An in vivo map of the yeast protein interactome

Protein interactions regulate the systems-level behavior of cells; thus, deciphering the structure and dynamics of protein interaction networks in their cellular context is a central goal in biology. We have performed a genome-wide in vivo screen for protein-protein interactions in Saccharomyces cerevisiae by means of a protein-fragment complementation assay (PCA). We identified 2770 interactions among 1124 endogenously expressed proteins. Comparison with previous studies confirmed known interactions, but most were not known, revealing a previously unexplored subspace of the yeast protein interactome. The PCA detected structural and topological relationships between proteins, providing an 8-nanometer-resolution map of dynamically interacting complexes in vivo and extended networks that provide insights into fundamental cellular processes, including cell polarization and autophagy, pathways that are evolutionarily conserved and central to both development and human health.     

Evidence for network evolution in an Arabidopsis interactome map

Plants have unique features that evolved in response to their environments and ecosystems. A full account of the complex cellular networks that underlie plant-specific functions is still missing. We describe a proteome-wide binary protein-protein interaction map for the interactome network of the plant Arabidopsis thaliana containing about 6200 highly reliable interactions between about 2700 proteins. A global organization of plant biological processes emerges from community analyses of the resulting network, together with large numbers of novel hypothetical functional links between proteins and pathways. We observe a dynamic rewiring of interactions following gene duplication events, providing evidence for a model of evolution acting upon interactome networks. This and future plant interactome maps should facilitate systems approaches to better understand plant biology and improve crops.     

酵母重复基因在蛋白质互作网络中的分歧进化

【目的】分析全基因组重复后,蛋白质互作网络对重复基因分歧模式的作用机制。【方法】结合高精度的蛋白质互作数据集和具有相同进化年代的重复基因数据集,在全基因组范围关联分析拷贝间进化距离与网络结构的相关性,并通过对拷贝间连接水平的差异程度分类,分析不同阶段网络结构对基因功能的影响。【结果】重复基因两拷贝间的进化距离与其祖先基因在网络中的连接水平呈显著负相关,与重复基因间的连接度差异率呈显著正相关;网络结构完全歧化的重复基因间的非同义替换均值,较未完全歧化的重复基因显著高出30.2%。【结论】网络结构对重复基因的进化起调节作用,网络系统在保持核心稳定的同时,使外围组分发生了更大变化;重复基因在网络结构改变的前期为基因组提供功能冗余,但在网络结构差别较大后,显著增加的突变更有利于基因新功能的产生。     

Global mapping of the yeast genetic interaction network

A genetic interaction network containing approximately 1000 genes and approximately 4000 interactions was mapped by crossing mutations in 132 different query genes into a set of approximately 4700 viable gene yeast deletion mutants and scoring the double mutant progeny for fitness defects. Network connectivity was predictive of function because interactions often occurred among functionally related genes, and similar patterns of interactions tended to identify components of the same pathway. The genetic network exhibited dense local neighborhoods; therefore, the position of a gene on a partially mapped network is predictive of other genetic interactions. Because digenic interactions are common in yeast, similar networks may underlie the complex genetics associated with inherited phenotypes in other organisms.     

Evolutionary rate in the protein interaction network

High-throughput screens have begun to reveal the protein interaction network that underpins most cellular functions in the yeast Saccharomyces cerevisiae. How the organization of this network affects the evolution of the proteins that compose it is a fundamental question in molecular evolution. We show that the connectivity of well-conserved proteins in the network is negatively correlated with their rate of evolution. Proteins with more interactors evolve more slowly not because they are more important to the organism, but because a greater proportion of the protein is directly involved in its function. At sites important for interaction between proteins, evolutionary changes may occur largely by coevolution, in which substitutions in one protein result in selection pressure for reciprocal changes in interacting partners. We confirm one predicted outcome of this process-namely, that interacting proteins evolve at similar rates.     

蛋白质相互作用网络研究的引文分析

目的：通过对蛋白质相互作用网络文献的同被引分析,得出其研究热点。方法：下载SCI数据库中蛋白质相互作用网络文献及其引文,统计引文频次,取被引频次超过33、累计百分比约为10%的58篇文献作为高被引论文,对来源-引文矩阵进行层次聚类分析,利用Ucinet软件对高被引文献的同被引矩阵进行k核分析,阅读文献得到该主题的研究热点。结果：高被引文献聚类分析得到6个研究热点。结论：蛋白质相互作用网络的热点主要集中于蛋白质相互作用网络数据的分析处理、生物网络中功能模块的研究、蛋白质相互作用的数据库建立、蛋白质相互作用网络拓扑结构的分析、关于蛋白质相互作用数据的分析软件、蛋白质相互作用网络的预测。     

A probabilistic functional network of yeast genes

A conceptual framework for integrating diverse functional genomics data was developed by reinterpreting experiments to provide numerical likelihoods that genes are functionally linked. This allows direct comparison and integration of different classes of data. The resulting probabilistic gene network estimates the functional coupling between genes. Within this framework, we reconstructed an extensive, high-quality functional gene network for Saccharomyces cerevisiae, consisting of 4681 (approximately 81%) of the known yeast genes linked by approximately 34,000 probabilistic linkages comparable in accuracy to small-scale interaction assays. The integrated linkages distinguish true from false-positive interactions in earlier data sets; new interactions emerge from genes' network contexts, as shown for genes in chromatin modification and ribosome biogenesis.     

