Facilitating folding of outer membrane proteins, roles of the periplasmic chaperone Skp and the outer membrane lipoprotein BamD

This thesis describes several important advancements in the understanding of the assembly of outer membrane proteins of Gram-negative bacteria like Escherichia coli. A first study was performed to identify binding regions in the trimeric chaperone Skp for outer membrane proteins. Skp is known to facilitate the passage of unfolded outer membrane proteins (OMPs) through the periplasm to the outer membrane (OM). A gene construct named “synthetic chaperone protein (scp)” gene was used to express a fusion protein (Scp) into the cytoplasm of E. coli. The scp gene was used as a template to design mutants of Scp suitable for structural and functional studies using site-directed spectroscopy. Fluorescence resonance energy transfer (FRET) was used to identify distances in Skp-OmpA complexes that separate regions in Scp and in outer membrane protein A (OmpA) from E. coli. For this study, single cysteine (Cys) mutants and single Cys - single tryptophan (Trp) double mutants of Scp were prepared. For FRET experiments, the cysteines were labeled with the tryptophan fluorescence energy acceptor IAEDANS. Single Trp mutants of OmpA were used as fluorescence energy donors. In the second part of this thesis, the function of BamD and the structure of BamD-Scp complexes were examined. BamD is an essential component of the β-barrel assembly machinery (BAM) complex of the OM of Gram-negative bacteria. Fluorescence spectroscopy was used to probe the interactions of BamD with lipid membranes and to investigate the interactions of BamD with possible partner proteins from the periplasm and from the OM. A range of single cysteine (Cys) and single tryptophan (Trp) mutants of BamD were prepared. A very important conclusion from the extensive FRET study is that the essential lipoprotein BamD interacts and binds to the periplasmic chaperone Skp. BamD contains tetratrico peptide repeat (TPR) motifs that are suggested to serve as docking sites for periplasmic chaperones such as Skp.

Anàlisi de les revistes indexades al Journal of Citation Reports del Social Science Citation Index. Període 1997-2005

En aquest estat de la qüestió, s’hi presenten els resultats d’una anàlisi sobre l’evolució i les característiques principals de les revistes de geografia incloses al Journal of Citation Reports dins de la versió del Social Science Citation Index i, per tant, amb factor d’impacte. El període d’estudi escollit ha estat el que va de 1997 a 2005, és a dir, al llarg dels darrers nou anys amb dades disponibles. En total, hi han aparegut incloses trenta-nou revistes, una bona part de les quals ha romàs a la llista durant tot el temps estudiat. Hi ha hagut deu publicacions que han estat situades entre les cinc amb més factor d’impacte de cada any, i cap no ha estat la primera més de dos anys seguits. S’han trobat divuit temàtiques diferents en el conjunt de les revistes, en destaquen les de caire generalista i les de geografia econòmica i regional. Una gran majoria dels volums està publicada per editorials, Blackwell Publishing n’és la més destacada. L’origen de les revistes és clarament anglosaxó, només n’hi trobem dues d’escrites en una altra llengua. La segona part de l’article descriu totes les publicacions contemplades en els nou anys estudiats, amb una petita ressenya de cadascuna

La Geografia i l'estudi dels boscos a Espanya

This article makes a revision of the most eminent contributions in Geography in relation to the forest study, starting with principal Spanish geographical journals, congress transactions and other bibliography about forest questions. A selection of the most eminent bibliography has been made paying special attention to three main subjects: forest and forest science history, forest and landscape description, and forest management

