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1.
BMC Bioinformatics ; 19(1): 390, 2018 Oct 23.
Artigo em Inglês | MEDLINE | ID: mdl-30352578

RESUMO

BACKGROUND: The Ageing Factor Database AgeFactDB contains a large number of lifespan observations for ageing-related factors like genes, chemical compounds, and other factors such as dietary restriction in different organisms. These data provide quantitative information on the effect of ageing factors from genetic interventions or manipulations of lifespan. Analysis strategies beyond common static database queries are highly desirable for the inspection of complex relationships between AgeFactDB data sets. 3D visualisation can be extremely valuable for advanced data exploration. RESULTS: Different types of networks and visualisation strategies are proposed, ranging from basic networks of individual ageing factors for a single species to complex multi-species networks. The augmentation of lifespan observation networks by annotation nodes, like gene ontology terms, is shown to facilitate and speed up data analysis. We developed a new Javascript 3D network viewer JANet that provides the proposed visualisation strategies and has a customised interface for AgeFactDB data. It enables the analysis of gene lists in combination with AgeFactDB data and the interactive visualisation of the results. CONCLUSION: Interactive 3D network visualisation allows to supplement complex database queries by a visually guided exploration process. The JANet interface allows gaining deeper insights into lifespan data patterns not accessible by common database queries alone. These concepts can be utilised in many other research fields.


Assuntos
Envelhecimento/genética , Gráficos por Computador , Bases de Dados Factuais , Redes Reguladoras de Genes , Software , Ontologia Genética , Humanos , Longevidade/genética , Interface Usuário-Computador
2.
Nucleic Acids Res ; 42(Database issue): D892-6, 2014 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-24217911

RESUMO

AgeFactDB (http://agefactdb.jenage.de) is a database aimed at the collection and integration of ageing phenotype data including lifespan information. Ageing factors are considered to be genes, chemical compounds or other factors such as dietary restriction, whose action results in a changed lifespan or another ageing phenotype. Any information related to the effects of ageing factors is called an observation and is presented on observation pages. To provide concise access to the complete information for a particular ageing factor, corresponding observations are also summarized on ageing factor pages. In a first step, ageing-related data were primarily taken from existing databases such as the Ageing Gene Database--GenAge, the Lifespan Observations Database and the Dietary Restriction Gene Database--GenDR. In addition, we have started to include new ageing-related information. Based on homology data taken from the HomoloGene Database, AgeFactDB also provides observation and ageing factor pages of genes that are homologous to known ageing-related genes. These homologues are considered as candidate or putative ageing-related genes. AgeFactDB offers a variety of search and browse options, and also allows the download of ageing factor or observation lists in TSV, CSV and XML formats.


Assuntos
Envelhecimento/genética , Bases de Dados Genéticas , Animais , Humanos , Internet , Longevidade/genética , Fenótipo , Integração de Sistemas
3.
Nucleic Acids Res ; 41(Database issue): D692-9, 2013 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-23193285

RESUMO

Many sequence data repositories can give a quick and easily accessible overview on genomes and their annotations. Less widespread is the possibility to compare related genomes with each other in a common database environment. We have previously described the GenColors database system (http://gencolors.fli-leibniz.de) and its applications to a number of bacterial genomes such as Borrelia, Legionella, Leptospira and Treponema. This system has an emphasis on genome comparison. It combines data from related genomes and provides the user with an extensive set of visualization and analysis tools. Eukaryote genomes are normally larger than prokaryote genomes and thus pose additional challenges for such a system. We have, therefore, adapted GenColors to also handle larger datasets of small eukaryotic genomes and to display eukaryotic gene structures. Further recent developments include whole genome views, genome list options and, for bacterial genome browsers, the display of horizontal gene transfer predictions. Two new GenColors-based databases for two fungal species (http://fgb.fli-leibniz.de) and for four social amoebas (http://sacgb.fli-leibniz.de) were set up. Both new resources open up a single entry point for related genomes for the amoebozoa and fungal research communities and other interested users. Comparative genomics approaches are greatly facilitated by these resources.


