Nucleosome arrays reveal the two-start organization of the chromatin fiber

Chromatin folding determines the accessibility of DNA constituting eukaryotic genomes and consequently is profoundly important in the mechanisms of nuclear processes such as gene regulation. Nucleosome arrays compact to form a 30-nanometer chromatin fiber of hitherto disputed structure. Two competing classes of models have been proposed in which nucleosomes are either arranged linearly in a one-start higher order helix or zigzag back and forth in a two-start helix. We analyzed compacted nucleosome arrays stabilized by introduction of disulfide cross-links and show that the chromatin fiber comprises two stacks of nucleosomes in accord with the two-start model.     

Histone H4-K16 acetylation controls chromatin structure and protein interactions

Acetylation of histone H4 on lysine 16 (H4-K16Ac) is a prevalent and reversible posttranslational chromatin modification in eukaryotes. To characterize the structural and functional role of this mark, we used a native chemical ligation strategy to generate histone H4 that was homogeneously acetylated at K16. The incorporation of this modified histone into nucleosomal arrays inhibits the formation of compact 30-nanometer-like fibers and impedes the ability of chromatin to form cross-fiber interactions. H4-K16Ac also inhibits the ability of the adenosine triphosphate-utilizing chromatin assembly and remodeling enzyme ACF to mobilize a mononucleosome, indicating that this single histone modification modulates both higher order chromatin structure and functional interactions between a nonhistone protein and the chromatin fiber.     

Correct folding of circularly permuted variants of a beta alpha barrel enzyme in vivo

An important question in protein folding is whether the natural amino and carboxyl termini and the given order of secondary structure segments are critical to the stability and to the folding pathway of proteins. Here it is shown that two circularly permuted versions of the gene of a single-domain beta alpha barrel enzyme can be expressed in Escherichia coli. The variants are enzymically active and are practically indistinguishable from the original enzyme by several structural and spectroscopic criteria, despite the creation of new termini and the cleavage of a surface loop. This novel genetic approach should be useful for protein folding studies both in vitro and in vivo.     

Visualizing the higher order folding of a catalytic RNA molecule

The higher order folding process of the catalytic RNA derived from the self-splicing intron of Tetrahymena thermophila was monitored with the use of Fe(II)-EDTA-induced free radical chemistry. The overall tertiary structure of the RNA molecule forms cooperatively with the uptake of at least three magnesium ions. Local folding transitions display different metal ion dependencies, suggesting that the RNA tertiary structure assembles through a specific folding intermediate before the catalytic core is formed. Enzymatic activity, assayed with an RNA substrate that is complementary to the catalytic RNA active site, coincides with the cooperative structural transition. The higher order RNA foldings produced by Mg(II), Ca(II), and Sr(II) are similar; however, only the Mg(II)-stabilized RNA is catalytically active. Thus, these results directly demonstrate that divalent metal ions participate in general folding of the ribozyme tertiary structure, and further indicate a more specific involvement of Mg(II) in catalysis.     

Heterochromatin and epigenetic control of gene expression

Eukaryotic DNA is organized into structurally distinct domains that regulate gene expression and chromosome behavior. Epigenetically heritable domains of heterochromatin control the structure and expression of large chromosome domains and are required for proper chromosome segregation. Recent studies have identified many of the enzymes and structural proteins that work together to assemble heterochromatin. The assembly process appears to occur in a stepwise manner involving sequential rounds of histone modification by silencing complexes that spread along the chromatin fiber by self-oligomerization, as well as by association with specifically modified histone amino-terminal tails. Finally, an unexpected role for noncoding RNAs and RNA interference in the formation of epigenetic chromatin domains has been uncovered.     

Mechanism of Supercontraction in a Striated Muscle Fiber

Cross-striated muscle fibers may contract reversibly to less than 30 percent of their rest length and it is not easy to reconcile this fact with the sliding filament model of muscular contraction. The mechanism of supercontraction has been studied in fibrils obtained from the giant muscle fibers of the barnacle Balanus nubilus. They were examined by phase-contrast light microscopy and electron microscopy. Contraction beyond the 50-percent stage was found to be achieved largely by the passage of thick filaments through the Z-disks, which are perforated. The overlap of thick filaments from adjacent sarcomeres causes the appearance of the contraction bands about the Z-disks. Subsequent contraction is associated with a folding and loose coiling, but not a shortening, of the thick filaments.     

