脑红蛋白和细胞红蛋白：携氧蛋白质家族2个新成员

脑红蛋白(neuroglobin, Ngb)和细胞红蛋白(cytoglobin, Cygb)是新发现的2个携氧蛋白家族的成员.脑红蛋白主要存在于脑中,而细胞红蛋白在全身各个组织都含有,它们和另外2个携氧蛋白——血红蛋白和肌红蛋白的同源性<25%,但它们在种属之间的同源性很高(>95%).脊椎动物脑红蛋白基因定位于14q24,细胞红蛋白基因定位于17q25,都含有4个外显子和3个内含子.2种蛋白在生理条件下含有6个配位键,不同于血红蛋白和肌红蛋白的5个配位键结构.这2种新蛋白和氧都具有很高的亲和力,在缺氧条件下其基因及蛋白表达都有明显的提升,对细胞的存活有一定保护作用.对于脑红蛋白和细胞红蛋白的功能研究,有助于更好地了解机体氧代谢和氧利用过程,并为临床在缺氧损伤时的治疗提供新的观点和途径.     

Role of Protein Cavities on Unfolding Volume Change and on Internal Dynamics under Pressure

The effects of two single point cavity forming mutations, F110S and I7S, on the unfolding volume change (DeltaV(0)) of azurin from Pseudomonas aeruginosa and on the internal dynamics of the protein fold under pressure were probed by the fluorescence and phosphorescence emission of Trp-48, deeply buried in the compact hydrophobic core of the macromolecule. Pressure-induced unfolding, monitored by the shift of the center of mass of the fluorescence spectrum, showed that DeltaV(0) is in the range of 60-70 mL/mol, not significantly different between cavity mutants and compact azurin species such as the wild-type and the mutant C3A/C26A, in which the superficial disulphide has been removed. The lack of extra volume in F110S and I7S proves that the engineered cavities, 40 A(3) in I7S and 100 A(3) in F110S, are filled with water molecules. Changes in flexibility of the protein matrix around the chromophore were monitored by the intrinsic phosphorescence lifetime (tau(0)). The application of pressure in the predenaturation range initially decreases the internal flexibility of azurin, the trend eventually reverting on approaching unfolding. The main difference between compact folds, wild-type and C3A/C26A, and cavity mutants is that the inversion point is powered from approximately 3 kbar to 1.5 kbar for F110S and <0.1 kbar for I7S, meaning that in the latter species pressure-induced internal hydration dominates very early over any compaction of the globular fold resulting from the reduction of internal free volume. The similar response between wild-type and the significantly less-stable C3A/C26A mutant suggests that thermodynamic stability per se is not the dominant factor regulating pressure-induced internal hydration of proteins.     

Molecular Dynamics Study on Protein and it's Water Structure at High Pressure

Abstract

We have performed NPT molecular dynamics simulations (Langevin Piston Method) on two types of solvated proteins-‘denaturation-unfavorable’ protein (insulin) and ‘denaturation-favorable protein’ (ribonuclease A) at high pressure (from 1 bar up to 20 kbar). The method is based on the extended system formalism introduced by Andersen, where the deterministic equations of motion for the piston degree of freedom are replaced by Langevin equation. We report the structural changes of proteins (ribonuclease A and insulin) and water molecules through radius of gyration, solvent accessible surface area, hydrogen bond pattern, and the topology of water clusters connected by the hydrogen bonded circular network. The solvent accessibility of ribonuclease A is mainly decreased by hydrophilic residues rather than hydrophobic residues under high pressure. From the results of hydrogen bond analysis, we have found that α-helix is more stable than β-sheet under high pressure. In addition, from the analysis of the water cluster, we have observed that for ribonuclease A, 5-membered ring structure is more favorable than 6-membered ring at higher pressure. However, for insulin, the ratio of 5 to 6-ring is constant over the pressure ranges for which we have performed MD simulation. This indicates that the water structure around insulin does not change under high pressure.     

