Is there more to enamel matrix proteins than biomineralization?

Enamel proteins are proteins synthesized by ameloblast cells. These proteins are secreted into the enamel extracellular matrix where they nucleate and regulate the growth of hydroxyapatite crystals to form the mineralized enamel covering the crown of the teeth. Although the exact role of these proteins in enamel mineralization is just beginning to be elucidated, new studies suggest that these proteins might have functions outside enamel formation. Furthermore, extracts of enamel proteins are currently being used to regenerate periodontal tissues destroyed by periodontal disease and new studies suggest that they might have chondrogenic and osteogenic properties. These new functions of enamel proteins will be the focus of this review.     

New tools for in vivo fluorescence tagging

Engineering of fluorescent proteins continues to produce new tools for in vivo studies. The current selection contains brighter, monomeric, spectral variants that will facilitate multiplex imaging and FRET, and a collection of optical highlighter proteins that might replace photoactivatable-GFP. These new highlighter proteins, which include proteins that have photoswitchable fluorescence characteristics and a protein whose fluorescence can be repeatedly turned on and off, should simplify refined analyses of protein dynamics and kinetics. Fluorescent protein-based systems have also been developed to allow facile detection of protein-protein interactions in planta. In addition, new tags in the form of peptides that bind fluorescent ligands and quantum dots offer the prospect of overcoming some of the limitations of fluorescent proteins such as excessive size and insufficient brightness.     

Identification and developmental expression of new biomineralization proteins in the sea urchin Strongylocentrotus purpuratus

The endoskeleton of the sea urchin larva is a network of calcareous rods secreted by primary mesenchyme cells (PMCs). In this study, we identified seven new biomineralization-related proteins through an analysis of a large database of gene products expressed by PMCs. The proteins include three new spicule matrix proteins (SpSM29, SpSM32, and SpC-lectin), two proteins related to the PMC-specific cell surface glycoprotein MSP130 (MSP130-related-1 and -2), and two novel proteins (SpP16 and SpP19). The genes encoding these proteins are expressed specifically by cells of the large micromere-PMC lineage and are activated zygotically beginning at the blastula stage, prior to PMC ingression. Several of the mRNAs show regulated patterns of expression within the PMC syncytium that correlate with the pattern of skeletal rod growth. This work identifies new proteins that may regulate the process of biomineralization in this tractable model system.     

The generation of new protein functions by the combination of domains

During evolution, many new proteins have been formed by the process of gene duplication and combination. The genes involved in this process usually code for whole domains. Small proteins contain one domain; medium and large proteins contain two or more domains. We have compared homologous domains that occur in both one-domain proteins and multidomain proteins. We have determined (1) how the functions of the individual domains in the multidomain proteins combine to produce their overall functions and (2) the extent to which these functions are similar to those in the one-domain homologs. We describe how domain combinations increase the specificity of enzymes; act as links between domains that have functional roles; regulate activity; combine within one chain functions that can act either independently, in concert or in new contexts; and provide the structural framework for the evolution of entirely new functions.     

Proteins induced by DNA-damaging agents in cultured Drosophila cells

In Drosophila cultured cells, the effects of several DNA-damaging agents on the expression of proteins were investigated. Poly(A+) RNA prepared from both untreated cells and cells treated with DNA-damaging agents was translated in vitro. The translation products were analyzed by two-dimensional electrophoresis. Methyl methanesulfonate, the most potent agent used, induced about 25 proteins, some new and some enhanced pre-existing proteins. Angelicin plus near UV irradiation, 4-nitroquinoline N-oxide and ethyl methanesulfonate were efficient inducers. Mitomycin C, UV irradiation and hydrogen peroxide were poor inducers, inducing only a few proteins at low levels. A tumor promoter, 12-O-tetradecanoylphorbol-13-acetate, and a DNA gyrase inhibitor, nalidixic acid, also were used. In this system they were weak inducers of new proteins. Several of the new or enhanced proteins were common to several agents, but others were agent specific. The distribution of mutagen-induced proteins was compared with that of proteins induced in cells heated at 37 degrees C. Some of the proteins induced by DNA-damaging agents were found to overlap heat-shock proteins. These results suggest that there are sets of induced genes that are regulated differently.     

