细胞外钙受体相互作用蛋白的研究进展

细胞外钙受体(CaR)为G蛋白偶联受体超家族中的成员,它的大部分作用是以Gαi,Gαq和Gα12/13为中介的,但由G蛋白α亚基介导的作用并不能完全解释CaR的生物学效应.与CaR相互作用蛋白如抑制蛋白、G蛋白受体激酶、受体激活修饰蛋白、丝蛋白、钾通道、小窝蛋白等结构和信号蛋白赋予CaR独特的信号转导特征,并能够更充分说明CaR在不同组织和细胞中所发挥的作用.本文将对上述几种与其相互作用蛋白及它们所产生的生物学效应做一综述.     

Recombinant DNA production of spider silk proteins

Spider dragline silk is considered to be the toughest biopolymer on Earth due to an extraordinary combination of strength and elasticity. Moreover, silks are biocompatible and biodegradable protein-based materials. Recent advances in genetic engineering make it possible to produce recombinant silks in heterologous hosts, opening up opportunities for large-scale production of recombinant silks for various biomedical and material science applications. We review the current strategies to produce recombinant spider silks.     

免疫共沉淀筛选细胞内与A型流感病毒M2蛋白相互作用的蛋白

摘要：【目的】筛选细胞内与A型流感病毒M2蛋白（A/M2）相互作用的蛋白质。【方法】将A/M2编码序列插入真核表达载体pCAGGS-CFlag,重组质粒pCAGGS-CFlag-A/M2转染HEK-293T细胞,裂解细胞,以Flag单抗偶联的琼脂糖球珠免疫沉淀A/M2-Flag蛋白,清洗去除非特异性结合的杂蛋白后,SDS-PAGE银染法显示与A/M2共沉淀的蛋白,从胶上切下此蛋白条带进行质谱分析。【结果】成功构建了A/M2的表达质粒,免疫印迹证实了A/M2蛋白在293T细胞中能够表达,免疫共沉淀筛选到与A/M2结合的多种蛋白,分析质谱结果,确定ataxin 10和3个真核翻译起始因子(eIF)为候选蛋白。【结论】ataxin 10与A/M2相互作用为流感病毒感染或接种流感疫苗引发小脑性共济失调提供了解释,eIF与A/M2相互作用表明A/M2可能在调控病毒蛋白合成方面起重要作用。     

The stretched intermediate model of B-Z DNA transition

There have been numerous attempts to describe the mechanism of B-Z transition. Our simulations based on the stochastic difference equation with length algorithm show that a short DNA oligomer will tend to unwind and overstretch during the transition. The overstretching of DNA is then understood from the Zhou, Zhang, and Ou-Yang model. Unlike the Harvey model, the stretched intermediate model does not pose any steric dilemma; we are able to show that the chain sense reversal progresses spontaneously using the stretched intermediate model. A nonlinear DNA model is used to describe the origins and mechanism of base rotation in the stretched intermediate state of DNA. We also propose an experiment that can verify the existence of a stretched intermediate state during B-Z transition, thus opening up fresh grounds for experimentation in this field.     

Electron microscopic mapping of proteins bound to herpes simplex virus DNA.

Exonuclease digestion experiments have suggested that there is a protein(s) bound close to one or both ends of herpes simplex virus-1 (HSV) DNA. The existence of such bound proteins has been positively demonstrated and their positions on the HSV genome determined by application of a newly developed method for electron microscopic mapping of proteins bound to nucleic acids. Purified HSV DNA was treated with dinitrofluorobenzene under conditions that covalently attach the dinitrophenyl (DNP) group to the proteins in a protein-nucleic acid complex. The HSV DNA-protein-(DNP)n complex was treated with rabbit anti-DNP IgG, and, in some cases, additionally treated with monovalent Fab fragments of goat anti-rabbit IgG, and mounted for examination in the electron microscope. Electron opaque dots representing the protein-(DNP)n-(IgG)m complex were seen on the HSV DNA. Direct measurements of the positions of the protein, as well as partial denaturation mapping, indicate that there are four positions for protein bound to HSV DNA: two near but not at the two ends and two at sites corresponding to the internal inverted repeats of the ends. These results suggest that there is a specific protein binding sequence within the direct terminal repeat of HSV DNA. The previous observation that HSV DNA is more sensitive to digestion by a 3' than by a 5' exonuclease then indicates that the bound protein(s) is more intimately associated with one strand of the specific sequence than with the complementary strand.     

