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.     

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.     

Communication network formation with link specificity and value transferability

We model strategic communication network formation with (i) link specificity: link maintenance lowers specific attention and thus value (negative externality previously ignored for communication) and (ii) value transferability via indirect links for informational but not for social value (positive externality modeled uniformly before). Assuming only social value, the pairwise stable set includes many nonstandard networks under high and particular combinations of complete components under low link specificity. Allowing for social and informational value reduces this set to certain fragmented networks under high and the complete network under low link specificity. These extremes are efficient, whereas intermediate link specificity generates inefficiency.     

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。     

Sequence‐Specific DNA Alkylation Targeting for Kras Codon 13 Mutation by Pyrrole–Imidazole Polyamide seco‐CBI Conjugates

Hairpin N‐methylpyrrole‐N‐methylimidazole polyamide seco‐CBI conjugates 2 – 6 were designed for synthesis by Fmoc solid‐phase synthesis, and their DNA‐alkylating activities against the Kras codon 13 mutation were compared by high‐resolution denaturing gel electrophoresis with 225 base pair (bp) DNA fragments. Conjugate 5 had high reactivity towards the Kras codon 13 mutation site, with alkylation occurring at the A of the sequence 5′‐ACGTCACC A ‐3′ (site 2), including minor 1 bp‐mismatch alkylation against wild type 5′‐ACG C CACC A ‐3′ (site 3). Conjugate 6 , which differs from conjugate 5 by exchanging one Py unit with a β unit, showed high selectivity but only weakly alkylated the A of 5′‐ACGTCACC A ‐3′ (site 2). The hairpin polyamide seco‐CBI conjugate 5 thus alkylates according to Dervan′s pairing rule with the pairing recognition which β/β pair targets T–A and A–T pairs. SPR and a computer‐minimized model suggest that 5 binds to the target sequence with high affinity in a hairpin conformation, allowing for efficient DNA alkylation.     

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.     

Broad specificity indirect competitive immunoassay for determination of nitrofurans in animal feeds

A generic hapten of nitrofurans was synthesized by derivatization of 5-nitrofurfural with diamine, and the hapten was coupled to carrier protein to prepare different immunogens and coating antigens by using diazotization method and glutaraldehyde method. The obtained novel polyclonal antibodies from immunized rabbits showed broad cross reactivity among seven nitrofurans. After assessment of four coating antigen/antibody combinations, an indirect competitive immunoassay was developed to simultaneously detect the seven nitrofurans in animal feeds. The limits of detection for these analytes were in the range of 5-16 μg kg⁻¹ depending on the compound. Recoveries from nitrofurans fortified blank feeds at levels of 30 and 100 ng g ⁻¹ were in a range of 82.6-108.4% with coefficients of variation lower than 11.4%. The immunoassay was further validated by a HPLC method and the two methods showed good correlation (r = 0.9924). Therefore, the proposed immunoassay could be used as a practical method to monitor the illicit use of nitrofurans in animal feeds.     

Effect of single active-site cleft mutation on product specificity in a thermostable bacterial cellulase

Mutation of a single active-site cleft tyrosyl residue to a glycyl residue significantly changes the mixture of products released from phosphoric acidswollen cellulose (PSC) by EIcd, the catalytic domain of the endoglucanase-I from Acidothermus cellulolyticus. The percentage of glucose in the product stream is almost 40% greater for the Y245G mutant (and for an additional double mutant, Y245G/Q204A) than for the wild type enzyme. Comparisons of results for digestion PSC and of pretreated yellow poplar suggest that the observed shifts in product specificity are connected to the hydrolysis of a more easily digestible fraction of both substrates. A model is presented that relates the changes in product specificity to a mutation-driven shift in indexing of the polymeric substrate along the extended binding-site cleft.