Assuntos
Bases de Dados Genéticas , Eucariotos/genética , Genômica , Amebozoários/genética , Genoma Fúngico , Internet , Anotação de Sequência Molecular
4.
Nucleic Acids Res ; 37(Database issue): D37-40, 2009 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-18805906

RESUMO

DiProDB (http://diprodb.fli-leibniz.de) is a database of conformational and thermodynamic dinucleotide properties. It includes datasets both for DNA and RNA, as well as for single and double strands. The data have been shown to be important for understanding different aspects of nucleic acid structure and function, and they can also be used for encoding nucleic acid sequences. The database is intended to facilitate further applications of dinucleotide properties. A number of property datasets is highly correlated. Therefore, the database comes with a correlation analysis facility. Authors having determined new sets of dinucleotide property values are invited to submit these data to DiProDB.


Assuntos
DNA/química , Bases de Dados de Ácidos Nucleicos , Fosfatos de Dinucleosídeos/química , RNA/química , Conformação de Ácido Nucleico , Termodinâmica , Interface Usuário-Computador
5.
Bioinformatics ; 25(19): 2603-4, 2009 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-19605418

RESUMO

MOTIVATION: DiProGB is an easy to use new genome browser that encodes the primary nucleotide sequence by thermodynamical and geometrical dinucleotide properties. The nucleotide sequence is thus converted into a sequence graph. This visualization, supported by different graph manipulation options, facilitates genome analyses, because the human brain can process visual information better than textual information. Also, DiProGB can identify genomic regions where certain physical properties are more conserved than the nucleotide sequence itself. Most of the DiProGB tools can be applied to both, the primary nucleotide sequence and the sequence graph. They include motif and repeat searches as well as statistical analyses. DiProGB adds a new dimension to the common genome analysis approaches by taking into account the physical properties of DNA and RNA. AVAILABILITY AND IMPLEMENTATION: Source code and binaries are freely available for download at http://diprogb.fli-leibniz.de, implemented in C++ and supported on MS Windows and Linux (using e.g. WineHQ).


Assuntos
Biologia Computacional/métodos , Genoma , Genômica/métodos , Análise de Sequência de DNA/métodos , Análise de Sequência de RNA/métodos , Software , Sequência de Bases , Bases de Dados Genéticas , Internet , Nucleotídeos/química , Alinhamento de Sequência , Interface Usuário-Computador
6.
Nat Commun ; 10(1): 2459, 2019 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-31150008

RESUMO

The original version of this Article contained an error in the spelling of the author Jule Müller, which was incorrectly given as Julia Müller. Additionally, in Fig. 4a, the blue-red colour scale for fold change in ageing/disease regulation included a blue stripe in place of a red stripe at the right-hand end of the scale. These errors have been corrected in both the PDF and HTML versions of the Article.

7.
J Phys Chem A ; 112(18): 4336-41, 2008 May 08.
Artigo em Inglês | MEDLINE | ID: mdl-18380490

RESUMO

The structure and energy of A-tetrads with N6-H6...N3 H-bonds was studied using B3LYP and BH&H density functional theory. The planar A-tetrad with C(4h) symmetry is more stable than the nonplanar structures at C4 and S4 symmetry. This structure corresponds to a local energy minimum. The energies of the structures with N6-H6...N1 and N6-H6...N7 H-bonds studied previously are of similar magnitude. Structures of A-tetrad complexes with sodium and potassium were most stable at S4 symmetry, and similarly, sandwich complexes consisting of two tetrads and a single cation were most stable at S8 symmetry. Relative energies of sandwich complexes with different symmetries obtained with the B3LYP and BH&H methods were quite different. BH&H overestimates the interaction energies between hydrogen-bonded neighbor bases relative to B3LYP.


