Protein inference: A protein quantification perspective

In mass spectrometry-based shotgun proteomics, protein quantification and protein identification are two major computational problems. To quantify the protein abundance, a list of proteins must be firstly inferred from the raw data. Then the relative or absolute protein abundance is estimated with quantification methods, such as spectral counting. Until now, most researchers have been dealing with these two processes separately. In fact, the protein inference problem can be regarded as a special protein quantification problem in the sense that truly present proteins are those proteins whose abundance values are not zero. Some recent published papers have conceptually discussed this possibility. However, there is still a lack of rigorous experimental studies to test this hypothesis.In this paper, we investigate the feasibility of using protein quantification methods to solve the protein inference problem. Protein inference methods aim to determine whether each candidate protein is present in the sample or not. Protein quantification methods estimate the abundance value of each inferred protein. Naturally, the abundance value of an absent protein should be zero. Thus, we argue that the protein inference problem can be viewed as a special protein quantification problem in which one protein is considered to be present if its abundance is not zero. Based on this idea, our paper tries to use three simple protein quantification methods to solve the protein inference problem effectively. The experimental results on six data sets show that these three methods are competitive with previous protein inference algorithms. This demonstrates that it is plausible to model the protein inference problem as a special protein quantification task, which opens the door of devising more effective protein inference algorithms from a quantification perspective. The source codes of our methods are available at: http://code.google.com/p/protein-inference/.     

富硒灵芝中一种新含硒蛋白的纯化、性质及其自由基清除活性研究

通过硫酸铵沉淀、离子交换层析和分子排阻层析等方法, 从富硒灵芝中获得了一种新的含硒蛋白, 命名为Se-GL-P, 并研究了此蛋白的性质、抗氧化活性与其硒含量间的关系. 结果表明, 此蛋白的分子量为36600, 分子中约含有19.8%的糖链, N端的氨基酸残基序列为DINGGGATLPQKLYLTPDVL, 属于DING蛋白家族. 硒含量为4.87 mg/g, 具有较高的羟自由基和超氧自由基清除活性. 研究发现, Se-GL-P的抗氧化活性的提高与其中硒含量的提高相关.     

Two-dimensionally self-arranged protein nanoarrays on diblock copolymer templates

Novel methods for creating protein arrays with two-dimensional control can significantly enhance basic biological research as well as various bioarray applications. We demonstrate that the structural variety and chemical heterogeneity of self-assembled, hexagonal polystyrene-b-poly(vinylpyridine) micelles can be successfully exploited as templates for easy and rapid fabrication of functional protein arrays over a large scale. Spontaneous formation of such polymeric template-guided protein molecules yields high-density protein arrays that exhibit repeat spacings in a nanoscopic dimension. The ensuing self-assembled protein molecules in the array maintain their natural conformation and activity over a very long time period. By tuning the size of the underlying block copolymer templates, our amphiphilic diblock copolymer-based approach to create high-density protein patterns also permits spatial control over two-dimensional repeat spacings of protein nanoarrays. These unique advantages of polystyrene-b-poly(vinylpyridine) templates make the spontaneously constructed protein nanoarrays highly suitable as functional protein sensor substrates. Therefore, our novel two-dimensional protein assembly method can be greatly beneficial for high-throughput proteomic assays and multiplexed high-density protein sensing applications.     

A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis

Study of the complexome - all the protein complexes of the cell - is essential for a better understanding and more global vision of cell function. Using two-dimensional blue native/SDS-PAGE (2-D BN/SDS-PAGE) technology, the cytosolic and membrane protein complexes of Escherichia coli were separated. Then, the different partners of each protein complex were identified by LC-MS/MS. In this report, 306 protein complexes were separated and identified. Among these protein complexes, 50 heteromultimeric and 256 homomultimeric protein complexes were found. Among the 50 heteromultimeric protein complexes, 18 previously described protein complexes validate the technology. In this study, 109 new protein complexes were found, providing insight into the function of previously uncharacterized bacterial proteins.     