Long-time stretched exponential kinetics in single DNA duplex dissociation

We probe DNA hybridization kinetics by measuring the lifetime distribution of single 16-bp duplexes under thermal dissociation. Our unique approach, based on two DNA-coated microspheres in an extended optical tweezer, allows the study of single duplex DNA molecules under negligible molecular tension. In contrast to earlier experiments, we find a stretched exponential lifetime distribution, which is likely due to dissociation proceeding via a number of competing pathways between highly force-sensitive intermediate states. Similar measurements of microspheres linked by multiple DNA bridges find they have unexpected short bound lifetimes, also consistent with force sensitivity.     

Method for patterning stretched DNA molecules on mica surfaces by soft lithography

Lambda DNA was stretched and patterned on mica surface using soft lithography. A highly diluted solution of amino propyl trimethoxy silane in hexane was deposited on a line patterned polydimethylsiloxane (PDMS) stamp. The functionalized stamp was then used to pick up DNA by molecular combing while the line patterns are parallel to the liquid surface. The stamp was then microcontact printed on freshly cleaved mica. We successfully obtained stretched DNA pattern on mica surface. DNA was found to be stretched in patterns perpendicular to those carved on the stamp. The stretched DNA population was large enough to be used for molecular biology mapping studies. Furthermore, the possibility of locating stretched DNA molecules in the desired position by stamping makes this method a good candidate for assembling non-semiconductor molecular devices.     

'Footprinting' proteins on DNA with peroxonitrous acid.

The peroxonitrite anion (ONOO-) is a stable species in alkaline solution that quickly generates a strong oxidant at neutral pH. A convenient procedure for the preparation of ONOOK has been developed based on the procedure of Keith & Powell [(1969) J. Chem. Soc. A, 90], which when added to a sample of duplex DNA buffered at neutral pH rapidly generates a strong oxidant capable of nonspecifically cleaving the DNA present. We show that this solution containing ONOOK can be used to hydroxyl radical footprint the binding the cl-repressor (cl) of phage lambda with the right operator, OR. In addition, we show that the individual-site binding isotherms determined by quantitative DNase I, Fe-EDTA and ONOOK footprinting are identical within experimental error. The identical isotherms obtained with the three different reagents with greatly differing sampling times indicates that the sampling time of the footprinting probe need not be short relative to the kinetic dissociation constants that govern protein-DNA interactions.     

Glycome mapping on DNA sequencing equipment

Here we provide a detailed protocol for the analysis of protein-linked glycans on DNA sequencing equipment. This protocol satisfies the glyco-analytical needs of many projects and can form the basis of 'glycomics' studies, in which robustness, high throughput, high sensitivity and reliable quantification are of paramount importance. The protocol routinely resolves isobaric glycan stereoisomers, which is much more difficult by mass spectrometry (MS). Earlier methods made use of polyacrylamide gel-based sequencers, but we have now adapted the technique to multicapillary DNA sequencers, which represent the state of the art today. In addition, we have integrated an option for HPLC-based fractionation of highly anionic 8-amino-1,3,6-pyrenetrisulfonic acid (APTS)-labeled glycans before rapid capillary electrophoretic profiling. This option facilitates either two-dimensional profiling of complex glycan mixtures and exoglycosidase sequencing, or MS analysis of particular compounds of interest rather than of the total pool of glycans in a sample.     