Assuntos
Adenina/química , Hidrogênio/química , Nitrogênio/química , Teoria Quântica , Ligação de Hidrogênio , Substâncias Intercalantes/química , Potássio/química , Sódio/química
8.
Mol Immunol ; 44(13): 3398-406, 2007 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-17399790

RESUMO

The common variant in the human complement Factor H gene (CFH), with Tyr402His, is linked to age-related macular degeneration (AMD), a prevalent disorder leading to visual impairment and irreversible blindness in elderly patients. Here we show that the risk variant CFH 402His displays reduced binding to C reactive protein (CRP), heparin and retinal pigment epithelial cells. This reduced binding can cause inefficient complement regulation at the cell surface, particularly when CRP is recruited to injured sites and tissue. In addition, we identify the Factor H-like protein 1 (FHL-1), an alternative splice product of the CFH gene as an additional protein that includes the risk residue 402, and thus confers risk for AMD. FHL-1 is expressed in the eye and the FHL-1 402His risk variant shows similar reduced cell binding and likely reduced complement regulatory functions on the cell surface. CFH and FHL-1 may act in concert in the eye and the reduced surface binding may result in inappropriate local complement control, which in turn can lead to inflammation, disturbance of local physiological homeostasis and progression to cell damage. As a consequence, these processes may lead to AMD pathogenesis.


Assuntos
Substituição de Aminoácidos/genética , Fator H do Complemento/deficiência , Fator H do Complemento/genética , Degeneração Macular/genética , Degeneração Macular/imunologia , Idoso de 80 Anos ou mais , Envelhecimento/genética , Animais , Linhagem Celular , Células Cultivadas , Proteínas Inativadoras do Complemento C3b , Fator H do Complemento/metabolismo , Fator H do Complemento/fisiologia , Feminino , Histidina/genética , Humanos , Degeneração Macular/metabolismo , Isoformas de Proteínas/deficiência , Isoformas de Proteínas/genética , Isoformas de Proteínas/fisiologia , Spodoptera/genética , Tirosina/genética
9.
Nat Commun ; 9(1): 327, 2018 01 30.
Artigo em Inglês | MEDLINE | ID: mdl-29382830

RESUMO

Disease epidemiology during ageing shows a transition from cancer to degenerative chronic disorders as dominant contributors to mortality in the old. Nevertheless, it has remained unclear to what extent molecular signatures of ageing reflect this phenomenon. Here we report on the identification of a conserved transcriptomic signature of ageing based on gene expression data from four vertebrate species across four tissues. We find that ageing-associated transcriptomic changes follow trajectories similar to the transcriptional alterations observed in degenerative ageing diseases but are in opposite direction to the transcriptomic alterations observed in cancer. We confirm the existence of a similar antagonism on the genomic level, where a majority of shared risk alleles which increase the risk of cancer decrease the risk of chronic degenerative disorders and vice versa. These results reveal a fundamental trade-off between cancer and degenerative ageing diseases that sheds light on the pronounced shift in their epidemiology during ageing.


Assuntos
Envelhecimento/genética , Doenças Cardiovasculares/genética , Diabetes Mellitus/genética , Neoplasias/genética , Doenças Neurodegenerativas/genética , Transcriptoma , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Envelhecimento/metabolismo , Envelhecimento/patologia , Animais , Encéfalo/crescimento & desenvolvimento , Encéfalo/metabolismo , Doenças Cardiovasculares/sangue , Doenças Cardiovasculares/patologia , Criança , Pré-Escolar , Doença Crônica , Diabetes Mellitus/sangue , Diabetes Mellitus/patologia , Fundulidae/genética , Fundulidae/crescimento & desenvolvimento , Fundulidae/metabolismo , Ontologia Genética , Genoma Humano , Humanos , Lactente , Fígado/crescimento & desenvolvimento , Fígado/metabolismo , Camundongos , Pessoa de Meia-Idade , Anotação de Sequência Molecular , Neoplasias/metabolismo , Neoplasias/patologia , Doenças Neurodegenerativas/sangue , Doenças Neurodegenerativas/patologia , Pele/crescimento & desenvolvimento , Pele/metabolismo , Peixe-Zebra/genética , Peixe-Zebra/crescimento & desenvolvimento , Peixe-Zebra/metabolismo
10.
Methods Mol Biol ; 395: 75-96, 2007.
Artigo em Inglês | MEDLINE | ID: mdl-17993668