超声和高压处理对牛血清白蛋白结构的影响

目的:研究牛血清白蛋白经过超声和高压处理前后的结构变化,以及自由基清除剂对其结构变化的影响.为进一步研究细胞破碎和乳化蛋白时超声和高压处理对蛋白的影响提供参考.方法:将BSA溶液经过超声和高压处理,然后利用高效液相色谱(HPLC)、动态光散射(DLS)、非变性聚丙烯酰胺凝胶电泳(nondenaturing SDS-PAGE)以及园二色谱(CD)等手段检测处理前后的结构变化.结果:发现超声使BSA严重聚集,加入自由基清除剂可以减少聚集的产生.而高压处理后的BSA未出现聚集,但二级结构发生了变化.结论:超声和高压这两种处理方法对蛋白损伤机理不同,所以选择合适的破碎方法要根据蛋白自身的性质而定.     

The Hemoglobin Conformation in Erythrocytes at Different Levels of Oxygen Partial Pressure

Biophysics - The variation in the conformations of hemoglobin heme and globin in response to different oxygen partial pressures (pO2) has been studied by Raman spectroscopy inside erythrocytes and...     

Growth of Streptococcus faecalis under High Hydrostatic Pressure and High Partial Pressures of Inert Gases

Growth of Streptococcus faecalis in a complex medium was inhibited by xenon, nitrous oxide, argon, and nitrogen at gas pressures of 41 atm or less. The order of inhibitory potency was: xenon and nitrous oxide > argon > nitrogen. Helium appeared to be impotent. Oxygen also inhibited streptococcal growth and it acted synergistically with narcotic gases. Growth was slowed somewhat by 41 atm hydrostatic pressure in the absence of narcotic gases, but the gas effects were greater than those due to pressure. In relation to the sensitivity of this bacterium to pressure, we found that the volume of cultures increased during growth in a volumeter or dilatometer, and that this dilatation was due mainly to glycolysis. A volume increase of 20.3 ± 3.6 ml/mole of lactic acid produced was measured, and this value was close to one of 24 ml/mole lactic acid given for muscle glycolysis, and interestingly, close to the theoretic volume increase of activation calculated from the depression of growth rate by pressure.     

Photosynthetic Acclimation in Pea and Soybean to High Atmospheric CO2 Partial Pressure

Nonnodulated pea (Pisum sativum L. cv Frosty) and soybean (Glycine max [L.] Merr. cv Wye) plants were grown under artificial lights from germination with ample nutrients, 600 [mu]mol photons m-2 s-1, and either 34 to 36 (control) or 64 to 68 Pa (enriched) CO2. For soybean, pod removal and whole-plant shading treatments were used to alter the source-sink balance and carbohydrate status of the plants. Growth of both species was substantially increased by CO2 enrichment despite some down-regulation of photosynthesis rate per unit leaf area ("acclimation"). Acclimation was observed in young pea leaves but not old and in old soybean leaves but not young. Acclimation was neither evident in quantum yield nor was it related to triose phosphate limitation of net photosynthesis. A correlation between levels of starch and sugars in the leaf and the amount of acclimation was apparent but was loose and only weakly related to the source-sink balance of the plant. A consistent feature of acclimation was reduced ribulose bisphosphate carboxylase (RuBPCase) content, although in vivo RuBPCase activity was not necessarily diminished by elevated growth CO2 owing to increased percentage of activation of the enzyme. A proposal is discussed that the complexity of photosynthetic acclimation responses to elevated CO2 is as an expression of re-optimization of deployment of within-plant resources at three levels of competition.     

