黄素依赖型卤化酶及其应用研究进展

卤化物是农业、制药业和化学工业的重要原料,主要以化学法合成,该法具有环境不友好和合成条件苛刻等劣势。天然卤化物生物合成途径的关键酶为卤化酶,包括卤过氧化物酶(haloperoxidase,HPO)、α-酮戊二酸依赖型卤化酶(α-ketoglutarate dependent halogenase,KG-Hal)、S-腺苷甲硫氨酸依赖型卤化酶(S-adenosylmethionine-dependenthalogenase)和黄素依赖型卤化酶(flavin-dependent halogenase,FDH)。其中,黄素依赖型卤化酶因其分布广泛、具有底物特异性和卤化位点选择性,是最具开发潜力的卤化酶。因此,本文对黄素依赖型卤化酶的结构、类型、催化机制及其应用研究进展进行综述,对利用基因分析和基因筛选方法寻找新型黄素依赖型卤化酶进行了展望。本综述有助于拓展黄素依赖型卤化酶的类型及其催化机制的知识,推动黄素依赖型卤化酶及其酶工程的研究,为新型卤化物的合成提供技术思路。     

酶分子体外定向进化的研究方法*

酶分子体外定向进化不仅可大幅度提高酶分子的进化效率,短期内在实验室完成自然状态下需要千百万年的进化过程,还可使酶分子按照人们期望的特定目标进化,因此对酶工程今后的发展非常重要。本对酶分子体外定向进化的研究方法进行了归纳总结。     

基于序列和结构分析的酶热稳定性改造策略*

功能酶被广泛应用于食品、化工、医药等领域,但却容易受高温环境限制,导致催化效率降低。以分子改造为目的的蛋白质工程技术是解决这一问题的关键环节,其能够对酶结构和功能进行改造,获得热稳定性好的工业酶。传统的定向进化方法只能依靠随机突变进行人工筛选,具有效率低、针对性差等缺点;理性设计作为酶热稳定性改造的主要方法,可借助各种计算机程序和软件预测潜在突变位点,但其要求对酶的催化机制、热稳定性机制有深入了解。对于大多数天然酶而言,酶的序列和晶体结构是最容易获取的信息,也是预测功能的重要基础。从酶的序列和晶体结构入手,重点介绍了共识突变、基于序列偏好性的突变、截短柔性区域、优化分子内相互作用力、刚化催化活性区域及计算机辅助筛选柔性位点等常用策略,这些策略具有筛选效率高、改造准确性高、实用性强等优点。结合多种酶的热稳定性改造案例进行分析,旨在为不同酶的改造策略选择提供有效参考,同时也为工业酶的耐热性研究提供理论支持。     

琼胶酶研究进展*

琼胶酶是一种多糖水解酶,根据降解琼脂糖的作用方式不同,可以分为α-琼胶酶（EC3.2.1.-）和β-琼胶酶（EC3.2.1.81）。中从琼胶酶的分类及酶活测定,酶的来源,产酶微生物的酶系及酶学性质,琼胶酶的分子生物学研究,酶的应用几个方面综述了琼胶酶的研究进展。     

杆状病毒几丁质酶基因结构与功能的研究进展*

杆状病毒几丁质酶基因是杆状病毒的非必需基因 ,是高度保守的基因。该基因在杆状病毒复制晚期表达产生几丁质酶 ,该酶N端具信号肽 ,中部是酶的活性区 ,C端是酶的内质网结合区。杆状病毒几丁质酶同时具有内切和外切几丁质酶活性 ,主要功能是水解昆虫体内的组成型几丁质。杆状病毒几丁质酶对于虫体液化是必需的 ,同时它还是原组织蛋白酶 (pro V Cath)的分子伴侣 ,并与病毒侵染机制相关联。杆状病毒的几丁质酶基因与细菌的几丁质酶基因可能源于共同的祖先。     

