用网络方法识别生物序列motif

生物序列motif的识别是后基因组时代的一个核心问题。本文首先回顾了识别motif的几种主要算法,然后根据motif的重要性和随机性介绍了利用网络识别motif的两种具有代表性的方法：一种是建立一个随机网络混合模型,利用EM算法识别其中随机的网络motif;另一种用修正的参数流算法过滤出其中的最大密度予图,即为生物序列motif,并指出这两种方法的优劣,最后还对今后研究方向给出了讨论。     

富脯氨酸模体研究进展

综述了近年来富脯氨酸模体的研究进展状况,并将其分为PxxP核心序列模体、聚脯氨酸模体、PPxY核心序列模体以及其他类型的模体4类,论述了富脯氨酸膜体的生物学功能及其常出现的原因.     

Motifs in brain networks

Complex brains have evolved a highly efficient network architecture whose structural connectivity is capable of generating a large repertoire of functional states. We detect characteristic network building blocks (structural and functional motifs) in neuroanatomical data sets and identify a small set of structural motifs that occur in significantly increased numbers. Our analysis suggests the hypothesis that brain networks maximize both the number and the diversity of functional motifs, while the repertoire of structural motifs remains small. Using functional motif number as a cost function in an optimization algorithm, we obtain network topologies that resemble real brain networks across a broad spectrum of structural measures, including small-world attributes. These results are consistent with the hypothesis that highly evolved neural architectures are organized to maximize functional repertoires and to support highly efficient integration of information.     

A Screen for Endocytic Motifs

Sorting signals for cargo selection into coated vesicles are usually in the form of short linear motifs. Three motifs for clathrin‐mediated endocytosis have been identified: YXXΦ, [D/E]XXXL[L/I] and FXNPXY. To search for new endocytic motifs, we made a library of CD8 chimeras with random sequences in their cytoplasmic tails, and used a novel fluorescence‐activated cell sorting (FACS)‐based assay to select for endocytosed constructs. Out of the five tails that were most efficiently internalized, only one was found to contain a conventional motif. Two contain dileucine‐like sequences that appear to be variations on the [D/E]XXXL[L/I] motif. Another contains a novel internalization signal, YXXXΦN, which is able to function in cells expressing a mutant µ2 that cannot bind YXXΦ, indicating that it is not a variation on the YXXΦ motif. Similar sequences are present in endogenous proteins, including a functional YXXXΦN (in addition to a classical YXXΦ) in cytotoxic T‐lymphocyte‐associated protein 4 (CTLA‐4). Thus, the repertoire of endocytic motifs is more extensive than the three well‐characterized sorting signals.     

CpG特征结构与树突状细胞

近年来的研究表明 :ＣｐＧ特征结构是脊椎动物免疫系统识别微生物ＤＮＡ并产生针对抗原的保护性免疫反应的主要机制 ,它在体内及体外均能诱导以Ｔｈ1细胞为主的高水平、高特异性的细胞免疫应答 ;是质粒ＤＮＡ疫苗及裸ＤＮＡ疫苗诱导机体免疫应答的原因之一 ,在临床实验中ＣｐＧ ＯＤＮ已被用作抗原疫苗、ＤＮＡ疫苗治疗肿瘤、变态反应性疾病的强有力佐剂。ＣｐＧ特征结构能够诱导机体产生以Ｔｈ1细胞为主的细胞免疫应答是因为它能够作用于Ｔ细胞、Ｂ细胞、ＮＫ细胞、巨噬细胞及树突状细胞等免疫细胞。树突状细胞是机体最主要的专职抗原呈递…     

Motifs of the caldesmon family

Seven highly conserved regions were found in caldesmon molecules from various sources using the multiple sequence alignment method. Their localization coincides with regions where the binding sites to other proteins were postulated. Less conserved and highly divergent regions of the sequences are described as well. These results could refine the planning of caldesmon gene manipulations and accelerate the precise localization of binding sites in the caldesmon molecule and, as a consequence, this could help to elucidate its function in smooth muscle contraction.     

Motifs involved in protein-protein interactions

Summary Interactions between proteins are extremely variable. However, in the dimeric proteins comprised of regular motifs, interface interactions are similar to those that stabilize monomers. Additional stability is gained by converting loops within motifs or domains to linkers across interfaces. In multi-domain proteins, interactions can be greatly effected by the conformation of linkers between domains. Complex association of subunits, involving higher rotational symmetry or cubic symmetry, frequently involves motif sharing across interfaces.     

DNA Intercalated Motifs with Non-Nucleoside Inserts

Russian Journal of Bioorganic Chemistry - A cytosine-rich sequence from the human genome that is presumably involved in the regulation of SHANK1 gene expression through the formation of an...     

蛋白质结构层次中的超二级结构

近年来关于蛋白质超二级结构(supersecondary motifs,Motifs)的研究已成为国际上一个热点课题,国内也开始出现有关的研究论文,蛋白质超二级结构是两个或几个规则二级结构单元的进一步组合,或看成是二级结构的局域折叠.文章就蛋白质Motifs结构的定义,特点,及对这一结构层次开展研究的意义作了综述,并对蛋白质Motifs研究的进展作了简要的介绍．     

Decorative Motifs On Great Oasis Pottery

Abstract

Decorative design motifs on Great Oasis Incised rim sherds from the Great Oasis site in Minnesota are illustrated and described. The usefulness of using decorative modes in ceramic comparisons with pottery of the Over focus is suggested.     

Aggregation-Prone Motifs in Human Immunoglobulin G

Therapeutic antibodies of many different IgG subclasses (IgG1, IgG2 and IgG4) are used in the treatment of various cancers, rheumatoid arthritis and other inflammatory and infectious diseases. These antibodies are stored for long durations under high concentrations as required in the disease treatment. Unfortunately, these antibodies aggregate under these storage conditions, leading to a decrease in antibody activity and raising concerns about causing an immunological response. Thus, there is a tremendous need to identify the aggregation-prone regions in different classes of antibodies. We use the SAP (spatial-aggregation-propensity) technology based on molecular simulations to determine the aggregation-prone motifs in the constant regions of IgG1 classes of antibodies. Mutations engineered on these aggregation-prone motif regions led to antibodies of enhanced stability. Fourteen aggregation-prone motifs are identified, with each motif containing one to seven residues. While some of these motifs contain residues that are neighbors in primary sequence, others contain residues that are far apart in primary sequence but are close together in the tertiary structure. Comparison of the IgG1 sequence with those of other subclasses (IgG2, IgG3 and IgG4) showed that these aggregation-prone motifs are largely preserved among all IgG subclasses. Other broader classes of antibodies (IgA1, IgD, IgE and IgM), however, differed in these motif regions. The aggregation-prone motifs identified were therefore common to all IgG subclasses, but differ from those of non-IgG classes. Moreover, since the motifs identified are in the constant regions, they are applicable for all antibodies within the IgG class irrespective of the variable region. Thus, the motif regions identified could be modified on all IgGs to yield antibodies of enhanced stability.