Highly Accurate Prediction of Protein-Protein Interactions via Incorporating Evolutionary Information and Physicochemical Characteristics

Protein-protein interactions (PPIs) occur at almost all levels of cell functions and play crucial roles in various cellular processes. Thus, identification of PPIs is critical for deciphering the molecular mechanisms and further providing insight into biological processes. Although a variety of high-throughput experimental techniques have been developed to identify PPIs, existing PPI pairs by experimental approaches only cover a small fraction of the whole PPI networks, and further, those approaches hold inherent disadvantages, such as being time-consuming, expensive, and having high false positive rate. Therefore, it is urgent and imperative to develop automatic in silico approaches to predict PPIs efficiently and accurately. In this article, we propose a novel mixture of physicochemical and evolutionary-based feature extraction method for predicting PPIs using our newly developed discriminative vector machine (DVM) classifier. The improvements of the proposed method mainly consist in introducing an effective feature extraction method that can capture discriminative features from the evolutionary-based information and physicochemical characteristics, and then a powerful and robust DVM classifier is employed. To the best of our knowledge, it is the first time that DVM model is applied to the field of bioinformatics. When applying the proposed method to the Yeast and Helicobacter pylori (H. pylori) datasets, we obtain excellent prediction accuracies of 94.35% and 90.61%, respectively. The computational results indicate that our method is effective and robust for predicting PPIs, and can be taken as a useful supplementary tool to the traditional experimental methods for future proteomics research.     

蛋白质含量测定方法

蛋白质与生命的起源、存在和进化都密切相关,蛋白质测定涉及到生产和科研的众多领域。本实验用定氮法、紫外吸收法、双缩脲法、考马斯亮蓝法分别对牛奶、酸奶、豆浆进行蛋白质含量的测定。依此分析比较各种测定蛋白质的方法,总结出各方法的特点及适用条件。     

含能材料物理化学性能理论预估研究进展

从含能材料领域的最近发展成果出发,讨论了该领域的主要研究方向,重点论述了当前含能材料物理化学性能理论预估的最新成果,主要包括量子化学、分子动力学或者半经验QSPR建模的方法预估含能材料的感度、燃烧爆轰性能、反应活性、固化机制与力学性能的研究进展。总结了目前存在的主要技术壁垒,包括缺乏完备统一的含能材料性能标准实验数据库,没有自主知识产权的商业化含能材料性能计算软件,且国际上商业软件对含能材料的物理化学性能的可靠预测仅局限于爆轰性能和燃烧性能。文献调研表明,我国需要进一步加强该领域研究,最终建立一个能评价含能材料性能与安全的综合软件平台。     

Structural Aspects and Prediction of Calmodulin-Binding Proteins

Calmodulin (CaM) is an important intracellular protein that binds Ca²⁺ and functions as a critical second messenger involved in numerous biological activities through extensive interactions with proteins and peptides. CaM’s ability to adapt to binding targets with different structures is related to the flexible central helix separating the N- and C-terminal lobes, which allows for conformational changes between extended and collapsed forms of the protein. CaM-binding targets are most often identified using prediction algorithms that utilize sequence and structural data to predict regions of peptides and proteins that can interact with CaM. In this review, we provide an overview of different CaM-binding proteins, the motifs through which they interact with CaM, and shared properties that make them good binding partners for CaM. Additionally, we discuss the historical and current methods for predicting CaM binding, and the similarities and differences between these methods and their relative success at prediction. As new CaM-binding proteins are identified and classified, we will gain a broader understanding of the biological processes regulated through changes in Ca²⁺ concentration through interactions with CaM.     

Proteins as emulsifiers: Methods for assessing the role

The objective of this review is to present a variety of surface and colloid chemical methodologies, in brief, with which one may study the role of proteins as emulsifiers and co-emulsifiers. The techniques range from microtechniques aimed at single interfaces (film balance) and double interfaces (tensiolaminometry) to macrotechniques aimed at the gross emulsion (microcalorimetry, electrophoresis, pulsed, nuclear magnetic resonance, microwaves). Equipment, procedures, typical results, and interpretation of the data are reviewed. Some results with commercially available proteinaceous materials are presented. A link between emulsion formation and stability theory, experimental methods, and food applications is made through the examples of a salad dressing emulsion and a foamable emulsion.     

Application of Fluorescent Proteins for Functional Dissection of the Drosophila Visual System

The Drosophila eye has been used extensively to study numerous aspects of biological systems, for example, spatio-temporal regulation of differentiation, visual signal transduction, protein trafficking and neurodegeneration. Right from the advent of fluorescent proteins (FPs) near the end of the millennium, heterologously expressed fusion proteins comprising FPs have been applied in Drosophila vision research not only for subcellular localization of proteins but also for genetic screens and analysis of photoreceptor function. Here, we summarize applications for FPs used in the Drosophila eye as part of genetic screens, to study rhodopsin expression patterns, subcellular protein localization, membrane protein transport or as genetically encoded biosensors for Ca²⁺ and phospholipids in vivo. We also discuss recently developed FPs that are suitable for super-resolution or correlative light and electron microscopy (CLEM) approaches. Illustrating the possibilities provided by using FPs in Drosophila photoreceptors may aid research in other sensory or neuronal systems that have not yet been studied as well as the Drosophila eye.     

