Structural biology of plasmodial proteins

Malaria is a global disease infecting several million individuals annually. Malarial infection is particularly severe in the poorest parts of the world and is a major drain on their limited resources. Development of drug resistance and absence of a preventive vaccine have led to an immediate necessity for identifying new drug targets to combat malaria. Understanding the intricacies of parasite biology is essential to design novel intervention strategies that can prevent the growth of the parasite. The structural biology approach towards this goal involves the identification of key differences in the structures of the human and parasite enzymes and the determination of unique protein structures essential for parasite survival. This review covers the work on structural biology of plasmodial proteins carried out during the period of January 2006 to June 2007.     

Structural biology of plasmid segregation proteins

DNA segregation, or partition, ensures stable genome transmission during cell division. In prokaryotes, partition is best understood for plasmids, which serve as tractable model systems to decipher the molecular underpinnings of this process. Plasmid partition is mediated by par systems, composed of three essential elements: a centromere-like site and the proteins ParA and ParB. In the first step, ParB binds the centromere to form a large segrosome. Subsequently, ParA, an ATPase, binds the segrosome and mediates plasmid separation. Recently determined ParB-centromere structures have revealed key insights into segrosome assembly, whereas ParA structures have shed light on the mechanism of plasmid separation. These structures represent important steps in elucidating the molecular details of plasmid segregation.     

Structural biology of the Bcl-2 family of proteins

The proteins of the Bcl-2 family are important regulators of programmed cell death. Structural studies of Bcl-2 family members have provided many important insights into their molecular mechanism of action and how members of this family interact with one another. To date, structural studies have been performed on six Bcl-2 family members encompassing both anti- (Bcl-x(L), Bcl-2, KSHV-Bcl-2, Bcl-w) and pro-apoptotic (Bax, Bid) members. They all show a remarkably similar fold despite an overall divergence in amino acid sequence and function (pro-apoptotic versus anti-apoptotic). The three-dimensional structures of Bcl-2 family members consist of two central, predominantly hydrophobic alpha-helices surrounded by six or seven amphipathic alpha-helices of varying lengths. A long, unstructured loop is present between the first two alpha-helices. The structures of the Bcl-2 proteins show a striking similarity to the overall fold of the pore-forming domains of bacterial toxins. This finding led to experiments which demonstrated that Bcl-x(L), Bcl-2, and Bax all form pores in artificial membranes. A prominent hydrophobic groove is present on the surface of the anti-apoptotic proteins. This groove is the binding site for peptides that mimic the BH3 region of various pro-apoptotic proteins such as Bak and Bad. Structures of Bcl-x(L) in complex with these BH3 peptides showed that they bind as an amphipathic alpha-helix and make extensive hydrophobic contacts with the protein. These data have not only helped to elucidate the interactions important for hetero-dimerization of Bcl-2 family members but have also been used to guide the discovery of small molecules that block Bcl-x(L) and Bcl-2 function. In the recently determined structure of the anti-apoptotic Bcl-w protein, the protein was also found to have a hydrophobic groove on its surface capable of binding BH3-containing proteins and peptides. However, in the native protein an additional carboxy-terminal alpha-helix interacts with the hydrophobic groove. This is reminiscent of how the carboxy-terminal alpha-helix of the pro-apoptotic protein Bax binds into its hydrophobic groove. This interaction may play a regulatory role and for Bax may explain why it is found predominately in the cytoplasm prior to activation. The hydrophobic groove of the pro-apoptotic protein, Bid protein, is neither as long nor as deep as that found in Bcl-x(L), Bcl-2, or Bax. In addition, Bid contains an extra alpha-helix, which is located between alpha1 and alpha2 with respect to Bcl-x(L), Bcl-2, and Bax. Although there are still many unanswered questions regarding the exact mechanism by which the Bcl-2 family of proteins modulates apoptosis, structural studies of these proteins have deepened our understanding of apoptosis on the molecular level.     

