A pre-existing hydrophobic collapse in the unfolded state of an ultrafast folding protein

Insights into the conformational passage of a polypeptide chain across its free energy landscape have come from the judicious combination of experimental studies and computer simulations. Even though some unfolded and partially folded proteins are now known to possess biological function or to be involved in aggregation phenomena associated with disease states, experimentally derived atomic-level information on these structures remains sparse as a result of conformational heterogeneity and dynamics. Here we present a technique that can provide such information. Using a 'Trp-cage' miniprotein known as TC5b (ref. 5), we report photochemically induced dynamic nuclear polarization NMR pulse-labelling experiments that involve rapid in situ protein refolding. These experiments allow dipolar cross-relaxation with hyperpolarized aromatic side chain nuclei in the unfolded state to be identified and quantified in the resulting folded-state spectrum. We find that there is residual structure due to hydrophobic collapse in the unfolded state of this small protein, with strong inter-residue contacts between side chains that are relatively distant from one another in the native state. Prior structuring, even with the formation of non-native rather than native contacts, may be a feature associated with fast folding events in proteins.     

利用生物-生态修复技术治理城市污染河道

开发生物-生态水体修复技术,是当前水环境技术的研究热点之一。这种技术具有投资省、能耗低、效果好、长期稳定等优势,因此在污水治理工程中得到了广泛应用。本文主要介绍了生物-生态水体修复技术的原理和主要方法,给出了利用此技术修复温州滨海园区蓄水河(10 000 m3/d)的工艺设计方案。实际运行结果表明,各项出水水质指标均可达到应有的设计水质标准。     

Adaptive eradication of methionine and cysteine from cyanobacterial light-harvesting proteins

Sulphur is unique among the main elements of living cells in that it is covalently bound to biopolymers but does not occur in the biopolymer backbone. Indeed, most of the bacterial sulphur content resides in the methionine and cysteine side-chains of proteins. The growth yield of an organism under conditions of sulphur limitation could therefore be greatly enhanced by mutations that substitute Met and Cys in the organism's proteins for sulphur-free amino acids. Because the saving in sulphur would increase with such accumulating mutations, Met and Cys changes could be progressively selected. Abundant proteins should be the prime targets of such a selection. A few published observations give credence to this scenario. Sulphate permease, which is abundantly produced by sulphur-starved Salmonella typhimurium, lacks Met and Cys residues. Also, two species of marine purple bacteria synthesize more protein than can be expected from a limited sulphate supply. We now report that the cyanobacterium Calothrix sp. PCC 7601 (referred to here as Calothrix) encodes sulphur-depleted versions of its most abundant proteins--phycocyanin and its auxiliary polypeptides--which it specifically expresses under conditions of sulphur limitation. Although these proteins do not take part in the fixation of sulphur, their elevated synthesis affects the sulphur budget of cyanobacterial cells. Direct evidence is thus provided that the structure of macromolecules can be subject to metabolic optimization.     

猪脂肪细胞生脂及其调控研究进展

肥胖已成为严重威胁人类健康的流行病,猪作为研究肥胖及相关疾病的动物模型已引起人们的关注.通过介绍碳水化合物、蛋白质、激素等因素对猪脂肪生成的调控,期待为预防和治疗威胁人类健康的疾病提供有益的帮助.     

Aggregation and vesiculation of membrane proteins by curvature-mediated interactions

Membrane remodelling plays an important role in cellular tasks such as endocytosis, vesiculation and protein sorting, and in the biogenesis of organelles such as the endoplasmic reticulum or the Golgi apparatus. It is well established that the remodelling process is aided by specialized proteins that can sense as well as create membrane curvature, and trigger tubulation when added to synthetic liposomes. Because the energy needed for such large-scale changes in membrane geometry significantly exceeds the binding energy between individual proteins and between protein and membrane, cooperative action is essential. It has recently been suggested that curvature-mediated attractive interactions could aid cooperation and complement the effects of specific binding events on membrane remodelling. But it is difficult to experimentally isolate curvature-mediated interactions from direct attractions between proteins. Moreover, approximate theories predict repulsion between isotropically curving proteins. Here we use coarse-grained membrane simulations to show that curvature-inducing model proteins adsorbed on lipid bilayer membranes can experience attractive interactions that arise purely as a result of membrane curvature. We find that once a minimal local bending is realized, the effect robustly drives protein cluster formation and subsequent transformation into vesicles with radii that correlate with the local curvature imprint. Owing to its universal nature, curvature-mediated attraction can operate even between proteins lacking any specific interactions, such as newly synthesized and still immature membrane proteins in the endoplasmic reticulum.     

