固氮酶晶体学研究进展

生物大分子的功能取决于它的空间结构。X射线衍射分析是获得生物大分子结构信息的常用方法。本文对固氮酶晶体的生长及其X射线衍射分析的主要进展简要地进行了介绍和评论。最后展望了今后的发展及问题。     

固氮酶晶体学研究进展

生物大分子的功能取决于它的空间结构.X射线衍射分析是获得生物大分子结构信息的常用方法.本文对固氮酶晶体的生长及其X射线衍射分析的主要进展简要地进行了介绍和评论.最后展望了今后的发展及问题.     

Current advances in research of cytochrome c oxidase

The function of cytochrome c oxidase as a biomolecular nanomachine that transforms energy of redox reaction into protonmotive force across a biological membrane has been subject of intense research, debate, and controversy. The structure of the enzyme has been solved for several organisms; however details of its molecular mechanism of proton pumping still remain elusive. Particularly, the identity of the proton pumping site, the key element of the mechanism, is still open to dispute. The pumping mechanism has been for a long time one of the key unsolved issues of bioenergetics and biochemistry, but with the accelerating progress in this field many important details and principles have emerged. Current advances in cytochrome oxidase research are reviewed here, along with a brief discussion of the most complete proton pumping mechanism proposed to date, and a molecular basis for control of its efficiency.     

Insights into nucleotide signal transduction in nitrogenase: structure of an iron protein with MgADP bound

Coupling the energy of nucleoside triphosphate binding and hydrolysis to conformational changes is a common mechanism for a number of proteins with disparate cellular functions, including those involved in DNA replication, protein synthesis, and cell differentiation. Unique to this class of proteins is the dimeric Fe protein component of nitrogenase in which the binding and hydrolysis of MgATP controls intermolecular electron transfer and reduction of nitrogen to ammonia. In the work presented here, the MgADP-bound (or "off") conformational state of the nitrogenase Fe protein has been captured and a 2.15 A resolution X-ray crystal structure is presented. The structure described herein reveals likely mechanisms for long-range communication from the nucleotide-binding sites for controlling the affinity of association with the MoFe protein component. Two pathways, termed switches I and II, appear to be integral to this nucleotide signal transduction mechanism. In addition, the structure provides the basis for the changes in the biophysical properties of the [4Fe-4S] cluster observed when Fe protein binds nucleotides. The structure of the MgADP-bound Fe protein provides important insights into the respective contributions of nucleotide interaction and complex formation in defining the conformational states that are the keys to nitrogenase catalysis.     

衰老的分子机制与干预研究的最新进展

随着全球老龄化时代的到来,衰老和衰老相关疾病带来的健康问题日益突出。如何最大限度地维持老龄人口健康、干预衰老相关疾病并延缓衰老的发生对于医疗系统、科研机构乃至整个社会都是巨大的挑战。目前,对于衰老的分子机制研究已经有长足的进步,对于衰老进程的生物学和遗传学机制已有突破性的认识,对于衰老相关疾病的发病机制也有了深刻的理解。但这些研究成果还远远达不到能够延缓人类衰老并遏制衰老相关疾病的发生的要求。该文将从衰老的分子机制和干预手段这两个方面入手,综述衰老的理论研究和实际应用中的主要成果和最新进展。     

Structural basis for the changes in redox potential in the nitrogenase Phe135Trp Fe protein with MgADP Bound

The crystal structure of the Azotobacter vinelandii nitrogenase Fe protein with phenylalanine at position 135 substituted by tryptophan has been determined in MgADP-bound form by X-ray diffraction methods. Amino acid substitution studies have suggested that the phenylalanine at position 135 located near the [4Fe-4S] cluster contributes to both the midpoint potential and nucleotide-induced changes of the [4Fe-4S] cluster. Substitution of tryptophan for phenylalanine at position 135 resulted in a significant positive shift in the midpoint potential in both the isolated and nucleotide-bound states. The factors thought to control the midpoint potential of the [FeS] cluster include solvent accessibility, dipolar environment, and structural strain. The structure derived in the present work provides an explanation for the more positive midpoint potential observed in the nucleotide-bound state, and suggests important insights into the contributions of the nucleotide interaction to the conformational states that are the keys to nitrogenase catalysis. The presence of MgADP in Phe135Trp Fe protein reveals the mechanism of the long-range communication from the nucleotide-binding site that controls its affinity for the MoFe protein component.     

