的,且可以定量计算出蛋白与PEG-600之间的吸附亲和能与水分子的解吸能.结合与吸附等温线相同条件下焓变测量数据表明,随盐浓度增大熵值增加,是因为去水合作用导致的熵增大为吸附提供了驱动力的缘故.其结果可以很好地解释液/固界面上折叠吸附的规律.     

麦芽糖在CdS量子点表面吸附的荧光光谱

用巯基丙酸作稳定剂,合成了水溶性好、单分散的Cd S量子点,利用麦芽糖对Cd S量子点的荧光猝灭效应,研究了麦芽糖在Cd S量子点表面的吸附行为.结果表明:量子点的荧光猝灭效应受到p H值和量子点浓度的显著影响,并且与吸附在量子点表面的麦芽糖分子数有关,麦芽糖分子在Cd S量子点表面吸附符合Langmuir等温吸附方程.c/ΔF与浓度c成很好的直线关系,浓度的变化范围达到3个数量级.根据Langmuir等温吸附方程式,在较低的浓度范围内,ΔF与浓度c也成很好的直线关系,利用这种直线关系可以建立麦芽糖的定量分析方法,检出限达到nmol级.     

A pre-existing hydrophobic collapse in the unfolded state of an ultrafast folding protein

Insights into the conformational passage of a polypeptide chain across its free energy landscape have come from the judicious combination of experimental studies and computer simulations. Even though some unfolded and partially folded proteins are now known to possess biological function or to be involved in aggregation phenomena associated with disease states, experimentally derived atomic-level information on these structures remains sparse as a result of conformational heterogeneity and dynamics. Here we present a technique that can provide such information. Using a 'Trp-cage' miniprotein known as TC5b (ref. 5), we report photochemically induced dynamic nuclear polarization NMR pulse-labelling experiments that involve rapid in situ protein refolding. These experiments allow dipolar cross-relaxation with hyperpolarized aromatic side chain nuclei in the unfolded state to be identified and quantified in the resulting folded-state spectrum. We find that there is residual structure due to hydrophobic collapse in the unfolded state of this small protein, with strong inter-residue contacts between side chains that are relatively distant from one another in the native state. Prior structuring, even with the formation of non-native rather than native contacts, may be a feature associated with fast folding events in proteins.     

Hydrogen bonding at the water surface revealed by isotopic dilution spectroscopy

The air-water interface is perhaps the most common liquid interface. It covers more than 70 per cent of the Earth's surface and strongly affects atmospheric, aerosol and environmental chemistry. The air-water interface has also attracted much interest as a model system that allows rigorous tests of theory, with one fundamental question being just how thin it is. Theoretical studies have suggested a surprisingly short 'healing length' of about 3??ngstr?ms (1?? = 0.1?nm), with the bulk-phase properties of water recovered within the top few monolayers. However, direct experimental evidence has been elusive owing to the difficulty of depth-profiling the liquid surface on the ?ngstr?m scale. Most physical, chemical and biological properties of water, such as viscosity, solvation, wetting and the hydrophobic effect, are determined by its hydrogen-bond network. This can be probed by observing the lineshape of the OH-stretch mode, the frequency shift of which is related to the hydrogen-bond strength. Here we report a combined experimental and theoretical study of the air-water interface using surface-selective heterodyne-detected vibrational sum frequency spectroscopy to focus on the 'free OD' transition found only in the topmost water layer. By using deuterated water and isotopic dilution to reveal the vibrational coupling mechanism, we find that the free OD stretch is affected only by intramolecular coupling to the stretching of the other OD group on the same molecule. The other OD stretch frequency indicates the strength of one of the first hydrogen bonds encountered at the surface; this is the donor hydrogen bond of the water molecule straddling the interface, which we find to be only slightly weaker than bulk-phase water hydrogen bonds. We infer from this observation a remarkably fast onset of bulk-phase behaviour on crossing from the air into the water phase.     

Role of ATP and disulphide bonds during protein folding in the endoplasmic reticulum.

Being topologically equivalent to the extracellular space, the lumen of the endoplasmic reticulum (ER) provides a unique folding environment for newly synthesized proteins. Unlike other compartments in the cell where folding occurs, the ER is oxidizing and therefore can promote the formation of disulphide bonds. The reducing agent dithiothreitol, when added to living cells, inhibits disulphide formation with profound effects on folding. Taking advantage of this effect, we demonstrate here that folding of influenza haemagglutinin is energy dependent. Metabolic energy is required to support the correct folding and disulphide bond formation in this well characterized viral glycoprotein, to rescue misfolded proteins from disulphide-linked aggregates, and to maintain the oxidized protein in its folded and oligomerization-competent state.     

Estimation of the polarity of the protein interior by optical spectroscopy

Crystallographic studies of myoglobin have shown that the haem pocket is lined with nonpolar amino-acid residues. In order to estimate the true polarity of the interior of proteins, certain studies have used bound fluorophores, the spectroscopic properties of which reflect the polarity of their environment. These studies have most often used 1-amino-8-naphthalene sulphonate (ANS) as a probe, but a more suitable probe, in principle, is 6-propionyl 2-(N,N-dimethyl)aminonaphthalene (PRODAN). We have synthesized a molecule with the advantageous spectroscopic properties of PRODAN but with a higher affinity for apomyogloblin: 2'-(N,N-dimethyl)amino-6-naphthopyl-4-trans-cyclohexanoic acid (DANCA), and report here its use to determine the polarity of the myoglobin haem pocket. Our results show that the pocket is actually a polar environment, and the polarity can be accounted for by peptide amide dipoles.