冠状病毒基因组特征及感染特点比较*

冠状病毒是一种可以引起人呼吸系统、消化系统等疾病的病原体。目前,对冠状病毒的了解还不够深入,尚不清楚新型冠状病毒(SARS-CoV-2)与其他人冠状病毒在生物学特点和感染机制、流行病学与临床特点等方面的异同,通过概括包括SARS-CoV-2在内的几种冠状病毒的特点,并分析SARS-CoV-2在特殊人群中的易感性及预后等特点,为临床研究和鉴别诊断提供参考和依据。     

冠状病毒基因组特征及感染特点比较*

冠状病毒是一种可以引起人呼吸系统、消化系统等疾病的病原体。目前,对冠状病毒的了解还不够深入,尚不清楚新型冠状病毒(SARS-CoV-2)与其他人冠状病毒在生物学特点和感染机制、流行病学与临床特点等方面的异同,通过概括包括SARS-CoV-2在内的几种冠状病毒的特点,并分析SARS-CoV-2在特殊人群中的易感性及预后等特点,为临床研究和鉴别诊断提供参考和依据。     

真菌花色素苷酶研究进展*

花色素苷酶是一类能催化花色素苷水解、褪色的糖苷酶,目前仅发现真菌有该酶的存在。本综述了真菌花色素苷酶在食品工业上应用,花色素苷酶的来源、种类、催化花色素苷降解的模式,花色素苷酶活力测定方法、分离纯化方法及酶学性质。     

微生物几丁质酶研究进展及应用*

几丁质由N-乙酰-D-氨基葡萄糖聚合而成,是自然界中仅次于纤维素的第二大类聚合物。微生物几丁质酶来源丰富,是生物降解或利用几丁质的主要媒介。野生型菌株几丁质酶产量低、活性弱,故近年来有关几丁质酶的研究侧重于对其产量及催化活性的提升等方面。此外,几丁质酶具有水解病原真菌细胞壁、破坏害虫体壁、生产N-乙酰氨基葡萄糖寡聚体或单体的应用价值,在医药、农业、食品加工等领域表现出巨大的市场潜力。综述微生物几丁质酶的来源、分类及工程改造,为后续几丁质酶的研究及开发利用提供参考。     

螺旋藻过氧化氢酶的比较研究*

采用碘量法对毛乌素沙地碱湖的钝顶螺旋藻S1 与国外引进的钝顶螺旋藻S2 和极大螺旋藻S3 的过氧化氢酶 (CAT)进行了比较研究。结果表明 :S1 、S2 和S3CAT活性在 2 5℃、pH 7 0时分别为 41 0 7U/g·FW、 550 4U/g·FW和 370 3U/g·FW ;Km值分别为 5 0× 1 0 ^{- 2}mol/L、 5 4× 1 0 ^{- 2} mol/L和 3 8× 1 0 ^{- 2} mol/L ;最适温度分别为 2 5℃     

稀有海洋放线菌Salinispora arenicola非核糖体肽合成酶和卤代酶生物合成基因簇核心区的克隆及序列分析

克隆稀有海洋放线菌Salinispora arenicola的非核糖体肽合成酶(NRPS)和卤代酶生物合成基因簇核心区基因片段。根据已发表的放线菌NRPS和卤代酶生物合成基因簇核心区的核苷酸序列保守区设计两对简并性引物,采用PCR的方法扩增NRPS和卤代酶生物合成基因簇核心区基因片段,使用分子生物学软件进行序列分析。获得两段大小分别为662bp和557bp的基因片段,编码220个和185个氨基酸。这两段序列与海洋放线菌Salinispora arenicola CNS-205的NRPS和卤代酶生物合成基因簇核心区基因核苷酸序列的同源性分别为99%和98%。成功地获得了稀有海洋放线菌Salinispora arenicola的NRPS和卤代酶生物合成基因簇核心区基因片段,该基因片段的获取将为分离全长基因簇以及研究该基因簇在生物合成中的功能奠定基础。     

Structure and Action of the Myxobacterial Chondrochloren Halogenase CndH: A New Variant of FAD-dependent Halogenases