Compact sources as the origin of the soft gamma-ray emission of the Milky Way

The Milky Way is known to be an abundant source of gamma-ray photons, now determined to be mainly diffuse in nature and resulting from interstellar processes. In the soft gamma-ray domain, point sources are expected to dominate, but the lack of sensitive high-resolution observations did not allow for a clear estimate of the contribution from such sources. Even the best imaging experiment revealed only a few point sources, accounting for about 50% of the total Galactic flux. Theoretical studies were unable to explain the remaining intense diffuse emission. Investigating the origin of the soft gamma-rays is therefore necessary to determine the dominant particle acceleration processes and to gain insights into the physical and chemical equilibrium of the interstellar medium. Here we report observations in the soft gamma-ray domain that reveal numerous compact sources. We show that these sources account for the entirety of the Milky Way's emission in soft gamma-rays, leaving at most a minor role for diffuse processes.     

High brightness electron beam from a multi-walled carbon nanotube

Carbon nanotubes can act as electron sources with very rigid structures, making them particularly interesting for use as point electron sources in high-resolution electron-beam instruments. Promising results have been reported with respect to some important requirements for such applications: a stable emitted current and a long lifetime. Two parameters of an electron source affect the resolution of these instruments: the energy spread of the emitted electrons and a parameter called the reduced brightness, which depends on the angular current density and the virtual source size. Several authors have measured a low energy spread associated with electron emission. Here we measure the reduced brightness, and find a value that is more than a factor of ten larger than provided by state-of-the-art electron sources in electron microscopes. In addition, we show that an individual multi-walled carbon nanotube emits most current into a single narrow beam. On the basis of these results, we expect that carbon nanotube electron sources will lead to a significant improvement in the performance of high-resolution electron-beam instruments.     

A Reliable Neighbor-Based Method for Identifying Essential Proteins by Integrating Gene Expressions,Orthology,and Subcellular Localization Information

Essential proteins are those necessary for the survival or reproduction of species and discovering such essential proteins is fundamental for understanding the minimal requirements for cellular life, which is also meaningful to the disease study and drug design. With the development of high-throughput techniques, a large number of Protein-Protein Interactions(PPIs) can be used to identify essential proteins at the network level. Up to now, though a series of network-based computational methods have been proposed, it is still a challenge to improve the prediction precision as the high false positives in PPI networks. In this paper, we propose a new method GOS to identify essential proteins by integrating the Gene expressions, Orthology, and Subcellular localization information.The gene expressions and subcellular localization information are used to determine whether a neighbor in the PPI network is reliable. Only reliable neighbors are considered when we analyze the topological characteristics of a protein in a PPI network. We also analyze the orthologous attributes of each protein to reflect its conservative features, and use a random walk model to integrate a protein's topological characteristics and its orthology. The experimental results on the yeast PPI network show that the proposed method GOS outperforms the ten existing methods DC, BC, CC, SC, EC, IC, NC, Pe C, ION, and CSC.     

Localization of p53, retinoblastoma and host replication proteins at sites of viral replication in herpes-infected cells.

Replication of DNA occurs at discrete sites in eukaryotic cell nuclei, where replication proteins are clustered into large complexes, or 'replicases'. Similarly, viral DNA replication is a highly structured process, notably in herpes simplex virus type-1 (HSV-1; reviewed in ref. 4) in which large globular 'replication compartments' containing the viral replication machinery exist. Replicating cellular DNA redistributes to these compartments upon HSV-1 infection. We have now used antibodies raised against several cellular proteins to detect changes in their subnuclear localization on HSV-1 infection. We found that various proteins involved in cellular DNA replication move to sites of viral DNA synthesis, whereas a selection of non-replication proteins do not. The retinoblastoma protein and p53 (the products of two putative anti-oncogenes) relocate to the same sites as known DNA replication proteins, suggesting that they may be associated with DNA replication complexes in normal, uninfected cells.     

