The effect of calcium on the conformation of cobalamin transporter BtuB

BtuB is a β‐barrel membrane protein that facilitates transport of cobalamin (vitamin B12) from the extracellular medium across the outer membrane of Escherichia coli. It is thought that binding of B12 to BtuB alters the conformation of its periplasm‐exposed N‐terminal residues (the TonB box), which enables subsequent binding of a TonB protein and leads to eventual uptake of B12 into the cytoplasm. Structural studies determined the location of the B12 binding site at the top of the BtuB's β‐barrel, surrounded by extracellular loops. However, the structure of the loops was found to depend on the method used to obtain the protein crystals, which—among other factors—differed in calcium concentration. Experimentally, calcium concentration was found to modulate the binding of the B12 substrate to BtuB. In this study, we investigate the effect of calcium ions on the conformation of the extracellular loops of BtuB and their possible role in B12 binding. Using all‐atom molecular dynamics, we simulate conformational fluctuations of several X‐ray structures of BtuB in the presence and absence of calcium ions. These simulations demonstrate that calcium ions can stabilize the conformation of loops 3–4, 5–6, and 15–16, and thereby prevent occlusion of the binding site. Furthermore, binding of calcium ions to extracellular loops of BtuB was found to enhance correlated motions in the BtuB structure, which is expected to promote signal transduction. Finally, we characterize conformation dynamics of the TonB box in different X‐ray structures and find an interesting correlation between the stability of the TonB box structure and calcium binding. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

An efficient system to detect protein ubiquitination by agroinfiltration in Nicotiana benthamiana

The ubiquitination proteasome pathway has been demonstrated to regulate all plant developmental and signaling processes. E3 ligase/substrate‐specific interactions and ubiquitination play important roles in this pathway. However, due to technical limitations only a few instances of E3 ligase–substrate binding and protein ubiquitination in plants have been directly evidenced. An efficient in vivo and in vitro ubiquitination assay was developed for analysis of protein ubiquitination reactions by agroinfiltration expression of both substrates and E3 ligases in Nicotiana benthamiana. Using a detailed analysis of the well‐known E3 ligase COP1 and its substrate HY5, we demonstrated that this assay allows for fast and reliable detection of the specific interaction between the substrate and the E3 ligase, as well as the effects of MG132 and substrate ubiquitination and degradation. We were able to differentiate between the original and ubiquitinated forms of the substrate in vivo with antibodies to ubiquitin or to the target protein. We also demonstrated that the substrate and E3 ligase proteins expressed by agroinfiltration can be applied to analyze ubiquitination in in vivo or in vitro reactions. In addition, we optimized the conditions for different types of substrate and E3 ligase expression by supplementation with the gene‐silencing suppressor p19 and by time‐courses of sample collection. Finally, by testing different protein extraction buffers, we found that different types of buffer should be used for different ubiquitination analyses. This method should be adaptable to other protein modification studies.     

环境因素对短命植物抱茎独行菜抽薹开花节律的影响

以新疆十字花科典型早春短命植物抱茎独行菜(Lepidium perfoliatum L.)为材料,分别在不同环境、不同土壤基质及不同春化时间下栽培,以探讨环境因素对抱茎独行菜抽薹开花的影响。结果表明:抱茎独行菜种子在蛭石∶珍珠岩(3∶1)中的出苗率显著高于营养土和自然生境土壤,基质对抱茎独行菜植株是否抽薹无显著影响,但影响其抽薹的早晚及结实特性;人工4℃春化对3种不同栽培环境中于阳台生长植株的抽薹有明显促进作用,而对培养室及户外环境中栽培植株是否抽薹无显著影响;抱茎独行菜抽薹开花对光照和温度的响应最明显,光照时间由短变长与苗期一定时间的低温之间的相互作用是促使抱茎独行菜抽薹开花的关键因素。     

Substrate specificity of a recombinant d‐lyxose isomerase from Serratia proteamaculans that produces d‐lyxose and d‐mannose

