钝顶螺旋藻C—藻蓝蛋白分子的STM研究

钝顶螺旋藻Ｃ┐藻蓝蛋白分子的ＳＴＭ研究张玉忠＊１,２时东霞１周百成２曾呈奎２庞世瑾１（１中国科学院北京真空物理实验室,北京２７２４信箱,北京１０００８０）（２中国科学院海洋研究所,青岛２６６０７１）关键词钝顶螺旋藻;Ｃ－藻蓝蛋白;扫描隧道显微镜藻胆蛋...     

STM and AFM images of nucleosome DNA under water

We have imaged DNA from the calf thymus nucleosome using a scanning tunneling microscope (STM) operated in water. The fragments are deposited onto the interface between a buffer solution and an epitaxially grown gold surface using an electrochemical tecnique. Most of the fragments are fairly straight, and when individual polymers can be identified, their length is consistent with the expected 146 basepairs (approximately 500 A). The resolution is often adequate to show signs of the 36 A helical pitch. Some images show a structure which appears to have abrupt kinks of the sort predicted by Crick and Klug (Nature 255, 530-533, 1975). In order to check that this shape is not a consequence of binding to underlying structure on the gold substrate, we have also made images of kinked structures using an atomic force microscope (AFM) with the DNA bound to glass.     

STM and AFM Images of Nucleosome DNA Under Water

Abstract

We have imaged DNA from the calf thymus nucleosome using a scanning tunneling microscope (STM) operated in water. The fragments are deposited onto the interface between a buffer solution and an epitaxially grown gold surface using an electrochemical technique. Most of the fragments are fairly straight, and when individual polymers can be identified, their length is consistent with the expected 146 basepairs (～ 500 Å). The resolution is often adequate to show signs of the 36 Å helical pitch. Some images show a structure which appears to have abrupt kinks of the sort predicted by Crick and Klug (Nature 255, 530–533,1975). In order to check that this shape is not a consequence of binding to underlying structure on the gold substrate, we have also made images of kinked structures using an atomic force microscope (AFM) with the DNA bound to glass.     

Response to “Critical Assessment of the Evidence for Striped Nanoparticles”

Stirling et al., (10.1371/journal.pone.0108482) presented an analysis on some of our publications on the formation of stripe-like domains on mixed-ligand coated gold nanoparticles. The authors shed doubts on some of our results however no valid argument is provided against what we have shown since our first publication: scanning tunneling microscopy (STM) images of striped nanoparticles show stripe-like domains that are independent of imaging parameters and in particular of imaging speed. We have consistently ruled out the presence of artifacts by comparing sets of images acquired at different tip speeds, finding invariance of the stipe-like domains. Stirling and co-workers incorrectly analyzed this key control, using a different microscope and imaging conditions that do not compare to ours. We show here data proving that our approach is rigorous. Furthermore, we never solely relied on image analysis to draw our conclusions; we have always used the chemical nature of the particles to assess the veracity of our images. Stirling et al. do not provide any justification for the spacing of the features that we find on nanoparticles: ~1 nm for mixed ligand particles and ~ 0.5 nm for homoligand particles. Hence our two central arguments remain unmodified: independence from imaging parameters and dependence on ligand shell chemical composition. The paper report observations on our STM images; none is a sufficient condition to prove that our images are artifacts. We thoroughly addressed issues related to STM artifacts throughout our microscopy work. Stirling et al. provide guidelines for what they consider good STM images of nanoparticles, such images are indeed present in our literature. They conclude that the evidences we provided to date are insufficient, this is a departure from one of the authors’ previous article which concluded that our images were composed of artifacts. Given that four independent laboratories have reproduced our measurements and that no scientifically rigorous argument is presented to invalidate our STM images, and also given that Stirling et al. do not contest the quality of our recent STM images, we re-affirm that specific binary mixture of ligands spontaneously form features in their ligand shell that we describe as stripe-like domains ~1 nm in width.     

A study of lignin formation at the molecular level by scanning tunneling microscopy.

