The investigation of the secondary structure propensities and free-energy landscapes of peptide ligands by replica exchange molecular dynamics simulations

The conformational states of two peptide sequences that bind to staphylococcal enterotoxin B are sampled by replica exchange molecular dynamic (REMD) simulations in explicit water. REMD simulations were treated with 52 replicas in the range of 280–501 K for both peptides. The conformational ensembles of both peptides are dominated by random coil, bend and turn structures with a small amount of helical structures for each temperature. In addition, while an insignificant presence of β-bridge structures were observed for both peptides, the β-sheet structure was observed only for peptide 3. The results obtained from simulations at 300 K are consistent with the experimental results obtained from circular dichroism spectroscopy. From the analysis of REMD results, we also calculated hydrophobic and hydrophilic solvent accessible surface areas for both peptides, and it was observed that the hydrophobic segments of the peptides tend to form bend or turn structures. Moreover, the free-energy landscapes of both peptides were obtained by principal component analysis to understand how the secondary structural properties change according to their complex space. From the free-energy analysis, we have found several minima for both peptides at decreased temperature. For these obvious minima of both peptides, it was observed that the random coil, bend and turn structures are still dominant and the helix, β-bridge or β-sheet structures can appear or disappear with respect to minima. On the other hand, when we compare the results of REMD with conventional MD simulations for these peptides, the configurations of peptide 3 might be trapped in energy minima during the conventional MD simulations. Hence, it can be said that the REMD simulations have provided a sufficiently high sampling efficiency.     

Interpopulation variability on embryo growth,seed dormancy break,and germination in the endangered Iberian daffodil Narcissus eugeniae (Amaryllidaceae)

The main goal of the study was to assess germination requirements in a threatened daffodil to elaborate a detailed protocol for plant production from seeds, a key tool for conservation. Experiments were carried out both in the laboratory and outdoor conditions. In Pseudonarcissi section, endemic Iberian species of Narcissus studied heretofore have different levels of morphophysiological dormancy (MPD). Embryo length, radicle emergence, and shoot emergence were analyzed to determine the level of MPD. Both interpopulational variability and seed storage duration were also studied. Mean embryo length in fresh seeds was 1.32 mm and the embryo had to grow until it reached at least 2.00 mm to germinate. Embryo growth occurs during warm stratification, after which the radicle emerges when temperatures go down. Seed dormancy was broken in the laboratory at 28/14°C in darkness followed by 15/4°C, but the germination percentage varies depending on the population. In outdoor conditions, seed dispersal occurs in June, the embryo grows during the summer and then the radicle emerges in autumn. The radicle system continues to grow during the winter months, but the shoot does not emerge until the beginning of the spring because it is physiologically dormant and requires a cold period to break dormancy. Early cold temperatures interrupt embryo growth and induce dormancy in seeds with an advanced embryo development. Seeds of N. eugeniae have deep simple epicotyl MPD. In addition, we found that embryo growth and germination were improved by seed storage duration.     

Floral and mating system divergence in secondary sympatry: testing an alternative hypothesis to reinforcement in Clarkia

Background and Aims

Reproductive character displacement (RCD) is often an important signature of reinforcement when partially cross-compatible taxa meet in secondary sympatry. In this study, floral evolution is examined during the Holocene range expansion of Clarkia xantiana subsp. parviflora from eastern Pleistocene refugia to a western zone of sympatry with its sister taxon, subsp. xantiana. Floral divergence between the two taxa is greater in sympatry than allopatry. The goal was to test an alternative hypothesis to reinforcement – that floral divergence of sympatric genotypes is simply a by-product of adaptation to pollination environments that differ between the allopatric and sympatric portions of the subspecies'' range.

Methods

Floral trait data from two common garden studies were used to examine floral divergence between sympatric and allopatric regions and among phylogeographically defined lineages. In natural populations of C. x. parviflora, the magnitude of pollen limitation and reproductive assurance were quantified across its west-to-east range. Potted sympatric and allopatric genotypes were also reciprocally translocated between geographical regions to distinguish between the effects of floral phenotype versus contrasting pollinator environments on reproductive ecology.

Key Results

Sympatric populations are considerably smaller flowered with reduced herkogamy. Pollen limitation and the reproductive assurance value of selfing are greater in sympatric than in allopatric populations. Most significantly, reciprocal translocation experiments showed these differences in reproductive ecology cannot be attributed to contrasting pollinator environments between the sympatric and allopatric regions, but instead reflect the effects of flower size on pollinator attraction.

