干扰素-λ的生物学作用

Ⅲ型干扰素（Interferon,IFN）,即IFN-λ,是一种新型干扰素,其家族包括IFN-λ1,IFN-λ2和IFN-λ3（也可分别称作IL-29,IL-28α和IL-28β）.IFN-λ的功能性受体复合物是由IL-28Rα（又称IFN-λR1或CRF2-12）和IL-10Rβ（又称CRF2-4）链组成的异二聚体,IFN-λ结合到受体上诱导受体异二聚体化,导致Jak-STAT信号转导途径的激活,从而发挥与Ⅰ型IFN相似的生物学效应.IFN-λ的生物学效应包括抗病毒、抗肿瘤和调节免疫活性等方面.IFN-λ很多生物学活性与临床上应用广泛的 IFN-α/β十分相似,但其受体表达局限,毒副作用相对较小,因此在抗病毒和抗肿瘤方面具有广阔的应用前景.     

IL-31及其受体研究进展

IL-31是一种最近被发现的细胞因子,主要由活化的Th2细胞产生.其功能受体是由IL-31R和OSMR两个亚基组成的异源二聚体复合物.上皮细胞和角质化细胞能组成性地表达这两种受体亚基,而单核细胞只有在活化状态下才能表达.IL-31通过其受体可以激活JAK-STAT、MAPK和PI3K/Akt三条信号通路,在皮炎等疾病中发挥作用,同时还具有调节抗原递呈、造血作用、细胞增殖及迁移,诱导趋化因子表达等生物学活性.     

IL-15和IL-T与IL-2共有活性与受体

两组研究人员报道发现了新的细胞因子,一个称之为IL-15,另一个称作IL-(?)。二者均有类似IL-2的活性,均通过部分IL-2受体刺激细胞,它们可能是同一种蛋白质,因而有助于澄清某些相互纠缠的观察。例如,IL-2缺陷小鼠令人惊奇地显示正常的免疫应答,这与IL2在体外起关键作用形成鲜明对照IL-2的作用是否受某些已知细胞因子组合或受一种未知因子的支持?答案可能就在IL-15/IL-1之中。 Grabstein等人培养的猿肾Ⅰ皮细胞系的上清液中分离出一种称作IL-15的因子能支持IL-2依赖细胞系的增殖,其表观分子量(SDS-PAGE)为14～15kD。N-     

IL－2部分拮抗剂可用于IL－2突变体对受体亚基结合能力的初步鉴定

用定点突变法分别得到了两个人白细胞介素-2(IL-2)的部分拮抗剂15Val-IL-2和126Asp-IL-2以及一个为IL-2受体α亚基结合缺陷型的突变体62Leu-IL-2,当将15Val-IL-2或126Asp-IL-2与62Leu-IL-2共同保温时,62Leu-IL-2的活性受到明显抑制,对此现象机理的分析表明15Val-IL-2或126Asp-IL-2可用于IL-2受体亚基结合缺陷型突变体的初步鉴定.同时,这一思路在其它受体-配基系统中具有一定的适用性.     

白介素-33与炎症

白介素-33（interleukin-33,IL-33）是最近发现的一种前炎症细胞因子,它结合IL-1受体家族成员ST2,活化NF-κB和MAPK信号通路,促进Th2细胞因子的产生,参与多种炎症与免疫反应过程。本文就IL-33的分子结构、编码蛋白、产生及调节、受体信号与生物学活性等作综述。     

白介素-33与炎症

自介紊-33(interleukin.33,IL-33)是最近发现的一种前炎症细胞因子,它结合IL-1受体家族成员ST2,活化NF-w.B和MAPK信号通路,促进Th2细胞因子的产生,参与多种炎症与免疫反应过程.本文就IL-33的分子结构、编码蛋白、产生及调节,受体信号与生物学活性等作综述.     