A scanning tunneling microscope (STM) was used to observe the temporal formation and organization of dehydrogenative polymer (DHP) synthesized from coniferyl alcohol. The images obtained elucidate this structure for the first time. The structure of DHP, as seen from STM images, shows long-range order. It appears that DHP consists of building units or modules assembled into larger assemblies called supermodules. Supermodules are interconnected into the overall lattice-like polymer structure with or without spherical regions. One module consists of about 20 monomers, while the supermodule contains about 500 monomers. Calculated molecular weights for modules and supermodules agree with DHP molecular weight distribution peaks. Samples prepared at two different pH values, 6.4 and 7.6, have the same characteristics. The results presented demonstrate that the process of lignification, even in in vitro conditions, is highly ordered, and as such contribute to our understanding of the structure of lignin, a significant constitutive and functional element of cell walls.     

Transmission electron microscopy, scanning tunneling microscopy, and atomic force microscopy of the cell envelope layers of the archaeobacterium Methanospirillum hungatei GP1.

Methanospirillum hungatei GP1 possesses paracrystalline cell envelope components including end plugs and a sheath formed from stacked hoops. Both negative-stain transmission electron microscopy (TEM) and scanning tunneling microscopy (STM) distinguished the 2.8-nm repeat on the outer surface of the sheath, while negative-stain TEM alone demonstrated this repeat around the outer circumference of individual hoops. Thin sections revealed a wave-like outer sheath surface, while STM showed the presence of deep grooves that precisely defined the hoop-to-hoop boundaries at the waveform nodes. Atomic force microscopy of sheath tubes containing entrapped end plugs emphasized the end plug structure, suggesting that the sheath was malleable enough to collapse over the end plugs and deform to mimic the shape of the underlying structure. High-resolution atomic force microscopy has revised the former idea of end plug structure so that we believe each plug consists of at least four discs, each of which is approximately 3.5 nm thick. PT shadow TEM and STM both demonstrated the 14-nm hexagonal, particulate surface of an end plug, and STM showed the constituent particles to be lobed structures with numerous smaller projections, presumably corresponding to the molecular folding of the particle.     

Sequence, packing and nanometer scale structure in STM images of nucleic acids under water

Scanning tunneling microscope (STM) images of random-sequence nucleic acid polymers under water show internal structure which depends strongly on the packing density of the polymer. Images of dense aggregates have a semicrystalline order with the individual polymers adopting simple periodic structures. Loose aggregates (or isolated molecules) show structural variability with considerable local bending and curving on a nanometer scale. It is not clear to what extent this structure is induced by the operation of the microscope. In order to investigate the possibility that the structure is sequence directed, we have imaged various DNA and RNA polymers at low packing densities. We present results here for random sequence DNA, poly(dAT).poly(dAT), poly(dA).poly(dT), poly(dCG).poly(dCG) and for random sequence RNA and poly(U). In contrast to loose aggregates of the random sequence material, the homopolymers show few sharp bends. Furthermore, the homopolymers appear to yield characteristic backbone patterns, usually at resolutions in excess of that obtained with random sequence polymers. The random sequence polymers show much more evidence of image distortion due to tip-molecule interactions, suggesting that they are, on average, mechanically less stable in the STM tunnel-gap than the homopolymers. Thus, while some of the structure observed in STM images is a consequence of tip-molecule interactions, it is related to sequence-directed properties of the polymer.     

Sequence,Packing and Nanometer Scale Structure in STM Images of Nucleic Acids Under Water

Abstract

Scanning tunneling microscope (STM) images of random-sequence nucleic acid polymers under water show internal structure which depends strongly on the packing density of the polymer. Images of dense aggregates have a semicrystalline order with the individual polymers adopting simple periodic structures. Loose aggregates (or isolated molecules) show structural variability with considerable local bending and curving on a nanometer scale. It is not clear to what extent this structure is induced by the operation of the microscope. In order to investigate the possibility that the structure is sequence directed, we have imaged various DNA and RNA polymers at low packing densities. We present results here for random sequence DNA, poly(dAT) · poly(dAT), poly(dA) · poly(dT), poly(dCG) · poly(dCG) and for random sequence RNA and poly(U). In contrast to loose aggregates of the random sequence material, the homopolymers show few sharp bends. Furthermore, the homopolymers appear to yield characteristic backbone patterns, usually at resolutions in excess of that obtained with random sequence polymers. The random sequence polymers show much more evidence of image distortion due to tip-molecule interactions, suggesting that they are, on average, mechanically less stable in the STM tunnel-gap than the homopolymers. Thus, while some of the structure observed in STM images is a consequence of tip-molecule interactions, it is related to sequence-directed properties of the polymer.     