A new tool for G protein analysis.

G proteins play a pivotal role in cellular signaling by acting as molecular switches that undergo conformational changes upon binding GTP. The primary sequence constituting the binding cleft among the >160 G proteins in the human genome is highly conserved, consistent with the fact that these proteins share similar guanine nucleotide-binding characteristics. Recent work has demonstrated the feasibility of designing new analogs of GTP that can specifically activate G proteins whose nucleotide-binding sites have been remodeled through mutagenesis. This strategy has the potential to provide new insights into how G proteins act as molecular switches that engage their downstream target/effector proteins to generate specific signaling outputs.     

The plant mitochondrial proteome

The plant mitochondrial proteome might contain as many as 2000-3000 different gene products, each of which might undergo post-translational modification. Recent studies using analytical methods, such as one-, two- and three-dimensional gel electrophoresis and one- and two-dimensional liquid chromatography linked on-line with tandem mass spectrometry, have identified >400 mitochondrial proteins, including subunits of mitochondrial respiratory complexes, supercomplexes, phosphorylated proteins and oxidized proteins. The results also highlight a range of new mitochondrial proteins, new mitochondrial functions and possible new mechanisms for regulating mitochondrial metabolism. More than 70 identified proteins in Arabidopsis mitochondrial samples lack similarity to any protein of known function. In some cases, unknown proteins were found to form part of protein complexes, which allows a functional context to be defined for them. There are indications that some of these proteins add novel activities to mitochondrial protein complexes in plants.     

Patch engineering: a general approach for creating proteins that have new binding activities

Patch engineering is a technique for creating folded proteins that have new binding activities. Different protein scaffolds are used to present a patch of discontinuous residues on a folded-protein surface. By varying simultaneously the residues in these patches and displaying these mutant proteins on phage, one can select proteins that have new binding activities. Patch engineering is applicable to any protein fold. Novel proteins derived by this approach might replace antibodies in certain applications or provide lead molecules for the design of non-peptide analogues.     

Antifreeze proteins in overwintering plants: a tale of two activities

Antifreeze proteins are found in a wide range of overwintering plants where they inhibit the growth and recrystallization of ice that forms in intercellular spaces. Unlike antifreeze proteins found in fish and insects, plant antifreeze proteins have multiple, hydrophilic ice-binding domains. Surprisingly, antifreeze proteins from plants are homologous to pathogenesis-related proteins and also provide protection against psychrophilic pathogens. In winter rye (Secale cereale), antifreeze proteins accumulate in response to cold, short daylength, dehydration and ethylene, but not pathogens. Transferring single genes encoding antifreeze proteins to freezing-sensitive plants lowered their freezing temperatures by approximately 1 degrees C. Genes encoding dual-function plant antifreeze proteins are excellent models for use in evolutionary studies to determine how genes acquire new expression patterns and how proteins acquire new activities.     

Zizimin1, a novel Cdc42 activator,reveals a new GEF domain for Rho proteins

The Rho family GTPases Rac, Rho and Cdc42 are critical in regulating the actin-based cytoskeleton, cell migration, growth, survival and gene expression. These GTPases are activated by guanine nucleotide-exchange factors (GEFs). A biochemical search for Cdc42 activators led to the cloning of zizimin1, a new protein whose overexpression induces Cdc42 activation. Sequence comparison combined with mutational analysis identified a new domain, which we named CZH2, that mediates direct interaction with Cdc42. CZH2-containing proteins constitute a new superfamily that includes the so-called 'CDM' proteins that bind to and activate Rac. Together, the results suggest that CZH2 is a new GEF domain for the Rho family of proteins.     

