Statistical analysis on protein-protein interface in crystals： Specific and non-specific interfaces are differentially distributed

The distribution of contact areas, or fractions of contacting, of protein-protein interfaces in crystals of pure polypeptides contains two components: a major exponential distribution and a minor flatter distribution. Suppose the two components belong to specific and non-specific contacts,respectively, then the probability of a contact with a givena rea, or fraction of contacting, can be estimated. By dividing the whole database into two sub-databases, one of them is known to contain more specific contacts than the other, this hypothesis is confirmed and it is also proved that the fraction of contacting is more effective than the contact area on discriminating specific and non-specific contacts in protein crystals.     

Prediction and systematic study of protein-protein interaction networks of Leptospira interrogans

Leptospirosis, a serious and contagious zoonotic bacterial disease that havocs livers and kidneys in hu-mans and some animals, occurs in both urban and rural environments worldwide. It is caused by the genus lep- tospira, a corkscrew-shaped bacterium[1]. Though the genomes of Leptospira interrogans serovars Lai strain lai[2] and Leptospira interrogans serovars Copenhageni strain L1-130[3] were recently sequenced and many molecular and cellular studies on leptospires have been conducted, the …     

自分泌运动因子(ATX)抑制剂结合位点的预测及其与rPAI-1的分子对接

利用复合物指纹的虚拟筛选预测自分泌运动因子(ATX)抑制剂的结合位点,并通过与24个抑制剂(10个脂质和脂基抑制剂,14个小分子抑制剂)分子对接和动力学模拟表明,Thr209,Asp172,Tyr306,Phe210,Leu243,Leu213和Phe274是抑制剂结合位点的重要残基,且这些残基均通过侧链与抑制剂作用.利用3D-partner预测出与ATX结合的蛋白为纤溶酶原激活物抑制剂1(rPAI-1),并通过同源模拟,得到rPAI-1的分子结构.利用软件GRAMM将ATX与rPAI-1分子结构相结合,并通过分子动力学模拟确定与大分子抑制剂rPAI-1作用的ATX重要残基Glu155和Ala158.     

莱茵衣藻腺苷二磷酸葡萄糖焦磷酸化酶的相互作用蛋白组分析

微藻利用光能和CO₂合成淀粉作为藻细胞的储能物质,是以燃料乙醇为代表的液体生物燃料的可持续原料来源.理解微藻淀粉代谢关键酶的催化机制和调控方式是基因工程操作以提高藻细胞淀粉积累能力的前提. 基于此,以莱茵衣藻淀粉合成代谢中的关键酶腺苷二磷酸葡萄糖焦磷酸化酶(AGPase)催化亚基为探针蛋白,获取该酶的GST融合蛋白后使用GST沉降分析实验结合HPLC-MS/MS的蛋白质检测技术及生物信息学分析方法获得一组与AGPase催化亚基存在相互作用蛋白质,主要包含分子伴侣蛋白、光合作用相关蛋白和信号蛋白分子等. 通过综合分析上述蛋白组的生理功能及亚细胞定位,揭示了它们通过与AGPase相互作用在淀粉合成代谢中的生物学意义.      

基于疏肝解郁功效的逍遥散寒苦肝和温辛肝性效关系研究

为探讨逍遥散中疏肝解郁中药的寒温差异与其功效的内在联系,通过数据库检索获取寒苦肝和温辛肝药性的主要有效成分及作用靶点,基于STRING平台构建蛋白质-蛋白质相互作用网络,采用Metascape对识别出的药性组合蛋白质-蛋白质相互作用网络进行京都基因与基因组百科全书通路注释和统计分析。结果表明:逍遥散中归肝经药性主要通过HTR2B等靶点参与神经递质、信号通路、内分泌发挥疏肝解郁的功效特点;逍遥散中寒苦药性主要通过CREBRF等靶点参与能量代谢、炎症反应发挥疏肝解郁的功效特点;逍遥散中温辛组合药性主要通过ADCY5等靶点参与炎症反应神经营养、氨基酸代谢发挥疏肝解郁的功效特点。该研究从分子网络水平阐释了逍遥散中归肝经药性的共性特征和寒苦药性、温辛药性的特异性特征,为逍遥散的药性与功效的内在联系研究提供了新思路和新方法。