生物制剂在草本纤维质农产品加工业中的应用进展

为了阐明生物制剂在草本纤维质农产品加工业中应用的研究范围与进展,采用系统信息学技术原理,围绕生物制剂在脱胶、纺织、造纸、轻工制造等学科领域中应用的主线,对近40年的相关研究报道进行分类整理与凝练。分析结果表明,在草本纤维原料脱胶及其类似初级加工过程中应用菌制剂具有节能、减排、降耗、高效利用资源等优点;在草本纤维纺织、造纸、轻工制造等深加工领域里应用酶制剂可以充分发挥酶的专一性、高效性作用,说明生物制剂在草本纤维质农产品加工业中应用的前景十分广阔。     

The nucleosomal surface as a docking station for Kaposi's sarcoma herpesvirus LANA

Kaposi's sarcoma-associated herpesvirus (KSHV) latency-associated nuclear antigen (LANA) mediates viral genome attachment to mitotic chromosomes. We find that N-terminal LANA docks onto chromosomes by binding nucleosomes through the folded region of histones H2A-H2B. The same LANA residues were required for both H2A-H2B binding and chromosome association. Further, LANA did not bind Xenopus sperm chromatin, which is deficient in H2A-H2B; chromatin binding was rescued after assembly of nucleosomes containing H2A-H2B. We also describe the 2.9-angstrom crystal structure of a nucleosome complexed with the first 23 LANA amino acids. The LANA peptide forms a hairpin that interacts exclusively with an acidic H2A-H2B region that is implicated in the formation of higher order chromatin structure. Our findings present a paradigm for how nucleosomes may serve as binding platforms for viral and cellular proteins and reveal a previously unknown mechanism for KSHV latency.     

蛋白质的品质管理

概述了蛋白质品质管理中涉及的分子伴侣、激发未折叠蛋白反应(unfolded protein response,UPR)和内质网相关性蛋白质降解途径(ER-associated degradation,ERAD)等的研究进展,并探讨了该领域存在的问题以及发展前景。指出蛋白质的生命过程经历生成、折叠、组装和降解,每个过程都有严格控制。内质网中,各种蛋白质合成、折叠并经修饰形成具有一定构象的功能性蛋白。其在内质网折叠受阻碍时,未折叠的蛋白聚集,激发UPR,使一系列分子伴侣和蛋白质折叠所需修饰酶类表达上调,帮助其完成折叠和装配。如果这些蛋白仍不能正确折叠,则进入ERAD被降解。     

立体分子伴侣-脂肪酶特异折叠酶

细菌脂肪酶是一类重要的工业用酶,尤其以来源于假单孢杆菌Pseudomonas与伯克霍尔德菌Burkholderia的脂肪酶应用最为广泛。然而,这类脂肪酶折叠过程中存在一个巨大的能障而无法自发正确折叠。研究发现,这类脂肪酶的编码基因所在操纵子中往往存在一个与其折叠相关的基因,编码一种脂肪酶特异折叠酶。该类蛋白为脂肪酶的立体分子伴侣,可与脂肪酶的折叠中间体相互作用,帮助脂肪酶越过折叠过程中的能量障碍,为其获得正确构象提供必要的空间信息。详细阐述了脂肪酶特异折叠酶的发现、分类、作用机制与应用前景。     

Chaperone selection during glycoprotein translocation into the endoplasmic reticulum

A variety of molecular chaperones and folding enzymes assist the folding of newly synthesized proteins in the endoplasmic reticulum. Here we investigated why some glycoproteins interact with the molecular chaperone BiP, and others with the calnexin/calreticulin pathway. The folding of Semliki forest virus glycoproteins and influenza hemagglutinin was studied in living cells. The initial choice of chaperone depended on the location of N-linked glycans in the growing nascent chain. Direct interaction with calnexin and calreticulin without prior interaction with BiP occurred if glycans were present within about 50 residues of the protein's NH2-terminus.     

