Using orthologous and paralogous proteins to identify specificity determining residues

Background  

Concepts of orthology and paralogy are become increasingly important as whole-genome comparison allows their identification in complete genomes. Functional specificity of proteins is assumed to be conserved among orthologs and is different among paralogs. We used this assumption to identify residues which determine specificity of protein-DNA and protein-ligand recognition. Finding such residues is crucial for understanding mechanisms of molecular recognition and for rational protein and drug design.     

Using GO-PseAA predictor to identify membrane proteins and their types

Cell membranes are crucial to the life of a cell. Although the basic structure of biological membrane is provided by the lipid bilayer, most of the specific functions are carried out by membrane proteins. Knowledge of membrane protein type often offers important clues toward determining the function of an uncharacterized protein. Therefore, predicting the type of a membrane protein from its primary sequence, or even just identifying whether the uncharacterized protein belongs to a membrane protein or not, is an important and challenging problem in bioinformatics and proteomics. To deal with these problems, the GO-PseAA predictor is introduced that is operated in a hybridization space by combining the gene ontology and pseudo amino acid composition. Meanwhile, to test the prediction quality, a dataset was constructed that contains 6476 non-membrane proteins and 5122 membrane proteins classified into five different types. To avoid redundancy and bias, none of the proteins included has > or = 40% sequence identity to any other. It has been observed that the overall success rate by the jackknife cross-validation test in identifying non-membrane proteins and membrane proteins was 94.76%, and that in identifying the five membrane protein types was 95.84%. The high success rates suggest that the GO-PseAA predictor can catch the core feature of the statistical samples concerned and may become an automated high throughput toll in molecular and cell biology.     

脂肪细胞分化相关转录因子的结构和功能

关于脂肪细胞分化调控的研究主要集中在转录因子的作用上。目前了解得比较清楚的分化转录因子有多种,其中CAAT增强子结合蛋白家族（C/EBPs）中的C／EBPα和过氧化物酶体增殖物激活受体家族（PPARs）中的PPARy是转录调控中起主要作用的两种因子。两者有各自的结构特点和功能,但在脂肪细胞中它们之间相互协同促进细胞的分化成熟。本文主要就C／EBPs和PPARs家族中主要成员的结构和功能及相互作用进行综述。     

Reactivity of histidine and lysine side-chains with diethylpyrocarbonate -- a method to identify surface exposed residues in proteins

The chemical modification of amino acid side-chains followed by mass spectrometric detection can reveal at least partial information about the 3-D structure of proteins. In this work we tested diethylpyrocarbonate, as a common histidyl modification agent, for this purpose. Appropriate conditions for the reaction and detection of modified amino acids were developed using angiotensin II as a model peptide. We studied the modification of several model proteins with a known spatial arrangement (insulin, cytochrome c, lysozyme and human serum albumin). Our results revealed that the surface accessibility of residues is a necessary, although in itself insufficient, condition for their reactivity; the microenvironment of side-chains and the dynamics of protein structure also affect the ability of residues to react. However the detection of modified residues can be taken as proof of their surface accessibility, and of direct contact with solvent molecules.     

NAC转录因子在植物抗病和抗非生物胁迫反应中的作用

NAC转录因子是植物特有的一类转录因子,其共同特点是在N端含有一段高度保守、由约150个氨基酸组成的NAC结构域,而C端为高度变异的转录调控区。研究表明,NAC转录因子不仅参与植物生长发育的调控,而且在植物抗逆反应中具有重要的调控作用。文章着重介绍NAC转录因子在植物抗逆反应中的作用及其调控机制,并简要讨论NAC转录因子生物学功能的研究方向。