The crystal structure of DNA mismatch repair protein MutS binding to a G x T mismatch

DNA mismatch repair ensures genomic integrity on DNA replication. Recognition of a DNA mismatch by a dimeric MutS protein initiates a cascade of reactions and results in repair of the newly synthesized strand; however, details of the molecular mechanism remain controversial. Here we present the crystal structure at 2.2 A of MutS from Escherichia coli bound to a G x T mismatch. The two MutS monomers have different conformations and form a heterodimer at the structural level. Only one monomer recognizes the mismatch specifically and has ADP bound. Mismatch recognition occurs by extensive minor groove interactions causing unusual base pairing and kinking of the DNA. Nonspecific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. The interleaved nucleotide-binding sites are located far from the DNA. Mutations in human MutS alpha (MSH2/MSH6) that lead to hereditary predisposition for cancer, such as hereditary non-polyposis colorectal cancer, can be mapped to this crystal structure.     

Unusual helical packing in crystals of DNA bearing a mutation hot spot

The target sequence of the restriction enzyme NarI (GGCGCC) is a hot spot for the -2 frameshift mutagenesis (GGCGCC----GGCC) induced by the chemical carcinogens such as N-2-acetyl-aminofluorene. Of the guanine residues, all of which show equal reactivity towards the carcinogen, only binding to the 3'-most proximal guanine within the NarI site is able to trigger the frameshift event. We selected the non-palindromic dodecamer d(ACCGGCGCCACA), whose sequence corresponds to the most mutagenic NarI site in pBR322 DNA; for X-ray structure analysis. Its molecular structure determined at 2.8 A resolution reveals significant deviations from the structure of canonical B-form DNA, with partial opening of three G-C base pairs, high propeller twist values and sequence-dependent three-centred hydrogen bonds. This crystal structure shows a novel kind of packing in which helices are locked together by groove-backbone interactions. The partial opening of G-C base pairs is induced by interactions of phosphate anionic oxygen atoms with the amino group of cytosine bases. This provides a model for close approach of DNA molecules during biological processes, such as recombination.     

Hypervariable ultra-long telomeres in mice

Telomere structure and behaviour is less well understood in vertebrates than it is in ciliates and yeasts (reviewed in ref. 1). Like all other eukaryotic chromosomes, those of vertebrates terminate in an array of a short repeated sequence. In vertebrates this sequence is (TTAGGG)n, as shown by in situ hybridization. In humans, these terminal repeats are heterogeneous in length, averaging about 10 kilobases in blood cells. Here we report the structure and inheritance of the terminal repeats present at mouse telomeres. The (TTAGGG)n tracts are many times larger than those present at human telomeres. Because of their constancy in length through somatic cell divisions, they are resolved as multiple discrete restriction fragments of up to 150 kilobases. Strikingly, this banding pattern is highly polymorphic within populations of inbred mice, suggesting an unusually high mutation rate. Indeed, although the banding pattern is inherited in a largely mendelian fashion, (TTAGGG)n tracts of new size appear frequently in family studies.     

The locus of sequence-directed and protein-induced DNA bending

The bending locus of trypanosome kinetoplast DNA, identified by gel electrophoresis, has tracts of a simple repeat sequence (CA5-6 T) symmetrically distributed about it, with a repeat interval of 10 base pairs. The analogous bending induced when catabolite gene activating protein binds to its recognition sequence near the promoter of the Escherichia coli lac operon is centred on a site about 5-7 base pairs away from the centre of the protein binding site.     

Crystal structure of an RNA double helix incorporating a track of non-Watson-Crick base pairs

The crystal structure of the RNA dodecamer duplex (r-GGACUUCGGUCC)2 has been determined. The dodecamers stack end-to-end in the crystal, simulating infinite A-form helices with only a break in the phosphodiester chain. These infinite helices are held together in the crystal by hydrogen bonding between ribose hydroxyl groups and a variety of donors and acceptors. The four noncomplementary nucleotides in the middle of the sequence did not form an internal loop, but rather a highly regular double-helix incorporating the non-Watson-Crick base pairs, G.U and U.C. This is the first direct observation of a U.C (or T.C) base pair in a crystal structure. The U.C pairs each form only a single base-base hydrogen bond, but are stabilized by a water molecule which bridges between the ring nitrogens and by four waters in the major groove which link the bases and phosphates. The lack of distortion introduced in the double helix by the U.C mismatch may explain its low efficiency of repair in DNA. The G.U wobble pair is also stabilized by a minor-groove water which bridges between the unpaired guanine amino and the ribose hydroxyl of the uracil. This structure emphasizes the importance of specific hydrogen bonding between not only the nucleotide bases, but also the ribose hydroxyls, phosphate oxygens and tightly bound waters in stabilization of the intramolecular and intermolecular structures of double helical RNA.     