Nitrate reduction and nitrogen fixation in symbiotic association Rhizobium-legumes

The inhibitory effect of nitrate on nitrogenase activity in root nodules of legume plants has been known for a long time. The major factor inducing changes in nitrogenase activity is the concentration of free oxygen inside nodules. Oxygen availability in the infected zone of nodule is limited, among others, by the gas diffusion resistance in nodule cortex. The presence of nitrate may cause changes in the resistance to O2 diffusion. The aim of this paper is to review literature data concerning the effect of nitrate on the symbiotic association between rhizobia and legume plants, with special emphasis on nitrogenase activity. Recent advances indicate that symbiotic associations of Rhizobium strains characterized by a high nitrate reductase activity are less susceptible to inhibition by nitrate. A thesis may be put forward that dissimilatory nitrate reduction, catalyzed by bacteroid nitrate reductase, significantly facilitates the symbiotic function of bacteroids.     

Insights into the role of nucleotide-dependent conformational change in nitrogenase catalysis: Structural characterization of the nitrogenase Fe protein Leu127 deletion variant with bound MgATP

In the present work, determination of the structure of the nitrogenase Leu 127 deletion variant Fe protein with MgATP bound is presented, along with density functional theory calculations, to provide insights into the roles of MgATP in the nitrogenase reaction mechanism. Comparison of the MgATP-bound structure of this Fe protein to the nucleotide-free form indicates that the binding of MgATP does not alter the overall structure of the variant significantly with only small differences in the conformation of amino acids in direct contact with the two bound MgATP molecules being seen. The earlier observation of splitting of the [4Fe-4S] cluster into two [2Fe-2S] clusters was observed to be unaltered upon binding MgATP. Density functional theory was used to probe the assignment of ligands to the two [2Fe-2S] rhombs. The Mg(2+) environment in the MgATP-bound structure of the Leu127 deletion Fe protein is similar to that observed for the Fe protein in the nitrogenase Fe protein: MoFe protein complex stabilized by MgADP and tetrafluoroaluminate suggesting that large scale conformational change implicated for the Fe protein may not be mediated by changes in the Mg(2+) coordination. The results presented here indicated that MgATP may enhance the stability of an open conformation and prohibit intersubunit interactions, which have been implicated in promoting nucleotide hydrolysis. This could be critical to the tight control of MgATP hydrolysis observed within the nitrogenase complex and may be important for maintaining unidirectional electron flow toward substrate reduction.     

Biochemistry and genetics of Klebsiella pneumoniae mutant strains unable to fix N2.

Selected mutant strains of Klebsiella pneumoniae that are unable to fix nitrogen have been characterized according to nitrogenase component activity as well as antigenic cross-reacting material. The lesions in these strains have been mapped by transduction, and the results indicate that there are at least five genes specifically responsible for nitrogen fixation in vivo. Besides genes that specify the structure of the two nitrogenase components, there is a gene for a factor that is required for component I activity and a gene that codes for a factor possibly involved in electron transport to component II. A mutation in another site does not allow the organism to produce either of the nitrogenase components. All of these genes are co-transducible with the gene that specifics the structure of histidinol dehydrogenase.     