The stretched DNA geometry of recombination and repair nucleoprotein filaments

The RecA protein of Escherichia coli plays essential roles in homologous recombination and restarting stalled DNA replication forks. In vitro, the protein mediates DNA strand exchange between single-stranded (ssDNA) and homologous double-stranded DNA (dsDNA) molecules that serves as a model system for the in vivo processes. To date, no high-resolution structure of the key intermediate, comprised of three DNA strands simultaneously bound to a RecA filament (RecA x tsDNA complex), has been elucidated by classical methods. Here we review the systematic characterization of the helical geometries of the three DNA strands of the RecA x tsDNA complex using fluorescence resonance energy transfer (FRET) under physiologically relevant solution conditions. Measurements of the helical parameters for the RecA x tsDNA complex are consistent with the hypothesis that this complex is a late, poststrand-exchange intermediate with the outgoing strand shifted by about three base pairs with respect to its registry with the incoming and complementary strands. All three strands in the RecA x tsDNA complex adopt extended and unwound conformations similar to those of RecA-bound ssDNA and dsDNA.     

Atomic force microscopy of DNA molecules stretched by spin-coating technique

We have developed an effective approach to stretching DNA molecules with the flow of fluid generated by spin coating. Well-stretched A DNA molecules were observed using atomic force microscopy. Substrate properties sensitively affected the stretching behavior of DNA. Our experimental findings revealed that a mica surface treated with crystal violet, a cationic dye molecule, is suitable to the spin-coating procedure for stretching DNA. Moreover, compared with relaxed DNA, we observed reduced height of the stretched DNA, which was attributed mainly to elongation force applied to the DNA molecules from the fluid flow and strong adhesion force between DNA and the substrate. This simple and effective method for preparing stretched DNA could be useful in physically mapping genomic DNA in a high throughput.     

Behavior of DNA fibers stretched by precise meniscus motion control

A modified DNA combing method, which can precisely locate straightened DNA fibers on a substrate, has been developed. Precise motion control of a DNA solution droplet on hydrophobic surfaces has allowed detailed analyses of DNA straightening behavior. Our method provides a technique for consistently straightening λ phage DNA on a trace of droplet motion, though the straightened DNAs had several variations in their alignments. The dependence of the straightened DNA frequency upon motion rate, fluidity in the droplet and environmental humidity was investigated. Visualization of the solution flow in the moving droplet indicated that flows circulating parallel to the contour of the droplet markedly bias the direction of straightening in relation to the site in the droplet. As a result, the alignment variations caused by the site specificity of the bias direction revealed that environmental humidity significantly alters the straightening behavior.     

Interaction of contractile proteins with DNA

The interaction of contractile proteins (myosin, actin, tropomyosin and troponin) with DNA was studied in vitro using a nitrocellulose filter binding technique. The data indicate a high affinity of myosin and troponin for DNA, a lesser interaction between DNA and tropomyosin and the absence of binding of actin to DNA. When binding to DNA was detected, the interaction was higher with single-stranded DNA than with RNA or double-stranded DNA, although in some conditions myosin binds equally as well to native as to denatured eukaryotic DNA. Myosin binds better to eukaryotic than to phage native DNA.     

Proteomics of chondrocytes with special reference to phosphorylation changes of proteins in stretched human chondrosarcoma cells

