Determination of the pH dependence,substrate specificity,and turnovers of alternative substrates for human ornithine aminotransferase

Hepatocellular carcinoma (HCC) is the most common primary cancer of the liver and occurs predominantly in patients with underlying chronic liver diseases. Over the past decade, human ornithine aminotransferase (hOAT), which is an enzyme that catalyzes the metabolic conversion of ornithine into an intermediate for proline or glutamate synthesis, has been found to be overexpressed in HCC cells. hOAT has since emerged as a promising target for novel anticancer therapies, especially for the ongoing rational design effort to discover mechanism-based inactivators (MBIs). Despite the significance of hOAT in human metabolism and its clinical potential as a drug target against HCC, there are significant knowledge deficits with regard to its catalytic mechanism and structural characteristics. Ongoing MBI design efforts require in-depth knowledge of the enzyme active site, in particular, pKa values of potential nucleophiles and residues necessary for the molecular recognition of ligands. Here, we conducted a study detailing the fundamental active-site properties of hOAT using stopped-flow spectrophotometry and X-ray crystallography. Our results quantitatively revealed the pH dependence of the multistep reaction mechanism and illuminated the roles of ornithine α-amino and δ-amino groups in substrate recognition and in facilitating catalytic turnover. These findings provided insights of the catalytic mechanism that could benefit the rational design of MBIs against hOAT. In addition, substrate recognition and turnover of several fragment-sized alternative substrates of hOATs, which could serve as structural templates for MBI design, were also elucidated.     

DeepMHADTA: Prediction of Drug-Target Binding Affinity Using Multi-Head Self-Attention and Convolutional Neural Network

Drug-target interactions provide insight into the drug-side effects and drug repositioning. However, wet-lab biochemical experiments are time-consuming and labor-intensive, and are insufficient to meet the pressing demand for drug research and development. With the rapid advancement of deep learning, computational methods are increasingly applied to screen drug-target interactions. Many methods consider this problem as a binary classification task (binding or not), but ignore the quantitative binding affinity. In this paper, we propose a new end-to-end deep learning method called DeepMHADTA, which uses the multi-head self-attention mechanism in a deep residual network to predict drug-target binding affinity. On two benchmark datasets, our method outperformed several current state-of-the-art methods in terms of multiple performance measures, including mean square error (MSE), consistency index (CI), rm2, and PR curve area (AUPR). The results demonstrated that our method achieved better performance in predicting the drug–target binding affinity.     

典型河床底质组成中底栖动物群落及多样性

底栖动物是河流生态系统中食物链的重要环节。通过对长江、黄河、东江和拒马河等河流野外调查和采样分析研究了河床底质组成对底栖动物群落结构的影响规律。研究结果发现,不同河床底质组成中的底栖动物结构差别很大,不同地理位置而相同底质条件和水力条件的河流底栖动物群落组成相似,说明河床底质是影响河流底栖动物群落结构的关键因素,受地理位置和大气候的影响不大;利用多项生物指标分析了不同河床底质组成中底栖动物群落的多样性,卵石河床且有水生植物生长的河流底栖动物物种组成最丰富,大河中沙质河床不稳定,未采集到底栖动物;不同底质类型河床中的优势种群亦不同。并分析了采样所得底栖动物物种数与采样面积之间的关系,符合前者随后者呈幂指数增加的规律,当实测采样面积为1～2m^2时物种数变化不大,建议一般情况下最小采样面积应为1m^2。     

威廉环毛蚯蚓对土壤微生物量及活性的影响

探讨威廉环毛蚯蚓（Ｐｈｅｒｅｔｉｍａ ｇｕｉｌｌｅｌｍｉ）对土壤总微生物量,活性微生物量的影响,蚯蚓处理中（土壤与蚯蚓的比例为５：１,干重：活体重,处理时间为２４ｈ）,用熏蒸提取法测定的土壤总微生物量下降,用底物诱导呼吸法测定的活性微生物量和真菌与细菌比例无显著变化;蚯蚓处理土壤促进了被微生物固持的养分的释放和土壤微生物群体年轻化,增强了微生物的代谢商和纤维素分解活性,结合对文献资料的分析,讨论了     

万古霉素的磁性亲和吸附分离

磁性亲和分离技术是近年新兴的一个分离方法,它可直接从初始样品液体中(无论是浑浊或清亮液)分离目标产物,克服了传统色谱方法需要离心和过滤除杂质的步骤,分离过程所用仪器极其简单,大大降低了操作费用,且易于实现规模化;此外,同亲和色谱一样也具有高的特异性及应用范围广等优点.使其在蛋白质、细胞的分离方面表现出了巨大的应用前景[1-4].万古霉素是一个多肽类的抗菌素,临床上用于治疗耐甲氧苯青霉素葡萄糖球菌的感染.目前虽有多种纯化方法[5,],但大多工艺复杂,回收率较低,尤其是在纯化过程中,万古霉素极易降解,迫使人们寻求更好的纯化方法来解决这个问题.     

