国外科技期刊亮点

蛋白活性研究新进展 作为一个非常有效的机制,变构调节能够控制诸多生物过程中的蛋白质活动,包括信号转导、新陈代谢、催化和基因调控等。其原理是一些酶除了有活性中心外,还有所谓的变构中心,与配体（或底物）结合可使酶的构象发生改变,影响酶活性中心与底物的亲和力及酶的活性。     

内生枯草芽孢杆菌HD-1β-甘露聚糖酶基因的克隆及结构生物学分析

采用PCR技术从一株内生枯草芽孢杆菌HD-1基因组DNA中扩增出β-甘露聚糖酶基因核苷酸编码序列.序列分析表明,该基因全长1 089bp,编码362个氨基酸和一个终止密码子,N端前27个氨基酸为其信号肽.该酶氨基酸序列与相同来源的β-甘露糖苷酶同源性最高达98.34%,具有ManB保守结构域,属于糖苷水解酶家族26的一员.通过对该酶分子三维结构的预测分析,该酶的催化域形成TIM桶状结构,Cys92和Cys112形成二硫键,它们之间的部分构成该酶的氧化还原反应的活性中心,Glu100和Glu292分别为该酶的酸碱催化位点和亲核催化位点.三维结构的分析为提高酶的催化活性的和功能方面的定向改造提供了依据.     

基于生物新陈代谢中酶的高效催化性研究

酶是生物新陈代谢的保障条件之一,在生物的新陈代谢过程中,主要起到催化生物化学反应的作用,从而保证新陈代谢顺利进行.酶的催化作用具有高效性的特点,而这一特性又取决于酶的高效催化机理.本文从酶改变化学反应历程,与底物的结合理论及结合途径方面阐述了生物新陈代谢中酶的高效催化性.     

溶液粘度和EcoRI限制性核酸内切酶—P_2-DNA复合物解离的动力学

Eco.RI限制性内切酶像所有球蛋白一样是动力学系统,并且存在着大量的构象底物。酶和底物之间能够发生反应,仅仅在酶蛋白被底物诱导而变构以后,变构能克服起动化学反应的阈值。粘度不仅影响扩散和分子彼此碰撞,而且也影响酶的变构。温度影响溶液粘度,从而也可间接地影响酶的变构。为了证明这种观点,我们在不同粘度和温度条件下,用Eco.RI限制性内切酶切割P_2—DNA,研究了酶——底物复合物催化速度常数的改变。一起考虑来自所有溶液的资料,酶——底物复合物的解离速度常数作为固定粘度下的温度函数和固定温度下的粘度函数被研究。酶——底物复合物的转变速度依赖于溶液粘度,溶液粘度在测定蛋白质动力学状态中起着重要的作用。我们的实验资料表明,最大的催化速度常数Kc值,出现在20%(V/V)的甘油溶液中,在不同温度下,Kc值在高于最适粘度的广大粘度范围内,将随粘度的增加而下降,反之,在低于最适粘度时,Kc值将随粘度的下降而下降。实验结果暗示,EcoRI酶——P_2—DNA复合物解离速度常数值,对于粘度和周围介质产生的酶的调控作用是敏感的。可能的机制将被讨论。     

腺苷化酶的研究进展

腺苷化修饰(AMPylation)是一种由腺苷化酶(AMPylators)催化的翻译后修饰.腺苷化酶是一类催化底物蛋白的某些残基侧链共价结合(或去除)一磷酸腺苷(adenosine 5'-monophosphate,AMP)的酶.腺苷化酶主要属于Fido结构域超家族和类DNA聚合酶家族(DNA-polymerase-β-like family).致病菌表达腺苷化酶调控宿主细胞的信号机制,达到利于致病菌繁殖和生存的目的.真核生物中也存在一些腺苷化酶参与感知和调控细胞应激.从腺苷化酶的分类、催化机理、调控方式和去腺苷化修饰活性等方面综述了腺苷化酶的研究进展.     

组蛋白H3K36位点甲基转移酶识别组蛋白底物的分子机制研究进展

组蛋白H3第36位赖氨酸的甲基化修饰在染色质上含量丰富,与活跃转录以及DNA损伤修复等重要生理过程相关．H3K36位点可以被一甲基化、二甲基化和三甲基化3种形式修饰,目前已知的负责组蛋白H3K36三甲基化修饰的人源蛋白是SETD2,负责组蛋白H3K36二甲基化修饰的酶包含NSD1、NSD2和NSD3和ASH1L共4名成员．这些H3K36甲基转移酶都具有非常特异的H3K36位点选择性,因此,对调控体内H3K36甲基化修饰的水平和分布十分重要．此外,它们的表达异常与人类的多种疾病相关．因此,解析组蛋白H3K36甲基转移酶识别并修饰组蛋白底物的分子机制,对揭示这些酶参与的表观遗传调控机制及其在体内的生理功能都具有十分重要的意义．早期的研究使得人们对组蛋白H3K36甲基转移酶催化底物的机制有了较深入的认识,但是由于解析的修饰酶与底物复合物的结构较少,对这些酶特异识别组蛋白底物分子机制的认识尚有很多不足．近年来,随着冷冻电镜技术的应用,H3K36甲基转移酶与核小体底物的复合物结构相继取得了突破,极大地推进了人们对这些酶识别并催化组蛋白底物分子机制的认识．本文以这几个组蛋白H3K36甲基转移酶为主要目标,对其分子机制的最新进展进行介绍总结．      

