Single molecule studies of antibody-antigen interaction strength versus intra-molecular antigen stability

We investigated molecular recognition of antibodies to membrane-antigens and extraction of the antigens out of membranes at the single molecule level. Using dynamic force microscopy imaging and enzyme immunoassay, binding of anti-sendai antibodies to sendai-epitopes genetically fused into bacteriorhodopsin molecules from purple membranes were detected under physiological conditions. The antibody/antigen interaction strength of 70-170 pN at loading rates of 2-50 nN/second yielded a barrier width of x = 0.12 nm and a kinetic off-rate (corresponding to the barrier height) of k(off) = 6s(-1), respectively. Bacteriorhodopsin unfolding revealed a characteristic intra-molecular force pattern, in which wild-type and sendai-bacteriorhodopsin molecules were clearly distinguishable in their length distributions, originating from the additional 13 amino acid residues epitope in sendai purple membranes. The inter-molecular antibody/antigen unbinding force was significantly lower than the force required to mechanically extract the binding epitope-containing helix pair out of the membrane and unfold it (126 pN compared to 204 pN at the same loading rate), meeting the expectation that inter-molecular unbinding forces are weaker than intra-molecular unfolding forces responsible for stabilizing native conformations of proteins.     

Contributions of Theodor Wilhelm Engelmann on phototaxis,chemotaxis, and photosynthesis

Theodor Wilhelm Engelmann (1843–1909), who had a creative life in music, muscle physiology, and microbiology, developed a sensitive method for tracing the photosynthetic oxygen production of unicellular plants by means of bacterial aerotaxis (chemotaxis). He discovered the absorption spectrum of bacteriopurpurin (bacteriochlorophyll a) and the scotophobic response, photokinesis, and photosynthesis of purple bacteria.     

Structure of the dimeric RC–LH1–PufX complex from Rhodobaca bogoriensis investigated by electron microscopy

Electron microscopy and single-particle averaging were performed on isolated reaction centre (RC)—antenna complexes (RC–LH1–PufX complexes) of Rhodobaca bogoriensis strain LBB1, with the aim of establishing the LH1 antenna conformation, and, in particular, the structural role of the PufX protein. Projection maps of dimeric complexes were obtained at 13 Å resolution and show the positions of the 2 × 14 LH1 α- and β-subunits. This new dimeric complex displays two open, C-shaped LH1 aggregates of 13 αβ polypeptides partially surrounding the RCs plus two LH1 units forming the dimer interface in the centre. Between the interface and the two half rings are two openings on each side. Next to the openings, there are four additional densities present per dimer, considered to be occupied by four copies of PufX. The position of the RC in our model was verified by comparison with RC–LH1–PufX complexes in membranes. Our model differs from previously proposed configurations for Rhodobacter species in which the LH1 ribbon is continuous in the shape of an S, and the stoichiometry is of one PufX per RC.     

<Emphasis Type="Italic">Rhodobaca barguzinensis</Emphasis> sp. nov., a new alkaliphilic purple nonsulfur bacterium isolated from a soda lake of the Barguzin Valley (Buryat Republic,Eastern Siberia)

A novel strain, alga-05, of alkaliphilic purple nonsulfur bacteria was isolated from sediments of a small saline (60 g/l) soda lake near Lake Algin (Barguzin Valley, Buryat Republic, Russia). These bacteria contain bacteriochlorophyll a and carotenoids of the alternative spirilloxanthin group with predominating demethylspheroidenone. They are facultative anaerobes; their photosynthetic structures are of the vesicular type and arranged along the cell periphery. Growth of this strain is possible in a salinity range of 5–80 g/l NaCl, with an optimum at 20 g/l NaCl. Best growth occurred at 20–35°C. Analysis of the 16S rRNA gene sequences demonstrated that the studied isolate is closely related to the alkaliphilic purple nonsulfur bacterium Rhodobaca bogoriensis (99% similarity) isolated from soda lakes of the African Rift Zone. According to the results of DNA-DNA hybridization, strain alga-05 has a 52% similarity with the type species of the genus Rhodobaca. On the basis of the obtained genotypic data and some phenotypic properties (dwelling in a hypersaline soda lake of Siberia, moderate halophily, ability to grow at relatively low temperatures, etc.), the isolated strain of purple bacteria was described as a new species of the genus Rhodobaca, Rca. barguzinensis sp. nov.     

紫色甘薯品系6种酶的同工酶分析

采用聚丙烯酰胺凝胶电泳技术,选用过氧化物酶(POD)、超氧化物歧化酶(SOD)、细胞色素氧化酶(CYT)、淀粉酶(AMY)、酯酶(EST)、苹果酸脱氢酶(MDH)等六种酶的同工酶系统对14个紫色甘薯品种(系)进行了同工酶分析.结果表明:过氧化物酶(POD)、细胞色素氧化酶(CYT) 、超氧化物歧化酶(SOD)等三种酶的同工酶酶谱很丰富,分别有13、11、10条酶带;淀粉酶(AMY)、酯酶(EST)、苹果酸脱氢酶(MDH)等三种酶的同工酶酶带相对较少,分别为4、7、7条.聚类分析结果表明,所有供试紫色甘薯品系或品种分成7类:I类包括品系A1、A2、A7;II类包括品系B1～B3;III类包括品系B7和B8;IV类只有品系B9;V类包括品系A3、A4、A6;VI类只有品系A5;VII类只有品种"山川紫".     