RESUMO

GenColors (gencolors.fli-leibniz.de) is a new web-based software/database system aimed at an improved and accelerated annotation of prokaryotic genomes considering information on related genomes and making extensive use of genome comparison. It offers a seamless integration of data from ongoing sequencing projects and annotated genomic sequences obtained from GenBank. A variety of export/import filters manages an effective data flow from sequence assembly and manipulation programs (e.g., GAP4) to GenColors and back as well as to standard GenBank file(s). The genome comparison tools include best bidirectional hits, gene conservation, syntenies, and gene core sets. Precomputed UniProt matches allow annotation and analysis in an effective manner. In addition to these analysis options, base-specific quality data (coverage and confidence) can also be handled if available. The GenColors system can be used both for annotation purposes in ongoing genome projects and as an analysis tool for finished genomes. GenColors comes in two types, as dedicated genome browsers and as the Jena Prokaryotic Genome Viewer (JPGV). Dedicated genome browsers contain genomic information on a set of related genomes and offer a large number of options for genome comparison. The system has been efficiently used in the genomic sequencing of Borrelia garinii and is currently applied to various ongoing genome projects on Borrelia, Legionella, Escherichia, and Pseudomonas genomes. One of these dedicated browsers, the Spirochetes Genome Browser (sgb.fli-leibniz.de) with Borrelia, Leptospira, and Treponema genomes, is freely accessible. The others will be released after finalization of the corresponding genome projects. JPGV (jpgv.fli-leibniz.de) offers information on almost all finished bacterial genomes, as compared to the dedicated browsers with reduced genome comparison functionality, however. As of January 2006, this viewer includes 632 genomic elements (e.g., chromosomes and plasmids) of 293 species. The system provides versatile quick and advanced search options for all currently known prokaryotic genomes and generates circular and linear genome plots. Gene information sheets contain basic gene information, database search options, and links to external databases. GenColors is also available on request for local installation.


Assuntos
Bases de Dados Genéticas , Genômica , Internet
11.
BMC Genomics ; 7: 211, 2006 Aug 16.
Artigo em Inglês | MEDLINE | ID: mdl-16914037

RESUMO

BACKGROUND: At least three species of Borrelia burgdorferi sensu lato (Bbsl) cause tick-borne Lyme disease. Previous work including the genome analysis of B. burgdorferi B31 and B. garinii PBi suggested a highly variable plasmid part. The frequent occurrence of duplicated sequence stretches, the observed plasmid redundancy, as well as the mainly unknown function and variability of plasmid encoded genes rendered the relationships between plasmids within and between species largely unresolvable. RESULTS: To gain further insight into Borreliae genome properties we completed the plasmid sequences of B. garinii PBi, added the genome of a further species, B. afzelii PKo, to our analysis, and compared for both species the genomes of pathogenic and apathogenic strains. The core of all Bbsl genomes consists of the chromosome and two plasmids collinear between all species. We also found additional groups of plasmids, which share large parts of their sequences. This makes it very likely that these plasmids are relatively stable and share common ancestors before the diversification of Borrelia species. The analysis of the differences between B. garinii PBi and B. afzelii PKo genomes of low and high passages revealed that the loss of infectivity is accompanied in both species by a loss of similar genetic material. Whereas B. garinii PBi suffered only from the break-off of a plasmid end, B. afzelii PKo lost more material, probably an entire plasmid. In both cases the vls gene locus encoding for variable surface proteins is affected. CONCLUSION: The complete genome sequences of a B. garinii and a B. afzelii strain facilitate further comparative studies within the genus Borrellia. Our study shows that loss of infectivity can be traced back to only one single event in B. garinii PBi: the loss of the vls cassettes possibly due to error prone gene conversion. Similar albeit extended losses in B. afzelii PKo support the hypothesis that infectivity of Borrelia species depends heavily on the evasion from the host response.