Atomic simulation of Xe and Kr separation in silica-templated amorphous mesoporous carbons CMK-3 and CMK-5

We perform a molecular simulation study on adsorption and separation of the noble gases Xe and Kr in silica-templated amorphous mesoporous carbons (CMK) materials. We generate the atomic models of CMK-3 and CMK-5 materials by adsorbing carbon in a model MCM-41 pore. Our carbon structures can capture the surface roughness and the disordered nature of the carbon rods and carbon pipes as reported in the experiment. The adsorption isotherms and isosteric heats of pure gases have been examined further. We find that the existence of the carbon interconnections between nanorods for CMK-3 and between nanopipes for CMK-5 will reduce the excess uptakes of the noble gases, whereas the isosteric heats are favoured in the materials with interconnections. The carbon interconnections are not advantageous to the adsorption storage of pure gases, but they can improve the separation ability of Xe for gas-mixture adsorption. The effects of temperature and concentration on the Xe separation are investigated and it is shown that the selectivities of Xe in the CMK-5 materials are insensitive to the two factors. We also find that both gas storage and separation of CMK materials are comparable to IRMOF-1 and UMCM-1 metal-organic frameworks.     

Ultra-Deep Sequencing of HIV-1 near Full-Length and Partial Proviral Genomes Reveals High Genetic Diversity among Brazilian Blood Donors

Background

Here, we aimed to gain a comprehensive picture of the HIV-1 diversity in the northeast and southeast part of Brazil. To this end, a high-throughput sequencing-by-synthesis protocol and instrument were used to characterize the near full length (NFLG) and partial HIV-1 proviral genome in 259 HIV-1 infected blood donors at four major blood centers in Brazil: Pro-Sangue foundation (São Paulo state (SP), n 51), Hemominas foundation (Minas Gerais state (MG), n 41), Hemope foundation (Recife state (PE), n 96) and Hemorio blood bank (Rio de Janeiro (RJ), n 70).

Materials and Methods

A total of 259 blood samples were obtained from 195 donors with long-standing infections and 64 donors with a lack of stage information. DNA was extracted from the peripheral blood mononuclear cells (PBMCs) to amplify the HIV-1 NFLGs from five overlapping fragments. The amplicons were molecularly bar-coded, pooled, and sequenced by Illumina paired-end protocol.

Results

Of the 259 samples studied, 208 (80%) NFLGs and 49 (18.8%) partial fragments were de novo assembled into contiguous sequences and successfully subtyped. Of these 257 samples, 183 (71.2%) were pure subtypes consisting of clade B (n = 167, 65%), C (n = 10, 3.9%), F1 (n = 4, 1.5%), and D (n = 2, 0.7%). Recombinant viruses were detected in 74 (28.8%) samples and consist of unique BF1 (n = 41, 15.9%), BC (n = 7, 2.7%), BCF1 (n = 4, 1.5%), CF1 and CDK (n = 1, 0.4%, each), CRF70_BF1 (n = 4, 1.5%), CRF71_BF1 (n = 12, 4.7%), and CRF72_BF1 (n = 4, 1.5%). Evidence of dual infection was detected in four patients coinfected with the same subtype (n = 3) and distinct subtype (n = 1).

Conclusion

Based on this work, subtype B appears to be the prevalent subtype followed by a high proportion of intersubtype recombinants that appeared to be arising continually in this country. Our study represents the largest analysis of the viral NFLG ever undertaken worldwide and provides insights into the understanding the genesis of the HIV-1 epidemic in this particular area of South America and informs vaccine design and clinical trials.     