免疫球蛋白G(IgG)分子结构的扫描隧道显微镜观察

把溶于双蒸水的兔IgG铺展在高定向石墨(HOPG)底载上,直接用扫描隧道显微镜(Scanning Tunneling Microscopy,简称STM)在大气环境中观察,得到了IgG分子的表面结构图像。从图像上可清晰地分辨出IgG分子的Fab及Fc片段,片段连接处的"铰链区"以及Fab和F_e片段的某些精细结构(IgG分子功能辖区)。本工作表明STM在研究生物大分子天然结构方面有巨大潜力。     

Structure of a mouse immunoglobulin G that lacks the entire CH1 domain: protein sequencing and small-angle X-ray scattering studies

The structure of a short-chain IgG2a antibody, which is a member of the family of mouse anti-dansyl switch variant antibodies with identical variable regions but different heavy-chain constant regions [Dangl, J.L., Parks, D. R., Oi, V. T., & Herzenberg, L. A. (1982) Cytometry 2, 395-401], is reported. Amino acid sequencing analyses have demonstrated that in the short-chain IgG2a antibody the entire CH1 domain is deleted whereas the hinge region remains intact. Small-angle X-ray scattering data were collected for the short-chain IgG2a antibody and compared with those for the switch variant IgG1, IgG2a, and IgG2b antibodies with the normal heavy chain. It has been concluded that deletion of the CH1 domain results in a large structural change and the short-chain IgG2a antibody possesses an elongated molecular shape with a much smaller hinge angle as compared with the normal IgG2a antibody that is a Y-shaped molecule.     

胆固醇对脂双层结构影响的SAXS和STM研究

用小角X射线散射（SAXS)和扫描隧道显微镜（STM）技术分别研究了模拟生物膜脂质体的结构以及胆固醇对生物膜双层结构的影响。结果表明,在扫描隧道显微镜照片中,磷脂分子在石墨表面形成规则的二维点状排列图像;磷脂胆固醇脂质体在石墨表面形成规则的二维波纹状排列图像。用小角X射线散射研究结果表明,DPPC脂质体是片层相结构,DPPC＋Chol脂质体是复相片层结构,DPPE＋Chol脂质体是片层立方相结构,DPPC＋DPPE＋Chol脂质体是立方六角形相结构。     

Structural characteristics of the beta-sheet-like human and rat islet amyloid polypeptides as determined by scanning tunneling microscopy

We demonstrate in this work that scanning tunneling microscopy (STM) provides a useful approach to obtaining structural information about human islet amyloid polypeptide (hIAPP) and rat islet amyloid polypeptide (rIAPP) assembly on highly oriented pyrolytic graphite (HOPG) with sub-molecular resolution. The observed hIAPP and rIAPP lamellae consisted of parallel stripes. The STM images of hIAPPs show multiple molecular folding structures, with an average of 11 amino acid residues for the core regions. In addition, the STM images also reveal the assembly characteristics of rIAPP lamellae and may indicate a secondary structural conformation from random coil to beta-sheet-like on the graphite surface.     

High resolution scanning tunnelling microscopy of the beta-amyloid protein (Abeta1-40) of Alzheimer's disease suggests a novel mechanism of oligomer assembly

The aggregation of the beta-amyloid protein (Abeta) is an important step in the pathogenesis of Alzheimer's disease. There is increasing evidence that lower molecular weight oligomeric forms of Abeta may be the most toxic species in vivo. However, little is known about the structure of Abeta oligomers. In this study, scanning tunnelling microscopy (STM) was used to examine the structure of Abeta monomers, dimers and oligomers. Abeta1-40 was visualised by STM on a surface of atomically flat gold. At low concentrations (0.5 microM) small globular structures were observed. High resolution STM of these structures revealed them to be monomers of Abeta. The monomers measured approximately 3-4 nm in diameter. Internal structure was seen in many of the monomers consistent with a conformation in which the polypeptide chain is folded into 3 or 4 domains. Oligomers were seen after ageing the Abeta solution for 24 h. The oligomers were also 3-4 nm in width and appeared to be formed by the end-to-end association of monomers with the polypeptide chain oriented at 90 degrees to the axis of the oligomer. The results suggest that the oligomer formation can proceed through a mechanism involving the linear association of monomers.     