Assuntos
Borrelia/genética , Genoma Bacteriano/genética , Seleção Genética , Borrelia/patogenicidade , Infecções por Borrelia/microbiologia , Borrelia burgdorferi/genética , Borrelia burgdorferi/patogenicidade , Cromossomos Bacterianos/genética , DNA Bacteriano/química , DNA Bacteriano/genética , Genes Bacterianos/genética , Humanos , Doença de Lyme/microbiologia , Plasmídeos/química , Plasmídeos/genética , Análise de Sequência de DNA , Especificidade da Espécie , Fatores de Tempo , Virulência
12.
Nucleic Acids Res ; 30(1): 253-4, 2002 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-11752308

RESUMO

The IMB Jena Image Library of Biological Macromolecules (http://www.imb-jena.de/IMAGE.html) is aimed at a better dissemination of information on three-dimensional biopolymer structures with an emphasis on visualization and analysis. It provides access to all structure entries deposited at the Protein Data Bank (PDB) and Nucleic Acid Database (NDB). In addition, basic information on the architecture of biological macromolecules is offered. Recent developments include a site database and an analysis tool that identifies all residues surrounding hetero components or sites according to geometrical criteria. This enables one to search for all structures with a certain pattern of amino acids/nucleotides/water adjacent to hetero components or sites. A new PDB/SWISS-PROT cross-reference database combines information from both PDB and SWISS-PROT, thus providing significantly more cross-references than either PDB or SWISS-PROT. The existing brief descriptions of X-ray, NMR and FTIR methods for structure determination are supplemented by information on circular dichroism.


Assuntos
Bases de Dados de Ácidos Nucleicos , Bases de Dados de Proteínas , Nucleotídeos/química , Proteínas/química , Animais , Carboidratos/química , Dicroísmo Circular , Gráficos por Computador , Cristalografia por Raios X , Imageamento Tridimensional , Armazenamento e Recuperação da Informação , Internet , Substâncias Macromoleculares , Ressonância Magnética Nuclear Biomolecular , Conformação de Ácido Nucleico , Polímeros/química , Conformação Proteica , Espectroscopia de Infravermelho com Transformada de Fourier
13.
Nat Commun ; 6: 10043, 2015 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-26620638

RESUMO

Ageing has been defined as a global decline in physiological function depending on both environmental and genetic factors. Here we identify gene transcripts that are similarly regulated during physiological ageing in nematodes, zebrafish and mice. We observe the strongest extension of lifespan when impairing expression of the branched-chain amino acid transferase-1 (bcat-1) gene in C. elegans, which leads to excessive levels of branched-chain amino acids (BCAAs). We further show that BCAAs reduce a LET-363/mTOR-dependent neuro-endocrine signal, which we identify as DAF-7/TGFß, and that impacts lifespan depending on its related receptors, DAF-1 and DAF-4, as well as ultimately on DAF-16/FoxO and HSF-1 in a cell-non-autonomous manner. The transcription factor HLH-15 controls and epistatically synergizes with BCAT-1 to modulate physiological ageing. Lastly and consistent with previous findings in rodents, nutritional supplementation of BCAAs extends nematodal lifespan. Taken together, BCAAs act as periphery-derived metabokines that induce a central neuro-endocrine response, culminating in extended healthspan.


Assuntos
Envelhecimento/metabolismo , Aminoácidos de Cadeia Ramificada/metabolismo , Caenorhabditis elegans/metabolismo , Envelhecimento/genética , Animais , Caenorhabditis elegans/genética , Caenorhabditis elegans/crescimento & desenvolvimento , Proteínas de Caenorhabditis elegans/genética , Proteínas de Caenorhabditis elegans/metabolismo , Feminino , Longevidade , Masculino , Camundongos/genética , Camundongos/crescimento & desenvolvimento , Camundongos/metabolismo , Camundongos Endogâmicos C57BL , Transaminases/genética , Transaminases/metabolismo , Peixe-Zebra/genética , Peixe-Zebra/crescimento & desenvolvimento , Peixe-Zebra/metabolismo
14.
J Biomol Struct Dyn ; 20(4): 507-17, 2003 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-12529150