Conclusions

Floral evolution occurred during the westward range expansion of parviflora, particularly in the zone of sympatry with xantiana. No evidence was found that strongly reduced flower size in sympatric parviflora (and RCD between parviflora and xantiana) is due to adaptation to limited pollinator availability. Rather, floral divergence appears to have been driven by other factors, such as interactions with congenerics in secondary sympatry.     

毛白杨PtoNAC157基因的克隆与表达分析

NAC是植物特有的一类转录因子,在植物生长发育和抗逆过程中有重要作用。本研究从毛白杨中克隆出一个NAC转录因子基因,并根据同源性分析将其命名为PtoNAC157,开放阅读框为942 bp,能编码一个由313个氨基酸残基组成的蛋白质,预测蛋白分子量为35.5 kDa,等电点为7.22。氨基酸同源性分析显示,该蛋白N-端具有保守的NAC结构域。实时荧光定量PCR结果表明：PtoNAC157在毛白杨幼根、茎和叶中均有表达,在茎中的表达量最高。PtoNAC157响应低温、NaCl（300mmol.L-1）、干旱和ABA（200μmol.L-1）胁迫。由此推测该基因在林木次生生长及响应胁迫信号转导过程中发挥作用。     

自复寄生蜂的生殖特性及其对生物防治的影响

自复寄生蜂营雌雄异律发育,雌蜂为初级寄生蜂,雄蜂为复寄生蜂。依据寄主类型产下的相应性别的后代,其性比受到寄主数量、初级寄主与二级寄主的相对丰度等因素影响。自复寄生蜂能够寄生和取食初级寄主,抑制有害昆虫的种群数量,同时能够寄生和取食同种和异种寄生蜂幼虫,产生致死干扰竞争作用。复寄生二级寄主时,易感时间窗口主要集中在老熟幼虫至预蛹阶段。与同种二级寄主相比,自复寄生蜂更倾向于寄生异种二级寄主或无选择倾向性,取食时,更倾向于异种二级寄主。自复寄生蜂特殊的生殖方式使其对生物防治的影响备受争议。在评价其生物防治价值时,应对其正面影响和负面影响做出全面权衡。本文对自复寄生蜂的生殖特性、对同种和其他种类寄生蜂产生的致死干扰竞争作用及其对生物防治的影响等问题的国内外研究进展进行了综述,以期为利用这种天敌资源开展有害生物综合治理提供依据。     

磨盘山天然次生林凋落物数量及动态

以磨盘山5.76hm2天然次生林群落固定监测样地为平台,均匀布设144个凋落物收集器,于2006年每月末(4—11月)连续收集其凋落物,用以分析群落尺度上的凋落物产量、组成及时空变化。结果表明,天然次生林年凋落量为3039.6 kg/hm2,以凋落叶(2499.2 kg/hm2)所占的比例最大,占年凋落量的82.22%,而凋落枝仅占年凋落量的9.92%,花果皮等所占比例更小,占总量的5%以下。1a内,凋落物收集器内共收集到42种树木的凋落叶,占样地内树种总数(46种)的91.30%,其中花曲柳(Fraxinus rhynchophylla)、核桃楸(Juglans mandshurica)和蒙古栎(Quercus mongolica)3个树种的凋落叶占落叶总量的82.97%,为叶凋落量的主要来源。不同收集器之间凋落量存在较大差异,99个收集器的年凋落量在200—400 g,2个收集器超过600 g;单个收集器全年最多可收集到19种树种的凋落叶,收集到凋落叶种数12种的收集器最多(29个)。凋落量月动态呈单峰型,69.78%的凋落量产生于9—10月份,叶凋落量月动态与凋落总量变化相同。落叶以秋季为主,但树种间叶凋落节律存在差异,其中核桃楸叶的凋落高峰集中在8—9月,花曲柳和春榆(Ulmus japonica)集中在9—10月,色木槭(Acer mono)为10月,蒙古栎叶为10—11月。     