Plakalbumin, alpha 1-antitrypsin, antithrombin and the mechanism of inflammatory thrombosis

An old puzzle in protein biochemistry concerns the ready conversion of ovalbumin, by proteolysis, to the much more stable derivative, plakalbumin. Ovalbumin is now known to belong to the serpin superfamily, most of which are serine proteinase inhibitors. We report here studies of two such members of the family, the human plasma proteins alpha 1-antitrypsin and antithrombin, and show that they undergo a similar change in stability on selective proteolysis. This change, which is accompanied by a loss of inhibitory activity, can best be considered as an irreversible molecular transition from a native stressed (S) conformation, to a more ordered relaxed (R) form. The maintenance of the native S conformation, and hence the maintenance of inhibitory activity, is critically dependent on the integrity of an exposed loop of polypeptide. We propose that the susceptibility of this peptide loop to proteolytic cleavage gives it an incidental role as a physiological switch which allows the inactivation of individual inhibitors by specific proteolysis. The vulnerability of this exposed loop in each inhibitor also explains the pathological action of a number of venoms and toxins. In particular, the demonstration here of the cleavage of antithrombin, by leukocyte elastase, explains an observed change in blood coagulation that accompanies severe inflammation and which can result in fatal thrombosis.     

Nuclear fission modes and fragment mass asymmetries in a five-dimensional deformation space

Nuclei undergoing fission can be described by a multi-dimensional potential-energy surface that guides the nuclear shape evolution--from the ground state, through intermediate saddle points and finally to the configurations of separated fission fragments. Until now, calculations have lacked adequate exploration of the shape parameterization of sufficient dimensionality to yield features in the potential-energy surface (such as multiple minima, valleys, saddle points and ridges) that correspond to characteristic observables of the fission process. Here we calculate and analyse five-dimensional potential-energy landscapes based on a grid of 2,610,885 deformation points. We find that observed fission features--such as the distributions of fission fragment mass and kinetic energy, and the different energy thresholds for symmetric and asymmetric fission--are very closely related to topological features in the calculated five-dimensional energy landscapes.     

Coherent control of pulsed X-ray beams.

Synchrotrons produce continuous trains of closely spaced X-ray pulses. Application of such sources to the study of atomic-scale motion requires efficient modulation of these beams on timescales ranging from nanoseconds to femtoseconds. However, ultrafast X-ray modulators are not generally available. Here we report efficient subnanosecond coherent switching of synchrotron beams by using acoustic pulses in a crystal to modulate the anomalous low-loss transmission of X-ray pulses. The acoustic excitation transfers energy between two X-ray beams in a time shorter than the synchrotron pulse width of about 100 ps. Gigahertz modulation of the diffracted X-rays is also observed. We report different geometric arrangements, such as a switch based on the collision of two counter-propagating acoustic pulses: this doubles the X-ray modulation frequency, and also provides a means of observing a localized transient strain inside an opaque material. We expect that these techniques could be scaled to produce subpicosecond pulses, through laser-generated coherent optical phonon modulation of X-ray diffraction in crystals. Such ultrafast capabilities have been demonstrated thus far only in laser-generated X-ray sources, or through the use of X-ray streak cameras.     

Crystal symmetry and the reversibility of martensitic transformations

Martensitic transformations are diffusionless, solid-to-solid phase transitions, and have been observed in metals, alloys, ceramics and proteins. They are characterized by a rapid change of crystal structure, accompanied by the development of a rich microstructure. Martensitic transformations can be irreversible, as seen in steels upon quenching, or they can be reversible, such as those observed in shape-memory alloys. In the latter case, the microstructures formed on cooling are easily manipulated by loads and disappear upon reheating. Here, using mathematical theory and numerical simulation, we explain these sharp differences in behaviour on the basis of the change in crystal symmetry during the transition. We find that a necessary condition for reversibility is that the symmetry groups of the parent and product phases be included in a common finite symmetry group. In these cases, the energy barrier to lattice-invariant shear is generically higher than that pertaining to the phase change and, consequently, transformations of this type can occur with virtually no plasticity. Irreversibility is inevitable in all other martensitic transformations, where the energy barrier to plastic deformation (via lattice-invariant shears, as in twinning or slip) is no higher than the barrier to the phase change itself. Various experimental observations confirm the importance of the symmetry of the stable states in determining the macroscopic reversibility of martensitic transformations.     