人白细胞介素-2结构与镇痛功能关系的研究

免疫调节因子白细胞介素-2(IL-2)具有中枢镇痛功能。实验采用基因定位突变技术,获得系列IL-2突变体,并测定其免疫学活性和镇痛能力,发现无免疫学活性的IL-2突变体20Leu-IL-2仍具有中枢镇痛能力,而44Leu-IL-2,45 Val-IL-2虽保留了免疫学活性,但其镇痛能力显著性下降或消失,阿片受体拮抗剂纳洛酮能够阻断IL-2的中枢镇痛作用,而不能影响IL-2对CTLL-2细胞的增殖作用。抗内源性阿片肽血清与IL-2能发生明显的交叉反应。实验结果提示,IL-2分子是通过由第45位Tyr残基及空间上相近的Phe残基等组成的镇痛功能位点与阿片受体相结合而发挥镇痛效应。     

白细胞介素－2受体γ链研究新进展

白细胞介素－2受体γ链（interleukin-2 receptorγchain,IL-2Rγc）是约3年前发现的IL-2受体亚单位之一,它不但参与高、中亲和力IL-2R的形成,而且作为细胞因子受体超家族成员参与IL－4、IL－7、IL－9和IL－15受体以及可能的IL－13受体功能性复合物的形成．IL-2Rγc基因结构与功能和蛋白质分子结构以及染色体定位已阐明．IL-2Rγc及信号传导的异常导致人类Ｘ染色体连锁重度联合免疫缺陷病(X-linked severe combined immunodeficiency XSCID)．因此,阐明IL-2Rγc在生理及病理状态下的生物学作用,对了解淋巴细胞的生长发育和分化成熟、免疫应答及其调控等问题都有重要的指导意义．     

新型的干扰素λ家族

干扰素λ为一类新型的干扰素家族,分IFN-λ1、IFN-λ2和IFN一λ3等3种,也分别称为IL-29,IL-28A和IL-28B;其功能受体复合物是由新鉴定的CRF2—12和IL-10R2组成的异二聚体。配体与受体相互作用能活化Jak—STAT通路,并起抗病毒或其他防御功能作用。     

人可溶性白介素-4受体(sIL-4R)在甲醇酵母中的表达

白细胞介素-4(IL-4)作为一种多功能的细胞因子在哮喘等变态性炎症反应中具有关键作用。IL-4通过结合细胞表面的白介素-4受体(IL-4R)发挥其生物学效应。sIL-4R缺少跨膜和胞内结构域,结合IL-4后不能产生信号传递来介导IL-4的生物学活性,但sIL-4R与IL-4结合的高度特异性和极高的亲和力使它非常适合作为理想的IL-4拮抗剂应用于哮喘等疾病的治疗。采用RT-PCR方法以人的单核细胞总RNA为模板扩增得到编码sIL-4R的基因片段,经测序证实后插入到甲醇酵母分泌表达质粒pPIC9K中,得到重组质粒pPIC9K／sIL-4R,利用限制性内切酶BalⅡ将其线性化后用电穿孔法导入Pichia pastoris GS115。分别用SDS-PAGE、Western blot和Ligand bioding blot对重组菌发酵上清中的sIL-4R进行鉴定。结果表明,在分子量约为30kD处有sIL-4R特异条带出现,并具有结合其配基IL-4的生物学活性。     

Contact patterns between helices and strands of sheet define protein folding patterns

Comparing and classifying protein folding patterns allows organizing the known structures and enumerating possible protein structural patterns including those not yet observed. We capture the essence of protein folding patterns in a concise tableau representation based on the order and contact patterns of secondary structures: helices and strands of sheet. The tableaux are intelligible to both humans and computers. They provide a database, derived from the Protein Data Bank, mineable in studies of protein architecture. Using this database, we have: (i) determined statistical properties of secondary structure contacts in an unbiased set of protein domains from ASTRAL, (ii) observed that in 98% of cases, the tableau is a faithful representation of the folding pattern as classified in SCOP, (iii) demonstrated that to a large extent the local structure of proteins indicates their complete folding topology, and (iv) studied the use of the representation for fold identification.     

Left-handed polyproline II helix formation is (very) locally driven

The left-handed polyproline II helix (PPII) is believed to be the preferred conformation for proline-rich regions of sequence in proteins. Such regions have been postulated to be protein-protein interaction domains. The formation of this structure is studied here using simple Monte Carlo computer simulations employing the hard sphere potential. It is found that polyproline sequences adopt only the PPII structure in the simulations. Non-proline, non-glycine residues inserted as guests into polyproline host peptides are conformationally restricted by the following proline residues and tend to be part of the PPII helix. It is found through insertion of two alanine residues into polyproline that the PPII structure is not propagated through more than one non-proline residue. This finding calls into question the hypothesis that proline-rich regions will preferentially adopt this structure since many such sequences are comprised of less than 50% proline residues. Proteins 33:218–226, 1998. © 1998 Wiley-Liss, Inc.     