小麦多聚半乳糖醛酸酶抑制蛋白的部分结构

为了弄清小麦多聚半乳糖醛酸酶抑制蛋白 (polygalacturonase inhibitingprotein ,PGIP)的作用机制 ,并为其在基因工程中的应用提供依据 ,对其结构进行了研究 .用Edman降解法测得小麦PGIP的N端序列为Lys Pro Leu Leu Thr Lys Ile Thr Lys Gly Ala Ala Ser Thr .用CD谱研究其二级结构 ,发现小麦PGIP天然态含有 4 3 7%的 β折叠和 13 1%的α螺旋 .酸碱和温度变性引起了二级结构改变 .不完全变性阶段 ,二级结构的变化表现为α螺旋无明显变化 ,β折叠遭到破坏 ;活性完全丧失阶段 ,β折叠变化很小 ,α螺旋含量明显减少 .用NR R(非还原 还原 )双向对角线SDS PAGE鉴定出小麦PGIP含有链内二硫键 .用去糖基化法确证了小麦PGIP的糖含量为 2 2 %.小麦PGIP与双子叶植物PGIP相比 ,一级结构差异较大 ,同源性由 36 %变为 9%;二级结构相似 ,都是高 β 折叠的蛋白 ;均具有链内二硫键 ;在糖含量上也相似 .研究结果为进一步弄清小麦PGIP作用机理打下了基础 ,同时对于植物抗赤霉病基因工程具有重要意义 .     

Interactions of Oxygen at High Pressure and Radiation in Drosophila

Oxygen at high pressure (OHP) and X-irradiation can interact in the fruit fly Drosophila melanogaster to potentiate toxic actions characteristic of one agent alone. 1000 kvp X-irradiation in doses of 30, 60, and 75 kr accelerated the acute immobilization of young male Drosophila by oxygen at 7.8 atm, up to rates twice that observed with such oxygen pressure alone. X-irradiation alone in these dosages did not acutely immobilize the Drosophila. X-irradiation during exposure to 7.8 atm pO₂ was more effective and consistent in producing this potentiation than was X-irradiation that preceded exposure to OHP. Acute OHP toxicity in young female Drosophila was not potentiated by 75 kr of X-irradiation. On the other hand, shortening of the life span of young male Drosophila by the above doses of X-irradiation was augmented significantly by a concurrent 40 min exposure to OHP (which alone did not significantly decrease life span). This shows, for the first time, that oxygen can affect not only the acute effects of radiation, but also the residual irreversible effects indicated by the life span shortening.     

Crystal Structure of Arabidopsis Deg2 Protein Reveals an Internal PDZ Ligand Locking the Hexameric Resting State

Eukaryotic organelles have developed elaborate protein quality control systems to ensure their normal activity, among which Deg/HtrA proteases play an essential role. Plant Deg2 protease is a homologue of prokaryotic DegQ/DegP proteases and is located in the chloroplast stroma, where its proteolytic activity is required to maintain the efficiency of photosynthetic machinery during stress. Here, we demonstrate that Deg2 exhibits dual protease-chaperone activities, and we present the hexameric structure of Deg2 complexed with co-purified peptides. The structure shows that Deg2 contains a unique second PDZ domain (PDZ2) following a conventional PDZ domain (PDZ1), with PDZ2 orchestrating the cage assembly of Deg2. We discovered a conserved internal ligand for PDZ2 that mediates hexamer formation and thus locks the protease in the resting state. These findings provide insight into the diverse modes of PDZ domain-mediated regulation of Deg proteases.     

The Stability of Clathrate Hydrates: Temperature Dependence of Dissociation Pressure in Xe and Ar Hydrate

Abstract

The thermodynamic stability of clathrate hydrates I and II encaging xenon or argon has been investigated by examining the temperature dependence of the dissociation pressure. The evaluation of the stability is made based on the generalized van der Waals and Platteeuw theory developed by Tanaka and Kiyohara [J. Chem. Phys. 98, 4098 (1993)]. In the new treatment, the free energy of formation of hydrates in equilibrium with ice is calculated by taking the coupling of the host lattice vibrations with guests into consideration. The predicted dissociation pressures of Xe and Ar hydrates agree well with experiments in higher temperature range. A poor agreement between experiment and calculation for Ar clathrate hydrate at low temperature is improved by the use of a quantum mechanical partition function for a harmonic oscillator in evaluating the free energy difference between ice and empty hydrate.     