Shoot apical meristem and cotyledon formation during Arabidopsis embryogenesis: interaction among the CUP-SHAPED COTYLEDON and SHOOT MERISTEMLESS genes

The shoot apical meristem and cotyledons of higher plants are established during embryogenesis in the apex. Redundant CUP-SHAPED COTYLEDON 1 (CUC1) and CUC2 as well as SHOOT MERISTEMLESS (STM) of Arabidopsis are required for shoot apical meristem formation and cotyledon separation. To elucidate how the apical region of the embryo is established, we investigated genetic interactions among CUC1, CUC2 and STM, as well as the expression patterns of CUC2 and STM mRNA. Expression of these genes marked the incipient shoot apical meristem as well as the boundaries of cotyledon primordia, consistent with their roles for shoot apical meristem formation and cotyledon separation. Genetic and expression analyses indicate that CUC1 and CUC2 are redundantly required for expression of STM to form the shoot apical meristem, and that STM is required for proper spatial expression of CUC2 to separate cotyledons. A model for pattern formation in the apical region of the Arabidopsis embryo is presented.     

The Y. bercovieri Anbu crystal structure sheds light on the evolution of highly (pseudo)symmetric multimers

Ancestral β-subunit (Anbu) is homologous to HslV and 20S proteasomes. Based on its phylogenetic distribution and sequence clustering, Anbu has been proposed as the “ancestral” form of proteasomes. Here, we report biochemical data, small-angle X-ray scattering results, negative-stain electron microscopy micrographs and a crystal structure of the Anbu particle from Yersinia bercovieri (YbAnbu). All data are consistent with YbAnbu forming defined 12–14 subunit multimers that differ in shape from both HslV and 20S proteasomes. The crystal structure reveals that YbAnbu subunits form tight dimers, held together in part by the Anbu specific C-terminal helices. These dimers (“protomers”) further assemble into a low-rise left-handed staircase. The lock-washer shape of YbAnbu is consistent with the presence of defined multimers, X-ray diffraction data in solution and negative-stain electron microscopy images. The presented structure suggests a possible evolutionary pathway from helical filaments to highly symmetric or pseudosymmetric multimer structures. YbAnbu subunits have the Ntn-hydrolase fold, a putative S₁ pocket and conserved candidate catalytic residues Thr1, Asp17 and Lys32(33). Nevertheless, we did not detect any YbAnbu peptidase or amidase activity. However, we could document orthophosphate production from ATP catalyzed by the ATP-grasp protein encoded in the Y. bercovieri Anbu operon.     

Solution conformation of wild-type and mutant IgG3 and IgG4 immunoglobulins using crystallohydrodynamics: possible implications for complement activation

We have employed the recently described crystallohydrodynamic approach to compare the time-averaged domain orientation of human chimeric IgG3wt (wild-type) and IgG4wt as well as two hinge mutants of IgG3 and an IgG4S331P (mutation from serine to proline at position 331, EU numbering) mutant of IgG4. The approach involves combination of the known shape of the Fab and Fc regions from crystallography with hydrodynamic data for the Fab and Fc fragments and hydrodynamic and small angle x-ray scattering data for the intact IgG structures. In this way, ad hoc assumptions over hydration can be avoided and model degeneracy (uniqueness problems) can be minimized. The best fit model for the solution structure of IgG3wt demonstrated that the Fab regions are directed away from the plane of the Fc region and with a long extended hinge region in between. The best fit model of the IgG3m15 mutant with a short hinge (and enhanced complement activation activity) showed a more open, but asymmetric structure. The IgG3HM5 mutant devoid of a hinge region (and also devoid of complement-activation activity) could not be distinguished at the low-resolution level from the structure of the enhanced complement-activating mutant IgG3m15. The lack of inter-heavy-chain disulphide bond rather than a significantly different domain orientation may be the reason for the lack of complement-activating activity of the IgG3HM5 mutant. With IgG4, there are significant and interesting conformational differences between the wild-type IgG4, which shows a symmetric structure, and the IgG4S331P mutant, which shows a highly asymmetric structure. This structural difference may explain the ability of the IgG4S331P mutant to activate complement in stark contrast to the wild-type IgG4 molecule which is devoid of this activity.     

Scanning tunneling microscopy of mercapto-hexyl-oligonucleotides attached to gold.