带电粒子束在真空中传输时的扩散研究

根据相对论力学对带电粒子束在其自生场作用下通过外层空间的真空中传输时束的扩散进行了研究。提出了一种计算粒子束径向半径扩散的方法;计算并讨论了粒子束类型、能量、流强和出口初始半径等各种因素对束扩散的影响;得出了尽可能减少粒子束扩散的束参数,所得结果同现有公布的数据相符合。     

Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation

Both prokaryotic and eukaryotic organisms contain DNA bridging proteins, which can have regulatory or architectural functions. The molecular and mechanical details of such proteins are hard to obtain, in particular if they involve non-specific interactions. The bacterial nucleoid consists of hundreds of DNA loops, shaped in part by non-specific DNA bridging proteins such as histone-like nucleoid structuring protein (H-NS), leucine-responsive regulatory protein (Lrp) and SMC (structural maintenance of chromosomes) proteins. We have developed an optical tweezers instrument that can independently handle two DNA molecules, which allows the systematic investigation of protein-mediated DNA-DNA interactions. Here we use this technique to investigate the abundant non-specific nucleoid-associated protein H-NS, and show that H-NS is dynamically organized between two DNA molecules in register with their helical pitch. Our optical tweezers also allow us to carry out dynamic force spectroscopy on non-specific DNA binding proteins and thereby to determine an energy landscape for the H-NS-DNA interaction. Our results explain how the bacterial nucleoid can be effectively compacted and organized, but be dynamic in nature and accessible to DNA-tracking motor enzymes. Finally, our experimental approach is widely applicable to other DNA bridging proteins, as well as to complex DNA interactions involving multiple DNA molecules.     

基因和蛋白质的批量注释系统UBROAD

以DNA微阵列、二维电泳、二维高压液相色谱和质谱等技术为代表的转录组和蛋白质组高通 量实验技术,能够产生海量的基因或蛋白质数据,对这些基因或蛋白质的注释是对相关数据 进 行后期处理的基础和必要条件.海量数据的注释人工难以完成,而目前基因和蛋白质的批量 注释网站给出的注释又往往不够全面.在比较常用基因和蛋白质的批量注释网站的基础上, 本工作研发了基因和蛋白质的批量注释系统UBROAD(Unified Batch Retriever of Annotati on Data),该系统整合了NCBI、Swiss Prot、BIND、enzyme -expasy、gene2accession 和gene2Unig ene 6个有关基因和蛋白质的数据源;支持Uniprot/trEMBL AC、 Uniprot Entryname、Genb ank Protein Accession Number、Genbank mRNA gi、Genbank mRNA Accession Number、 G ene name、 Gene ID和Unigene ID 8种登录号混合查询;含有各种登录号以及基 因或蛋白质的基本信息、功能分类、相互作用共38项注释项供选择;提供微软电子表格形式 的注释结果.可以通过访问网页http://www.bioscience.org.cn/ubroad免费使用该系统.     

论我国建立统一应急救援体系之"急"

现代化大生产以能量巨大输入为突出特征，生产过程中潜伏着重大火灾、爆炸、毒物泄漏等危险。根据国外经验，建立统一应急救援体系是当务之“急”。本文着重就该体系的机构设置及职能、运行机制、保障制度、实施手段等内容作了论述。     

Recruitment of cytosolic proteins to a secretory granule membrane depends on Ca2+-calmodulin

An increase in free calcium triggers catecholamine secretion from chromaffin cells and calmodulin is strongly implicated as the intracellular Ca2+ receptor. In our recent studies of calmodulin action in the chromaffin cell, micromolar Ca2+ concentrations resulted in calmodulin and cytosolic proteins becoming bound to the chromaffin granule membranes. We now report that calmodulin is bound with high affinity to granule membrane proteins of molecular weights (Mrs) 25,000 and 22,000 (25K and 22K) at low Ca2+ (less than 10(-8) M) and to proteins with Mrs 69K and 50K at high Ca2+ (greater than 1 microM). Other cytosolic components (Mrs 70K, 36K, 34K and 32K) require calmodulin for their interfraction with membrane. These proteins separately bound to calmodulin-Sepharose at high Ca2+ concentrations. Although the functions of these adrenal proteins have not been established, the 34K and 32K Mr components co-migrate with clathrin light chains isolated from medullary coated vesicles and the Mr 34K components from both sources share the same one-dimensional peptide map. These interactions were observed at micromolar Ca2+ levels at 'intracellular' conditions of pH and ionic strength and would be expected to occur during secretion from the chromaffin cell.