盐离子对次壶腹腺丝蛋白重组模块的影响

为研究不同生理环境对蛛丝蛋白组装及成丝的影响,首次以MiSp序列为对象,研究其NTR1SR2CT重组模块在不同种类(浓度)盐离子条件下的聚集和成纤维特性及其在成纤维过程中二级结构的变化。基于大腹园蛛MiSp全长序列构建NTR1SR2CT模块,并在大肠杆菌Escherichia coli BL21中成功表达。借助8 mol/L尿素裂解包涵体进行变性纯化得到NTR1SR2CT重组蛋白。NTR1SR2CT重组蛋白二级结构主要为无规则卷曲(Random coil)或α螺旋(Helix),在自然成丝及冻干过程中部分random coil或helix转变为β折叠(β-sheet),甲醇能促进该转变过程。另外,钾离子和磷酸根离子有利于NTR1SR2CT重组蛋白聚集从而促进丝纤维的形成。研究结果为成丝机理研究奠定了基础,同时也为工业化生产高品质的蛛丝纤维提供了条件。     

雷公藤内生细菌的促生作用及其对雷公藤甲素生成的影响

从健康雷公藤植株体内分离得到23株内生细菌,对其有益生物学特征及对小麦萌发能力的影响进行评价,得出3株益生效果显著的内生细菌.这3株内生细菌均能产生植物生长素和铁载体,其中LG3、LJ10具有溶磷特性,LG3、LY4具有固氮功能并同时具有1-氨基环丙烷-1-羧酸脱氨酶(ACC脱氨酶)活性.经细菌16S rDNA序列鉴定及同源性分析发现, LG3、LY4属于肠杆菌属,LJ10属于泛菌属.回接试验表明,3株内生细菌不但能够促进雷公藤植株的生长,还能显著提高不同器官内雷公藤甲素的含量.
     

Genetic structure of Pseudo-nitzschia pungens (Bacillariophyceae) populations: Implications of a global diversification of the diatom

Pseudo-nitzschia pungens is a planktonic marine diatom known to be widespread in tropical and temperate coastal waters. We examined the population genetic structure of tropical Southeast Asian populations of P. pungens and compared it with those of northern and southern temperate populations. The secondary structures of the nuclear encoded internal transcribed spacer (ITS) region of 164 strains of P. pungens were modeled and analyzed. The tree revealed three ITS entities: clade I (comprised of P. pungens var. pungens) was distributed mainly in northern temperate waters; clade II (comprised of both P. pungens var. pungens and var. cingulata) was mainly from the NE Pacific; and clade III (comprised of both P. pungens var. pungens and var. aveirensis) was restricted to tropical and warm-temperate waters. Hybrids of both P. pungens var. pungens and var. cingulata co-occurred in clades I and II. Sixty haplotypes were revealed from the sequences of 164 strains. Haplotype diversity inferred from the median-joining network was in accordance with phylogenetic analysis, further supporting the grouping of the P. pungens haplogroups. Our results revealed limited gene flow between P. pungens from tropical and temperate waters, and significant population structure, as estimated by an analysis of molecular variance (AMOVA), with 75% of the total ITS variation found among populations (Ф_ST = 0.75). This study suggests that distinct environmental clines, such as ocean thermohaline circulation, have a potential for fragmenting and dispersing global populations of P. pungens. Formation of the Isthmus of Panama, in particular, is speculated to play a role in this allopatric differentiation in P. pungens populations worldwide.     

Extended secondary structures in proteins

Supersecondary structures of proteins have been systematically searched and classified, but not enough attention has been devoted to such large edifices beyond the basic identification of secondary structures. The objective of the present study is to show that the association of secondary structures that share some of their backbone residues is a commonplace in globular proteins, and that such deeper fusion of secondary structures, namely extended secondary structures (ESSs), helps stabilize the original secondary structures and the resulting tertiary structures. For statistical purposes, a set of 163 proteins from the protein databank was randomly selected and a few specific cases are structurally analyzed and characterized in more detail. The results point that about 30% of the residues from each protein, on average, participate in ESS. Alternatively, for the specific cases considered, our results were based on the secondary structures produced after extensive Molecular Dynamics simulation of a protein–aqueous solvent system. Based on the very small width of the time distribution of the root mean squared deviations, between the ESS taken along the simulation and the ESS from the mean structure of the protein, for each ESS, we conclude that the ESSs significantly increase the conformational stability by forming very stable aggregates. The ubiquity and specificity of the ESS suggest that the role they play in the structure of proteins, including the domains formation, deserves to be thoroughly investigated.