Autocatalytic Sets and Biological Specificity

A universal feature of the biochemistry of any living system is that all the molecules and catalysts that are required for reactions of the system can be built up from an available food source by repeated application of reactions from within that system. RAF (reflexively autocatalytic and food-generated) theory provides a formal way to study such processes. Beginning with Kauffman’s notion of “collectively autocatalytic sets,” this theory has been further developed over the last decade with the discovery of efficient algorithms and new mathematical analysis. In this paper, we study how the behaviour of a simple binary polymer model can be extended to models where the pattern of catalysis more precisely reflects the ligation and cleavage reactions involved. We find that certain properties of these models are similar to, and can be accurately predicted from, the simple binary polymer model; however, other properties lead to slightly different estimates. We also establish a number of new results concerning the structure of RAFs in these systems.     

Dermorphins are Natural Opioids with an Unique Primary Structure That Determines Their Biological Specificity

Based on the authors" and published data, the spectrum of biological activities of dermorphins was theoretically analyzed for the first time from the viewpoint of specific structural features of their molecule that determine selective affinity to -opiate receptors. It was shown that specific distribution of dermorphins and corresponding opiate receptors in tissues and organs, especially in the CNS structures, determines the role of dermorphins in the regulation of functions of the most important physiological systems.     

Mutational Tuning of Galectin-3 Specificity and Biological Function

Galectins are defined by a conserved β-galactoside binding site that has been linked to many of their important functions in e.g. cell adhesion, signaling, and intracellular trafficking. Weak adjacent sites may enhance or decrease affinity for natural β-galactoside-containing glycoconjugates, but little is known about the biological role of this modulation of affinity (fine specificity). We have now produced 10 mutants of human galectin-3, with changes in these adjacent sites that have altered carbohydrate-binding fine specificity but that retain the basic β-galactoside binding activity as shown by glycan-array binding and a solution-based fluorescence anisotropy assay. Each mutant was also tested in two biological assays to provide a correlation between fine specificity and function. Galectin-3 R186S, which has selectively lost affinity for LacNAc, a disaccharide moiety commonly found on glycoprotein glycans, has lost the ability to activate neutrophil leukocytes and intracellular targeting into vesicles. K176L has increased affinity for β-galactosides substituted with GlcNAcβ1–3, as found in poly-N-acetyllactosaminoglycans, and increased potency to activate neutrophil leukocytes even though it has lost other aspects of galectin-3 fine specificity. G182A has altered carbohydrate-binding fine specificity and altered intracellular targeting into vesicles, a possible link to the intracellular galectin-3-mediated anti-apoptotic effect known to be lost by this mutant. Finally, the mutants have helped to define the differences in fine specificity shown by Xenopus, mouse, and human galectin-3 and, as such, the evidence for adaptive change during evolution.     

Cell Specificity of Molecular Changes During Memory Storage

Abstract: The aeolid nudibranch, Hermissenda crassicornis , exhibits Pavlovian conditioning to paired light and rotational stimuli and it has been suggested that protein kinase C (PKC) may play a critical role in the cellular mechanism for this conditioned behavioral response in the B-cell photoreceptor. The present study was designed to further examine learning-specific PKC involvement in identified cellular areas, particularly those in the visual-vestibular network, of the Hermissenda nervous system after Pavlovian conditioning. As used in previous vertebrate studies, the highly specific PKC radioligand, [³H]phorbol-12,13-dibutyrate ([³H]-PDBU), was used to determine the binding characteristics of the molluscan protein receptor considered to be PKC. The binding was specific, saturable, and could be displaced by a soluble diacylglycerol analogue. The binding activity was distributed evenly between the cytosol and the membrane. All of these analyses suggest that [³H]PDBU binds primarily to PKC in Hermissenda as it does in many other systems. Computerized grain image analysis was then used to determine the cellular localization of PKC as a function of Pavlovian conditioning. The medial and intermediate B photoreceptor and the optic ganglion showed significantly increased [³H]PDBU binding in conditioned animals. The present results provide the first report of an associative learning change of a key signal transduction component in identified neurons.     

噬藻体的分子生物学研究进展

噬藻体是一种侵染原核藻类的病毒,可能是控制蓝藻水华生消的重要生态因子,在自然水体中大量存在.随着分子生物学和遗传学技术的不断发展,噬藻体的不断分离和发现,水生生态系统的研究内容更加丰富.对近年来国内外有关噬藻体分子生物学、遗传标记和分子生物学检测等方面的最新研究进展作了综述,并对今后研究工作进行了展望.     

转基因的分子生物学特性

现代分子生物学研究中,转基因概念的出现越来越频繁,它渐渐被用来表示所有的用基因工程手段构建、导入高等真核生物细胞,并稳定地整合入受体基因组的外源DNA．文章较系统地总结了已见报道的转基因的结构类型、它在受体细胞内的遗传学行为、表达特性和影响因素及其相应的生物学效应;分析了转基因研究中尚待研究的问题,提出了系统地进行转基因本身的分子生物学特性研究的必要性.     