Site‐directed analysis on protein hydrophobicity

Hydrophobicity of a protein is considered to be one of the major intrinsic factors dictating the protein aggregation propensity. Understanding how protein hydrophobicity is determined is, therefore, of central importance in preventing protein aggregation diseases and in the biotechnological production of human therapeutics. Traditionally, protein hydrophobicity is estimated based on hydrophobicity scales determined for individual free amino acids, assuming that those scales are unaltered when amino acids are embedded in a protein. Here, we investigate how the hydrophobicity of constituent amino acid residues depends on the protein context. To this end, we analyze the hydration free energy—free energy change on hydration quantifying the hydrophobicity—of the wild‐type and 21 mutants of amyloid‐beta protein associated with Alzheimer's disease by performing molecular dynamics simulations and integral‐equation calculations. From detailed analysis of mutation effects on the protein hydrophobicity, we elucidate how the protein global factor such as the total charge as well as underlying protein conformations influence the hydrophobicity of amino acid residues. Our results provide a unique insight into the protein hydrophobicity for rationalizing and predicting the protein aggregation propensity on mutation, and open a new avenue to design aggregation‐resistant proteins as biotherapeutics. © 2014 Wiley Periodicals, Inc.     

Inhibition of protein interactions: co-crystalized protein–protein interfaces are nearly as good as holo proteins in rigid-body ligand docking

Modulating protein interaction pathways may lead to the cure of many diseases. Known protein–protein inhibitors bind to large pockets on the protein–protein interface. Such large pockets are detected also in the protein–protein complexes without known inhibitors, making such complexes potentially druggable. The inhibitor-binding site is primary defined by the side chains that form the largest pocket in the protein-bound conformation. Low-resolution ligand docking shows that the success rate for the protein-bound conformation is close to the one for the ligand-bound conformation, and significantly higher than for the apo conformation. The conformational change on the protein interface upon binding to the other protein results in a pocket employed by the ligand when it binds to that interface. This proof-of-concept study suggests that rather than using computational pocket-opening procedures, one can opt for an experimentally determined structure of the target co-crystallized protein–protein complex as a starting point for drug design.     

Identification of Proteins Using Affinity Affi-Gel Simultaneously with Acrylamide Electrophoresis

Abstract

This work presents a method in which a desired protein may be separated from a biological protein preparation and identified by highly specific monoclonal antibody. The desired protein may be isolated from crude protein preparations by this method. The protein remains intact and stable throughout the procedure. This method utilizes common nonreducing conditions of polyacrylamide gel electrophoresis (PAGE), and Western Blot transfer of protein. This isolation of the desired protein can be accomplished for a microgram or tens of micrograms of material. The application of Western blot technique with monoclonal antibody permits the highest specificity in terms of identifying the target protein. In addition to identifying the target protein the method can isolate sufficient amounts for further characterization.     

蛋白质快速检测仪测定乳及乳制品中蛋白质

采用研制的蛋白质快速检测仪,系统地考察了温度、时间和干扰物质等因素对蛋白质测定的影响及检测仪的重复性,并将检测仪应用于新鲜乳、纯牛奶、牛奶饮料(核桃、燕麦、红枣)、牛初乳、奶粉、豆奶粉、豆浆粉和鸡蛋等样品中蛋白质的定量测定.实验结果表明,在17～40℃条件下,蛋白质试剂与蛋白质在1 min内即可完成反应,整个蛋白质含量...     

Modulator binding protein antagonizes activation of (Ca2+ + Mg2+)-ATPase and Ca2+ transport of red blood cell membranes.

Red blood cells contain a protein that activates membrane-bound (Ca2+ + Mg2+)-ATPase and Ca2+ transport. The red blood cell activator protein is similar to a modulator protein that stimulates cyclic AMP phosphodiesterase. Wang and Desai [Journal of Biological Chemistry 252:4175--4184, 1977] described a modulator-binding protein that antagonizes the activation of cyclic AMP phosphodiesterase by modulator protein. In the present work, modulator-binding protein was shown to antagonize the activation of (Ca2+ + Mg2+)-ATPase and Ca2+ transport by red blood cell activator protein. The results further demonstrate the similarity between the activator protein from human red blood cells and the modulator protein from bovine brain.     