PvRON2, a new Plasmodium vivax rhoptry neck antigen

Background: Rhoptries are specialized organelles from parasites belonging to the phylum Apicomplexa; they secrete their protein content during invasion of host target cells and are sorted into discrete subcompartments within rhoptry neck or bulb. This distribution is associated with these proteins’ role in tight junction (TJ) and parasitophorous vacuole (PV) formation, respectively. Methods: Plasmodium falciparum RON2 amino acid sequence was used as bait for screening the codifying gene for the homologous protein in the Plasmodium vivax genome. Gene synteny, as well as identity and similarity values, were determined for ron2 and its flanking genes among P. falciparum, P. vivax and other malarial parasite genomes available at PlasmoDB and Sanger Institute databases. Pvron2 gene transcription was determined by RT-PCR of cDNA obtained from the P. vivax VCG-1 strain. Protein expression and localization were assessed by Western blot and immunofluorescence using polyclonal anti-PvRON2 antibodies. Co-localization was confirmed using antibodies directed towards specific microneme and rhoptry neck proteins. Results and discussion: The first P. vivax rhoptry neck protein (named here PvRON2) has been identified in this study. PvRON2 is a 2,204 residue-long protein encoded by a single 6,615 bp exon containing a hydrophobic signal sequence towards the amino-terminus, a transmembrane domain towards the carboxy-terminus and two coiled coil a-helical motifs; these are characteristic features of several previously described vaccine candidates against malaria. This protein also contains two tandem repeats within the interspecies variable sequence possibly involved in evading a host’s immune system. PvRON2 is expressed in late schizonts and localized in rhoptry necks similar to what has been reported for PfRON2, which suggests its participation during target cell invasion. Conclusions: The identification and partial characterization of the first P. vivax rhoptry neck protein are described in the present study. This protein is homologous to PfRON2 which has previously been shown to be associated with PfAMA-1, suggesting a similar role for PvRON2.

Development of designed site-directed pseudopeptide-peptido-mimetic immunogens as novel minimal subunit-vaccine candidates for malaria

Synthetic vaccines constitute the most promising tools for controlling and preventing infectious diseases. When synthetic immunogens are designed from the pathogen native sequences, these are normally poorly immunogenic and do not induce protection, as demonstrated in our research. After attempting many synthetic strategies for improving the immunogenicity properties of these sequences, the approach consisting of identifying high binding motifs present in those, and then performing specific changes on amino-acids belonging to such motifs, has proven to be a workable strategy. In addition, other strategies consisting of chemically introducing non-natural constraints to the backbone topology of the molecule and modifying the a-carbon asymmetry are becoming valuable tools to be considered in this pursuit. Non-natural structural constraints to the peptide backbone can be achieved by introducing peptide bond isosters such as reduced amides, partially retro or retro-inverso modifications or even including urea motifs. The second can be obtained by strategically replacing L-amino-acids with their enantiomeric forms for obtaining both structurally site-directed designed immunogens as potential vaccine candidates and their Ig structural molecular images, both having immunotherapeutic effects for preventing and controlling malaria.

Producció i caracterització de variants de la ribonucleasa pancreàtica humana dissenyades per a adquirir propietats citotòxiques