6-mercapto hexyl-oligonucleotides bind to a gold surface strongly enough to permit imaging by a scanning tunneling microscope (STM). STM images showed worm-like chains that were approximately 12-(A-wide for single-stranded DNA and 20-(A-wide for double-stranded DNA. The chain lengths corresponded to 3.4 +/- 0.4 A per basepair for double-stranded DNA and 2.2 +/- 0.4 A per base for single-stranded DNA. This unexpectedly short length for single-stranded DNA was confirmed using oligomers with both single- and double-stranded regions. When the attachment of the samples was weakened (by imaging in water or scraping with the STM tip) the images changed to pairs of "blobs," apparently reflecting the attachment points of the molecules to the gold surface. Given this interpretation, images of DNA containing a five-base bulge imply that the bulge bends the oligomer by 90 degrees +/- 20 degrees.     

Voltammetry and in situ scanning tunneling microscopy of cytochrome C nitrite reductase on Au(111) electrodes

Escherichia coli cytochrome c nitrite reductase (NrfA) catalyzes the six-electron reduction of nitrite to perform an important role in the biogeochemical cycling of nitrogen. Here we describe NrfA adsorption on single-crystal Au(111) electrodes as an electrocatalytically active film in which the enzyme undergoes direct electron exchange with the electrode. The adsorbed NrfA has been imaged to molecular resolution by in situ scanning tunneling microscopy (in situ STM) under full electrochemical potential control and under conditions where the enzyme is electrocatalytically active. Details of the density and orientational distribution of NrfA molecules are disclosed. The submonolayer coverage resolved by in situ STM is readily reconciled with the failure to detect nonturnover signals in cyclic voltammetry of the NrfA films. The molecular structures show a range of lateral dimensions. These are suggestive of a distribution of orientations that could account for the otherwise anomalously low turnover number calculated for the total population of adsorbed NrfA molecules when compared with that determined for solutions of NrfA. Thus, comparison of the voltammetric signals and in situ STM images offers a direct approach to correlate electrocatalytic and molecular properties of the protein layer, a long-standing issue in protein film voltammetry.     

A smart membrane based on an antigen-responsive hydrogel

Hydrogel membranes have been fabricated that incorporate antibody/antigen moieties. The permeability of large solutes through these membranes is dependent on the presence of soluble antigen that can compete with the internal interactions between antibody and antigen leading to an increase in gel mesh size. Specifically, the membrane's structure is based on a dextran backbone grafted with a fluorescein isothiocyanate (FITC) antigen and a sheep anti-FITC IgG antibody. The backbone is covalently cross-linked by conjugated divinyl sulfone (DVS) groups. The gel structure is additionally stabilized by affinity crosslinks formed by biospecific interactions between the bound IgG and FITC. FTIR spectra of the gel are consistent with formation of covalent bonds between cysteine groups in the IgG and DVS groups in the dextran. Results obtained using isothermal titration calorimetry (ITC) confirmed the competitive interaction binding between IgG-FITC-dextran and free sodium fluorescein at pH 5.0. Scanning electron microscopy (SEM) of samples prepared using cryofixation and cryofracturing techniques showed that observed changes in permeability correlate with free fluorescein-dependent structural changes in the gel. Three-dimensional images obtained from confocal laser scanning microscopy show that these changes occur throughout the gel and indicate that SEM results are not artifacts of sample preparation. The permeability of these gels, as shown by blue-dextran (12 kDa) diffusion, increases in response to the presence of free fluorescein of the external medium, which causes competitive displacement of the affinity cross-links. Sequential addition and removal of sodium fluorescein showed that these permeability changes are reversible.     

Conformation of DNA-DNA polymerase I complex observed by scanning tunneling microscopy.

The conformation of a complex of a 41 mer/31 mer DNA fragment and the Klenow fragment of DNA polymerase I of Escherichia coli was studied by scanning tunnelling microscopy (STM). The results shows that near two turns of double helix of this DNA fragment was outside of enzyme while another part containing more than one turn of helix and 10 nucleotides single strand was combined with enzyme. The dimension and shape of DNA polymerase I (KF) in complex were different from that of free enzyme. The conformation of DNA-DNA polymerase I (KF) complex and the application of STM in studying structure of complex of DNA polymerase with DNA were discussed.