Structure of the repressor-operator complex of bacteriophage 434

The crystal structure of a specific complex between the DNA-binding domain of phage 434 repressor and a synthetic 434 operator DNA shows interactions that determine sequence-dependent affinity. The repressor recognizes its operators by its complementarity to a particular DNA conformation as well as by direct interaction with base pairs in the major groove.     

Interplay of electron-lattice interactions and superconductivity in superconductivity in Bi2Sr2CaCu2O8+delta

Formation of electron pairs is essential to superconductivity. For conventional superconductors, tunnelling spectroscopy has established that pairing is mediated by bosonic modes (phonons); a peak in the second derivative of tunnel current d2I/dV2 corresponds to each phonon mode. For high-transition-temperature (high-T(c)) superconductivity, however, no boson mediating electron pairing has been identified. One explanation could be that electron pair formation and related electron-boson interactions are heterogeneous at the atomic scale and therefore challenging to characterize. However, with the latest advances in d2I/dV2 spectroscopy using scanning tunnelling microscopy, it has become possible to study bosonic modes directly at the atomic scale. Here we report d2I/dV2 imaging studies of the high-T(c) superconductor Bi2Sr2CaCu2O8+delta. We find intense disorder of electron-boson interaction energies at the nanometre scale, along with the expected modulations in d2I/dV2 (refs 9, 10). Changing the density of holes has minimal effects on both the average mode energies and the modulations, indicating that the bosonic modes are unrelated to electronic or magnetic structure. Instead, the modes appear to be local lattice vibrations, as substitution of 18O for 16O throughout the material reduces the average mode energy by approximately 6 per cent--the expected effect of this isotope substitution on lattice vibration frequencies. Significantly, the mode energies are always spatially anticorrelated with the superconducting pairing-gap energies, suggesting an interplay between these lattice vibration modes and the superconductivity.     

Structure of the immature retroviral capsid at 8 Å resolution by cryo-electron microscopy

The assembly of retroviruses such as HIV-1 is driven by oligomerization of their major structural protein, Gag. Gag is a multidomain polyprotein including three conserved folded domains: MA (matrix), CA (capsid) and NC (nucleocapsid). Assembly of an infectious virion proceeds in two stages. In the first stage, Gag oligomerization into a hexameric protein lattice leads to the formation of an incomplete, roughly spherical protein shell that buds through the plasma membrane of the infected cell to release an enveloped immature virus particle. In the second stage, cleavage of Gag by the viral protease leads to rearrangement of the particle interior, converting the non-infectious immature virus particle into a mature infectious virion. The immature Gag shell acts as the pivotal intermediate in assembly and is a potential target for anti-retroviral drugs both in inhibiting virus assembly and in disrupting virus maturation. However, detailed structural information on the immature Gag shell has not previously been available. For this reason it is unclear what protein conformations and interfaces mediate the interactions between domains and therefore the assembly of retrovirus particles, and what structural transitions are associated with retrovirus maturation. Here we solve the structure of the immature retroviral Gag shell from Mason-Pfizer monkey virus by combining cryo-electron microscopy and tomography. The 8-? resolution structure permits the derivation of a pseudo-atomic model of CA in the immature retrovirus, which defines the protein interfaces mediating retrovirus assembly. We show that transition of an immature retrovirus into its mature infectious form involves marked rotations and translations of CA domains, that the roles of the amino-terminal and carboxy-terminal domains of CA in assembling the immature and mature hexameric lattices are exchanged, and that the CA interactions that stabilize the immature and mature viruses are almost completely distinct.     

