Molecular structure of a left-handed double helical DNA fragment at atomic resolution

The DNA fragment d(CpGpCpGpCpG) crystallises as a left-handed double helical molecule with Watson-Crick base pairs and an antiparallel organisation of the sugar phosphate chains. The helix has two nucleotides in the asymmetric unit and contains twelve base pairs per turn. It differs significantly from right-handed B-DNA.     

Glutamate receptors at atomic resolution

At synapses throughout the brain and spinal cord, the amino-acid glutamate is the major excitatory neurotransmitter. During evolution, a family of glutamate-receptor ion channels seems to have been assembled from a kit consisting of discrete ligand-binding, ion-channel, modulatory and cytoplasmic domains. Crystallographic studies that exploit this unique architecture have greatly aided structural analysis of the ligand-binding core, but the results also pose a formidable challenge, namely that of resolving the allosteric mechanisms by which individual domains communicate and function in an intact receptor.     

Reaction path of protein farnesyltransferase at atomic resolution

Protein farnesyltransferase (FTase) catalyses the attachment of a farnesyl lipid group to numerous essential signal transduction proteins, including members of the Ras superfamily. The farnesylation of Ras oncoproteins, which are associated with 30% of human cancers, is essential for their transforming activity. FTase inhibitors are currently in clinical trials for the treatment of cancer. Here we present a complete series of structures representing the major steps along the reaction coordinate of this enzyme. From these observations can be deduced the determinants of substrate specificity and an unusual mechanism in which product release requires binding of substrate, analogous to classically processive enzymes. A structural model for the transition state consistent with previous mechanistic studies was also constructed. The processive nature of the reaction suggests the structural basis for the successive addition of two prenyl groups to Rab proteins by the homologous enzyme geranylgeranyltransferase type-II. Finally, known FTase inhibitors seem to differ in their mechanism of inhibiting the enzyme.     

Replication of a cis-syn thymine dimer at atomic resolution

Ultraviolet light damages DNA by catalysing covalent bond formation between adjacent pyrimidines, generating cis-syn cyclobutane pyrimidine dimers (CPDs) as the most common lesion. CPDs block DNA replication by high-fidelity DNA polymerases, but they can be efficiently bypassed by the Y-family DNA polymerase pol eta. Mutations in POLH encoding pol eta are implicated in nearly 20% of xeroderma pigmentosum, a human disease characterized by extreme sensitivity to sunlight and predisposition to skin cancer. Here we have determined two crystal structures of Dpo4, an archaeal pol eta homologue, complexed with CPD-containing DNA, where the 3' and 5' thymine of the CPD separately serves as a templating base. The 3' thymine of the CPD forms a Watson-Crick base pair with the incoming dideoxyATP, but the 5' thymine forms a Hoogsteen base pair with the dideoxyATP in syn conformation. Dpo4 retains a similar tertiary structure, but each unusual DNA structure is individually fitted into the active site for catalysis. A model of the pol eta-CPD complex built from the crystal structures of Saccharomyces cerevisiae apo-pol eta and the Dpo4-CPD complex suggests unique features that allow pol eta to efficiently bypass CPDs.     

Crystal structure of trp repressor/operator complex at atomic resolution

The crystal structure of the trp repressor/operator complex shows an extensive contact surface, including 24 direct and 6 solvent-mediated hydrogen bonds to the phosphate groups of the DNA. There are no direct hydrogen bonds or non-polar contacts to the bases that can explain the repressor's specificity for the operator sequence. Rather, the sequence seems to be recognized indirectly through its effects on the geometry of the phosphate backbone, which in turn permits the formation of a stable interface. Water-mediated polar contacts to the bases also appear to contribute part of the specificity.     

Magnetic exchange force microscopy with atomic resolution

The ordering of neighbouring atomic magnetic moments (spins) leads to important collective phenomena such as ferromagnetism and antiferromagnetism. A full understanding of magnetism on the nanometre scale therefore calls for information on the arrangement of spins in real space and with atomic resolution. Spin-polarized scanning tunnelling microscopy accomplishes this but can probe only conducting materials. Force microscopy can be used on any sample independent of its conductivity. In particular, magnetic force microscopy is well suited to exploring ferromagnetic domain structures. However, atomic resolution cannot be achieved because data acquisition involves the sensing of long-range magnetostatic forces between tip and sample. Magnetic exchange force microscopy has been proposed for overcoming this limitation: by using an atomic force microscope with a magnetic tip, it should be possible to detect the short-range magnetic exchange force between tip and sample spins. Here we show for a prototypical antiferromagnetic insulator, the (001) surface of nickel oxide, that magnetic exchange force microscopy can indeed reveal the arrangement of both surface atoms and their spins simultaneously. In contrast with previous attempts to implement this method, we use an external magnetic field to align the magnetic polarization at the tip apex so as to optimize the interaction between tip and sample spins. This allows us to observe the direct magnetic exchange coupling between the spins of the tip atom and sample atom that are closest to each other, and thereby demonstrate the potential of magnetic exchange force microscopy for investigations of inter-spin interactions at the atomic level.     

