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/.     

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.     

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.     

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.     

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.     

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.     

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.     

Electrostatic interactions of charged dipolar proteins in reverse micelles

The electrostatic interactions in a reverse micelle containing a small-ionized protein are studied by Monte Carlo simulation. The electrostatic contribution to the potential of mean force of the protein in the reverse micelle is determined for a neutral protein, a uniformly charged protein, and a uniformly charged protein with a dipole moment. The effect of addition of a simple electrolyte is studied. While symmetrically distributed micellar charge exerts no force on enclosed ionic species, the protein is driven to the micellar wall due to interactions with simple ions. Protein binding to the inner wall of the micelle can be regulated by added salt. The presence of a dipole drives the protein further to the wall. These effects are studied for several proteins characterized by different charges and dipole moments. For a weakly charged protein with a strong dipole moment the contribution of dipolar interaction to the free energy can represent a major driving force for protein solubilization in the microemulsion.     

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.     

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。     

Adaptation of a fast Fourier transform-based docking algorithm for protein design

Designing proteins with novel protein/protein binding properties can be achieved by combining the tools that have been developed independently for protein docking and protein design. We describe here the sequence-independent generation of protein dimer orientations by protein docking for use as scaffolds in protein sequence design algorithms. To dock monomers into sequence-independent dimer conformations, we use a reduced representation in which the side chains are approximated by spheres with atomic radii derived from known C2 symmetry-related homodimers. The interfaces of C2-related homodimers are usually more hydrophobic and protein core-like than the interfaces of heterodimers; we parameterize the radii for docking against this feature to capture and recreate the spatial characteristics of a hydrophobic interface. A fast Fourier transform-based geometric recognition algorithm is used for docking the reduced representation protein models. The resulting docking algorithm successfully predicted the wild-type homodimer orientations in 65 out of 121 dimer test cases. The success rate increases to approximately 70% for the subset of molecules with large surface area burial in the interface relative to their chain length. Forty-five of the predictions exhibited less than 1 A C(alpha) RMSD compared to the native X-ray structures. The reduced protein representation therefore appears to be a reasonable approximation and can be used to position protein backbones in plausible orientations for homodimer design.     

PURIFICATION OF Cd-BINDING PROTEIN FROM MAIZE ROOTS BY REVERSE-PHASE HIGH-PERFORMANCE LIQUID CHROMATOGRAPHY

An efficient procedure of purification of Cd-binding protein in roots of maize has been established. Young seedlings of maize were exposed to a medium containing CdCl2 to induce the production of Cd-binding protein in their roots. The protein was purified after heat treatment by ion-exchange chromatography and reverse-phase HPLC. The resulting protein was identified as a purified product by N-terminal amino acid with the dansyl method. Its molecular weight was 3200 dalton, the cysteine content was 29.5%, about 3 Cd atoms were bound to one molecule of the protein and the Cd : cystine ratio was 1 : 2.3. According to its character, this protein could be a kind of plant metallothionein-like protein.     

Allosterically Activated Protein Self‐Assembly for the Construction of Helical Microfilaments with Tunable Helicity

Protein allostery, a chemical‐to‐mechanical effect that can precisely regulate protein structure, exists in many proteins. Herein, we demonstrate that protein allostery can be used to drive self‐assembly for the construction of tunable protein architectures. Calmodulin (CaM) was chosen as a model allosteric protein. Ca²⁺‐mediated contraction of CaM to a closed state can activate CaM and its ligand to self‐assemble into a 1D protein helical microfilament. Conversely, relaxation of CaM to the open state can unwind and further dissociate the helical assemblies. Fine regulation of the protein conformation by tuning the external Ca²⁺ level allows us to obtain various protein helical nanostructures with tunable helicity. This study offers a new approach toward chemomechanically controlled protein self‐assembly.     

Tuning substrate selectivity of a cationic enzyme using cationic polymers

Noncovalent interactions between an artificial molecular scaffold and a protein are interesting due to the possibility of reversible modulation of the activity of the protein. alpha-Chymotrypsin is a positively charged protein that has been shown to interact with negatively charged polymers. Here we show that positively charged polymers are also capable of electrostatically binding to this protein. The resulting experiments show that the ability of a polymer to bind a protein does not depend only on the pI of the protein. We also realized that the variations in charge density in the polymer backbone afford different selectivities of the enzyme toward charged substrates.     

Evaluation of protein modification during anti-viral heat bioprocessing by electrospray ionization mass spectrometry

During the preparation of therapeutic plasma and recombinant protein biopharmaceuticals heat-treatment is routinely applied as a means of viral inactivation. However, as most proteins denature and aggregate under heat stress, it is necessary to add thermostabilizing excipients to protein formulations destined for anti-viral heat-treatment in order to prevent protein damage. Anti-viral heat-treatment bioprocessing therefore requires that a balance be found between the bioprocessing conditions, virus kill and protein integrity. In this study we have utilized a simple model protein, beta-lactoglobulin, to investigate the relationship between virucidal heat-treatment conditions (protein formulation and temperature) and the type and extent of protein modification in the liquid state. A variety of industrially relevant heat-treatments were undertaken, using formulations that included sucrose as a thermostabilizing excipient. Using liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS) we show here that protein modifications do occur with increasingly harsh heat-treatment. The predominant modification under these conditions was protein glycation by either glucose or fructose derived from hydrolyzed sucrose. Advanced glycation end products and additional unidentified products were also present in beta-lactoglobulin protein samples subjected to extended heat-treatment. These findings have implications for the improvement of anti-viral heat-treatment bioprocesses to ensure the safety and efficacy of protein biopharmaceuticals. CopyrightCopyright 2001 John Wiley & Sons, Ltd.     

Closer look at the operating definition of protein recovery in CE

Analyte recovery is an important figure to assess protein adsorption on fused‐silica capillaries. In 1991, Regnier et al. estimated recovery by assuming the loss of analyte from adsorption and thus the decrease in peak area measured by two detectors to be proportional to the length of the capillary section between them. In this report, we closely examine this concept and its adaptation to commercial CE instruments to determine protein recovery. We hypothesize that, once a steady‐state migration is reached, protein adsorption is a first‐order process with respect to protein concentration and surface density of adsorbing sites. This hypothesis is shown to be valid over a reasonably wide range of capillary effective length and, as a result, protein recovery decreases exponentially with the migrated distance. However, unlike the traditional recovery figure obtained through a conventional spike process, protein recovery measured by this approach does not have the same merit since it is strongly dependent from capillary dimensions and applied electric field. Nevertheless, protein recovery and the slope of the logarithmic protein peak area versus length plot are useful figures to compare protein adsorption on different capillary surfaces. Several literature reports dealing with the application of Regnier concept to calculate protein recovery are discussed.     

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.     

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.     

Proteolytic cleavage reveals interaction patterns between silica nanoparticles and two variants of human carbonic anhydrase

To characterize the sites on the protein surface that are involved in the adsorption to silica nanoparticles and the subsequent rearrangements of the protein/nanoparticle interaction, a novel approach has been used. After incubation of protein with silica nanoparticles for 2 or 16 h, the protein was cleaved with trypsin and the peptide fragments were analyzed with mass spectrometry. The nanoparticle surface area was in 16-fold excess over available protein surface to minimize the probability that the initial binding would be affected by other protein molecules. When the fragment patterns obtained in the presence and absence of silica nanoparticles were compared, we were able to characterize the protein fragments that interact with the surface. This approach has allowed us to identify the initial binding sites on the protein structure and the rearrangement of the binding sites that occur upon prolonged incubation with the surface.