The crystal structure of the FAD-dependent chondrochloren halogenase CndH has been established at 2.1 Å resolution. The enzyme contains the characteristic FAD-binding scaffold of the glutathione reductase superfamily. Except for its C-terminal domain, the chainfold of CndH is virtually identical with those of FAD-dependent aromatic hydroxylases. When compared to the structurally known FAD-dependent halogenases PrnA and RebH, CndH lacks a 45 residue segment near position 100 and deviates in the C-terminal domain. Both variations are near the active center and appear to reflect substrate differences. Whereas PrnA and RebH modify free tryptophan, CndH halogenates the tyrosyl group of a chondrochloren precursor that is most likely bound to a carrier protein. In contrast to PrnA and RebH, which enclose their small substrate completely, CndH has a large non-polar surface patch that may accommodate the putative carrier. Apart from the substrate binding site, the active center of CndH corresponds to those of PrnA and RebH. At the halogenation site, CndH has the characteristic lysine (Lys76) but lacks the required base Glu346 (PrnA). This base may be supplied by a residue of its C-terminal domain or by the carrier. These differences were corroborated by an overall sequence comparison between the known FAD-dependent halogenases, which revealed a split into a PrnA-RebH group and a CndH group. The two functionally established members of the CndH group use carrier-bound substrates, whereas three members of PrnA-RebH group are known to accept a free amino acid. Given the structural and functional distinction, we classify CndH as a new variant B of the FAD-dependent halogenases, adding a new feature to the structurally established variant A enzymes PrnA and RebH.     

海洋链霉菌Streptomyces sp.B-17卤化酶基因的克隆及生物信息学分析

海洋放线菌是生理活性物质重要的产生菌,而海洋放线菌产生的卤化酶可催化生理活性物质的卤化,极大提高了其抑菌和抗癌活性。从大连海域分离出1株链霉菌Streptomyces sp.B-17,从其基因组DNA中扩增一524 bp的基因片段,经与pMD-19T载体连接,转化大肠埃希菌JM109感受态细胞,重组质粒经鉴定证明正向插入到pMD-19T载体。生物信息学分析表明该序列与Actinocorallia herbida DSM 44252的2个依赖FADH2卤化酶基因的同源性为88%,拟编码氨基酸与色氨酸卤化酶(CP001848)的相似性也达到74%,证明所克隆的基因片段为卤化酶基因片段,为后续的基因功能分析及表达奠定了基础。     

环糊精葡萄糖基转移酶的结构特征与催化机理

随着环糊精在食品、医药等领域的应用越来越广,生产环糊精所必需的环糊精葡萄糖基转移酶(CGT酶)已经成为当今研究的热点。特别是近二十年来,国外对该酶进行了比较深入的研究。首先介绍了CGT酶的功能特性与结构特征。CGT酶是一种多功能型酶,能催化三种转糖基反应(歧化、环化和耦合反应)和水解反应,其中,能将淀粉转化为环糊精的环化反应是特征反应;作为α-淀粉酶家族的成员,CGT酶除了具有与α-淀粉酶相同的A、B、C结构域外,还存在D和E结构域。另外,对CGT酶的催化机理包括底物结合方式、转糖苷反应机理以及环化机理等进行了详细的讨论。     

Chloramphenicol Biosynthesis: The Structure of CmlS, a Flavin-Dependent Halogenase Showing a Covalent Flavin-Aspartate Bond