Anomalous electrophoretic behavior of a very acidic protein: ribonuclease U2

Ribonuclease U2 is a low-molecular-weight acidic protein with three disulfide bridges. This protein displays an anomalous electrophoretic behavior on standard SDS-PAGE. The electrophoretic mobility of the nonreduced protein roughly corresponds to its molecular mass while the migration of the reduced protein would be in accordance with the expected molecular mass of the protein dimer. This study reveals that the protein does not bind SDS under the SDS-PAGE conditions, its electrophoretic mobility being only determined by its electrostatic charge and hydrodynamic properties. In addition, the nonreduced protein cannot be blotted to a membrane. Unfolding of the protein upon reduction of its disulfide bridges enables electrotransference to membranes due to a restricted diffusion along the electrophoresis gel.     

Interaction with the Surrounding Water Plays a Key Role in Determining the Aggregation Propensity of Proteins

Understanding the molecular determinants of the relative propensities of proteins to aggregate in a cellular environment is a central issue for treating protein‐aggregation diseases and developing peptide‐based therapeutics. Despite the expectation that protein aggregation can largely be attributed to direct protein–protein interactions, a crucial role the surrounding water in determining the aggregation propensity of proteins both in vitro and in vivo was identified. The overall protein hydrophobicity, defined solely by the hydration free energy of a protein in its monomeric state sampling its equilibrium structures, was shown to be the predominant determinant of protein aggregation propensity in aqueous solution. Striking discrimination of positively and negatively charged residues by the surrounding water was also found. This effect depends on the protein net charge and plays a crucial role in regulating the solubility of the protein. These results pave the way for the design of aggregation‐resistant proteins as biotherapeutics.     

Combined protein A imprinting and cryogelation for production of spherical affinity material

Cryogels have been demonstrated to be efficient when applied for protein isolation. Owing to their macroporous structure, cryogels can also be used for treating particle‐containing material, e.g. cell homogenates. Another challenging development in protein purification technology is the use of molecularly imprinted polymers (MIPs). These MIPs are robust and can be used repeatedly. The paper presents a new technology that combine the formation of cryogel beads concomitantly with making imprints of a protein. Protein A was chosen as the print molecule which was also be the target in the purification step. The present paper describes a new method to produce protein‐imprinted cryogel beads. The protein‐imprinted material was characterized and the separation properties were evaluated with regard to both the target protein and whole cells with target protein exposed on the cell surface. The maximum protein A adsorption was 18.1 mg/g of wet cryogel beads. The selectivity coefficient of protein A‐imprinted cryogel beads for protein A was 5.44 and 12.56 times greater than for the Fc fragment of IgG and protein G, respectively.     

蛋白质和变性蛋白质二级结构的FTIR分析进展

蛋白质结构的研究一直是人们研究的一个热点,蛋白质在发生变性后,二级结构会改变,从而导致生物活性丧失,这些与医药学及食品科学等领域密切相关。傅里叶变换红外光谱(FTIR)作为一种无损、快速的分析方法在蛋白质二级结构的研究中发挥重要的作用,本文就FTIR对于蛋白质二级结构的研究作一初步概述,主要介绍FTIR研究蛋白质结构的主要方法、红外光谱的谱学特点。     

An HBV large surface antigen protein which can be secreted from mammalian cells.

The N-terminal 54 base pairs (encoding amino acid residues 2-19) within the preS1 region of the human hepatitis B virus surface antigen gene were deleted by site-directed mutagenesis. Unlike the wild type large surface antigen protein, when this mutated gene was expressed in monkey kidney cell line COS-M6, the protein product (S301 protein) could be secreted from the cells. Moreover, the inhibition of the secretion of the major surface antigen protein by this altered large surface antigen protein was greatly reduced, suggesting that the deleted region contained a retention sequence which prevented the secretion of the large surface antigen. However, the coexpression of the major S protein was essential for the secretion of the S301 protein. When coexpressed, the secretion of these two proteins was synchronous. Like the wild type large surface antigen protein, the S301 protein could be translocated into endoplasmic reticulum and glycosylated after its synthesis in COS cells. The S301 protein was thermostable and proteinase-resistant. It also retained the antigenicity of the large S and major S proteins. Given the fact that the S301 protein is readily secretable, stable and identical to the large S protein in terms of their antigenicity, it may be developed into a new generation of recombinant vaccine for the prevention of viral hepatitis.     