Amb la finalitat d'aprofundir en les bases moleculars de la citotoxicitat de les ribonucleases pancreàtiques, es van construir variants derivades de l'HP-RNasa seguint dues estratègies. En la primera, es van generar variants de l'enzim resistents a l'acció de l'inhibidor proteic de les ribonucleases (hRI), substituint residus implicats en la interfície de contacte entre la ribonucleasa i l'hRI. En la segona, es va addicionar el motiu RGD en regions de superfície de la proteïna implicades en la formació del complex amb l'hRI, a fi de promoure la seva interacció amb la membrana plasmàtica de les cèl·lules i a la vegada disminuir l'afinitat de les variants per l'hRI. Es va comprovar que només les variants portadores de substitucions múltiples adquirien la capacitat de resistència a l'hRI. L'estudi del percentatge d'inhibició de la síntesi proteica en cèl·lules incubades amb cadascuna de les variants va mostrar que només dues de les variants construïdes havien adquirit propietats citotòxiques. La citotoxicitat més elevada la va presentar una variant que no era resistent a l'hRI, amb valors que eren només entre 5 i 15 vegades inferiors als de l'onconasa. Aquest resultat demostrà que la sensibilitat a l'hRI no és necessàriament un paràmetre limitant per a la citotoxicitat de les ribonucleases. Cap de les variants que incorporava un motiu RGD presentà citotoxicitat, evidenciant que aquest motiu no és efectiu a fi de dotar les ribonucleases pancreàtiques de propietats citotòxiques. Es van estudiar les bases moleculars de la citotoxicitat de la variant més citotòxica. En primer lloc, l'anàlisi de la internalització per marcatge radioactiu d'aquesta variant en relació amb l'onconasa i amb altres variants de l'HP-RNasa no citotòxiques, va posar en evidència que només l'onconasa era internalitzada eficientment. Es descartava així la possibilitat que l'acció citotòxica de l'enzim estudiat fos conseqüència d'una major eficiència d'endocitosi. També es va comprovar que l'addició del motiu RGD no era capaç de promoure la internalització de les proteïnes amb més eficàcia. Per microscòpia confocal de fluorescència, les variants humanes només es van començar a detectar a l'interior de la cèl·lula a partir de les 24 h d'incubació. Totes les variants generades van presentar una eficiència catalítica superior al 50 % de l'activitat de la seva proteïna parental, PM5, indicant que probablement l'estructura del centre actiu no havia estat afectada de manera dràstica per les substitucions introduïdes. No obstant, en tots els casos es va produir una disminució en la termoestabilitat respecte a PM5. Aquest resultat indicà que la correlació descrita a la bibliografia entre l'increment de termoestabilitat i l'increment de citotoxicitat per les ribonucleases no sempre es compleix. Per microscòpia confocal es va comprovar que tant la proteïna més citotòxica, com una variant no citotòxica resistent a l'hRI, així com la proteïna parental, seguien la via de degradació lisosomal. Aquesta ruta de trànsit no va ser afectada per l'addició de drogues que alteren les vies de trànsit retrògrad (monensina i brefeldina A), però sí per l'addició de la bafilomicina A1, una droga que neutralitza el pH endosomal i que va actuar alentint el trànsit de les proteïnes als lisosomes. D'acord amb aquests resultats, els valors de citotoxicitat de les variants es van incrementar de manera significativa només en presència de bafilomicina A1, suggerint que les ribonucleases transloquen al citoplasma a partir d'algun punt de la via de trànsit endosomal. Es va comprovar que l'acció de la variant més citotòxica era deguda a que l'addició d'un segon motiu de tres Arg en PE5 dota a aquesta proteïna amb un senyal de transport nuclear. La fracció d'enzim que aconsegueix translocar al citoplasma a partir d'algun punt de la via endosomal previ als lisosomes, és conduït ràpidament al nucli de la cèl·lula per mitjà del mecanisme clàssic de transport actiu. Per la seva afinitat amb l'rRNA, l'enzim es concentra en el nuclèol, on probablement duu a terme la seva activitat catalítica. La interacció d'aquesta variant amb els receptors nucleocitoplasmàtics, les importines, impediria per altra banda el bloqueig de l'enzim per part de l'hRI. Els resultats obtinguts presenten una nova estratègia de disseny de ribonucleases citotòxiques, basada en l'addició de segments NLS a fi de promoure el transport nuclear dels enzims. Aquesta estratègia podria permetre superar limitacions que fins al moment han estat descrites com a limitants de la citotoxicitat de les ribonucleases pancreàtiques, com la sensibilitat a l'hRI o la baixa eficiència d'internalització.

Determinantes sociais condicionantes das altas clínicas dos utentes da rede nas UCCI: um estudo de caso