RESUMO

We have carried out B3LYP hybrid density functional studies of complexes formed by cyclic cytosine-, guanine-, thymine-, uracil- and mixed guanine cytosine-tetrads with Li+, Na+ and K+ ions to determine their structures and interaction energies. The conformations studied have been restricted to a hydrogen bond pattern closely related to the tetrads observed in experimental nucleic acid structures. A comparison of the alkali metal ion/tetrad complexes with the tetrads without cations indicates that alkali metal ions modulate the tetrad structures significantly and that even the hydrogen bond pattern may change. Guanine-tetrad cation complexes show the strongest interaction energy compared to other tetrads that occur less frequently in experimental structures. The most stable G-tetrad/metal ion structure adopts a nearly planar geometry that is especially suitable for tetraplex formation, which requires approximately parallel tetrad planes. In the cytosine-tetrad there is a very large central cavity suitable for cation recognition, but the complexes adopt a non-planar structure unsuitable for stacking, except possibly for ions with very large radii. Uracil and thymine tetrads show a significant different characteristics which may contribute to the differences between DNA and RNA


Assuntos
Algoritmos , Citosina/química , Guanina/química , Modelos Químicos , Conformação Molecular , Timina/química , Uracila/química , Pareamento de Bases , Cátions Monovalentes/química , Ligação de Hidrogênio , Lítio/química , Modelos Moleculares , Potássio/química , Sódio/química , Eletricidade Estática , Termodinâmica
15.
Rejuvenation Res ; 15(6): 631-41, 2012 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-22950424

RESUMO

In an "aging society," health span extension is most important. As in 2010, talks in this series of meetings in Rostock-Warnemünde demonstrated that aging is an apparently very complex process, where computational work is most useful for gaining insights and to find interventions that counter aging and prevent or counteract aging-related diseases. The specific topics of this year's meeting entitled, "RoSyBA: Rostock Symposium on Systems Biology and Bioinformatics in Ageing Research," were primarily related to "Cancer and Aging" and also had a focus on work funded by the German Federal Ministry of Education and Research (BMBF). The next meeting in the series, scheduled for September 20-21, 2013, will focus on the use of ontologies for computational research into aging, stem cells, and cancer. Promoting knowledge formalization is also at the core of the set of proposed action items concluding this report.


Assuntos
Envelhecimento/fisiologia , Biologia Computacional , Pesquisa , Biologia de Sistemas , Animais , Caenorhabditis elegans/fisiologia , Senescência Celular , Dieta , Humanos , Camundongos , Estresse Fisiológico , Peixe-Zebra/fisiologia
16.
Rejuvenation Res ; 13(6): 763-7, 2010 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-21204651

RESUMO

Evidence is accumulating that the first genuine antiaging interventions (e.g., approved pharmaceutical, nutriceutical, and stem-cell-based therapies) will become available within the next decades. Model organism data, next-generation sequencing, and further advances call for sophisticated large-scale data analysis. To present the state-of-the art and to talk about upcoming tasks and challenges in the bioinformatics and systems biology of aging-related data, a workshop on Bioinformatics in Ageing Research convened leading experts from Europe on May 4-5, 2010, in Rostock/Warnemünde. This meeting report summarizes talks and gives some outlook into future developments.


Assuntos
Envelhecimento/fisiologia , Pesquisa Biomédica , Biologia Computacional , Congressos como Assunto , Animais , Bases de Dados como Assunto , Modelos Animais de Doenças , Drosophila melanogaster/fisiologia , Humanos , Camundongos , Transdução de Sinais , Células-Tronco/citologia , Biologia de Sistemas
18.
Brief Funct Genomic Proteomic ; 6(3): 220-39, 2007 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-17956938

RESUMO

The rapidly increasing amount of information on three-dimensional (3D) structures of biological macro-molecules has still an insufficient impact on genome analysis, functional genomics and proteomics as well as on many other fields in biomedicine including disease-related research. There are, however, attempts to make structural data more easily accessible to the bench biologist. As members of the world-wide Protein Data Bank (wwPDB), the RCSB Protein Data Bank (PDB), the Protein Data Bank Japan and the Macromolecular Structure Database are the primary information resources for 3D structures of proteins, nucleic acids, carbohydrates and complexes thereof. In addition, a number of secondary resources have been set up that also provide information on all currently known structures in a relatively comprehensive manner and not focusing on specific features only. They include PDBsum, the OCA browser-database for protein structure/function, the Molecular Modeling Database and the Jena Library of Biological Macromolecules--JenaLib. Both the primary and secondary resources often merge the information in the PDB files with data from other resources and offer additional analysis tools thereby adding value to the original PDB data. Here, we briefly describe these resources from a user's point of view and from a comparative perspective. It is our aim to guide researchers outside the structure biology field in getting the most out of the 3D structure resources.