多酚-肌原纤维蛋白互作对蛋白的影响

肌原纤维蛋白是组成肌肉纤维蛋白的其中一种,肌原纤维蛋白的空间结构,蛋白的氧化性、凝胶性、乳化性等功能特性对肉制品的品质有十分重要的影响。在日常生活中,蛋白质氧化是一种常见的现象,这一现象以前没有得到很好的认识,很大程度上被忽视但现在更好了,据了解,这是一个复杂的化学过程,比如我们经常在生活中发现肉储存久了,颜色会由鲜红色变成棕褐色,这就是蛋白质氧化的导致的。所以,在肉制品中加入合适的抗氧化剂来防止肉制品的氧化变质是非常重要的,也是现在科研正在积极探索的方向。据对食品蛋白质氧化的研究发现,茶多酚它具有极强的清除有害自由基的能力,可以有效的防止肉制品的颜色发生变化,延长了肉制品的保质期,故茶多酚是目前发现的一种可理想的运用在肉制品的天然抗氧化剂之一。这篇文章综述了近些年来国内外关于茶多酚与蛋白的相互作用方式,研究了茶多酚与肌原纤维蛋白相互作用的作用机理,及在肉制品中加入多酚后,多酚与肌原纤维蛋白形互作对蛋白质性能的影响。     

Structure-based assembly of protein complexes in yeast

Images of entire cells are preceding atomic structures of the separate molecular machines that they contain. The resulting gap in knowledge can be partly bridged by protein-protein interactions, bioinformatics, and electron microscopy. Here we use interactions of known three-dimensional structure to model a large set of yeast complexes, which we also screen by electron microscopy. For 54 of 102 complexes, we obtain at least partial models of interacting subunits. For 29, including the exosome, the chaperonin containing TCP-1, a 3'-messenger RNA degradation complex, and RNA polymerase II, the process suggests atomic details not easily seen by homology, involving the combination of two or more known structures. We also consider interactions between complexes (cross-talk) and use these to construct a structure-based network of molecular machines in the cell.     

Regulation of MAPK function by direct interaction with the mating-specific Galpha in yeast

The mating response of the budding yeast Saccharomyces cerevisiae is mediated by a prototypical heterotrimeric GTP-binding protein (G protein) and mitogen-activated protein kinase (MAPK) cascade. Although signal transmission by such pathways has been modeled in detail, postreceptor down-regulation is less well understood. The pheromone-responsive G protein alpha subunit (Galpha) of yeast down-regulates the mating signal, but its targets are unknown. We have found that Galpha binds directly to the mating-specific MAPK in yeast cells responding to pheromone. This interaction contributes both to modulation of the mating signal and to the chemotropic response, and it demonstrates direct communication between the top and bottom of a Galpha-MAPK pathway.     

二进制与十进制动态显示的关键技术

二进制是计算机中所采用的数据表示形式,在文章中介绍了基于VRML与JAVA的虚拟动态交互技术,分析了利用Java或JavaScript语言创建出新的内插节点和传感节点来驱动和控制整个虚拟空间的方法,研究了利用VRML和Java的技术去设计动态交互的场景,实现了二进制与十进制之间的动态交互显示,最后指出该系统已被成功运用于教学,文章的创新点在于利用PRO/E优化建模。     

网络教学师生互动平台的设计

师生互动平台是网络教学中必不可少的环节,便于教师与学生之间的信息交流,具有专题讨论、作业系统、资料上传与下载等功能.本文主要介绍了在网络教学中师生互动平台的设计内容.     

Crystal structures of the adenylate sensor from fission yeast AMP-activated protein kinase

The 5'-AMP (adenosine monophosphate)-activated protein kinase (AMPK) coordinates metabolic function with energy availability by responding to changes in intracellular ATP (adenosine triphosphate) and AMP concentrations. Here, we report crystal structures at 2.9 and 2.6 A resolution for ATP- and AMP-bound forms of a core alphabetagamma adenylate-binding domain from the fission yeast AMPK homolog. ATP and AMP bind competitively to a single site in the gamma subunit, with their respective phosphate groups positioned near function-impairing mutants. Unexpectedly, ATP binds without counterions, amplifying its electrostatic effects on a critical regulatory region where all three subunits converge.     

自组织神经影射网络排序及其在植物群落分析中的应用

自组织神经影射网络(SOFM)对复杂问题和非线性问题具有较强的分析和解决功能,其特征完全适合植物群落的排序研究。该文介绍了SOFM的基本原理和排序分析过程及方法,并应用SOFM网络排序对太行山中段植物群落进行了排序分析。其计算过程在Matlab 65神经网络工具箱中实现。结果将68个样方排列在SOFM拓扑空间,排序轴反映了明确的生态梯度,能够反映植物群落间的生态关系,生态意义明确,符合植被实际,表明SOFM网络是有效的植物群落排序方法。在SOFM排序过程中也很容易进行聚类,有利于群落分类和排序的结合。      

小立碗藓原生质体再生过程中蛋白质相互作用网络分析

[目的]探明蛋白质间的相互作用对于阐明细胞生命活动的分子机制具有重要意义.[方法]应用Cytoscape平台中MiMI插件,进行磷酸化修饰蛋白质之间的相互作用(protein-protein interaction,PPI)网络分析.采用基于DAVID分析系统对PPI网络中的蛋白质进行Gene Ontology (GO)富集分析.[结果]有5个磷酸化蛋白质(ATX1、AGL21、KNAT2、EOL2和VIP4)与其他33个蛋白质存在相互作用关系.这些PPI网络中的蛋白质主要参与分生组织的分生状态的维持,干细胞的发育以及基因的表达调控等生物过程.[结论]小立碗藓原生质体的再生机制可能与种子植物的胚后发育相似.