氮沉降对热带亚热带森林土壤氮循环微生物过程的影响研究进展

近年来,高速的城市化和工业化建设导致全球大气氮沉降量逐年递增,其中热带亚热带地区氮沉降量显著高于全球平均水平,而大部分热带亚热带森林土壤趋近氮饱和状态,氮沉降增加将持续向土壤输入外源活性氮,极易导致土壤氮过剩,进而破环整个森林生态系统氮循环的平衡。我国热带亚热带地区经济发展快速,氮沉降增加导致的土壤养分失衡和林地退化等生态问题日益凸显,森林土壤氮循环对大气氮沉降的响应及适应机制已引起了学术界的广泛关注。研究表明氮循环各环节均由特定的功能微生物驱动完成,明确氮沉降增加对热带亚热带森林土壤氮循环功能微生物及其介导的关键过程的影响,对评价未来氮沉降增加背景下全球森林土壤氮循环的响应及驱动机制有重要作用,可为促进我国热带亚热带地区森林修复、生态环境的改善与提升提供科学支撑。鉴于此,本文综述了热带亚热带森林土壤氮循环主要过程（如固氮、硝化、反硝化、厌氧氨氧化等）及其功能微生物群落丰度、活性、组成等对氮沉降增加的响应,同时分析了这些功能微生物的群落特征与主要环境因子（如NH₄⁺、NO₃^-、有机碳、pH、含水量等）的关联性。在此基础上探讨了氮沉降增加下功能微生物对热带亚热带森林土壤氮循环的调控作用,重点探讨了功能微生物如何通过改变丰度与群落组成而影响氮循环过程,并对目前研究中存在的主要问题与未来研究重点进行了简要剖析。     

禁牧对半干旱草地土壤氮循环功能基因丰度和氮储量的影响

以黄土高原云雾山不同禁牧(0、7、18、27和35年)草地为对象,研究禁牧对不同土层(0～10、10～20、20～40和40～60 cm)土壤氮循环微生物功能基因(nifH、amoA-AOA、amoA-AOB、narG、nirK、nirS和nosZ)丰度的影响,并分析了土壤氮循环微生物功能基因与土壤氮储量之间的关系.结果表明: 与放牧相比,禁牧35年提高了nifH和amoA-AOB的基因丰度,分别增加了67.8%和17.6%;禁牧降低了nirK基因丰度.表层土壤(0～10 cm)nifH、narG和nirS基因丰度显著高于深层土壤(20～40和40～60 cm),表明nifH、narG和nirS基因具有表聚效应.禁牧提高了土壤氮储量,在27年时0～60 cm土层土壤氮储量最高(20.96 mg·hm^-2),说明27年可能为最适禁牧年限.nifH、amoA-AOA和amoA-AOB基因丰度与氮储量具有显著线性关系,表明含有这些基因的微生物对于提高土壤氮储量具有重要作用.土壤全氮、容重以及速效磷含量是影响土壤氮循环基因的主要因素.本研究结果为深入理解土壤氮循环过程及退化草地的恢复提供了科学参考.     

Physiological function and catalytic versatility of bacterial multihaem cytochromes c involved in nitrogen and sulfur cycling

Bacterial MCCs (multihaem cytochromes c) represent widespread respiratory electron-transfer proteins. In addition, some of them convert substrates such as nitrite, hydroxylamine, nitric oxide, hydrazine, sulfite, thiosulfate or hydrogen peroxide. In many cases, only a single function is assigned to a specific MCC in database entries despite the fact that an MCC may accept various substrates, thus making it a multifunctional catalyst that can play diverse physiological roles in bacterial respiration, detoxification and stress defence mechanisms. The present article briefly reviews the structure, function and biogenesis of selected MCCs that catalyse key reactions in the biogeochemical nitrogen and sulfur cycles.     

Structural and functional diversity of adaptor proteins involved in tyrosine kinase signalling

Adaptors are proteins of multi-modular structure without enzymatic activity. Their capacity to organise large, temporary protein complexes by linking proteins together in a regulated and selective fashion makes them of outstanding importance in the establishment and maintenance of specificity and efficiency in all known signal transduction pathways. This review focuses on the structural and functional characterisation of adaptors involved in tyrosine kinase (TK) signalling. TK-linked adaptors can be distinguished by their domain composition and binding specificities. However, such structural classifications have proven inadequate as indicators of functional roles. A better way to understand the logic of signalling networks might be to look at functional aspects of adaptor proteins such as signalling specificity, negative versus positive contribution to signal propagation, or their position in the signalling hierarchy. All of these functions are dynamic, suggesting that adaptors have important regulatory roles rather than acting only as stable linkers in signal transduction.     