Crystal versus solution structures of enzymes: NMR spectroscopy of a crystalline serine protease

The hydrogen-bonding status of His57 in the catalytic triad (Asp-His-Ser) of serine protease has important mechanistic implications for this class of enzymes. Recent nitrogen-15 nuclear magnetic resonance (NMR) studies of alpha-lytic protease find His57 and Ser195 to be strongly hydrogen-bonded, a result that conflicts with the corresponding crystallographic studies, thereby suggesting that the crystal and solution structures may differ. This discrepancy is addressed and resolved in a nitrogen-15 NMR study of the enzyme in the crystalline state. The results show that the His-Ser and Asp-His interactions are identical in crystals and solutions, but that in crystals His57 titrates with a pKa of 7.9, nearly one pKa unit higher than in solution. This elevated pKa accounts for the absence of the His-Ser hydrogen bond in previous x-ray studies.     

Macroscopic fibers and ribbons of oriented carbon nanotubes

A simple method was used to assemble single-walled carbon nanotubes into indefinitely long ribbons and fibers. The processing consists of dispersing the nanotubes in surfactant solutions, recondensing the nanotubes in the flow of a polymer solution to form a nanotube mesh, and then collating this mesh to a nanotube fiber. Flow-induced alignment may lead to a preferential orientation of the nanotubes in the mesh that has the form of a ribbon. Unlike classical carbon fibers, the nanotube fibers can be strongly bent without breaking. Their obtained elastic modulus is 10 times higher than the modulus of high-quality bucky paper.     

Neutrophil extracellular traps kill bacteria

Neutrophils engulf and kill bacteria when their antimicrobial granules fuse with the phagosome. Here, we describe that, upon activation, neutrophils release granule proteins and chromatin that together form extracellular fibers that bind Gram-positive and -negative bacteria. These neutrophil extracellular traps (NETs) degrade virulence factors and kill bacteria. NETs are abundant in vivo in experimental dysentery and spontaneous human appendicitis, two examples of acute inflammation. NETs appear to be a form of innate response that binds microorganisms, prevents them from spreading, and ensures a high local concentration of antimicrobial agents to degrade virulence factors and kill bacteria.     

不同盐度对脊尾白虾非特异性免疫及抗氧化酶活性的影响

为了研究不同盐度对脊尾白虾免疫水平的影响,实验对5个盐度组脊尾白虾的肝胰腺和肌肉组织中的非特异性免疫及抗氧化酶相关的酶活性进行了比较分析。结果表明,除LSZ酶活外,不同酶活在肝胰腺中的分布均高于肌肉;除肌肉中的LSZ酶活外,不同盐度组间的免疫酶活性有显著差异。ACP、AKP酶活在肝胰腺中分布以26.6盐度组最高,显著高于11.0、16.2、21.4盐度组（P〈0.05）;不同盐度间脊尾白虾肝胰腺中LSZ酶活差异显著（P〈0.05）,以26.6盐度组酶活最高;T-AOC、SOD酶活在肝胰腺中的分布差异显著（P〈0.05）,以31.8盐度组最高,21.4盐度组最低。     

蛋白质分子的一生——蛋白质的品质管理(英文)

概述了蛋白质品质管理中涉及的分子伴侣、激发未折叠蛋白反应(unfolded protein response, UPR)和内质网相关性蛋白质降解途径(ER-associated degradation, ERAD)等的研究进展,并探讨了该领域存在的问题以及发展前景。指出蛋白质的生命过程经历生成、折叠、组装和降解,每个过程都有严格控制。内质网中,各种蛋白质合成、折叠并经修饰形成具有一定构象的功能性蛋白。其在内质网折叠受阻碍时,未折叠的蛋白聚集,激发 UPR,使一系列分子伴侣和蛋白质折叠所需修饰酶类表达上调,帮助其完成折叠和装配。如果这些蛋白仍不能正确折叠,则进入 ERAD 被降解。