运动后尿液蛋白质分子量与等电点的变化特征

通过对９名男性受试者在分别完成１００－２００ｍ,４００－８００ｍ和１ ５００－３ ０００ｍ跑步间歇训练后尿蛋白分子量和等电点的测定发现：①运动时尿液高、低分子量蛋白质排泄率均较运动前明显增加,但以高分子量蛋白质排泄为主;②运动时尿液高、低分子量蛋白质排泄率均以４００－８００ｍ间歇训练时最高,１００－２００ｍ间歇训练时次之,１ ５００－３ ０００ｍ间歇训练时最低;③运动时尿液排出的蛋白质以负离子为主     

Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking

Protein-protein association can frequently involve significant backbone conformational changes of the protein partners. A computationally rapid method has been developed that allows to approximately account for global conformational changes during systematic protein-protein docking starting from many thousands of start configurations. The approach employs precalculated collective degrees of freedom as additional variables during protein-protein docking minimization. The global collective degrees of freedom are obtained from normal mode analysis using a Gaussian network model for the protein. Systematic docking searches were performed on 10 test systems that differed in the degree of conformational change associated with complex formation and in the degree of overlap between observed conformational changes and precalculated flexible degrees of freedom. The results indicate that in case of docking searches that minimize the influence of local side chain conformational changes inclusion of global flexibility can significantly improve the agreement of the near-native docking solutions with the corresponding experimental structures. For docking of unbound protein partners in several cases an improved ranking of near native docking solutions was observed. This was achieved at a very modest ( approximately 2-fold) increase of computational demands compared to rigid docking. For several test cases the number of docking solutions close to experiment was also significantly enhanced upon inclusion of soft collective degrees of freedom. This result indicates that inclusion of global flexibility can facilitate in silico protein-protein association such that a greater number of different start configurations results in favorable complex formation.     

产碱杆菌Alcaligenes sp.KS-85来源肌酸酶活性中心的关键氨基酸功能研究

肌酸酶(Creatinase,EC 3.5.3.3)水解肌酸生成尿素和肌氨酸,是肌酐多酶级联检测中的关键酶.为进一步解析产碱杆菌来源肌酸酶的催化机理,利用蛋白质同源建模、分子对接、丙氨酸扫描技术分析了酶与底物的相互作用,并聚焦于酶活性中心4个功能未知的保守位点Phe64、Asp102、Phe252、Phe321,通过将...     

Plant‐based oral vaccines against zoonotic and non‐zoonotic diseases

The shared diseases between animals and humans are known as zoonotic diseases and spread infectious diseases among humans. Zoonotic diseases are not only a major burden to livestock industry but also threaten humans accounting for >60% cases of human illness. About 75% of emerging infectious diseases in humans have been reported to originate from zoonotic pathogens. Because antibiotics are frequently used to protect livestock from bacterial diseases, the development of antibiotic‐resistant strains of epidemic and zoonotic pathogens is now a major concern. Live attenuated and killed vaccines are the only option to control these infectious diseases and this approach has been used since 1890. However, major problems with this approach include high cost and injectable vaccines is impractical for >20 billion poultry animals or fish in aquaculture. Plants offer an attractive and affordable platform for vaccines against animal diseases because of their low cost, and they are free of attenuated pathogens and cold chain requirement. Therefore, several plant‐based vaccines against human and animals diseases have been developed recently that undergo clinical and regulatory approval. Plant‐based vaccines serve as ideal booster vaccines that could eliminate multiple boosters of attenuated bacteria or viruses, but requirement of injectable priming with adjuvant is a current limitation. So, new approaches like oral vaccines are needed to overcome this challenge. In this review, we discuss the progress made in plant‐based vaccines against zoonotic or other animal diseases and future challenges in advancing this field.     

Coarse-grained molecular dynamics simulation of interactions between cyclic lipopeptide Bacillomycin D and cell membranes

According to experimental studies, Bacillomycin D has strong antimicrobial activities, but the antimicrobial mechanism is still unknown. In this paper, the interaction mechanisms between this cyclic lipopeptide and three different charged cell membranes are studied via Coarse-Grained Molecular Dynamics (CG MD) simulations. A specific CG model for the cyclic lipopeptide Bacillomycin D was developed. The insertion of cyclic lipopeptide Bacillomycin D into DOPC, DOPC/DPPA and DOPC/DOTAP cell membranes was investigated. The position distribution and stability of Bacillomycin D in the three different cell membranes were analysed and compared based on density profile calculations. Additionally, we focused on the Radial Distribution Function (RDF) curves between amino acid residues with negative charges or strong hydrophobic properties and the head groups of two different cell membranes. Based on changes in the curvature of the three membranes, the cyclic lipopeptide Bacillomycin D can cause localised surface protrusions in DOPC/DOTAP membranes, inward depressions in the surface of DOPC/DPPA membranes and inhibition deformation in the surface of DOPC membranes. This study will help to further understand the antibacterial mechanism of the cyclic lipopeptide Bacillomycin D and provide a basis for the development of new antibiotics.     