For proteomic analysis, cartilage molecular composition is a challenging mixture of highly glycosylated proteoglycans and triple-helical collagens, which constitute the major part of cartilage macromolecules. Selective separation of these molecules from the minor components is generally needed before mass spectrometry-based identification of lower-abundancy proteins is possible. The cell density of cartilage is also very low, therefore, cell cultures offer an easier approach to study cellular responses of chondrocytic cells, e.g., to mechanical stimuli. In this study, we investigated the phosphorylation events in human chondrosarcoma cells during cellular stretching. Human chondrosarcoma cells were stretched to 8% strain at a frequency of 1 Hz. One set of experiments included cellular stretching which lasted 2 hours, and the other one included experiments of 2 hours daily treatment for up to 3 days. Two-dimensional polyacrylamide gel electrophoresis combined with chromatographic phosphoprotein pre-enrichment and electrospray ionization mass spectrometry-based protein identification was used to reveal changes of phosphoproteins in cells exposed to cyclic stretching. We discovered that 2 hours cyclic stretching increased the phosphorylation of moesin, elongation factor eEF1D and leprecan, while the phosphorylation of elongation factor eEF1B decreased after cellular stretching. Western blot analyses with phospho-specific antibodies suggested that stretching induces phosphorylation of ERK of the MAP kinase pathway, but did not induce phosphorylation of phosphatidylinositol 3-kinase. In conclusion, the proteomic approach revealed that cellular stretching induced specific phosphorylation changes in chondrosarcoma cells.     

Sarcomeric cytoskeletal proteins and myosin phenotype in stretched soleus of hindlimb-suspended rats

Changes in sarcomeric cytoskeletal proteins of rat m. soleus fibers upon the chronic stretching against the background of gravitational unloading were analyzed and compared with changes in fiber size and myosin phenotype. For rats exposed to gravitational unloading in the usual microgravity-simulating experimental model (hindlimb suspension (HS) according to Morey-Holten), a considerable reduction in the mass of m. soleus (by 54%) and the area of its fibers of both slow-twitch (by 47%) and fast-twitch (37%) types compared with control animals was revealed. Moreover, the percent of fibers containing only slow isoforms of myosin heavy chains (MHC) for suspended animals was slightly smaller and the portion of fibers interacting only with antibodies against fast myosin isoforms was significantly higher than for control animals. For hindlimb-suspended rats, the titin/MHC and nebulin/MHC ratios appeared to be reduced almost by two times as compared with those for the contriol group of animals. Chronic immobilization of m. soleus in stretched state against the background of suspension leads to a partial or complete prevention of the reduction in muscle fiber sizes, the transformation of the myosin phenotype into fast one, and a decrease in relative content of sarcomeric cytoskeletal proteins.     

Entropy loss in long-distance DNA looping

The entropy loss due to the formation of one or multiple loops in circular and linear DNA chains is calculated from a scaling approach in the limit of long chain segments. The analytical results allow us to obtain a fast estimate for the entropy loss for a given configuration. Numerical values obtained for some examples suggest that the entropy loss encountered in loop closure in typical genetic switches may become a relevant factor in comparison to both k(B)T and typical bond energies in biopolymers, which has to be overcome by the released bond energy between the looping contact sites.     

Translational Entropy and DNA Duplex Stability

Investigation of folding/unfolding DNA duplexes of various size and composition by superprecise calorimetry has revised several long-held beliefs concerning the forces responsible for the formation of the double helix. It was established that: 1) the enthalpy and the entropy of duplex unfolding are temperature dependent, increasing with temperature rise and having the same heat capacity increment for CG and AT pairs; 2) the enthalpy of AT melting is greater than that of the CG pair, so the stabilizing effect of the CG pair in comparison with AT results not from its larger enthalpic contribution (as expected from its extra hydrogen bond), but from the larger entropic contribution of the AT pair that results from its ability to fix ordered water in the minor groove and release it upon duplex unfolding; 3) the translation entropy, resulting from the appearance of a new kinetic unit on duplex dissociation, determines the dependence of duplex stability on its length and its concentration (it is an order-of-magnitude smaller than predicted from the statistical mechanics of gases and is fully expressed by the stoichiometric correction term); 4) changes in duplex stability on reshuffling the sequence (the “nearest-neighbor effect”) result from the immobilized water molecules fixed by AT pairs in the minor groove; and 5) the evaluated thermodynamic components permit a quantitative expression of DNA duplex stability.