肾上腺髓质素的分子特征及生物学功能

1993年日本学者Ｋｉｔａｍｕｒａ等首次从人的嗜铬细胞瘤(ｐｈｅｏｃｈｒｏｍｏｃｙｔｏｍａ,ＰＣ)组织中分离出一种新的活性多肽,它具有舒张体循环和肺循环的血管、明显降低血压的作用,称为肾上腺髓质素(ａｄｒｅｎｏｍｅｄｕｌｌｉｎ,ＡＤＭ)。ＡＤＭ广泛分布于机体多种组织如肾上腺髓质、肺、肾、脾、小肠、心肌、大脑皮质中,其中尤以肾上腺髓质含量最高,约为150±24ｐｍｏｌ/ｇ湿组织。血浆中ＡＤＭ的浓度约为收稿日期:19991228作者简介:朱赓伯(1934—),男,教授。9±5.4ｆｍｏｌ/Ｌ,它主要来自肺和血管内皮细胞。目前认为ＡＤＭ是一种参…     

Molecular Determinants of Substrate Specificity in Sodium-coupled Glutamate Transporters

Crystal structures of the archaeal homologue Glt_Ph have provided important insights into the molecular mechanism of transport of the excitatory neurotransmitter glutamate. Whereas mammalian glutamate transporters can translocate both glutamate and aspartate, Glt_Ph is only one capable of aspartate transport. Most of the amino acid residues that surround the aspartate substrate in the binding pocket of Glt_Ph are highly conserved. However, in the brain transporters, Thr-352 and Met-362 of the reentrant hairpin loop 2 are replaced by the smaller Ala and Thr, respectively. Therefore, we have studied the effects of T352A and M362T on binding and transport of aspartate and glutamate by Glt_Ph. Substrate-dependent intrinsic fluorescence changes were monitored in transporter constructs containing the L130W mutation. Glt_Ph-L130W/T352A exhibited an ∼15-fold higher apparent affinity for l-glutamate than the wild type transporter, and the M362T mutation resulted in an increased affinity of ∼40-fold. An even larger increase of the apparent affinity for l-glutamate, around 130-fold higher than that of wild type, was observed with the T352A/M362T double mutant. Radioactive uptake experiments show that Glt_Ph-T352A not only transports aspartate but also l-glutamate. Remarkably, Glt_Ph-M362T exhibited l-aspartate but not l-glutamate transport. The double mutant retained the ability to transport l-glutamate, but its kinetic parameters were very similar to those of Glt_Ph-T352A alone. The differential impact of mutation on binding and transport of glutamate suggests that hairpin loop 2 not only plays a role in the selection of the substrate but also in its translocation.     

细胞珠蛋白的结构及其生物学效应

细胞珠蛋白(cytoglobin,Cygb)是最近发现的脊椎动物珠蛋白超家族的一员,在体内分布广泛。人Cygb基因定位于染色体17q25,含有4个外显子和3个内含子,编码190个氨基酸残基(分子量20.9kD)。Cygb拥有经典的“three-over-three”α螺旋三明治折叠结构,同神经珠蛋白(Ngb)一样,Cygb血红素在缺乏外源性配体时呈“六配位”结构。Cygb的确切功能尚不十分清楚,目前主要有携氧与储氧、氧感受器、活性氧基团和NO的清道夫、NADH氧化酶或过氧化氢酶样作用和参与胶原形成等假说。     

Crystal Structure and Substrate Specificity of Drosophila 3,4-Dihydroxyphenylalanine Decarboxylase

Background

3,4-Dihydroxyphenylalanine decarboxylase (DDC), also known as aromatic L-amino acid decarboxylase, catalyzes the decarboxylation of a number of aromatic L-amino acids. Physiologically, DDC is responsible for the production of dopamine and serotonin through the decarboxylation of 3,4-dihydroxyphenylalanine and 5-hydroxytryptophan, respectively. In insects, both dopamine and serotonin serve as classical neurotransmitters, neuromodulators, or neurohormones, and dopamine is also involved in insect cuticle formation, eggshell hardening, and immune responses.

Principal Findings

In this study, we expressed a typical DDC enzyme from Drosophila melanogaster, critically analyzed its substrate specificity and biochemical properties, determined its crystal structure at 1.75 Angstrom resolution, and evaluated the roles residues T82 and H192 play in substrate binding and enzyme catalysis through site-directed mutagenesis of the enzyme. Our results establish that this DDC functions exclusively on the production of dopamine and serotonin, with no activity to tyrosine or tryptophan and catalyzes the formation of serotonin more efficiently than dopamine.

Conclusions

The crystal structure of Drosophila DDC and the site-directed mutagenesis study of the enzyme demonstrate that T82 is involved in substrate binding and that H192 is used not only for substrate interaction, but for cofactor binding of drDDC as well. Through comparative analysis, the results also provide insight into the structure-function relationship of other insect DDC-like proteins.     

柯萨奇B组病毒致病性的分子生物学研究

柯萨奇B组病毒（coxsackievirus group B,CVB）是微小RNA病毒科肠道病毒属成员,病毒性心肌炎的病例中大约有20％-25％是由柯萨奇B组病毒引起。CVB的致病机制十分复杂,病毒基因组以及病毒蛋白均在病毒致病过程中发挥重要作用。因此,对柯萨奇B组病毒的基因组、结构蛋白以及某些非结构蛋白与靶细胞内分子间相互作用生物信息的认识是阐述该病分子机制的基础。