Structure refined to 2A of a nicked DNA octanucleotide complex with DNase I

The cutting rates of bovine pancreatic deoxyribonuclease I (DNase I) vary along a given DNA sequence, indicating that the enzyme recognizes sequence-dependent structural variations of the DNA double-helix. In an attempt to define the helical parameters determining this sequence-dependence, we have co-crystallized a complex of DNase I with a self-complementary octanucleotide and refined the crystal structure at 2 A resolution. This structure confirms the basic features of an early model, namely that an exposed loop of DNase I binds in the minor groove of B-type DNA and that interactions do occur with the backbone of both strands. Nicked octamer duplexes that have lost a dinucleotide from the 3'-end of one strand are hydrogen-bonded across a two-fold axis in the crystal to form a quasi-continuous double helix of 14 base pairs. The DNA 14-mer has a B-type conformation and shows substantial distortion of both local and overall helix parameters, induced mainly by the tight interaction of Y73 and R38 in the unusually wide minor groove. Directly coupled to the widening of the groove by approximately 3A is a 21.5 degree bend of the DNA away from the bound enzyme towards the major groove, suggesting that both DNA stiffness and groove width are important in determining the sequence-dependence of the enzyme cutting rate. A second cut of the DNA which is induced by diffusion of Mn2+ into the co-crystals suggests that there are two active sites in DNase I separated by more than 15A.     

ATP-dependent assembly of double hexamers of SV40 T antigen at the viral origin of DNA replication

Simian virus 40 (SV40) replicates in nuclei of human and monkey cells. One viral protein, large tumour (T) antigen, is required for the initiation of DNA replication. The development of in vitro replication systems which retain this property has facilitated the identification of the cellular components required for replication. T antigen recognizes the pentanucleotide 5'-GAGGC-3' which is present in four copies within the 64 base-pairs (bp) of the core origin. In the presence of ATP it binds with increased affinity forming a distinctive, bilobed structure visible in electron micrographs. As a helicase, it unwinds SV40 DNA bidirectionally from the origin. We report here that in vitro and in the presence of ATP, T antigen assembles a double hexamer, centred on the core origin and extending beyond it by 12 bp in each direction. The assembly of this dodecamer initiates an untwisting of the duplex by 2-3 turns. In the absence of ATP, a tetrameric structure is the largest found at the core origin. In the absence of DNA, but in the presence of ATP or its non-hydrolysable analogues, T antigen assembles into hexamers. This suggests that ATP effects an allosteric change in the monomer. The change alters protein-protein interactions and allows the assembly of a double hexamer, which initiates replication at the core origin.     

Atomic-level modelling of the HIV capsid

The mature capsids of human immunodeficiency virus type 1 (HIV-1) and other retroviruses are fullerene shells, composed of the viral CA protein, that enclose the viral genome and facilitate its delivery into new host cells. Retroviral CA proteins contain independently folded amino (N)- and carboxy (C)-terminal domains (NTD and CTD) that are connected by a flexible linker. The NTD forms either hexameric or pentameric rings, whereas the CTD forms symmetric homodimers that connect the rings into a hexagonal lattice. We previously used a disulphide crosslinking strategy to enable isolation and crystallization of soluble HIV-1 CA hexamers. Here we use the same approach to solve the X-ray structure of the HIV-1 CA pentamer at 2.5?? resolution. Two mutant CA proteins with engineered disulphides at different positions (P17C/T19C and N21C/A22C) converged onto the same quaternary structure, indicating that the disulphide-crosslinked proteins recapitulate the structure of the native pentamer. Assembly of the quasi-equivalent hexamers and pentamers requires remarkably subtle rearrangements in subunit interactions, and appears to be controlled by an electrostatic switch that favours hexamers over pentamers. This study completes the gallery of substructures describing the components of the HIV-1 capsid and enables atomic-level modelling of the complete capsid. Rigid-body rotations around two assembly interfaces appear sufficient to generate the full range of continuously varying lattice curvature in the fullerene cone.     

新型空气静压推力轴承承载能力的实验研究

用弹性薄板实现的可变均压槽与固定均压槽结合应用的新型空气静压推力轴承具有高刚度的优点,本文运用空气静压推力轴承性能测试试验台测试空气推力轴承的气膜间隙,气膜压力分布,承载能力。对新型气体静压推力轴承的承载能力进行了实验研究和分析,结论证明该新型气体静压推力轴承的计方案能够提高轴承的承载能力。     

The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data

The classical RNA secondary structure model considers A.U and G.C Watson-Crick as well as G.U wobble base pairs. Here we substitute it for a new one, in which sets of nucleotide cyclic motifs define RNA structures. This model allows us to unify all base pairing energetic contributions in an effective scoring function to tackle the problem of RNA folding. We show how pipelining two computer algorithms based on nucleotide cyclic motifs, MC-Fold and MC-Sym, reproduces a series of experimentally determined RNA three-dimensional structures from the sequence. This demonstrates how crucial the consideration of all base-pairing interactions is in filling the gap between sequence and structure. We use the pipeline to define rules of precursor microRNA folding in double helices, despite the presence of a number of presumed mismatches and bulges, and to propose a new model of the human immunodeficiency virus-1 -1 frame-shifting element.     