Structural biology of solute carrier (SLC) membrane transport proteins

The human solute carriers (SLCs) comprise over 400 different transporters, organized into 65 families (http://slc.bioparadigms.org/) based on their sequence homology and transport function. SLCs are responsible for transporting extraordinarily diverse solutes across biological membranes, including inorganic ions, amino acids, lipids, sugars, neurotransmitters and drugs. Most of these membrane proteins function as coupled symporters (co-transporters) utilizing downhill ion (H⁺ or Na⁺) gradients as the driving force for the transport of substrate against its concentration gradient into cells. Other members work as antiporters (exchangers) that typically contain a single substrate-binding site with an alternating access mode of transport, while a few members exhibit channel-like properties. Dysfunction of SLCs is correlated with numerous human diseases and therefore they are potential therapeutic drug targets. In this review, we identified all of the SLC crystal structures that have been determined, most of which are from prokaryotic species. We further sorted all the SLC structures into four main groups with different protein folds and further discuss the well-characterized MFS (major facilitator superfamily) and LeuT (leucine transporter) folds. This review provides a systematic analysis of the structure, molecular basis of substrate recognition and mechanism of action in different SLC family members.     

The evolution of nitrogen cycling

Based upon arguments concerning properties of the environment and the energetics of nitrogen transformation reactions, new hypotheses regarding their evolution are presented. These hypotheses are supported by new calculations and observations germane to understanding the evolution of the nitrogen cycle. From calculations of shock production by meteor impact, we suggest that impact produced fixed nitrogen could have resulted in the entire reservoir of Earth's N₂ being converted into fixed nitrogen at the end of accretion. We have significantly improved upon previous calculations of the abiotic fixation rate on the early earth and find a rate of fixation by lightning of 1–3 × 10¹⁶ Molecules NO/J, which is 2 to 3 times greater than previous estimates. This strengthens the suggestion, corroborated by the predominance of a single nitrogenase enzyme, that biological nitrogen fixation may have been a late evolutionary development, after the development of an aerobic atmosphere. In addition, we show for the first time that HNO, predicted to be the main product of atmospheric photochemical reactions involving NO on the primitive Earth by photochemical models, would eventually become NO₂ ^– and NO₃ ^– after reaching the Earth's surface. Based upon microbe-environment interactions on an ecological as well as a biochemical scale we suggest that denitrification arose prior to aerobic respiration and that nitrification arose after the advent of an aerobic atmosphere. We hypothesize the following evolutionary sequence for the biological transformation of nitrogen compounds: Ammonification Denitrification Nitrification Nitrogen fixation.     

Structural biology

A selection of interesting papers that were published in the two months before our press date in major journals most likely to report significant results in structural biology.     

Structural biology

A selection of interesting papers that were published in the two months before our press date in major journals most likely to report significant results in structural biology.     

Structural biology

A selection of interesting papers that were published in the two months before our press date in major journals most likely to report significant results in structural biology.     

Structural biology

Protein crystallography has become a major technique for understanding cellular processes. This has come about through great advances in the technology of data collection and interpretation, particularly the use of synchrotron radiation. The ability to express eukaryotic genes in Escherichia coli is also important. Analysis of known structures shows that all proteins are built from about 1000 primeval folds. The collection of all primeval folds provides a basis for predicting structure from sequence. At present about 450 are known. Of the presently sequenced genomes only a fraction can be related to known proteins on the basis of sequence alone. Attempts are being made to determine all (or as many as possible) of the structures from some bacterial genomes in the expectation that structure will point to function more reliably than does sequence. Membrane proteins present a special problem. The next 20 years may see the experimental determination of another 40,000 protein structures. This will make considerable demands on synchrotron sources and will require many more biochemists than are currently available. The availability of massive structure databases will alter the way biochemistry is done.     

Structural biology

A selection of interesting papers that were published in the two months before our press date in major journals most likely to report significant results in structural biology.     

Structural biology

A selection of interesting papers that were published in the two months before our press date in major journals most likely to report significant results in structural biology.     

Structural biology

A selection of interesting papers that were published in the two months before our press date in major journals most likely to report significant results in structural biology.     

Structural biology

A selection of interesting papers that were published in the two months before our press date in major journals most likely to report significant results in structural biology.