SATB1在基因表达调控中作用的研究进展

SATB1是一种组织特异性的核基质结合蛋白,参与了染色质高级结构的形成和组织特异性基因的表达调控,对于胸腺细胞的发育和T细胞的成熟起到了尤为重要的作用。虽然已经知道SATB1可以通过与MAR序列结合,以促进染色质重塑,调节组蛋白乙酰化和甲基化水平等多种途径对基因的表达进行调控,但是对于该过程所涉及到的分子机制仍然不是很清楚。本文对SATB1在基因表达调控方面的研究进展作一综述。     

固氮酶的研究进展

固氮酶将N2还原为NH3的过程是自然界实现氮循环的重要环节。固氮酶是由γ2型二聚体组成的Fe蛋白和α2β2异四聚体组成的MoFe蛋白组成。固氮酶催化的机制包括铁蛋白的氧还循环和钼铁蛋白的氧还循环两部分。Klebsiella pneumoniae的nif基因簇由20个基因组成,构成了8个转录单位,总长度24206bp,其操控机制是多水平、多层次的调控过程。同时综述了固氮酶的多样性,目前已经发现的有钼铁固氮酶、钒铁固氮酶、铁铁固氮酶以及在Strpomyces thermoauophicus内存在的与已知的三种固氮酶体系明显不同的固氮体系。     

Thermodynamics of the mechanism of the nitrogenase reaction

The fixation of molecular nitrogen by nitrogenase requires a lot of energy because 16 mol of ATP are hydrolyzed per mole of nitrogen converted to ammonia. Kim and Dees determined the crystallograpic structure of nitrogenase and this has led to a three-step mechanism that involves Feprotein and MoFeprotein in addition to ferredoxin. Each of these steps can be interpreted in terms of two half reactions that are connected through their transfer of electrons. Estimates can be made of the standard apparent reduction potentials of these three steps and their dependencies on pH and ionic strength. This mechanism is compared with the same type of analysis of an alternative three-step mechanism in which the hydrolysis of ATP is coupled with the reduction of molecular nitrogen, rather than the reduction of Feprotein. The problem with the first mechanism is that the second step produces 12 mol of hydrogen ions per mole of nitrogen fixed and the third step consumes 10 mol of hydrogen ions per mole of nitrogen fixed. The alternative mechanism does not have this problem.     

Structure and function of the small ribozymes.

Recently, major advances have been made toward increasing our understanding of small ribozyme structure and function. The first general acid-base catalytic mechanism for a ribozyme has been defined. Shifted nucleotide pK(a) values have been found to be surprisingly frequent structural elements. Finally, the dynamic nature of RNA catalysis has been highlighted through new structural and biochemical information.     

Regulation of nitrogenase A and R concentrations in Rhodopseudomonas capsulata by glutamine synthetase.

Nitrogen-starved purple non-sulphur bacteria have an active unregulated form of nitrogenase (nitrogenase A); however, the nitrogenase of a glutamine synthetase-negative mutant of Rhodopseudomonas capsulata, when nitrogen-starved, was predominantly inactive and required activation by Mn2+ and activating-factor protein. This regulatory form of nitrogenase has been called nitrogenase R. Treatment of wild-type cells (containing nitrogenase A) with methionine sulphoximine, an inhibitor of glutamine synthetase, converted the enzyme into nitrogenase R. Glutamine synthetase thus appears to control the intracellular concentrations of nitrogenase A and R and in this way regulates nitrogenase activity in the photosynthetic bacterium.     

Microbial communities and diazotrophic activity differ in the root‐zone of Alamo and Dacotah switchgrass feedstocks

Nitrogen (N) bioavailability is a primary limiting nutrient for crop and feedstock productivity. Associative nitrogen fixation (ANF) by diazotrophic bacteria in root‐zone soil microbial communities have been shown to provide significant amounts of N to some tropical grasses, but this potential in switchgrass, a warm‐season, temperate, US native, perennial tallgrass has not been widely studied. ‘Alamo’ and ‘Dacotah’ are cultivars of switchgrass, adapted to the southern and northern regions of the United States, respectively, and offer an opportunity to better describe this plant–bacterial association. The nitrogenase enzyme activity, microbial communities, and amino acid profiles in the root‐zones of the two ecotypes were studied at three different plant growth stages. Differences in the nitrogenase enzyme activity and free soluble amino acid profiles indicated the potential for greater nitrogen fixation in the high productivity Alamo compared with the lower productivity Dacotah. Changes in the amino acid profiles and microbial community structure (rRNA genes) of the root‐zone suggest different plant–bacterial interactions can help to explain differences in nitrogenase activity. PICRUSt analysis revealed functional differences, especially nitrogen metabolism, that supported ecotype differences in root‐zone nitrogenase enzyme activity. It is thought that the greater productivity of Alamo increased the belowground flow of carbon into roots and root‐zone habitats, which in turn support the high energy demands needed to support nitrogen fixation. Further research is thus needed to understand plant ecotype and cultivar trait differences that can be used to breed or genetically modify crop plants to support root‐zone associations with diazotrophs.     