Enhanced Inter-helical Residue Contact Prediction in Transmembrane Proteins

In this paper, based on a recent work by McAllister and Floudas who developed a mathematical optimization model to predict the contacts in transmembrane alpha-helical proteins from a limited protein data set (McAllister and Floudas, 2008), we have enhanced this method by (1) building a more comprehensive data set for transmembrane alpha-helical proteins and this enhanced data set is then used to construct the probability sets, MIN-1N and MIN-2N, for residue contact prediction, (2) enhancing the mathematical model via modifications of several important physical constraints and (3) applying a new blind contact prediction scheme on different protein sets proposed from analyzing the contact prediction on 65 proteins from Fuchs et al. (2009). The blind contact prediction scheme has been tested on two different membrane protein sets. First, it is applied to five carefully selected proteins from the training set. The contact prediction of these five proteins uses probability sets built by excluding the target protein from the training set, and an average accuracy of 56% was obtained. Second, it is applied to six independent membrane proteins with complicated topologies, and the prediction accuracies are 73% for 2ZY9A, 21% for 3KCUA, 46% for 2W1PA, 64% for 3CN5A, 77% for 3IXZA and 83% for 3K3FA. The average prediction accuracy for the six proteins is 60.7%. The proposed approach is also compared with a support vector machine method (TMhit Lo et al., 2009) and it is shown that it exhibits better prediction accuracy.     

Function Prediction and Analysis of Mycobacterium tuberculosis Hypothetical Proteins

High-throughput biology technologies have yielded complete genome sequences and functional genomics data for several organisms, including crucial microbial pathogens of humans, animals and plants. However, up to 50% of genes within a genome are often labeled "unknown", "uncharacterized" or "hypothetical", limiting our understanding of virulence and pathogenicity of these organisms. Even though biological functions of proteins encoded by these genes are not known, many of them have been predicted to be involved in key processes in these organisms. In particular, for Mycobacterium tuberculosis, some of these "hypothetical" proteins, for example those belonging to the Pro-Glu or Pro-Pro-Glu (PE/PPE) family, have been suspected to play a crucial role in the intracellular lifestyle of this pathogen, and may contribute to its survival in different environments. We have generated a functional interaction network for Mycobacterium tuberculosis proteins and used this to predict functions for many of its hypothetical proteins. Here we performed functional enrichment analysis of these proteins based on their predicted biological functions to identify annotations that are statistically relevant, and analysed and compared network properties of hypothetical proteins to the known proteins. From the statistically significant annotations and network information, we have tried to derive biologically meaningful annotations related to infection and disease. This quantitative analysis provides an overview of the functional contributions of Mycobacterium tuberculosis "hypothetical" proteins to many basic cellular functions, including its adaptability in the host system and its ability to evade the host immune response.     

Filtering,Prediction and Simulation Methods for Noncausal Processes

This article discusses filtering, prediction and simulation in univariate and multivariate noncausal processes. A closed‐form functional estimator of the predictive density for noncausal and mixed processes is introduced that provides prediction intervals up to a finite horizon H. A state‐space representation of a noncausal and mixed multivariate vector autoregressive process is derived in two ways‐by the partial fraction decomposition or from the real Jordan canonical form. A recursive BHHH algorithm for the maximization of the approximate log‐likelihood function is proposed, which calculates the filtered values of the unobserved causal and noncausal components of the process. The new methods are illustrated by a simulation study involving a univariate noncausal process with infinite variance.     

理化因素对头发影响作用的研究方法与现状

利用头发研究成果为化妆品中发用品的开发服务在国际上起步较晚。本综述了头发的生物学特征、各理化因素对头发影响作用的研究方法及其研究现状,概述了法医学、生物学、环境科学和化妆品等领域毛发研究动态。     

Physicochemical and Functional Properties of Freeze-Dried and Oven Dried Corn Gluten Meals

ABSTRACT

The physicochemical and functional properties of convection oven- and freeze-dried gluten meals of two corn varieties were evaluated. The physicochemical properties (water solubility index, water absorption index, Hunter color parameters, and bulk density) and functional properties (water absorption, oil absorption, least gelation concentration, protein solubility, and emulsification properties) of convection-oven and freeze-dried corn gluten meals were compared with each other and soy flour. Freeze-dried corn gluten meals was observed to have lower bulk density (0.244–0.263 kg/m³) and was lighter in color (high L and ΔE) compared to their counterpart convection oven–dried gluten meals. Freeze-dried gluten meals from both corn varieties showed significantly higher oil absorption, water absorption, pH, emulsification, and protein solubility compared to oven-dried corn gluten meals. The gluten meals from both corn varieties had lower water absorption and bulk density but higher oil absorption than soy flour, suggesting the hydrophobic nature of corn proteins. Corn gluten meals formed thin (pourable) emulsions compared to soy flour emulsions, which were thick salad dressing type. Freeze- and convection oven–dried corn gluten meals showed significantly lower protein solubility measured at different pH than soy flour.     