丝氨酸/精氨酸富集蛋白与肿瘤发生

富含丝氨酸和精氨酸的SR蛋白（serine/arginine-rich protein）是重要的剪接因子家族,广泛参与RNA加工过程,包括剪接、出核、稳定性及翻译。近年来的研究发现,SR蛋白家族成员大多在肿瘤组织中存在异常表达,有些SR蛋白甚至能够作为原癌基因,通过调控肿瘤相关基因的选择性剪接而参与细胞转化和肿瘤发生。本文综述了SR蛋白的不同成员在肿瘤发生中的作用及其调控肿瘤相关基因的机制,以期为相关肿瘤的研究与诊治提供新思路和新靶点。     

Perspectives of immobilized-metal affinity chromatography.

Immobilized Metal-Affinity Chromatography (IMAC) represents a relatively new separation technique that is primarily appropriate for the purification of proteins with natural surface-exposed histidine residues and for recombinant proteins with engineered histidine tags or histidine clusters. Because the method has gained broad popularity in recent years, the main recent developments in the field of new sorbents, techniques and possible applications are discussed in this article. Advantages of the method and new prospects are described as well as the problems and concerns that appear when the method is to be used for production of pharmaceutical-grade proteins.     

蛋白质的二级结构预测研究进展

认识蛋白质的二级结构是了解蛋白质的折叠模式和三级结构的基础,并为研究蛋白质的功能以及它们之间的相互作用模式提供结构基础,同时还可以为新药研发提供帮助。故研究蛋白质的二级结构具有重要的意义。随着后基因组时代的到来,越来越多的蛋白质序列不断被发现,给蛋白质的二级结构研究带来巨大的挑战和研究空间。而依靠传统的实验方法很难获取大规模蛋白质的二级结构信息。目前,采用生物信息学手段仍然是获得大部分蛋白质二级结构的途径。近年来,许多研究者通过构建用于二级结构预测的蛋白质数据集,计算、提取蛋白质的各种特征信息,并采用不同的预测算法预测蛋白质的二级结构得到了快速的发展。本文拟从蛋白质的特征信息的提取与筛选、预测算法以及预测效果的检验方法等方面进行综述,介绍蛋白质二级结构预测领域的研究进展。相信随着基因组学、蛋白质组学和生物信息学的不断发展,蛋白质二级结构预测会不断取得新突破。     

兼职功能蛋白

兼职功能蛋白(moonlighting proteins)是指一类具有两种或两种以上功能的蛋白,且这些功能间没有直接相关性,此类蛋白能够通过多种形式转换其功能.随着科学研究的深入,越来越多的已知功能的蛋白被发现具有新型兼职功能,其兼职功能对生物体的意义绝不亚于其所谓本职功能.兼职功能蛋白的发现大大拓展了基因、蛋白质与生理功能一一对应的传统观念;特别是最近研究发现一类叫做无固有结构蛋白(intrinsically unstructured proteins,IUPs)表现出多功能性,向"蛋白质的功能等视于确定的三维结构"的经典定律发起了挑战.本文综述了兼职功能蛋白的功能转换机制、进化历程、研究方法等方面的最新研究进展,同时对兼职功能蛋白给生命科学研究带来的新思路和新挑战进行了深入的讨论.     

Differential induction of glucose-regulated and heat shock proteins: effects of pH and sulfhydryl-reducing agents on chicken embryo cells

Glucose-regulated and heat shock proteins are two subsets of eukaryotic stress proteins that can be induced differentially, simultaneously, and reciprocally. Two new inducers, low extracellular pH and 2-mercaptoethanol, that stimulate chicken embryo cells to synthesize glucose-regulated proteins rapidly were found. Two classes of cellular targets for mercaptoethanol were defined operationally, one dependent on and the other independent of protein synthesis. A new inducer of heat shock proteins, high extracellular pH, was found as well. Inductions by low and high extracellular pH were inhibited by actinomycin D but were insensitive to cycloheximide. Inductions of glucose-regulated and heat shock proteins are discussed in terms of changes in intracellular pH and sulfhydryl oxidation states.     