Introdução: O adiamento das altas clínicas nas Unidades de Cuidados Continuados Integrados (UCCI) por motivos sociais é actualmente considerado um dos principais motivos que impedem a integração atempada de novos clientes na Rede Nacional de Cuidados Continuados, RNCC, daqui em diante designada como a REDE. Este atraso tem impacto ao nível da recuperação e estabilização dos utentes, bem como ao nível de eficiência e eficácia da UCCI, não podendo deixar de se considerarem os aspectos sociais e económicos. Objectivo Geral: Identificar os determinantes que influenciam as altas clínicas em UCCI. Métodos e População do Estudo: Este é um estudo de caso colectivo, em que os dados observacionais, transversais, são recolhidos por meio de questionário de auto-relato (por cada área de intervenção directa) e por análise dos processos de consulta de pacientes. O objecto desta pesquisa abrange dois grupos: o grupo de amostra composto por 70 profissionais de saúde que lidam directamente com os utentes e o grupo amostra composto de utentes internados na UCCI L Nostrum, com alta clínica entre 1/1/2011 e 31/12/2012, e que foram integrados através da REDE. Foram recolhidos os dados de 293 utentes sendo objecto de estudo os casos de 83 utentes integrados através da REDE e com prolongamento de internamento por motivos sociais. Resultados: Na percepção dos profissionais de saúde, as respostas institucionais apresentam-se como a condicionante mais indicada, tanto para os utentes em geral, com 22 indicações (88%) como para os utentes da REDE, com 10 indicações (40%). Relativamente aos motivos familiares há referência de 76% para os utentes em geral e de 36% para os utentes da REDE. Os motivos económicos também apresentam, para os profissionais inquiridos, um valor expressivo (68%) nos utentes em geral, estando nos da REDE este factor condicionante a par com os motivos familiares (36%). Os motivos estruturais têm menor expressão tanto nos utentes em geral (32%) como nos utentes da REDE (16%). “Outros” para os utentes em geral, refere-se a dependência funcional (4%). Nos motivos familiares, para os utentes em geral, 23 (92%) foi mais vezes indicada a insuficiência de suporte familiar, para os utentes da REDE, 13 (52%). A ausência de suporte familiar, para os utentes em geral, representa 48% das respostas, seguindo-se o suporte inadequado (28%) e a ausência de cuidadores (24%). Para os utentes da REDE, o suporte inadequado apresenta-se como segundo motivo (7%), seguindo-se a ausência de suporte familiar (16%). Na percepção dos profissionais, os utentes da REDE estão também condicionados pela distância geográfica (8%) da sua área residencial. Em termos estruturais, os motivos mais assinalados pelos profissionais para a generalidade dos utentes foram as barreiras físicas à mobilidade (80%) e a habitação sem condições básicas de habitabilidade (78%). Os mesmos motivos foram assinalados para os utentes da REDE, barreiras físicas à mobilidade (40%) e habitação sem condições de habitabilidade (28%). No entanto, relativamente aos utentes em geral, a ausência de habitação (29%) e a distância geográfica (4%) também foram motivos assinalados. Dos motivos económicos percebidos pelos profissionais, a insuficiência de rendimentos é o factor mais assinalado pela generalidade dos utentes (84%) e pelos da REDE (68%), seguida da percepção da capacidade de reposta limitada das instituições, 64% para a generalidade dos utentes e 28% para os da REDE e por fim os tipos de respostas insuficientes para as necessidades individuais dos utentes (20% dos utentes em geral e 12% da REDE). No total dos dois anos, 2011 e 2012, verificaram-se na UCCI L Nostrum 293 prorrogações (100%) das quais 210 (71,6%) foram consideradas dentro do prazo e justificadas com motivos clínicos, enquanto 83 (28,3%) foram efectivamente protelamentos por motivos sociais, tendo em conta que nestes casos os utentes já não tinham critérios clínicos que justificassem a sua permanência na UCCI. Das 210 prorrogações consideradas dentro do prazo e justificadas com motivos clínicos, 93 (44,3%) foram-no por tempo de espera para transferência de UCCI. Em 2011, dos 146 utentes com alta protelada (100%), 50 utentes (34,2%) permaneceram na UCCI por motivos sociais, enquanto em 2012 houve registo de 33 casos de protelamento (22,4%) em 147 (100%) altas prorrogadas. Conclusões: Dos factores identificados como motivo de protelamento nos 83 utentes, estritamente por motivos sociais, destaca-se o protelamento de alta por espera de integração em equipamento/resposta adequada, nomeadamente lar ou serviços de apoio domiciliário (79,5%), seguindo-se a insuficiência de rendimentos do utente/familiares para contratação de serviços ou resposta institucional (74,7%), a inexistência de condições habitacionais para regresso ao domicílio (63,9%) e a insuficiência de suporte familiar (54,2%). Regista-se também a inadequação do suporte familiar (31,3%), a inexistência de suporte familiar (28,9%) e, em menor percentagem, a ausência de condições estruturais (13,3%). A ausência de domicílio (sem abrigo) (8,4%) e a ausência de rendimentos (4,8%) também foram factores inibidores da alta clínica. Dos 293 utentes identificados que tiveram protelamento da alta por motivos sociais verificou-se que 144 (49,1%) dos utentes permaneceram unicamente pela existência de condicionantes institucionais e familiares/estruturais. Aspectos éticos: ao longo deste estudo, foram assegurados e respeitados, todos os procedimentos de garantia da confidencialidade e rigor na recolha dos dados, e a não interferência nas dinâmicas da instituição, dos utentes e dos profissionais.