Taq酶体外合成DNA时模板错位机制的探讨

利用Taq DNA聚合酶体外合成DNA过程中,当反应体系中缺少与模板链互补配对的dNTP底物时,产物合成并不会在底物缺失位点处终止,聚合反应继续进行.为研究此复制缺陷现象,设计一系列模板用于DNA体外酶促合成.除了已知的碱基错配机制,笔者发现存在另一种"模板错位"机制,即模板中与底物非Watson-Crick互补配对的碱基位点首先进行收缩滑动,形成模板bulge结构后再继续进行酶促合成反应.这项研究有助于提高DNA样品合成保真度以及继续深入探索体外DNA合成的详细机制.     

酶催化功能混杂性研究进展

酶催化生物体内化学反应,是生命代谢形成运转的动力。与传统观点认为酶具有专一性催化功能相对,近年来生物信息与实验分析都证实了酶具有多种混杂催化功能是普遍存在的现象。在过去的几十亿年里,古老酶一直不断演化以适应变化的环境,形成现代功能多样的酶蛋白家族。基于独特底物结合模式和动态蛋白结构的催化功能混杂性是酶蛋白适应性演化的基础。酶的混杂活性有望被开发应用于药物酶法合成及环境修复领域。本文就酶催化功能混杂性的普遍性、分子机理、可进化性等方面的相关研究进展进行综述。     

胆色素原脱氨酶的研究进展

胆色素原脱氨酶是生物体内参与四吡咯化合物生物合成过程的关键酶之一,它催化了4个底物脱去4分子氨依次连接成线形的四吡咯产物羟甲基胆素．论文总结了胆色素原脱氨酶在生化性质、晶体结构、催化机理等方面的研究成果,并介绍了该酶的一些重要氨基酸．     

乙醇脱氢酶底物分子对接的优化

通过分子对接的方法,探寻乙醇脱氢酶催化底物脱氢时酶与底物分子的特定位点间存在作用力及其与底物亲和力之间的相关性.研究结果表明:影响乙醇脱氢酶催化底物与酶相互作用的主要因素并非是分子量或者分子间氢键的键能,而是分子间总的作用力及分子间形成氢键的个数,其相关系数可达0.63;辅酶及金属离子对酶与底物结合的抑制常数及结合位点具有十分显著的影响.     

Active-site mutants altering the cooperativity of E. coli phosphofructokinase

Crystal structures of the high- and low-activity states of the allosteric enzyme phosphofructokinase implicate three arginines in substrate binding, catalysis and cooperativity. Arginines 162 and 243 reach into the active site from an adjacent subunit and interact with the cooperative substrate fructose 6-phosphate. Mutation of these arginines to serine results in mutant enzymes with reduced substrate binding and lowered cooperativity, but with little change in their catalytic ability (kcat). Arg 72 bridges the two substrates fructose 6-phosphate and ATP, and interacts with the 1-phosphate of the product fructose 1,6-biphosphate. Mutation of this residue to serine reduces the catalytic activity, cooperativity and binding of fructose 6-phosphate and fructose 1,6-bisphosphate. In the reverse reaction, the kinetics of wild-type and the Ser 72 mutant with respect to fructose 1,6-bisphosphate are hyperbolic, whereas those of the Ser 162 and Ser 243 mutants are sigmoidal. These results show that each of the three arginines contributes to cooperativity and to the transmission of allosteric signals between the four subunit of the enzyme.     

Ribonucleotides in DNA newly synthesised in 3T6 cells in vivo.

Within the field of DNA replication, considerable interest has focused in recent years on the mechanism of initiation of synthesis of DNA molecules. In vitro replication systems from Escherichia coli have been instrumental in uncovering a priming function fo9r ribonucleotides on the earliest intermediates of DNA polymerisation in vitro and in identifying the proteins involved. In vitro replication systems from mammalian cells that permit the use of the phosphate-transfer method for detection of RNA-DNA junctions as well as direct labelling of the RNA moiety of the molecules have suggested a similar role for ribonucleotides in DNA synthesis in eukaryotes. However, the existence of this mechanism in mammalian cells in vivo has not been established. Here we report the first evidence that a significant proportion of the earliest intermediates in mammalian DNA polymerisation in vivo do, in fact, possess ribonucleotides, presumably because their synthesis was initiated with one or more ribonucleotides.     