Aims: Characterization of substrate specificity of a d ‐lyxose isomerase from Serratia proteamaculans and application of the enzyme in the production of d ‐lyxose and d ‐mannose. Methods and Results: The concentrations of monosaccharides were determined using a Bio‐LC system. The activity of the recombinant protein from Ser. proteamaculans was the highest for d ‐lyxose among aldoses, indicating that it is a d‐ lyxose isomerase. The native recombinant enzyme existed as a 54‐kDa dimer, and the maximal activity for d‐ lyxose isomerization was observed at pH 7·5 and 40°C in the presence of 1 mmol l^?1 Mn²⁺. The K_m values for d ‐lyxose, d ‐mannose, d ‐xylulose, and d ‐fructose were 13·3, 32·2, 3·83, and 19·4 mmol l^?1, respectively. In 2 ml of reaction volume at pH 7·5 and 35°C, d ‐lyxose was produced at 35% (w/v) from 50% (w/v) d ‐xylulose by the d‐ lyxose isomerase in 3 h, while d ‐mannose were produced at 10% (w/v) from 50% (w/v) d ‐fructose in 5 h. Conclusions: We identified the putative sugar isomerase from Ser. proteamaculans as a d ‐lyxose isomerase. The enzyme exhibited isomerization activity for aldose substrates with the C2 and C3 hydroxyl groups in the left‐hand configuration. High production rates of d‐ lyxose and d ‐mannose by the enzyme were obtained. Significance and Impact of the Study: A new d‐ lyxose isomerase was found, and this enzyme had higher activity for d ‐lyxose and d ‐mannose than previously reported enzymes. Thus, the enzyme can be applied in industrial production of d ‐lyxose and d ‐mannose.     

Organism–quartz interactions in structuring benthic communities: towards a marine bio-mineralogy?

Abiotic and biotic factors determine the distribution and structure of marine benthic communities but the processes invoked to explain such patterns are often inadequate. We demonstrate that the presence of quartz grains in sediments inhibits animal colonization on marine soft-bottoms. We suggest that this phenomenon may be related to the oxidant properties of the quartz crystal surface derived by the generation of silicon-based radicals due to water movement. The interaction between organisms and the crystallographic structure of substrata might play a neglected but important role in structuring coastal benthic communities.     

Interaction of pro-and eukaryotic DNA repair enzymes with oligodeoxyribonucleotides containing clustered lesions

A study was made of the interaction of 8-oxoguanine-DNA glycosylases of Escherichia coli (Fpg) and human (OGG1), as well as apurinic/apyrimidinic endonucleases of yeast (Apn1) and E. coli (Nfo), with oligodeoxyribonucleotides containing 8-oxoguaine (oxoG) and tetrahydrofuran (F, a stable analog of an apurinic site) separated by various numbers of nucleotides. Inhibitor analysis showed that the affinity of Fgp for single-stranded DNA ligands is virtually independent of the relative positions of oxoG and F. K _M and k _cat were determined for all the four enzymes and all double-stranded substrates studied. The effect of the second lesion strongly depended both on the relative position of the lesion and the enzyme of interest. The highest drop in the affinity of Fpg and OGG1 for the substrate (1.6-to 148-fold) and in the reaction rate (4.8-to 58-fold) was recorded for the oligonucleotides in which F was immediately 3′ or 5′ of oxoG. Introduction of the second lesion barely affected K _M for nucleases Apn1 and Nfo. The reaction rate was five-to tenfold lower for the substrates containing two adjacent lesions. For all enzymes studied, an increase in the distance between two lesions in double-stranded DNA decreased their contribution to K _M and k _cat.     

Probing of contacts between <Emphasis Type="Italic">Eco</Emphasis>RII DNA methyltransferase and DNA with the use of substrate analogs and molecular modeling

The molecular mechanisms of DNA recognition and modification by EcoRII DNA methyltransferase (M.EcoRII) were studied using 14-mer substrate analogs containing 2-aminopurine or 1′,2′-dideoxy-D-ribofuranose in the M.EcoRII recognition site. The efficiency of DNA binding and methylation depended on the position of a modified nucleoside residue in the recognition site. A structural model of M.EcoRII in complex with substrate DNA and the cofactor analog S-adenosyl-L-homocysteine (AdoHcy) was constructed using the available crystal structures of M.Hha and M.HaeIII and the recent Frankenstein’s monster approach. The amino acid residues interacting with DNA were predicted based on the model. In addition, theoretical and experimental findings made it possible to predict the groups of atoms of the heterocyclic bases of the M.EcoRII recognition site that are presumably involved in the interactions with the enzyme.