Influence of proline on the thermostability of the active site and membrane arrangement of transmembrane proteins

Proline residues play a fundamental and subtle role in the dynamics, structure, and function in many membrane proteins. Temperature derivative spectroscopy and differential scanning calorimetry have been used to determine the effect of proline substitution in the structural stability of the active site and transmembrane arrangement of bacteriorhodopsin. We have analyzed the Pro-to-Ala mutation for the helix-embedded prolines Pro⁵⁰, Pro⁹¹, and Pro¹⁸⁶ in the native membrane environment. This information has been complemented with the analysis of the respective crystallographic structures by the FoldX force field. Differential scanning calorimetry allowed us to determine distorted membrane arrangement for P50A and P186A. The protein stability was severely affected for P186A and P91A. In the case of Pro⁹¹, a single point mutation is capable of strongly slowing down the conformational diffusion along the denaturation coordinate, becoming a barrier-free downhill process above 371 K. Temperature derivative spectroscopy, applied for first time to study thermal stability of proteins, has been used to monitor the stability of the active site of bacteriorhodopsin. The mutation of Pro⁹¹ and Pro¹⁸⁶ showed the most striking effects on the retinal binding pocket. These residues are the Pro in closer contact to the active site (activation energies for retinal release of 60.1 and 76.8 kcal/mol, respectively, compared to 115.8 kcal/mol for WT). FoldX analysis of the protein crystal structures indicates that the Pro-to-Ala mutations have both local and long-range effects on the structural stability of residues involved in the architecture of the protein and the active site and in the proton pumping function. Thus, this study provides a complete overview of the substitution effect of helix-embedded prolines in the thermodynamic and dynamic stability of a membrane protein, also related to its structure and function.     

衡阳盆地土壤动物多样性研究

对衡阳盆地紫色页岩土壤 9种生境中的土壤动物进行了调查研究 ,共获得土壤动物35 85只 ,隶属于 4门 8纲 39目 ,其中线虫类、蜱螨类为优势类群 ,占总捕量的 5 0 2 4 % ;常见类群 1 2类 ,占总捕量的 4 4 0 1 %。从土壤动物水平分布上看 ,9种生境相似程度较大 ,其中尤以芦竹林和桃树林、阔叶林和桉树林、芦竹林和桉树林之间相似程度更突出。从土壤动物垂直分布上看 ,9种生境中只有桃树林、柑桔林垂直分布较为明显 ,而各种生境中土壤动物具有明显的表聚性。芦竹林、柑桔林、桉树林、菜地、阔叶林和桃树林 6种生境土壤动物群落的多样性及均匀度呈基本一致的趋势 ,且各生境间差别不大     

Cyperus Tubers Protect Meloidogyne incognita from 1,3-Dichloropropene

Meloidogyne incognita-infected and noninfected tubers of yellow nutsedge (Cyperus esculentus) and purple nutsedge (Cyperus rotundus) were treated with 56 L/ha 1,3-dichloropropene (1,3-D) in microplots and subsequently examined for tuber and nematode viability in the greenhouse using a chile pepper (Capsicum annuum) bioassay system. The study was conducted three times. Nutsedge tuber viability and M. incognita harbored in both yellow and purple nutsedge tubers were unaffected by 1,3-D treatment. Nematode reproduction on nutsedges and associated chile pepper plants varied among years, possibly due to differing levels of tuber infection or soil temperature, but was not affected by fumigation. The presence of M. incognita resulted in greater yellow nutsedge tuber germination and reproduction. The efficacy of 1,3-D for management of M. incognita in chile pepper production is likely to be reduced when nutsedges are present in high numbers, reinforcing the importance of managing these weeds and nematodes simultaneously.     

含奥氏酮嗜盐紫色硫细菌的分离鉴定及系统发育分析

[目的]为挖掘我国紫色硫细菌物种和光合蛋白基因资源.[方法]采用Pfennig紫色硫细菌无机选择性培养基和琼脂稀释法.[结果]从青岛东风盐场分离获得一株含奥氏酮、耐高浓度硫化物、嗜盐耐碱紫色硫细菌菌株283-1.该菌株能氧化硫化物产生硫粒储存在细胞内、嗜盐、细胞含有奥氏酮类胡萝卜素、细菌叶绿素a强吸收峰位于830 nm处、运动、不产生气囊,表明属于Marichromatium属.16S rDNA序列同源性比较和系统发育分析也表明这一点.但该菌株能在1%～15%NaCl、7.5 mmol/L 高浓度硫化物、45℃、5000lux、pH9.0条件下生长良好,能很好的光同化C3和C4有机酸和葡萄糖酸钠等特性,与Marichromatium属4个种有明显不同.[结论]菌株283-1是Marichromatium属一个新分离物,编号 Marichromatium sp.283-1.