Replication fork movement sets chromatin loop size and origin choice in mammalian cells

Genome stability requires one, and only one, DNA duplication at each S phase. The mechanisms preventing origin firing on newly replicated DNA are well documented, but much less is known about the mechanisms controlling the spacing of initiation events(2,3), namely the completion of DNA replication. Here we show that origin use in Chinese hamster cells depends on both the movement of the replication forks and the organization of chromatin loops. We found that slowing the replication speed triggers the recruitment of latent origins within minutes, allowing the completion of S phase in a timely fashion. When slowly replicating cells are shifted to conditions of fast fork progression, although the decrease in the overall number of active origins occurs within 2 h, the cells still have to go through a complete cell cycle before the efficiency specific to each origin is restored. We observed a strict correlation between replication speed during a given S phase and the size of chromatin loops in the next G1 phase. Furthermore, we found that origins located at or near sites of anchorage of chromatin loops in G1 are activated preferentially in the following S phase. These data suggest a mechanism of origin programming in which replication speed determines the spacing of anchorage regions of chromatin loops, that, in turn, controls the choice of initiation sites.     

Modular enzymes

Although modular macromolecular devices are encountered frequently in a variety of biological situations, their occurrence in biocatalysis has not been widely appreciated. Three general classes of modular biocatalysts can be identified: enzymes in which catalysis and substrate specificity are separable, multisubstrate enzymes in which binding sites for individual substrates are modular, and multienzyme systems that can catalyse programmable metabolic pathways. In the postgenomic era, the discovery of such systems can be expected to have a significant impact on the role of enzymes in synthetic and process chemistry.     

Active site-directed protein regulation

Regulation of protein function is vital for the control of cellular processes. Proteins are often regulated by allosteric mechanisms, in which effectors bind to regulatory sites distinct from the active sites and alter protein function. Intrasteric regulation, directed at the active site and thus the counterpart of allosteric control, is now emerging as an important regulatory mechanism.     

Crystal structure of the anti-viral APOBEC3G catalytic domain and functional implications

The APOBEC family members are involved in diverse biological functions. APOBEC3G restricts the replication of human immunodeficiency virus (HIV), hepatitis B virus and retroelements by cytidine deamination on single-stranded DNA or by RNA binding. Here we report the high-resolution crystal structure of the carboxy-terminal deaminase domain of APOBEC3G (APOBEC3G-CD2) purified from Escherichia coli. The APOBEC3G-CD2 structure has a five-stranded beta-sheet core that is common to all known deaminase structures and closely resembles the structure of another APOBEC protein, APOBEC2 (ref. 5). A comparison of APOBEC3G-CD2 with other deaminase structures shows a structural conservation of the active-site loops that are directly involved in substrate binding. In the X-ray structure, these APOBEC3G active-site loops form a continuous 'substrate groove' around the active centre. The orientation of this putative substrate groove differs markedly (by 90 degrees) from the groove predicted by the NMR structure. We have introduced mutations around the groove, and have identified residues involved in substrate specificity, single-stranded DNA binding and deaminase activity. These results provide a basis for understanding the underlying mechanisms of substrate specificity for the APOBEC family.     

Structural basis for the bifunctionality of fructose-1,6-bisphosphate aldolase/phosphatase

Enzymes catalyse specific reactions and are essential for maintaining life. Although some are referred to as being bifunctional, they consist of either two distinct catalytic domains or a single domain that displays promiscuous substrate specificity. Thus, one enzyme active site is generally responsible for one biochemical reaction. In contrast to this conventional concept, archaeal fructose-1,6-bisphosphate (FBP) aldolase/phosphatase (FBPA/P) consists of a single catalytic domain, but catalyses two chemically distinct reactions of gluconeogenesis: (1) the reversible aldol condensation of dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (GA3P) to FBP; (2) the dephosphorylation of FBP to fructose-6-phosphate (F6P). Thus, FBPA/P is fundamentally different from ordinary enzymes whose active sites are responsible for a specific reaction. However, the molecular mechanism by which FBPA/P achieves its unusual bifunctionality remains unknown. Here we report the crystal structure of FBPA/P at 1.5-? resolution in the aldolase form, where a critical lysine residue forms a Schiff base with DHAP. A structural comparison of the aldolase form with a previously determined phosphatase form revealed a dramatic conformational change in the active site, demonstrating that FBPA/P metamorphoses its active-site architecture to exhibit dual activities. Thus, our findings expand the conventional concept that one enzyme catalyses one biochemical reaction.