Structural basis of substrate specificity in the serine proteases.

Structure-based mutational analysis of serine protease specificity has produced a large database of information useful in addressing biological function and in establishing a basis for targeted design efforts. Critical issues examined include the function of water molecules in providing strength and specificity of binding, the extent to which binding subsites are interdependent, and the roles of polypeptide chain flexibility and distal structural elements in contributing to specificity profiles. The studies also provide a foundation for exploring why specificity modification can be either straightforward or complex, depending on the particular system.     

The Role of Microsite Conditions in Restoring Trembling Aspen (Populus tremuloides Michx) from Seed

Encouraging natural regeneration of Populus tremuloides Michx (trembling aspen) from seed is a largely unexplored means for reintroducing the species into reclamation areas. We evaluated the effects of microsite (surface contour and substrate type) on aspen seedling establishment and growth on a reclaimed coal mine. The 4.6 ha study site was divided into six 48 m‐wide strips that had 15 or 40 cm capping material salvaged from a nearby forest floor added to the mine surface. We surveyed 126 m long transects located in the center of each strip for microsite conditions, and the presence and height of aspen seedlings. We found that aspen seedlings generally preferred mineral‐organic substrates and concave microsites. To facilitate the regeneration of aspen by seed, we suggest that land managers increase small‐scale roughness and microtopographic diversity on reclaimed sites .     

Construction of a dual-tag system for gene expression, protein affinity purification and fusion protein processing

An E. coli vector system was constructed which allows the expression of fusion genes via a l-rhamnose-inducible promotor. The corresponding fusion proteins consist of the maltose-binding protein and a His-tag sequence for affinity purification, the Saccharomyces cerevisiae Smt3 protein for protein processing by proteolytic cleavage and the protein of interest. The Smt3 gene was codon-optimized for expression in E. coli. In a second rhamnose-inducible vector, the S. cerevisiae Ulp1 protease gene for processing Smt3 fusion proteins was fused in the same way to maltose-binding protein and His-tag sequence but without the Smt3 gene. The enhanced green fluorescent protein (eGFP) was used as reporter and protein of interest. Both fusion proteins (MalE-6xHis-Smt3-eGFP and MalE-6xHis-Ulp1) were efficiently produced in E. coli and separately purified by amylose resin. After proteolytic cleavage the products were applied to a Ni-NTA column to remove protease and tags. Pure eGFP protein was obtained in the flow-through of the column in a yield of around 35% of the crude cell extract.     

Targeted tandem affinity purification of PSD‐95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins

The molecular complexity of mammalian proteomes demands new methods for mapping the organization of multiprotein complexes. Here, we combine mouse genetics and proteomics to characterize synapse protein complexes and interaction networks. New tandem affinity purification (TAP) tags were fused to the carboxyl terminus of PSD‐95 using gene targeting in mice. Homozygous mice showed no detectable abnormalities in PSD‐95 expression, subcellular localization or synaptic electrophysiological function. Analysis of multiprotein complexes purified under native conditions by mass spectrometry defined known and new interactors: 118 proteins comprising crucial functional components of synapses, including glutamate receptors, K⁺ channels, scaffolding and signaling proteins, were recovered. Network clustering of protein interactions generated five connected clusters, with two clusters containing all the major ionotropic glutamate receptors and one cluster with voltage‐dependent K⁺ channels. Annotation of clusters with human disease associations revealed that multiple disorders map to the network, with a significant correlation of schizophrenia within the glutamate receptor clusters. This targeted TAP tagging strategy is generally applicable to mammalian proteomics and systems biology approaches to disease.     

用兔红细胞膜制备亲和树脂纯化红芸豆红细胞凝集素的方法

建立运用兔红细胞膜制备亲和树脂来纯化红芸豆中红细胞凝集素的方法。红芸豆经过浸提,(NH4)2SO4沉淀,红细胞膜亲和树脂吸附、洗脱得到红细胞凝集素(PHA-E)试样。采用电泳法测定其纯度、相对分子质量和等电点。用体积分数2%的兔红细胞悬液测定试样凝血活力及影响凝血因素。经PAGE分析PHA-E试样为单带,SDS-PAGE分析显示亚基相对分子质量为3.2×104,等电点为6.5。研究发现,促使50%兔红细胞产生凝集的试样蛋白质最低质量浓度为4μg/mL,单糖不影响PHA-E凝血活力,EDTA抑制其凝血活力,Zn2+促进其凝血。