Assuntos
Bases de Dados de Proteínas , Substâncias Macromoleculares/química , Conformação Proteica , Proteínas/química , Sequência de Aminoácidos , Gráficos por Computador , Bases de Dados Factuais , Modelos Moleculares , Dados de Sequência Molecular , Estrutura Molecular , Proteínas/genética , Alinhamento de Sequência , Análise de Sequência de Proteína , Homologia de Sequência de Aminoácidos
19.
J Mol Model ; 13(2): 335-45, 2007 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-17013632

RESUMO

Isoguanine tetraplexes and pentaplexes contain two or more stacked polyads with intercalating metal ions. We report here the results of a density functional study of sandwiched isoguanine tetrad and pentad complexes consisting of two polyads with Na(+), K(+) and Rb(+) ions at the B3LYP level. In comparison to single polyad metal ion complexes, there is a trend towards increased non-planarity of the polyads in the sandwich complexes. In general, the pentad sandwiches have relatively planar polyad structures, whereas the tetrad complexes contain highly non-planar polyad building blocks. As in other sandwich complexes and in metal ion complexes with single polyads, the metal ion-base interaction energy plays an essential role. In iG sandwich structures, this interaction energy is slightly larger than in the corresponding guanine sandwich complexes. Because the base-base interaction energy is even more increased in passing from guanine to isoguanine, the isoguanine sandwiches are thus far the only examples where the base-base interaction energy is larger than the base-metal ion interaction energy. Stacking interactions have been studied in smaller models consisting of two bases, retaining the geometry from the complete complex structures. From the data obtained at the B3LYP and BH&H levels and with Møller-Plesset perturbation theory, one can conclude that the B3LYP method overestimates the repulsion in stacked base dimers. For the complexes studied in this work, this is only of minor importance because the direct inter-tetrad or inter-pentad interaction is supplemented by a strong metal ion-base interaction. Using a microsolvation model, the metal ion preference K(+) approximately Rb(+) > Na(+) is found for tetrad complexes. On the other hand, for pentads the ordering is Rb(+) > K(+) > Na(+). In the latter case experimental data are available that agree with this prediction.


Assuntos
Guanina/química , Metais Alcalinos/química , Modelos Moleculares , Cátions/química , Ácidos Nucleicos/química , Termodinâmica
20.
J Comput Chem ; 26(4): 352-64, 2005 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-15648098

RESUMO

Nucleic acid tetraplexes and lipophilic self-assembling G-quadruplexes contain stacked base tetrads with intercalated metal ions as basic building blocks. Thus far, quantum-chemical studies have been used to explore the geometric and energetic properties of base tetrads with and without metal ions. Recently, for the first time, work on a sandwiched G-tetrad complex has been studied. We report here results of a systematic B3LYP density functional study on sandwiched G-, C-, U-, and T-tetrads with Na+ and K+ at different symmetries that substantially extend the recent work. The results include detailed information on total energies as well as on metal ion tetrad and base-base interaction energies. The geometrical parameters of the sandwiched metal ion complexes are compared to both experimental structures and to calculated geometries of complexes of single tetrads with metal ions. A microsolvation model explains the ion selectivity preference of K+ over Na+ in a qualitative sense.


Assuntos
Algoritmos , Citosina/química , Guanina/química , Modelos Moleculares , Conformação Molecular , Timina/química , Uracila/química , Pareamento de Bases , Ligação de Hidrogênio , Potássio/química , Sódio/química , Termodinâmica
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