Controlling the Substrate Specificity of an Enzyme through Structural Flexibility by Varying the Salt-Bridge Density

Many enzymes, particularly in one single family, with highly conserved structures and folds exhibit rather distinct substrate specificities. The underlying mechanism remains elusive, the resolution of which is of great importance for biochemistry, biophysics, and bioengineering. Here, we performed a neutron scattering experiment and molecular dynamics (MD) simulations on two structurally similar CYP450 proteins; CYP101 primarily catalyzes one type of ligands, then CYP2C9 can catalyze a large range of substrates. We demonstrated that it is the high density of salt bridges in CYP101 that reduces its structural flexibility, which controls the ligand access channel and the fluctuation of the catalytic pocket, thus restricting its selection on substrates. Moreover, we performed MD simulations on 146 different kinds of CYP450 proteins, spanning distinct biological categories including Fungi, Archaea, Bacteria, Protista, Animalia, and Plantae, and found the above mechanism generally valid. We demonstrated that, by fine changes of chemistry (salt-bridge density), the CYP450 superfamily can vary the structural flexibility of its member proteins among different biological categories, and thus differentiate their substrate specificities to meet the specific biological needs. As this mechanism is well-controllable and easy to be implemented, we expect it to be generally applicable in future enzymatic engineering to develop proteins of desired substrate specificities.     

磺胺间甲嘧啶单克隆抗体的制备

研究了磺胺间甲嘧啶单克隆抗体的制备。结果表明,得到三株单抗,其中3F7株抗体效价最高,细胞培养上清为1∶5.2×102,腹水为1∶5.5×105。通过交叉反应试验可知,单抗具有较好的特异性。     

甲氧基有机磷杀虫剂广谱特异性抗体的制备

以通用结构O,O-二甲基硫代磷酸酯为目标检测基团,制备针对甲氧基有机磷杀虫剂的广谱特异性抗体。利用O,O-二甲基硫代磷酸钠和氯乙酸合成半抗原S-羧甲基-O,O-二甲基二硫代磷酸酯(CMP),通过混合酸酐法(MA)和活性酯法(AE)分别与牛血清蛋白(BSA)和卵清蛋白(OVA)偶联。CMP-MA-BSA、CMP-AE-BSA作为免疫原均获得了免疫应答。其中,CMP-AE-BSA所获得的抗血清效价最高,为256000。研究了有机溶剂种类及含量、pH因素对ELISA曲线的影响,确定CMP酶联免疫分析方法(ELISA)的最佳工作条件,CMP的最低检测浓度为0.076μg/L,IC50为93.97μg/L。以14种常见有机磷杀虫剂为对象,检测抗体对其交叉反应,测定结果表明:抗体对马拉硫磷、稻丰散、乐果、亚胺硫磷、倍硫磷、甲基嘧啶磷、甲基对硫磷、杀螟硫磷及杀扑磷等均有识别作用。IC50分别为69.92、136.90、230.39、416.84、508.57、510.38、607.21、835.30和850.21μg/L。该技术可用于多种甲氧基有机磷杀虫剂的快速定性或半定量检测。     

Comparative docking studies on ligand binding to the multispecific antibodies IgE-La2 and IgE-Lb4

Summary A large comparative study is presented in which the binding of approximately 30 different ligands to two IgE antibodies (La2 and Lb4) is analyzed by means of an automated-docking procedure based on simulated annealing. The method is able to reproduce experimentally verified binding orientations, as shown by application to the Ig-AN02-hapten complex. The main address of the study is to investigate the concept of antibody multispecificity. Problems and usefulness of docking in this context are discussed. The results indicate reasons for multispecific binding properties and how they can be understood from the topology of the binding site. Though similar in general behaviour, the two antibodies show interesting differences in their binding characteristics. The binding sites of both antibodies are described and the main interacting residues revealed.     

Characterization of molecular complexity

We put forward a novel index of molecular complexity, ξ, taking into account the symmetry of a molecular graph and the specificity of structural components considered. The ξ index is defined as the sum of augmented valences of all mutually nonequivalent vertices in a molecular graph. The augmented valence of a vertex in a graph is the sum of its valence and valences of all neighboring vertices with the weight 1/2^d depending on their distance, d, from the vertex. The ξ index is examined on the set of octane isomers and some special classes of graphs. It is also compared with a certain number of alternative complexity measures considered in the literature. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003     

Ion-specific swelling behavior of uncharged poly(acrylic acid) gel

The ion-specific swelling behavior of poly(acrylic acid) (PAA) gel prepared by -ray irradiation was investigated as a function of salt concentration in the presence of 0.01 M HCl. The anion specificity for the swelling ratio was similar to that for many kinds of hydrogels, i.e., Cl^–<Br^–<NO₃ ^–<I^–, while the cation specificity proved to be rather unusual, i.e., Mg²⁺<Ca²⁺<Li⁺<Na⁺<K⁺<Cs⁺. In order to find any differences in the hydration of uncharged PAA from that of other polymers having typical polar groups, the hydrogen-bonding hydrations on the relevant polar groups were compared for small molecule analogues with an ab initio molecular orbital calculation. According to the results, the marked deswelling of PAA gel in the presence of strongly hydrated cations was ascribed to the unfavorable hydration to the acidic proton of PAA due to the reduced availability of water oxygen as well as to the destabilization of hydrophobic hydration developing around the uncharged PAA.     

Isolation, Purification, and Properties of α-Amylase from Bacillus subtilis-7A

Cultivation ofBacillus subtilis-7A on waste from alcohol production yielded an active extracellular enzyme -amylase with MW 75 kDa. The enzyme was isolated from the culture medium by 60% saturated ammonium sulfate and purified until homogeneous by gel filtration on Sephadex G-100 and ion-exchange chromatography on DEAE-cellulose. The optimum temperatures for the complex and purified enzyme are 30 and 50°C, respectively. The optimum activity for both preparations occurred at pH 6.5. The substrate specificity of the isolated preparations was studied.     

Ion-specific repulsive interactions in colloidal silica dispersions evidenced through osmotic compression measurements and implication in frontal ultrafiltration experiments

Comparative osmotic compression experiments were performed on colloidal silica dispersions in the presence of various chloride salts at the same 0.01 M concentration with different counterions and highlighted the influence of ionic specificity on the resistance to water removal. These results were complemented with frontal ultrafiltration measurements that demonstrate modulation of the permeate flux according to the salt used.     

分组检测方法综述

分组检测是一种经济且有效的检测算法。它在流行病学、农业及基因组学等领域有着广泛的应用。本文主要从分组检测的起源、发展及其应用着手,着重于介绍分组检测算法中的统计推断方法,并讨论了目前分组检测算法面临的一些问题和挑战。