Serial increase in the thermal stability of 3-isopropylmalate dehydrogenase from Bacillus subtilis by experimental evolution.

We improved the thermal stability of 3-isopropylmalate dehydrogenase from Bacillus subtilis by an in vivo evolutionary technique using an extreme thermophile, Thermus thermophilus, as a host cell. The leuB gene encoding B. subtilis 3-isopropylmalate dehydrogenase was integrated into the chromosome of a leuB-deficient strain of T. thermophilus. The resulting transformant showed a leucine-autotrophy at 56 degrees C but not at 61 degrees C and above. Phenotypically thermostabilized strains that can grow at 61 degrees C without leucine were isolated from spontaneous mutants. Screening temperature was stepwise increased from 61 to 66 and then to 70 degrees C and mutants that showed a leucine-autotrophic growth at 70 degrees C were obtained. DNA sequence analyses of the leuB genes from the mutant strains revealed three stepwise amino acid replacements, threonine-308 to isoleucine, isoleucine-95 to leucine, and methionine-292 to isoleucine. The mutant enzymes with these amino acid replacements were more stable against heat treatment than the wild-type enzyme. Furthermore, the triple-mutant enzyme showed significantly higher specific activity than that of the wild-type enzyme.     

period基因的Thr—Gly区段在果蝇和部分双翅目昆虫中的分子进化特征

以亲缘关系极近的近缘种类群、中等距离的远缘种类群为对象,分析生物钟基因period的Thr-Gly区段的分子进化特征,发现Thr-Gly区段在果蝇和部分双翅目昆虫中未曾经历性选择和其他定向的正选择。Thr-Gly区段在果蝇nasuta亚群中的分子进化速率为10.4×10     

Bioactive conformations of two seminal delta opioid receptor penta‐peptides inferred from free‐energy profiles

Delta‐opioid (DOP) receptors are members of the G protein‐coupled receptor (GPCR) sub‐family of opioid receptors, and are evolutionarily related, with homology exceeding 70%, to cognate mu‐opioid (MOP), kappa‐opioid (KOP), and nociceptin opioid (NOP) receptors. DOP receptors are considered attractive drug targets for pain management because agonists at these receptors are reported to exhibit strong antinociceptive activity with relatively few side effects. Among the most potent analgesics targeting the DOP receptor are the linear and cyclic enkephalin analogs known as DADLE (Tyr‐D ‐Ala‐Gly‐Phe‐D ‐Leu) and DPDPE (Tyr‐D ‐Pen‐Gly‐Phe‐D ‐Pen), respectively. Several computational and experimental studies have been carried out over the years to characterize the conformational profile of these penta‐peptides with the ultimate goal of designing potent peptidomimetic agonists for the DOP receptor. The computational studies published to date, however, have investigated only a limited range of timescales and used over‐simplified representations of the solvent environment. We provide here a thorough exploration of the conformational space of DADLE and DPDPE in an explicit solvent, using microsecond‐scale molecular dynamics and bias‐exchange metadynamics simulations. Free‐energy profiles derived from these simulations point to a small number of DADLE and DPDPE conformational minima in solution, which are separated by relatively small energy barriers. Candidate bioactive forms of these peptides are selected from identified common spatial arrangements of key pharmacophoric points within all sampled conformations. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 21–27, 2014.     

微阵列（microarrays）技术及其应用

微阵列分为cDNA微阵列和寡聚核苷酸微阵列,微阵列上“印”有大量已知部分序列的DNA探针,微阵列技术就是利用分子杂交原理,使同时被比较的标本（用同位素或荧光素标记）与微阵列杂交,通过检测杂交信号强度及数据处理,把他们转化成不同标本中特异基因的丰度,从而全国比较不同标本的基因表达水平的差异,微阵列技术是一种探索基因组功能的有力手段。