Chloramphenicol is a halogenated natural product bearing an unusual dichloroacetyl moiety that is critical for its antibiotic activity. The operon for chloramphenicol biosynthesis in Streptomyces venezuelae encodes the chloramphenicol halogenase CmlS, which belongs to the large and diverse family of flavin-dependent halogenases (FDH’s). CmlS was previously shown to be essential for the formation of the dichloroacetyl group. Here we report the X-ray crystal structure of CmlS determined at 2.2 Å resolution, revealing a flavin monooxygenase domain shared by all FDHs, but also a unique ‘winged-helix’ C-terminal domain that creates a T-shaped tunnel leading to the halogenation active site. Intriguingly, the C-terminal tail of this domain blocks access to the halogenation active site, suggesting a structurally dynamic role during catalysis. The halogenation active site is notably nonpolar and shares nearly identical residues with Chondromyces crocatus tyrosyl halogenase (CndH), including the conserved Lys (K71) that forms the reactive chloramine intermediate. The exception is Y350, which could be used to stabilize enolate formation during substrate halogenation. The strictly conserved residue E44, located near the isoalloxazine ring of the bound flavin adenine dinucleotide (FAD) cofactor, is optimally positioned to function as a remote general acid, through a water-mediated proton relay, which could accelerate the reaction of the chloramine intermediate during substrate halogenation, or the oxidation of chloride by the FAD(C4α)-OOH intermediate. Strikingly, the 8α carbon of the FAD cofactor is observed to be covalently attached to D277 of CmlS, a residue that is highly conserved in the FDH family. In addition to representing a new type of flavin modification, this has intriguing implications for the mechanism of FDHs. Based on the crystal structure and in analogy to known halogenases, we propose a reaction mechanism for CmlS.     

Asia1型口蹄疫病毒分离株结构蛋白基因的克隆与表达

口蹄疫病毒结构蛋白氨基酸的变化是病毒抗原性变异的分子基础,大部分抗原表位位于主要的免疫原蛋白VP1上,部分非线性抗原表位位于VP2和VP3上.本研究首次成功测定了Asia1型口蹄疫病毒(YNBS/58)四种结构蛋白基因(p1区)的核苷酸序列,全长2199个碱基,编码733个氨基酸,该基因与Ind63/72、Pka3/54、Israel、China/99、C1/Germany、A22、ZIM7/83/2毒株的p1基因核苷酸序列同源性分别为88.4%、86.0%、89.3%、68.6%、67.6%、66.8%、50.3%,推导的氨基酸序列同源性分别为94.1%、93.2%、95.1%、79.9%、77.0%、76.5%、58.1%;将YNBS/58株与Ind63/72、Pka3/54、Israel株的vp1、vp2、vp3、vp4基因和编码蛋白分别进行同源性比较,发现VP1的序列变异最大,VP2、VP3、VP4次之,且VP1的氨基酸变异主要集中在42-50位和137-156位.实现了YNBS/58株结构蛋白基因在大肠杆菌中的高效表达,其表达的融合蛋白以包涵体形式存在,分子量约为88kDa,占菌体总蛋白的16%左右,并利用镍柱对目的蛋白进行了纯化,纯度达90%以上,本实验为进一步研究A-sia1型口蹄疫病毒的分子流行病学、p1基因及其编码蛋白的生物学功能奠定了基础.     

不同干扰强度下江西武夷山河岸带阔叶林群落的结构与数量特征

为揭示中亚热带典型河岸带阔叶林群落的结构特征、数量特征和干扰强度的耦合关系,根据干扰强度的不同,在江西武夷山保护区内选取3条主要水系进行阔叶林群落调查,共统计到河岸带维管束植物93科174属304种,分别占保护区维管束植物总数的41.5%、18.0%、11.9%。物种组成以壳斗科（6属22种）、山茶科（7属22种）、樟科（6属16种）、蔷薇科（8属16种）为主。不同干扰强度下的河岸带植被群落相似性Jaccard系数均在0.2-0.3之间,各群落优势种完全不同,且存在特有分布的物种,但群落乔木层优势种优势度（重要值）差异不显著（P〉0.05）。不同干扰强度下,物种数量、群落Jaccard系数、丰富度指数、多样性指数、均匀度指数总体上为：轻微干扰〉中等干扰〉无干扰;而乔木的平均高度和平均胸径却为：无干扰〉中等干扰〉轻微干扰。研究结果表明,江西武夷山河岸带阔叶林以常绿阔叶树种为主,但不同干扰梯度下群落的结构和数量特征差异性较大。     