Comparative Study of Regulatory Circuits in Two Sea Urchin Species Reveals Tight Control of Timing and High Conservation of Expression Dynamics

Accurate temporal control of gene expression is essential for normal development and must be robust to natural genetic and environmental variation. Studying gene expression variation within and between related species can delineate the level of expression variability that development can tolerate. Here we exploit the comprehensive model of sea urchin gene regulatory networks and generate high-density expression profiles of key regulatory genes of the Mediterranean sea urchin, Paracentrotus lividus (Pl). The high resolution of our studies reveals highly reproducible gene initiation times that have lower variation than those of maximal mRNA levels between different individuals of the same species. This observation supports a threshold behavior of gene activation that is less sensitive to input concentrations. We then compare Mediterranean sea urchin gene expression profiles to those of its Pacific Ocean relative, Strongylocentrotus purpuratus (Sp). These species shared a common ancestor about 40 million years ago and show highly similar embryonic morphologies. Our comparative analyses of five regulatory circuits operating in different embryonic territories reveal a high conservation of the temporal order of gene activation but also some cases of divergence. A linear ratio of 1.3-fold between gene initiation times in Pl and Sp is partially explained by scaling of the developmental rates with temperature. Scaling the developmental rates according to the estimated Sp-Pl ratio and normalizing the expression levels reveals a striking conservation of relative dynamics of gene expression between the species. Overall, our findings demonstrate the ability of biological developmental systems to tightly control the timing of gene activation and relative dynamics and overcome expression noise induced by genetic variation and growth conditions.     

Sublethal High Hydrostatic Pressure Treatment Reveals the Importance of Genes Coding Cytoskeletal Protein in Escherichia Coli Morphogenesis

We studied morphologic changes after sublethal high hydrostatic pressure treatment (HPT) of Escherichia coli K-12 strains in which genes related to the cytoskeleton, cell wall, and cell division had been deleted. Some long filamentous and swelling cells were observed in wild-type bacteria, while some spherical, branched, or collapsed cells were observed in deletion mutants. In particular, ΔzapA and ΔrodZ showed distinguished morphologies. ZapA supports FtsZ, a cytoskeletal protein, forming ring with ZapB. RodZ, a cytoskeletal protein, interacts with MreB, also a cytoskeletal protein, and both factors are necessary for maintaining the rod shape of the cell. These results showed that insufficient formation of FtsZ rings induced cell elongation and that insufficient formation of MreB induced a branched and collapsed cell shape. Therefore, the correct formation of the bacteria cytoskeleton by FtsZ rings and MreB is important for keeping normal cell shape during growth after HPT, and the polymerization of cytoskeletal proteins was a critical target of sublethal HPT. These results indicate that sublethal HPT induces bacterial cell morphologic change and provide important information on the role of genes involved in morphogenesis. Therefore, sublethal HPT may be a good tool for studying the morphogenesis of bacterial cells.     

The Responses of Stomatal Density to CO2 Partial Pressure

Experiments on a range of species of tree, shrub and herb haveshown that stomatal density and stomatal index increase as thepartial pressure of CO₂ decreases over the range from the currentlevel of 34 Pa to 22.5 Pa. Stomatal density responds to thereduced partial pressure of CO₂ in a simulation of high altitude(3000 m), when the CO₂ mole fraction is unchanged. When the partial pressure of CO₂ is increased from 35 to 70Pa stomatal density decreases slightly, with a response to unitchange in CO₂ which is about 10% of that below 34 Pa. Measurements of gas exchange on leaves which had developed indifferent CO₂ partial pressures, but at low saturation vapourpressure deficits in the range of 0.7 to 0.9 kPa, indicatedlower photosynthetic rates but higher stomatal conductancesat reduced CO₂ partial pressures. Experiments on populations of Nardus stricta originating fromaltitudes of 366 m and 810 m in Scotland, indicated geneticdifferences in the responses of stomatal density to CO₂ in pressuressimulating altitudes of sea level and 2 000 m. Plants from thehigher altitude showed greater declines in stomatal densitywhen the CO₂ partial pressure was increased. Key words: Stomata, CO₂, gas exchange, altitude, atmospheric pressure