Two-dimensional crystallization of membrane proteins: the lipid layer strategy

Due to the difficulty to crystallize membrane proteins, there is a considerable interest to intensify research topics aimed at developing new methods of crystallization. In this context, the lipid layer crystallization at the air/water interface, used so far for soluble proteins, has been recently adapted successfully to produce two-dimensional (2D) crystals of membrane proteins, amenable to structural analysis by electron crystallography. Besides to represent a new alternative strategy, this approach gains the advantage to decrease significantly the amount of material needed in incubation trials, thus opening the field of crystallization to those membrane proteins difficult to surexpress and/or purify. The systematic studies that have been performed on different classes of membrane proteins are reviewed and the physico-chemical processes that lead to the production of 2D crystals are addressed. The different drawbacks, advantages and perspectives of this new strategy for providing structural information on membrane proteins are discussed.     

Novel purification method for mammalian seminal plasma phospholipid-binding proteins reveals the presence of a novel member of this family of protein in stallion seminal fluid

A family of bull seminal plasma (BSP) phospholipid-binding proteins (BSP proteins), potentiate heparin- and HDL-induced capacitation. The homologous proteins have been purified from stallion and boar seminal plasma, and detected in low concentrations in other mammalian seminal plasma. In this study, we developed a new isolation method for mammalian seminal plasma choline phospholipid-binding proteins wherein they are present in low concentrations. The method is based on the interaction of this family of proteins with egg yolk low-density lipoprotein fraction (LDF). In order to demonstrate the feasibility of the method, we incubated LDF with alcohol precipitates of bull, boar, and stallion seminal plasma. LDF were re-isolated by ultracentrifugation along with bound proteins. LDF with associated proteins were dialyzed, lyophilized, and delipidated. BSP homologous proteins were finally purified by p-aminophenyl phosphorylcholine (PPC)-agarose and/or gelatin-agarose chromatographies, and analyzed by SDS-PAGE. With this new protocol, phospholipid-binding proteins of bull, boar, and stallion seminal plasma were recovered almost 100%. A new 12 kDa stallion seminal plasma protein of the same family was also isolated and partially sequenced. The radio-immunoassay (RIA) data showed that 10 mg of LDF can bind all BSP proteins present in 120 mg of alcohol precipitated BSP proteins. These results confirm the efficiency of the method and that the LDF step could be used for the isolation of all BSP proteins homologs from different mammalian species.     

Network Propagation with Dual Flow for Gene Prioritization

Based on the hypothesis that the neighbors of disease genes trend to cause similar diseases, network-based methods for disease prediction have received increasing attention. Taking full advantage of network structure, the performance of global distance measurements is generally superior to local distance measurements. However, some problems exist in the global distance measurements. For example, global distance measurements may mistake non-disease hub proteins that have dense interactions with known disease proteins for potential disease proteins. To find a new method to avoid the aforementioned problem, we analyzed the differences between disease proteins and other proteins by using essential proteins (proteins encoded by essential genes) as references. We find that disease proteins are not well connected with essential proteins in the protein interaction networks. Based on this new finding, we proposed a novel strategy for gene prioritization based on protein interaction networks. We allocated positive flow to disease genes and negative flow to essential genes, and adopted network propagation for gene prioritization. Experimental results on 110 diseases verified the effectiveness and potential of the proposed method.     

Actin-binding proteins.

Much new information on the sequence, structure, and function of filament crosslinking, capping, and severing proteins is now known. Other significant findings include identification of a new abundant monomer-sequestering protein in platelets, and evidence that many actin-binding proteins interact with phosphoinositides and that this interaction may have metabolic consequences.