Asia1型口蹄疫病毒分离株结构蛋白基因的克隆与表达

口蹄疫病毒结构蛋白氨基酸的变化是病毒抗原性变异的分子基础,大部分抗原表位位于主要的免疫原蛋白VP1上,部分非线性抗原表位位于VP2和VP3上。本研究首次成功测定了 Asia1 型口蹄疫病毒(YNBS/58)四种结构蛋白基因( p1 区)的核苷酸序列,全长 2199 个碱基,编码 733 个氨基酸,该基因与 Ind63/72、Pka3/54、Israel、China/99、C1/Germany、A22、ZIM7/83/2 毒株的 p1 基因核苷酸序列同源性分别为 88. 4%、86. 0%、89. 3%、68.6%、67.6%、66.8%、50.3%,推导的氨基酸序列同源性分别为 94.1%、93.2%、95.1%、79.9%、77.0%、76.5%、58.1%;将YNBS/58株与 Ind63/72、Pka3/54、Israel株的 vp1、vp2、vp3、vp4 基因和编码蛋白分别进行同源性比较,发现VP1的序列变异最大,VP2、VP3、VP4次之,且VP1的氨基酸变异主要集中在 42-50 位和 137-156 位。实现了YNBS/58株结构蛋白基因在大肠杆菌中的高效表达,其表达的融合蛋白以包涵体形式存在,分子量约为88kDa,占菌体总蛋白的16%左右,并利用镍柱对目的蛋白进行了纯化,纯度达 90%以上,本实验为进一步研究 A sia1型口蹄疫病毒的分子流行病学、p1基因及其编码蛋白的生物学功能奠定了基础。     

Examination of structural stability and phase transitions in constant-pressure first-principles molecular dynamics simulations

Constant-pressure first-principles molecular dynamics (FPMD) simulation is a powerful tool for investigations of structures in crystals. However, it needs enourmous computations so that highly accurate calculations for electronic states cannot be employed at present. In this report, we examined the reliability and applicability of constant-pressure FPMD in the study of structural properties under this limitation. Crystalline silicon was employed as a benchmark to perform constant-pressure FPMD simulations (with a deformable simulation cell). It is found that, in high pressure (metallic) phases, crystalline symmetry is broken with the present simulation conditions. Several structural transformations were realized by compression and decompression, but they are not entirely consistent with experiment. We discuss this discrepancy and conclude that the number of k point sampling in the Brillouin zone is crucial. It is recommended that constant-pressure FPMD is employed to explore candidate structures for unknown solid phases at present computational resources.     

Structural Studies and Protein Engineering of Inositol Phosphate Multikinase

Inositol phosphates (IPs) regulate vital processes in eukaryotes, and their production downstream of phospholipase C activation is controlled through a network of evolutionarily conserved kinases and phosphatases. Inositol phosphate multikinase (IPMK, also called Ipk2 and Arg82) accounts for phosphorylation of IP₃ to IP₅, as well as production of several other IP molecules. Here, we report the structure of Arabidopsis thaliana IPMKα at 2.9 Å and find it is similar to the yeast homolog Ipk2, despite 17% sequence identity, as well as the active site architecture of human IP₃ 3-kinase. Structural comparison and substrate modeling were used to identify a putative basis for IPMK selectivity. To test this model, we re-engineered binding site residues predicted to have restricted substrate specificity. Using steady-state kinetics and in vivo metabolic labeling studies in modified yeast strains, we observed that K117W and K117W:K121W mutants exhibited nearly normal 6-kinase function but harbored significantly reduced 3-kinase activity. These mutants complemented conditional nutritional growth defects observed in ipmk null yeast and, remarkably, suppressed lethality observed in ipmk null flies. Our data are consistent with the hypothesis that IPMK 6-kinase activity and production of Ins(1,4,5,6)P₄ are critical for cellular signaling. Overall, our studies provide new insights into the structure and function of IPMK and utilize a synthetic biological approach to redesign inositol phosphate signaling pathways.