Honorarios [adaptaciones y refundiciones en De la Cuadra y Aguilera-Malta] (Dossier: Cuatro narradores del 30, relecturas en su centenario)

Se contrasta Honorarios, obra dramática de Aguilera-Malta, y «Honorarios», el cuento de José de la Cuadra que la inspiró. El diálogo entre los dos autores fue explícito en diversos textos, así como en sus respectivos mundos literarios: nombres de personajes, motivos, leyendas, mitos, formas, ideología y demandas, actitudes e intereses. De la Cuadra dialogó a su vez con otros creadores. «Honorarios», e.g., recrea y reinterpreta la figura del mítico fetiche Moloch, según lo representan Metrópolis, del cineasta Fritz Lang, y Salambó, de Gustave Flaubert, la narración aludida es también una refundición en torno al tema del poder omnipresente y cruel, que requiere insaciablemente de víctimas propiciatorias. De igual manera, en su proceso creativo y de búsqueda expresiva, Aguilera-Malta acostumbró remozar y reformular temas en diferentes géneros literarios –como el de la lucha del ser humano frente a las fuerzas hostiles de la naturaleza y la sociedad, interpretado en La isla virgen, El tigre y Jaguar–. En Honorarios, Aguilera-Malta se concentró en hallar la manera de transferir la trama del relato «Honorarios» al género dramático. El resultado es una eficaz refundición, en términos de la perspectiva histórico-política y de reflexiones sobre la función de la literatura.

A geometric algorithm for an artificial life form based on anachronistic methods

Modern methods of spawning new technological motifs are not appropriate when it is desired to realize artificial life as an actual real world entity unto itself (Pattee 1995; Brooks 2006; Chalmers 1995). Many fundamental aspects of such a machine are absent in common methods, which generally lack methodologies of construction. In this paper we mix classical and modern studies in order to attempt to realize an artificial life form from first principles. A model of an algorithm is introduced, its methodology of construction is presented, and the fundamental source from which it sprang is discussed.

Characterisation of an s-type low molecular weight glutenin subunit of wheat and its proline and glutamine-rich repetitive domain

The low molecular weight glutenin subunits (LMW-GS) are major components of the glutenin polymers which determine the elastomeric properties of wheat (Triticum aestivum L.) gluten and dough. They comprise a complex mixture of components and have proved to be difficult to purify for detailed characterisation. The mature LMW subunit proteins comprise two structural domains, with one domain consisting of repeated sequences based on short peptide motifs. DNA sequences encoding this domain and a whole subunit were expressed in Escherichia coli and the recombinant proteins purified. Detailed comparisons by spectroscopy (CD, FT-IR) and dynamic light scattering indicated that the repetitive and non-repetitive domains of the proteins formed different structures with the former having an extended conformation with an equilibrium between poly-L-proline II-like structure and type II’ b-turns, and the latter a more compact globular structure rich in a-helix. Although the structures of these two domains appear to form independently, dynamic light scattering of the whole subunit dissolved in trifluoroethanol(TFE) suggested that they interact, leading to a more compact conformation. These observations may have relevance to the role of the LMW-GS in gluten structure and functionality.