一个预测RNA二级结构的回溯算法

本文讨论了一个预测RNA二级结构的回溯算法。该算法根据极大基配对的原则按字典顺序产生所有可能的二级结构。它的时间复杂性是O(n~2),空间复杂性是O(n)。     

水溶液中阳离子Gemini表面活性剂与右旋糖苷相互作用

通过黏度、电导和紫外光谱方法研究了水溶液中阳离子Gem in i表面活性剂1,2-二亚甲基-双(烷基二甲基溴化铵)(简写为10-2-10和12-2-12)和右旋糖苷之间的相互作用.由于二者之间的相互作用,在Gem in i表面活性剂10-2-10和12-2-12存在下,右旋糖苷溶液表现出电粘效应;随着溶液中右旋糖苷浓度的增加,Gem in i表面活性剂10-2-10和12-2-12胶束电离度呈增加趋势,且右旋糖苷与Gem in i表面活性剂12-2-12之间的相互作用要强于与10-2-10间的相互作用.     

利用菲涅尔圆孔衍射探测AFeSe三元化合物超导配对对称性

提出了一个特殊菲涅尔圆孔衍射实验,核心由正常金属/绝缘层/超导体多层膜构成,用来精确探测超导配对对称性.理论分析表明,对于超导层是s波配对,△(-k)=△(k),且满足k·r=nπ的情况下,那么衍射图样的零阶为暗纹,其中k为波矢,n为整数.反之,如果△(-k)=-△(k),且在其他条件不变的情况下,那么零阶衍射图样为明纹.从而可以利用这种简单易行的实验途径,对超导电子的配对对称性进行无模棱两可的判定.最后把这套装置应用到最近发现的AFeSe三元化合物超导体,给出了可能的具体实验方案,来探测这种多费米面复杂的电子配对对称性.     

Attractive and repulsive Fermi polarons in two dimensions

The dynamics of a single impurity in an environment is a fundamental problem in many-body physics. In the solid state, a well known case is an impurity coupled to a bosonic bath (such as lattice vibrations); the impurity and its accompanying lattice distortion form a new entity, a polaron. This quasiparticle plays an important role in the spectral function of high-transition-temperature superconductors, as well as in colossal magnetoresistance in manganites. For impurities in a fermionic bath, studies have considered heavy or immobile impurities which exhibit Anderson's orthogonality catastrophe and the Kondo effect. More recently, mobile impurities have moved into the focus of research, and they have been found to form new quasiparticles known as Fermi polarons. The Fermi polaron problem constitutes the extreme, but conceptually simple, limit of two important quantum many-body problems: the crossover between a molecular Bose-Einstein condensate and a superfluid with BCS (Bardeen-Cooper-Schrieffer) pairing with spin-imbalance for attractive interactions, and Stoner's itinerant ferromagnetism for repulsive interactions. It has been proposed that such quantum phases (and other elusive exotic states) might become realizable in Fermi gases confined to two dimensions. Their stability and observability are intimately related to the theoretically debated properties of the Fermi polaron in a two-dimensional Fermi gas. Here we create and investigate Fermi polarons in a two-dimensional, spin-imbalanced Fermi gas, measuring their spectral function using momentum-resolved photoemission spectroscopy. For attractive interactions, we find evidence for a disputed pairing transition between polarons and tightly bound dimers, which provides insight into the elementary pairing mechanism of imbalanced, strongly coupled two-dimensional Fermi gases. Additionally, for repulsive interactions, we study novel quasiparticles--repulsive polarons--the lifetime of which determines the possibility of stabilizing repulsively interacting Fermi systems.     

A New Approach to Provide Global Certificate Service in Virtual Enterprise

Certificate Authority(CA)is the core of public key infrastructure.However,the traditional structure of CA is either hierarchical or reticular,and none of them is suitable for security requirements come from the new trend in enterprise cooperation,namely virtual enterprise(VE).In this paper a new idea-virtual certificate authority(VCA),is proposed,as well as its implementation.The goal of VCAis to provide global certificate service over vital enterprise while keeping CA of each participant intact as much as possible.Unlike PEM,PGP,and BCA,by using secret sharing scheme,virtual CA avoids the need for TTP and supports virtual enterprise′s feature of dynamical construction and destruction.