Extended secondary structures in proteins

Supersecondary structures of proteins have been systematically searched and classified, but not enough attention has been devoted to such large edifices beyond the basic identification of secondary structures. The objective of the present study is to show that the association of secondary structures that share some of their backbone residues is a commonplace in globular proteins, and that such deeper fusion of secondary structures, namely extended secondary structures (ESSs), helps stabilize the original secondary structures and the resulting tertiary structures. For statistical purposes, a set of 163 proteins from the protein databank was randomly selected and a few specific cases are structurally analyzed and characterized in more detail. The results point that about 30% of the residues from each protein, on average, participate in ESS. Alternatively, for the specific cases considered, our results were based on the secondary structures produced after extensive Molecular Dynamics simulation of a protein–aqueous solvent system. Based on the very small width of the time distribution of the root mean squared deviations, between the ESS taken along the simulation and the ESS from the mean structure of the protein, for each ESS, we conclude that the ESSs significantly increase the conformational stability by forming very stable aggregates. The ubiquity and specificity of the ESS suggest that the role they play in the structure of proteins, including the domains formation, deserves to be thoroughly investigated.     

Patterns of protein-fold usage in eight microbial genomes: A comprehensive structural census

Eight microbial genomes are compared in terms of protein structure. Specifically, yeast, H. influenzae, M. genitalium, M. jannaschii, Synechocystis, M. pneumoniae, H. pylori, and E. coli are compared in terms of patterns of fold usage—whether a given fold occurs in a particular organism. Of the ∼340 soluble protein folds currently in the structure databank (PDB), 240 occur in at least one of the eight genomes, and 30 are shared amongst all eight. The shared folds are depleted in all-helical structure and enriched in mixed helix-sheet structure compared to the folds in the PDB. The top-10 most common of the shared 30 are enriched in superfolds, uniting many non-homologous sequence families, and are especially similar in overall architecture—eight having helices packed onto a central sheet. They are also very different from the common folds in the PBD, highlighting databank biases. Folds can be ranked in terms of expression as well as genome duplication. In yeast the top-10 most highly expressed folds are considerably different from the most highly duplicated folds. A tree can be constructed grouping genomes in terms of their shared folds. This has a remarkably similar topology to more conventional classifications, based on very different measures of relatedness. Finally, folds of membrane proteins can be analyzed through transmembrane-helix (TM) prediction. All the genomes appear to have similar usage patterns for these folds, with the occurrence of a particular fold falling off rapidly with increasing numbers of TM-elements, according to a “Zipf-like” law. This implies there are no marked preferences for proteins with particular numbers of TM-helices (e.g. 7-TM) in microbial genomes. Further information pertinent to this analysis is available at http://bioinfo.mbb.yale.edu/genome. Proteins 33:518–534, 1998. © 1998 Wiley-Liss, Inc.     

Protein loop structure prediction with flexible stem geometries

The structure prediction of loops with flexible stem residues is addressed in this article. While the secondary structure of the stem residues is assumed to be known, the geometry of the protein into which the loop must fit is considered to be unknown in our methodology. As a consequence, the compatibility of the loop with the remainder of the protein is not used as a criterion to reject loop decoys. The loop structure prediction with flexible stems is more difficult than fitting loops into a known protein structure in that a larger conformational space has to be covered. The main focus of the study is to assess the precision of loop structure prediction if no information on the protein geometry is available. The proposed approach is based on (1) dihedral angle sampling, (2) structure optimization by energy minimization with a physically based energy function, (3) clustering, and (4) a comparison of strategies for the selection of loops identified in (3). Steps (1) and (2) have similarities to previous approaches to loop structure prediction with fixed stems. Step (3) is based on a new iterative approach to clustering that is tailored for the loop structure prediction problem with flexible stems. In this new approach, clustering is not only used to identify conformers that are likely to be close to the native structure, but clustering is also employed to identify far-from-native decoys. By discarding these decoys iteratively, the overall quality of the ensemble and the loop structure prediction is improved. Step (4) provides a comparative study of criteria for loop selection based on energy, colony energy, cluster density, and a hybrid criterion introduced here. The proposed method is tested on a large set of 3215 loops from proteins in the Pdb-Select25 set and to 179 loops from proteins from the Casp6 experiment.     