发菜固氮基因nifD和nifK克隆及其失水条件下的差异表达

nifD和nifK编码钼铁固氮酶中的钼铁蛋白。为了解发菜nifD和nifK分子信息及对水分胁迫的响应机制,该研究设计了简并性引物克隆发菜nifD和nifK全长,进行原核表达和生物信息学分析,并对不同失水状态下发菜nifD和nifK在转录水平的差异表达和固氮酶活性的变化进行分析。结果表明,发菜nifD和nifK全长分别为1 443 bp和1 536 bp (登陆号为分别为KU886164和KU886165);将nifD和nifK在大肠杆菌中表达,分别获得一个约57 kD和58 kD的外源蛋白;生物信息学分析表明,nifD和nifK核苷酸序列和推译的氨基酸序列均与点形念珠藻(Nostoc punctiforme PCC 73102)高度一致性;nifD和nifK的二级结构主要有α-螺旋、β-折叠、β-转角和随机卷曲。此外,随着藻体含水量的逐渐降低,发菜nifD和nifK在转录水平上的表达量逐渐增加,但固氮酶活性呈现先增加后下降的趋势。研究结果为深入全面研究发菜固氮酶基因结构及其响应水分胁迫的固氮机理及氮代谢途径提供了基础。     

Changes in the EPR signal of dinitrogenase from Azotobacter vinelandii during the lag period before hydrogen evolution begins.

During the lag period before H2 is evolved by the nitrogenase system, the EPR signal of dinitrogenase decreases steadily, indicating transfer of electrons into dinitrogenase. The rate constant for the decrease in amplitude of the EPR signal, the steady state rate of H2 evolution from nitrogenase, and the length of the lag period have been measured. The data suggest that H2 is evolved only after dinitrogenase has been reduced by 2 electrons/molybdenum. The electrons that have been transfered into dinitrogenase during the lag period are not evolved as H2 upon denaturation of dinitrogenase. The existence of a lag indicates that the two nitrogenase proteins dissociate after every electron transfer. The lag occurs and the nitrogenase proteins dissociate under a variety of conditions of pH and temperature.     

直接遗忘效应中认知抑制机制研究新进展

随着认知抑制研究的兴起,作为测量认知抑制能力的主要方法,直接遗忘效应得到了不断深入的研究。本文简要介绍了直接遗忘效应的研究范式,并就直接遗忘的内在机制是"选择性复述"的作用,还是"认知抑制"的作用展开讨论。在此基础上还就个体抑制能力的发展进程及其应用价值的研究进展做了简要介绍,并指出了已有研究存在的一些问题。     

Duplication and extension of the Thorneley and Lowe kinetic model for Klebsiella pneumoniae nitrogenase catalysis using a MATHEMATICA software platform

The Thorneley and Lowe kinetic model for nitrogenase catalysis was developed in the early to mid 1980s, and has been of value in accounting for many aspects of nitrogenase catalysis. It has also been of value by providing a model for predicting new catalytic behavior. Since its original publication, new results have been obtained and have been successfully incorporated into the model. However, the computer program used for nitrogenase simulations has not been generally available. Using kinetic schemes and assumptions previously outlined by Thorneley and Lowe, we report attempts to duplicate the original T&L kinetic simulation for Klebsiella pneumoniae nitrogenase catalysis using an updated simulation based on the MATHEMATICA programming format, which makes it more user-friendly and more readily available. Comparisons of our simulations with the original T&L simulations are generally in agreement, but in some cases serious discrepancy is observed. Possible reasons for the differences are discussed. In addition to duplicating the original T&L model, we report effects of updating it by including information that has come to light subsequent to its original publication.