Analysis of conformational motions and related key residue interactions responsible for a specific function of proteins with elastic network model

Protein collective motions play a critical role in many biochemical processes. How to predict the functional motions and the related key residue interactions in proteins is important for our understanding in the mechanism of the biochemical processes. Normal mode analysis (NMA) of the elastic network model (ENM) is one of the effective approaches to investigate the structure-encoded motions in proteins. However, the motion modes revealed by the conventional NMA approach do not necessarily correspond to a specific function of protein. In the present work, a new analysis method was proposed to identify the motion modes responsible for a specific function of proteins and then predict the key residue interactions involved in the functional motions by using a perturbation approach. In our method, an internal coordinate that accounts for the specific function was introduced, and the Cartesian coordinate space was transformed into the internal/Cartesian space by using linear approximation, where the introduced internal coordinate serves as one of the axes of the coordinate space. NMA of ENM in this internal/Cartesian space was performed and the function-relevant motion modes were identified according to their contributions to the specific function of proteins. Then the key residue interactions important for the functional motions of the protein were predicted as the interactions whose perturbation largely influences the fluctuation along the internal coordinate. Using our proposed methods, the maltose transporter (MalFGK₂) from E. Coli was studied. The functional motions and the key residue interactions that are related to the channel-gating function of this protein were successfully identified.     

Protein factors that bind to the murine 2',5'-oligoadenylate synthetase ME-12 gene 5' upstream regulatory region

The murine 2',5'-oligoadenylate synthetase ME-12 gene regulatory region AB forms six complexes with protein factors in murine BALB/c 3T3 cells as demonstrated by the mobility shift electrophoresis assay under the reaction conditions used. The complexes, designated C1-C6 in order of their decreasing electrophoretic mobility, showed three distinctive specificities with regulatory region AB, element A, and element B as probes or competing DNA: 1) C1 is region AB-specific (this complex did not form with either element A or B used alone or as a mixture); 2) C5 formed both with element A and element B; 3) C2, C3, C4, and C6 formed with element B, but not A. The protein factors that give rise to these complexes show differential DNA binding activities in various buffer solutions at different pH values. The C4-forming protein factor is the interferon (IFN)-alpha/beta-stimulated response factor (ISRF) which shows element B specificity. It preexists in the cytoplasm. ISRF appears to be complexed to an inhibitor (ISRFI) in the cytoplasm and to dissociate from the inhibitor and to translocate into the nucleus upon treatment of cells with IFN-alpha/beta. We propose that IFN-alpha/beta treatment of BALB/c 3T3 can trigger at least two events: 1) loosening of a tight inhibitor-ISRF complex with the release of free ISRF; this may be mediated via phosphorylation of ISRF or ISRFI; 2) translocation of ISRF into the nucleus and binding to the enhancer element B, which results in the activation of 2',5'-oligoadenylate synthetase gene expression.     

转基因大豆MON89788芯片式数字PCR定量方法的建立

针对抗虫耐除草剂大豆转基因品系MON89788,从转基因植物基因组DNA的提取、核酸模板的质量和浓度控制、引物探针的筛选、PCR反应过程的建立等方面建立了一套完整的转基因大豆芯片式dPCR定量检测方法。本实验也对该方法的重复性和定量检测限进行考察。10组5%转基因品系大豆MON89788样品定量重复性RSD在1.17%-9.97%之间,均满足国际上转基因定量结果RSD小于25%的要求。用该方法对转基因含量为5%、1%、0.1%的大豆MON89788进行定量检测,其定量结果为5.20%、0.94%和0.11%,RSD分别为6.2%、3.6%和15.2%。该检测方法的定量限达到0.1%,能满足欧盟对转基因定量标识0.9%的要求。将本实验建立的方法用于转基因大豆的定量检测,能为规范我国转基因监管工作的实施提供强有力的技术支撑。     

Monkeys pass the mirror test after training

<正>There is no experiencing without an experiencer,the self.Whether the experiencer knows it is"the self"that is experiencing is a different and tricky philosophical issue.Dating back to Ivan Pavlov’s dogs,the"experience"of animals has     

Foliar Spray with 24-Epibrassinolide Enhanced Strawberry Fruit Quality,Phytochemical Content,and Postharvest Life

Journal of Plant Growth Regulation - Activation of complex metabolic pathways and antioxidant activities is necessary for enhancing quality and health promoting capacity of food crops. Plant growth...     

Biomimetic Approaches to Functional Surfaces, Surface Wetting and Fluids Drag Reduction

In the natural world,plants and animals haveevolved over time to best adapt to the environment.Theyinteract very effectively with the surrounding environmentby exchanging energies and mass flow across theircuticles of specific micro structures and functions toachieve perfect energy balance.Such different functionsmay include the limitation of uncontrolled loss of water,protection from solar radiation,micro effect of inducedturbulence on flow drag reduction,defence againstpathogens,changing surface wettability and hydropho-     

Soluble expression and purification of Brucella cell surface protein (BCSP31) of Brucella melitensis and preparation of anti-BCSP31 monoclonal antibodies

Brucella cell surface protein (BCSP31) is potentially useful for diagnosing brucellosis. We aimed to establish a monoclonal antibody (MAb) against Brucella melitensis BCSP31 and to investigate its distribution in diagnosis. Soluble recombinant BCSP31 was successfully expressed and purified. Two MAbs (1F1 and 1E5) against B. melitensis BCSP31, effective in detecting both recombinant and cellular proteins, were obtained and characterized. The MAbs did not react with Escherichia coli, Staphylococcus aureus, Bacillus subtilis, Mycobacterium tuberculosis, or Bacillus aeruginosus, but strongly reacted with BCSP31 and B. melitensis by ELISA and Western blot analysis. We also tested different Brucella species and brucellosis using the prepared anti-BCSP31 MAbs. BCSP31 and anti-BCSP31 MAbs may play important roles in future research in diagnosing brucellosis.