New approaches to high-throughput structure characterization of SH3 complexes: the example of Myosin-3 and Myosin-5 SH3 domains from S. cerevisiae

SH3 domains are small protein modules that are involved in protein-protein interactions in several essential metabolic pathways. The availability of the complete genome and the limited number of clearly identifiable SH3 domains make the yeast Saccharomyces cerevisae an ideal proteomic-based model system to investigate the structural rules dictating the SH3-mediated protein interactions and to develop new tools to assist these studies. In the present work, we have determined the solution structure of the SH3 domain from Myo3 and modeled by homology that of the highly homologous Myo5, two myosins implicated in actin polymerization. We have then implemented an integrated approach that makes use of experimental and computational methods to characterize their binding properties. While accommodating their targets in the classical groove, the two domains have selectivity in both orientation and sequence specificity of the target peptides. From our study, we propose a consensus sequence that may provide a useful guideline to identify new natural partners and suggest a strategy of more general applicability that may be of use in other structural proteomic studies.     

Optimum allocation of conservation funds and choice of conservation programs for a set of African cattle breeds

Although funds for livestock conservation are limited there is little known about the optimal allocation of conservation funds. A new algorithm was used to allocate Mio US$ 1, 2, 3, 5 or unlimited funds, discounted over 50 years, on 23 African cattle breeds conserved with four different possible conservation programs. Additionally, Mio US$ 1 was preferably allocated to breeds with special traits. The conceptional in situ conservation programs strongly involve breeders and give them part of the responsibility for the conservation of the breed. Therefore, the pure in situ conservation was more efficient than cryoconservation or combined in situ and cryoconservation. The average annual discounted conservation cost for a breed can be as low as US$ 1000 to US$ 4400 depending on the design of the conservation program and the economic situation of the country of conservation. The choice of the breeds and the optimal conservation program and the amount of money allocated to each breed depend on many factors such as the amount of funds available, the conservation potential of each breed, the effects of the conservation program as well as its cost. With Mio US$ 1, 64% of the present diversity could be maintained over 50 years, which is 13% more than would be maintained if no conservation measures were implemented. Special traits could be conserved with a rather small amount of the total funds. Diversity can not be conserved completely, not even with unlimited funds. A maximum of 92% of the present diversity could be conserved with Mio US$ 10, leaving 8% of the diversity to unpredictable happenings. The suggested algorithm proved to be useful for optimal allocation of conservation funds. It allocated the funds optimally among breeds by identifying the most suited conservation program for each breed, also accounting for differences in currency exchange rates between the different countries.     

Characterization of a membrane protein folding motif, the Ser zipper, using designed peptides

Polar residues play important roles in the association of transmembrane helices and the stabilities of membrane proteins. Although a single Ser residue in a transmembrane helix is unable to mediate a strong association of the helices, the cooperative interactions of two or more appropriately placed serine hydroxyl groups per helix has been hypothesized to allow formation of a "serine zipper" that can stabilize transmembrane helix association. In particular, a heptad repeat Sera Xxx Xxx Leud Xxx Xxx Xxx (Xxx is a hydrophobic amino acid) appears in both antiparallel helical pairs of polytopic membrane proteins as well as the parallel helical dimerization motif found in the murine erythropoietin receptor. To examine the intrinsic conformational preferences of this motif independent of its context within a larger protein, we synthesized a peptide containing three copies of a SeraLeud heptad motif. Computational results are consistent with the designed peptide adopting either a parallel or antiparallel structure, and conformational search calculations yield the parallel dimer as the lowest energy configuration, which is also significantly more stable than the parallel trimer. Analytical ultracentrifugation indicated that the peptide exists in a monomer-dimer equilibrium in dodecylphosphocholine micelles. Thiol disulfide interchange studies showed a preference for forming parallel dimers in micelles. In phospholipid vesicles, only the parallel dimer was formed. The stability of the SerZip peptide was studied in vesicles prepared from phosphatidylcholine (PC) lipids of different chain length: POPC (C16:0C18:1 PC) and DLPC (C12:0PC). The stability was greater in POPC, which has a good match between the length of the hydrophobic region of the peptide and the bilayer length. Finally, mutation to Ala of the Ser residues in the SerZip motif gave rise to a relatively small decrease in the stability of the dimer, indicating that packing interactions rather than hydrogen-bonding provided the primary driving force for association.     