管道腐蚀剩余寿命预测方法对比研究

随着我国油气管道建设的不断推进,钢制管道也更普遍的应用于油、气输送行业。但是钢制管道在潮湿的环境下极易发生腐蚀,因腐蚀造成的穿孔现象给石化行业的安全生产带来了巨大的挑战。本文通过对几种腐蚀剩余寿命预测方法进行优化对比分析,并给出了个各自的适应范围。从理论上为油、气管道维护工作者提供必要的技术参考。从而可以根据理论的剩余寿命,加强对油气管道的维护,防止或减轻腐蚀速率。该方法的使用不仅可以产生显著的经济效益,而且还具有巨大的社会效益。     

热力学函数关系式与麦克斯韦关系式的简单记忆方法

物理化学向来以理论性强、公式繁多著称,学生在学习中普遍感觉记忆负担较重。为此文章介绍了两种巧记热力学重要函数关系式和麦克斯韦关系式的方法:公式对照法和参数组合法,经实践有助于学生记忆掌握这些公式。     

Physicochemical and Functional Properties of Freeze-Dried and Oven Dried Corn Gluten Meals

The physicochemical and functional properties of convection oven- and freeze-dried gluten meals of two corn varieties were evaluated. The physicochemical properties (water solubility index, water absorption index, Hunter color parameters, and bulk density) and functional properties (water absorption, oil absorption, least gelation concentration, protein solubility, and emulsification properties) of convection-oven and freeze-dried corn gluten meals were compared with each other and soy flour. Freeze-dried corn gluten meals was observed to have lower bulk density (0.244-0.263 kg/m³) and was lighter in color (high L and ΔE) compared to their counterpart convection oven-dried gluten meals. Freeze-dried gluten meals from both corn varieties showed significantly higher oil absorption, water absorption, pH, emulsification, and protein solubility compared to oven-dried corn gluten meals. The gluten meals from both corn varieties had lower water absorption and bulk density but higher oil absorption than soy flour, suggesting the hydrophobic nature of corn proteins. Corn gluten meals formed thin (pourable) emulsions compared to soy flour emulsions, which were thick salad dressing type. Freeze- and convection oven-dried corn gluten meals showed significantly lower protein solubility measured at different pH than soy flour.     

Bioactive and Physicochemical Properties of Persimmon as Affected by Drying Methods

In this study, the effects of three different drying methods (freeze drying, oven drying, and vacuum oven drying) on bioactive (total phenolics, total flavonoids, condensed tannin and total hydrolyzable tannin contents, antiradical activity, and antidiabetic activity) and some physicochemical (dry matter, ash, water activity (a _w ), color, protein, hydroxymethylfurfural, glucose and fructose content) properties of persimmon fruit were investigated. Simplex lattice mixture design methodology was applied to determine the best solvent mixture for the extraction of phenolics from the samples. It was found that the mixture of acetone:water at the ratio of 50:50 % (v/v) was the best solvent mixture for the extraction. The persimmon powder sample obtained from freeze drying showed significantly (p <0.05) higher bioactivity values than oven- and vacuum-oven-dried samples. Antiradical activity changed significantly depending on the drying method employed and it was superior in freeze-dried samples than that of the other drying methods.     

BIAPSS: A Comprehensive Physicochemical Analyzer of Proteins Undergoing Liquid–Liquid Phase Separation

The liquid–liquid phase separation (LLPS) of biomolecules is a phenomenon which is nowadays recognized as the driving force for the biogenesis of numerous functional membraneless organelles and cellular bodies. The interplay between the protein primary sequence and phase separation remains poorly understood, despite intensive research. To uncover the sequence-encoded signals of protein capable of undergoing LLPS, we developed a novel web platform named BIAPSS (Bioinformatics Analysis of LLPS Sequences). This web server provides on-the-fly analysis, visualization, and interpretation of the physicochemical and structural features for the superset of curated LLPS proteins.     

Chemical Synthesis of Integral Membrane Proteins: Methods and Applications

The development of efficient chemical methods for total synthesis or semisynthesis of integral membrane proteins is an important challenge at the interface between chemistry and biology. This review outlines the recent advances in the synthesis of integral membrane proteins, with particular focus on the methods for difficult peptide synthesis, purification, and enhancement of peptide solubility under the ligation conditions. The applications of these methods to the synthesis of integral membrane proteins with one or multiple transmembrane domains are also described.     

米糠蛋白的提取及功能性质研究

采用碱提法进行米糠蛋白的提取并对提取物进行红外光谱测定.实验结果表明,碱提法对米糠蛋白的提取效果较好.通过单因素分析,正交实验优化出最佳提取工艺:pH值6,液固比5∶1,提取时间2 h.此蛋白的功能性质较好,具有良好的开发前景.