Phylogeny, function, and evolution of the cupins, a structurally conserved, functionally diverse superfamily of proteins

The cupin superfamily is a group of functionally diverse proteins that are found in all three kingdoms of life, Archaea, Eubacteria, and Eukaryota. These proteins have a characteristic signature domain comprising two histidine- containing motifs separated by an intermotif region of variable length. This domain consists of six beta strands within a conserved beta barrel structure. Most cupins, such as microbial phosphomannose isomerases (PMIs), AraC- type transcriptional regulators, and cereal oxalate oxidases (OXOs), contain only a single domain, whereas others, such as seed storage proteins and oxalate decarboxylases (OXDCs), are bi-cupins with two pairs of motifs. Although some cupins have known functions and have been characterized at the biochemical level, the majority are known only from gene cloning or sequencing projects. In this study, phylogenetic analyses were conducted on the conserved domain to investigate the evolution and structure/function relationships of cupins, with an emphasis on single- domain plant germin-like proteins (GLPs). An unrooted phylogeny of cupins from a wide spectrum of evolutionary lineages identified three main clusters, microbial PMIs, OXDCs, and plant GLPs. The sister group to the plant GLPs in the global analysis was then used to root a phylogeny of all available plant GLPs. The resulting phylogeny contained three main clades, classifying the GLPs into distinct subfamilies. It is suggested that these subfamilies correlate with functional categories, one of which contains the bifunctional barley germin that has both OXO and superoxide dismutase (SOD) activity. It is proposed that GLPs function primarily as SODs, enzymes that protect plants from the effects of oxidative stress. Closer inspection of the DNA sequence encoding the intermotif region in plant GLPs showed global conservation of thymine in the second codon position, a character associated with hydrophobic residues. Since many of these proteins are multimeric and enzymatically inactive in their monomeric state, this conservation of hydrophobicity is thought to be associated with the need to maintain the various monomer- monomer interactions. The type of structure-based predictive analysis presented in this paper is an important approach for understanding gene function and evolution in an era when genomes from a wide range of organisms are being sequenced at a rapid rate.

Microbial relatives of the seed storage proteins of higher plants: conservation of structure and diversification of function during evolution of the cupin superfamily.

This review summarizes the recent discovery of the cupin superfamily (from the Latin term "cupa," a small barrel) of functionally diverse proteins that initially were limited to several higher plant proteins such as seed storage proteins, germin (an oxalate oxidase), germin-like proteins, and auxin-binding protein. Knowledge of the three-dimensional structure of two vicilins, seed proteins with a characteristic beta-barrel core, led to the identification of a small number of conserved residues and thence to the discovery of several microbial proteins which share these key amino acids. In particular, there is a highly conserved pattern of two histidine-containing motifs with a varied intermotif spacing. This cupin signature is found as a central component of many microbial proteins including certain types of phosphomannose isomerase, polyketide synthase, epimerase, and dioxygenase. In addition, the signature has been identified within the N-terminal effector domain in a subgroup of bacterial AraC transcription factors. As well as these single-domain cupins, this survey has identified other classes of two-domain bicupins including bacterial gentisate 1, 2-dioxygenases and 1-hydroxy-2-naphthoate dioxygenases, fungal oxalate decarboxylases, and legume sucrose-binding proteins. Cupin evolution is discussed from the perspective of the structure-function relationships, using data from the genomes of several prokaryotes, especially Bacillus subtilis. Many of these functions involve aspects of sugar metabolism and cell wall synthesis and are concerned with responses to abiotic stress such as heat, desiccation, or starvation. Particular emphasis is also given to the oxalate-degrading enzymes from microbes, their biological significance, and their value in a range of medical and other applications.