石榴籽油的微波提取和体外抗氧化作用研究

比较常规回流提取与微波提取法对石榴籽油的提取率,并采用正交实验法优选微波提取最佳工艺条件。结果表明,出油率有显著性差异(P<0.01),微波提取出油率高,其提取最佳工艺条件为:物液比为1:5(g:mL),微波处理时间为50s×5(即每次处理50s,间歇处理5次),微波功率为480w。用Schaal烘箱法(60±1℃)比较了石榴籽油和维生素E抗猪油和色拉油氧化的作用,石榴籽油的体外抗氧化作用优于维生素E,具有很好的应用前景。     

欧亚旋覆花总黄酮提取与富集工艺研究

为研究欧亚旋覆花总黄酮的最佳提取与大孔吸附树脂富集工艺,采用不同溶剂、多种提取方法、L9(34)正交实验优化及AB-8大孔吸附树脂富集,结果表明其最佳提取工艺为用10倍量水为溶剂回流提取3次,每次1h,再结合AB-8大孔吸附树脂富集,以70%乙醇洗脱效果最佳,总黄酮回收率达90%,总黄酮含量达50%以上。此工艺简便可行,符合工业化生产要求。     

锁阳多糖提取工艺的研究

以浸膏得率和浸膏中多糖质量分数综合评价,利用L9(34)正交实验从水提和醇沉两方面优选锁阳中水溶性多糖最佳提取工艺条件,为锁阳活性多糖的开发提供科学依据和实验基础。最佳水提工艺条件为:m(锁阳):v(水)=1:12,回流提取0.5 h,提取2次;最佳醇沉工艺条件为:在m(生药):v(水提液)=1 g:2 mL溶液中加入乙醇,使φ(乙醇)=70%,静置6 h。     

对Logistic增长的SIS模型实现反馈线性化和极点配置的一步设计

非线性系统极点配置状态反馈调节器的常用方法为两步设计,而且要求必须满足对合条件,对于一个高于二阶的实际系统很难满足这些严格的条件,精确线性化和极点配置一步设计的方法避免了严格的对合条件,本文将这种方法运用在非线性微分代数系统中,并将此法应用到生物系统上．     

平板式光生物反应器中紫球藻培养条件的优化

研究了平板式光生物反应器中紫球藻(Porphyridium cruentumNaegeli)的培养条件,运用均匀设计法对光照强度、通气速率、装液量、接种密度以及pH等影响紫球藻生长的因素进行优化,获得了在平板式光生物反应器中培养紫球藻的最佳条件:光照强度10 000 lx、通气速率350 L.h-1、装液量6 L、藻细胞接种密度1.1×106mL-1、pH9.0。在最佳条件下藻体的生物量产率和生物量产量分别达到0.431 g.L-1.d-1和3.240 g.L-1,最大生长速率达0.652 g.L-1.d-1,胞外多糖含量高达0.665 g.L-1。另外,在培养过程中隔天补充培养液有利于紫球藻生物量的增加和胞外多糖的产生。     

均匀设计法优化黄芩愈伤组织培养基

目的:优化黄芩愈伤组织培养条件。方法:采用均匀设计法,以黄芩甙含量为主要考察指标,对黄芩愈伤组织生长的MS培养基成分进行多因素多水平考察。结果:最佳培养基为MS附加0.25mg/L NAA、0.5mg/L 6-BA、17g/L葡萄糖和35g/L蔗糖。最佳培养基黄芩甙含量为27.44mg/gDW。结论:用均匀设计法优化愈伤组织培养基省时、方便,且最佳培养基黄芩甙含量与预测值相近,且明显高于均匀设计实验方案中的黄芩甙含量。经SAS软件分析得出的优化方程拟合度很好。     

醉马草毒性成分的提取研究

目的:为研究醉马草有毒成分的种类、特性及提取方法,达到最终纯化出有毒成分的目的。方法:结合系统预试验、全紫外波段扫描、多种方法对比提取效率、毒理实验等各种实验方法系统的对醉马草进行了研究。结果:醉马草含有生物碱、黄酮等多种成分,其中毒性成分主要是亲水部位的生物碱,中毒小白鼠表现为心跳呼吸加速、流泪、四肢无力嗜睡等症状,在醉马草整个生长期中,苗期所含总生物碱量最大,总生物碱在紫外波长为196nm、274nm和340nm有吸收峰,三种提取方法中乙醇煎煮法比较实用,正交实验法确定最佳提取工艺为80℃、50%的乙醇30倍体积下温育3h。