Molecular structure of r(GCG)d(TATACGC): a DNA--RNA hybrid helix joined to double helical DNA

The molecule r(GCG)d(TATACGC) is self-complementary and forms two DNA--RNA hybrid segments surrounding a central region of double helical DNA; its molecular structure has been solved by X-ray analysis. All three parts of the molecule adopt a conformation which is close to that seen in the 11-fold RNA double helix. The conformation of the ribonucleotides is partly determined by water molecules bridging between the ribose O2' hydroxyl group and cytosine O2. The hybrid-DNA duplex junction contains no structural discontinuities. However, the central DNA TATA sequence has some structural irregularities.     

毛细管电泳分离DNA片段的研究

以羟丙甲基纤维素作为筛分介质，３７ｃｍ×７５μｍ涂层石英毛细管，在 ７ ｋｖ电压下，毛细管电泳分离了 φ１７４ ＤＮＡ／ＨａｅⅢ Ｍａｒｋｅｒｓ．     

基于啮合特性的人字齿轮动力学建模与分析

利用人字齿轮啮合特性的分析结果,准确计算人字齿轮轮齿时变啮合刚度激励和误差激励。根据齿轮啮合冲击模型,计算人字齿轮啮入冲击激励。根据人字齿轮的均载传动特性,综合考虑上述3种激励,利用集中参数理论建立人字齿轮12自由度弯曲—扭转—轴向变形耦合的三维空间动力学模型。应用牛顿第二定律,建立系统的振动方程,对方程进行消除刚体位移和量纲归一化处理。采用变步长四阶龙格库塔法(Runge-Kutta)求解,得到系统的振动响应和动态特性。结果表明:人字齿轮动力学模型的建立、求解和分析为其动态设计奠定了基础。     

原子尺度上的波

提出全同粒子以及虚粒子假设,并推导了二维速度控制条件,再结合原子势函数,在原子尺度上描述了线性波的传播。考虑晶格非谐性以及位错的影响,进一步探究了二阶非线性波的产生机理。理论分析表明,晶格非谐性和位错引起的晶格畸变会诱发产生高阶虚粒子,高阶虚粒子是高阶非线性波产生的关键因素,位错等材料早期非线性或细微损伤导致高阶虚粒子增多而引发明显的高次谐波,因此,可以通过探测高次谐波诊断材料早期损伤。     

基于人字齿轮啮合特性的滑动摩擦功率损失

以空间多重共轭啮合理论为基础,利用人字齿轮副轮齿接触特性与承载接触特性,提出一种计算人字齿轮滑动摩擦功率损失的方法。首先,利用人字齿轮副轮齿接触分析(TCA),获得人字齿轮齿面接触路径和印痕。然后,利用人字齿轮副承载接触分析(LTCA),计算得到啮合齿面瞬时椭圆长轴(接触点)上离散点的法向载荷和瞬时接触点的传动误差,把所得到的离散点载荷和传动误差分别转换成齿面瞬时接触点的法向载荷和相对滑动速度,二者与摩擦因数相乘得到人字齿轮瞬时接触点的滑动摩擦功率损失。最后,对人字齿轮齿面所有瞬时接触点的滑动摩擦功率损失进行拟合并积分,最终获得1对人字齿轮轮齿从啮入到啮出的滑动摩擦功损。     

Structure of DNase I at 2.0 A resolution suggests a mechanism for binding to and cutting DNA

Bovine pancreatic deoxyribonuclease I (DNase I), an endonuclease that degrades double-stranded DNA in a nonspecific but sequence-dependent manner, has been used as a biochemical tool in various reactions, in particular as a probe for the structure of chromatin and for the helical periodicity of DNA on the nucleosome and in solution. Limited digestion by DNase I, termed DNase I 'footprinting', is routinely used to detect protected regions in DNA-protein complexes. Recently, we have solved the three-dimensional structure of this glycoprotein (relative molecular mass 30,400) by X-ray structure analysis at 2.5 A resolution and have subsequently refined it crystallographically at 2.0 A. Based on the refined structure and the binding of Ca2+-thymidine 3',5'-diphosphate (Ca-pTp) at the active site, we propose a mechanism of action and present a model for the interaction of DNase I with double-stranded DNA that involves the binding of an exposed loop region in the minor groove of B-DNA and electrostatic interactions of phosphates from both strands with arginine and lysine residues on either side of this loop. We explain DNase I cleavage patterns in terms of this model and discuss the consequences of the extended DNase I-DNA contact region for the interpretation of DNase I footprinting results.     

Crystal structure of the met repressor-operator complex at 2.8 A resolution reveals DNA recognition by beta-strands.

The crystal structure of the met repressor-operator complex shows two dimeric repressor molecules bound to adjacent sites 8 base pairs apart on an 18-base-pair DNA fragment. Sequence specificity is achieved by insertion of double-stranded antiparallel protein beta-ribbons into the major groove of B-form DNA, with direct hydrogen-bonding between amino-acid side chains and the base pairs. The repressor also recognizes sequence-dependent distortion or flexibility of the operator phosphate backbone, conferring specificity even for inaccessible base pairs.