Definition of a New Information-Based Per-Residue Quality Parameter

For biomolecular NMR structures typically only a poor correspondence is observed between statistics derived from the experimental input data and structural quality indicators obtained from the structure ensembles. Here, we investigate the relationship between the amount of available NMR data and structure quality. By generating datasets with a predetermined information content and evaluating the quality of the resulting structure ensembles we show that there is, in contrast to previous findings, a linear relation between the information contained in experimental data and structural quality. From this relation, a new quality parameter is derived that provides direct insight, on a per-residue basis, into the extent to which structural quality is governed by the experimental input data.     

Sequence-similar, structure-dissimilar protein pairs in the PDB

It is often assumed that in the Protein Data Bank (PDB), two proteins with similar sequences will also have similar structures. Accordingly, it has proved useful to develop subsets of the PDB from which "redundant" structures have been removed, based on a sequence-based criterion for similarity. Similarly, when predicting protein structure using homology modeling, if a template structure for modeling a target sequence is selected by sequence alone, this implicitly assumes that all sequence-similar templates are equivalent. Here, we show that this assumption is often not correct and that standard approaches to create subsets of the PDB can lead to the loss of structurally and functionally important information. We have carried out sequence-based structural superpositions and geometry-based structural alignments of a large number of protein pairs to determine the extent to which sequence similarity ensures structural similarity. We find many examples where two proteins that are similar in sequence have structures that differ significantly from one another. The source of the structural differences usually has a functional basis. The number of such proteins pairs that are identified and the magnitude of the dissimilarity depend on the approach that is used to calculate the differences; in particular sequence-based structure superpositioning will identify a larger number of structurally dissimilar pairs than geometry-based structural alignments. When two sequences can be aligned in a statistically meaningful way, sequence-based structural superpositioning provides a meaningful measure of structural differences. This approach and geometry-based structure alignments reveal somewhat different information and one or the other might be preferable in a given application. Our results suggest that in some cases, notably homology modeling, the common use of nonredundant datasets, culled from the PDB based on sequence, may mask important structural and functional information. We have established a data base of sequence-similar, structurally dissimilar protein pairs that will help address this problem (http://luna.bioc.columbia.edu/rachel/seqsimstrdiff.htm).     

Structure alignment via Delaunay tetrahedralization

A novel protein structure alignment technique has been developed reducing much of the secondary and tertiary structure to a sequential representation greatly accelerating many structural computations, including alignment. Constructed from incidence relations in the Delaunay tetrahedralization, alignments of the sequential representation describe structural similarities that cannot be expressed with rigid-body superposition and complement existing techniques minimizing root-mean-squared distance through superposition. Restricting to the largest substructure superimposable by a single rigid-body transformation determines an alignment suitable for root-mean-squared distance comparisons and visualization. Restricted alignments of a test set of histones and histone-like proteins determined superpositions nearly identical to those produced by the established structure alignment routines of DaliLite and ProSup. Alignment of three, increasingly complex proteins: ferredoxin, cytidine deaminase, and carbamoyl phosphate synthetase, to themselves, demonstrated previously identified regions of self-similarity. All-against-all similarity index comparisons performed on a test set of 45 class I and class II aminoacyl-tRNA synthetases closely reproduced the results of established distance matrix methods while requiring 1/16 the time. Principal component analysis of pairwise tetrahedral decomposition similarity of 2300 molecular dynamics snapshots of tryptophanyl-tRNA synthetase revealed discrete microstates within the trajectory consistent with experimental results. The method produces results with sufficient efficiency for large-scale multiple structure alignment and is well suited to genomic and evolutionary investigations where no geometric model of similarity is known a priori.     

蛋白质二级结构指定

蛋白质二级结构是指蛋白质骨架结构中有规律重复的构象。由蛋白质原子坐标正确地指定蛋白质二级结构是分析蛋白质结构与功能的基础,二级结构的指定对于蛋白质分类、蛋白质功能模体的发现以及理解蛋白质折叠机制有着重要的作用。并且蛋白质二级结构信息广泛应用到蛋白质分子可视化、蛋白质比对以及蛋白质结构预测中。目前有超过20种蛋白质二级结构指定方法,这些方法大体可以分为两大类:基于氢键和基于几何,不同方法指定结果之间的差异较大。由于尚没有蛋白质二级结构指定方法的综述文献,因此,本文主要介绍和总结已有蛋白质二级结构指定方法。