Sequence analysis of the cupin gene family in Synechocystis PCC6803

The recently described cupin superfamily of proteins includes the germin and germinlike proteins, of which the cereal oxalate oxidase is the best characterized. This superfamily also includes seed storage proteins, in addition to several microbial enzymes and proteins with unknown function. All these proteins are characterized by the conservation of two central motifs, usually containing two or three histidine residues presumed to be involved with metal binding in the catalytic active site. The present study on the coding regions of Synechocystis PCC6803 identifies a previously unknown group of 12 related cupins, each containing the characteristic two-motif signature. This group comprises 11 single-domain proteins, ranging in length from 104 to 289 residues, and includes two phosphomannose isomerases and two epimerases involved in cell wall synthesis, a member of the pirin group of nuclear proteins, a possible transcriptional regulator, and a close relative-of a cytochrome c551 from Rhodococcus. Additionally, there is a duplicated, two-domain protein that has close similarity to an oxalate decarboxylase from the fungus Collybia velutipes and that is a putative progenitor of the storage proteins of land plants.

Nuclear magnetic resonance structure shows that the severe acute respiratory syndrome coronavirus-unique domain contains a macrodomain fold

The nuclear magnetic resonance (NMR) structure of a central segment of the previously annotated severe acute respiratory syndrome (SARS)-unique domain (SUD-M, for "middle of the SARS-unique domain") in SARS coronavirus (SARS-CoV) nonstructural protein 3 (nsp3) has been determined. SUD-M(513-651) exhibits a macrodomain fold containing the nsp3 residues 528 to 648, and there is a flexibly extended N-terminal tail with the residues 513 to 527 and a C-terminal flexible tail of residues 649 to 651. As a follow-up to this initial result, we also solved the structure of a construct representing only the globular domain of residues 527 to 651 [SUD-M(527-651)]. NMR chemical shift perturbation experiments showed that SUD-M(527-651) binds single-stranded poly(A) and identified the contact area with this RNA on the protein surface, and electrophoretic mobility shift assays then confirmed that SUD-M has higher affinity for purine bases than for pyrimidine bases. In a further search for clues to the function, we found that SUD-M(527-651) has the closest three-dimensional structure homology with another domain of nsp3, the ADP-ribose-1 ''-phosphatase nsp3b, although the two proteins share only 5% sequence identity in the homologous sequence regions. SUD-M(527-651) also shows three-dimensional structure homology with several helicases and nucleoside triphosphate-binding proteins, but it does not contain the motifs of catalytic residues found in these structural homologues. The combined results from NMR screening of potential substrates and the structure-based homology studies now form a basis for more focused investigations on the role of the SARS-unique domain in viral infection.

Zea mays annexins modulate cytosolic free Ca2+ and generate a Ca2+-permeable conductance

Regulation of reactive oxygen species and cytosolic free calcium ([Ca2+](cyt)) is central to plant function. Annexins are small proteins capable of Ca2+-dependent membrane binding or membrane insertion. They possess structural motifs that could support both peroxidase activity and calcium transport. Here, a Zea mays annexin preparation caused increases in [Ca2+] cyt when added to protoplasts of Arabidopsis thaliana roots expressing aequorin. The pharmacological profile was consistent with annexin activation (at the extracellular plasma membrane face) of Arabidopsis Ca2+-permeable nonselective cation channels. Secreted annexins could therefore modulate Ca2+ influx. As maize annexins occur in the cytosol and plasma membrane, they were incorporated at the intracellular face of lipid bilayers designed to mimic the plasma membrane. Here, they generated an instantaneously activating Ca2+-permeable conductance at mildly acidic pH that was sensitive to verapamil and Gd3+ and had a Ca2+-to-K+ permeability ratio of 0.36. These results suggest that cytosolic annexins create a Ca2+ influx pathway directly, particularly during stress responses involving acidosis. A maize annexin preparation also demonstrated in vitro peroxidase activity that appeared independent of heme association. In conclusion, this study has demonstrated that plant annexins create Ca2+-permeable transport pathways, regulate [Ca2+] cyt, and may function as peroxidases in vitro.