分子动力学模拟极端嗜热核糖结合蛋白的热力学稳定性

采用分子动力学模拟方法研究极端嗜热性核糖结合蛋白(tteRBP)的嗜热机理.在常温(300 K)和最佳活性温度(375 K)时,分别对tteRBP分子进行动力学模拟,结果表明,整体分子均保持结构稳定,但分子内部的协调运动不同.在375 K时蛋白整体柔性显著提高,使分子能够局部调整构象以适应极端高温.蛋白结构变化的分析也确认了高温时构象局部微调对蛋白极端高温稳定性的关键作用.     

Applications of protein microarray technology

Protein microarrays, an emerging class of proteomic technologies, are quickly becoming essential tools for large-scale and high throughput biochemistry and molecular biology. Recent progress has been made in all the key steps of protein microarray fabrication and application, such as the large-scale cloning of expression-ready prokaryotic and eukaryotic ORFs, high throughput protein purification, surface chemistry, protein delivery systems, and detection methods. Two classes of protein microarrays are currently available: analytical and functional protein microarrays. In the case of analytical protein microarrays, well-characterized molecules with specific activity, such as antibodies, peptide-MHC complexes, or lectins, are used as immobilized probes. These arrays have become one of the most powerful multiplexed detection platforms. Functional protein microarrays are being increasingly applied to many areas of biological discovery, including drug target identification/validation and studies of protein interaction, biochemical activity, and immune responses. Great progress has been achieved in both classes of protein microarrays in terms of sensitivity and specificity, and new protein microarray technologies are continuing to emerge. Finally, protein microarrays have found novel applications in both scientific research and clinical diagnostics.     

Effect of arginine on stability of GST-ZNF191（243-368）

For better understanding the chemical or biological information of ZNF191(243-368), we expressed the fusion protein of GST and ZNF191(243-368), and used it to obtain the binding DNA sequence of this zinc finger protein. But in the process of expression and purification, we found this fusion protein slowly degradated. For resolving this problem, we simultaneously added charged amino acids L-Arg and L-Glu to the solution of fusion protein, and demonstrated that this method can dramatically increase the stability of this fusion protein. This method can make the fusion protein suitable for the continuous works, especially for situations where high protein concentration and long-term stability without precipitate and degradation of protein are required.     

Modeling of the salt effects on hydrophobic adsorption equilibrium of protein

A two-state protein model is proposed to describe the salt effects on protein adsorption equilibrium on hydrophobic media. This model assumes that protein molecules exist in two equilibrium states in a salt solution, that is, hydrated and dehydrated states, and only the dehydrated-state protein can bind to hydrophobic ligands. In terms of the two-state protein hypothesis and the steric mass-action theory, protein adsorption equilibrium on hydrophobic media is formulated by a five-parameter equation. The model is demonstrated with the adsorption of bovine serum albumin to Phenyl Sepharose gels as a model system. The effects of salt type (sodium chloride, sodium sulfate and ammonium sulfate) on the model parameters are discussed. Then, the model formulism is simplified in terms of the small magnitude of the protein dehydration equilibrium constant in the model. This simplification has returned the model derived on the basis of the two-state protein hypothesis to its original mechanism of salt effects on the hydrophobic adsorption of protein. This simplified model also creates satisfactory prediction of protein adsorption isotherms.     

Coupling between lysozyme and glycerol dynamics: microscopic insights from molecular-dynamics simulations

We explore possible molecular mechanisms behind the coupling of protein and solvent dynamics using atomistic molecular-dynamics simulations. For this purpose, we analyze the model protein lysozyme in glycerol, a well-known protein-preserving agent. We find that the dynamics of the hydrogen bond network between the solvent molecules in the first shell and the surface residues of the protein controls the structural relaxation (dynamics) of the whole protein. Specifically, we find a power-law relationship between the relaxation time of the aforementioned hydrogen bond network and the structural relaxation time of the protein obtained from the incoherent intermediate scattering function. We demonstrate that the relationship between the dynamics of the hydrogen bonds and the dynamics of the protein appears also in the dynamic transition temperature of the protein. A study of the dynamics of glycerol as a function of the distance from the surface of the protein indicates that the viscosity seen by the protein is not the one of the bulk solvent. The presence of the protein suppresses the dynamics of the surrounding solvent. This implies that the protein sees an effective viscosity higher than the one of the bulk solvent. We also found significant differences in the dynamics of surface and core residues of the protein. The former is found to follow the dynamics of the solvent more closely than the latter. These results allowed us to propose a molecular mechanism for the coupling of the solvent-protein dynamics.