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  • 1
    Online Resource
    Online Resource
    Origami in the outer membrane: the transmembrane arrangement of mitochondrial porins
    Canadian Science Publishing ; 2002
    In:  Biochemistry and Cell Biology Vol. 80, No. 5 ( 2002-10-01), p. 551-562
    Details
    In: Biochemistry and Cell Biology, Canadian Science Publishing, Vol. 80, No. 5 ( 2002-10-01), p. 551-562
    Abstract: Voltage-dependent anion-selective channels (VDAC), also known as mitochondrial porins, are key regulators of metabolite flow across the mitochondrial outer membrane. Porins from a wide variety of organisms share remarkably similar electrophysiological properties, in spite of considerable sequence dissimilarity, indicating that they share a common structure. Based on primary sequence considerations, analogy with bacterial porins, and circular dichroism analysis, it is agreed that VDAC spans the outer membrane as a β-barrel. However, the residues that form the antiparallel β-strands comprising this barrel remain unknown. Various predictive methods, largely based on the known structures of bacterial β-barrels, have been applied to the primary sequences of VDAC. Refinement and confirmation of these predictions have developed through numerous investigations of wild-type and variant porins, both in mitochondria and in artificial membranes. These experiments have involved VDAC from several sources, precluding the generation of a unified model. Herein, using the Neurospora VDAC sequence as a template, the published structural information and predictions have been reassessed to delineate a model that satisfies most of the available data.Key words: VDAC, mitochondrial porin, β-barrel.
    Type of Medium: Online Resource
    ISSN: 0829-8211 , 1208-6002
    URL: Article
    DOI: 10.1139/o02-149
    Language: English
    Publisher: Canadian Science Publishing
    Publication Date: 2002
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Homology Requirements for Double-Strand Break-Mediated Recombination in a Phage λ- td Intron Model System
    Oxford University Press (OUP) ; 1996
    In:  Genetics Vol. 143, No. 3 ( 1996-07-01), p. 1057-1068
    Details
    In: Genetics, Oxford University Press (OUP), Vol. 143, No. 3 ( 1996-07-01), p. 1057-1068
    Abstract: Many group I introns encode endonucleases that promote intron homing by initiating a double-strand break-mediated homologous recombination event. A td intron-phage λ model system was developed to analyze exon homology effects on intron homing and determine the role of the λ 5′–3′ exonuclease complex (Redαβ) in the repair event. Efficient intron homing depended on exon lengths in the 35- to 50-bp range, although homing levels remained significantly elevated above nonbreak-mediated recombination with as little as 10 bp of flanking homology. Although precise intron insertion was demonstrated with extremely limiting exon homology, the complete absence of one exon produced illegitimate events on the side of heterology. Interestingly, intron inheritance was unaffected by the presence of extensive heterology at the double-strand break in wild-type λ, provided that sufficient homology between donor and recipient was present distal to the heterologous sequences. However, these events involving heterologous ends were absolutely dependent on an intact Red exonuclease system. Together these results indicate that heterologous sequences can participate in double-strand break-mediated repair and imply that intron transposition to heteroallelic sites might occur at break sites within regions of limited or no homology.
    Type of Medium: Online Resource
    ISSN: 1943-2631
    URL: Article
    DOI: 10.1093/genetics/143.3.1057
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 1996
    detail.hit.zdb_id: 1477228-0
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    The evolutionary history of mitochondrial porins
    Springer Science and Business Media LLC ; 2007
    In:  BMC Evolutionary Biology Vol. 7, No. 1 ( 2007-12)
    Details
    In: BMC Evolutionary Biology, Springer Science and Business Media LLC, Vol. 7, No. 1 ( 2007-12)
    Abstract: Mitochondrial porins, or voltage-dependent anion-selective channels (VDAC) allow the passage of small molecules across the mitochondrial outer membrane, and are involved in complex interactions regulating organellar and cellular metabolism. Numerous organisms possess multiple porin isoforms, and initial studies indicated an intriguing evolutionary history for these proteins and the genes that encode them. Results In this work, the wealth of recent sequence information was used to perform a comprehensive analysis of the evolutionary history of mitochondrial porins. Fungal porin sequences were well represented, and newly-released sequences from stramenopiles, alveolates, and seed and flowering plants were analyzed. A combination of Neighbour-Joining and Bayesian methods was used to determine phylogenetic relationships among the proteins. The aligned sequences were also used to reassess the validity of previously described eukaryotic porin motifs and to search for signature sequences characteristic of VDACs from plants, animals and fungi. Secondary structure predictions were performed on the aligned VDAC primary sequences and were used to evaluate the sites of intron insertion in a representative set of the corresponding VDAC genes. Conclusion Our phylogenetic analysis clearly shows that paralogs have appeared several times during the evolution of VDACs from the plants, metazoans, and even the fungi, suggesting that there are no "ancient" paralogs within the gene family. Sequence motifs characteristic of the members of the crown groups of organisms were identified. Secondary structure predictions suggest a common 16 β-strand framework for the transmembrane arrangement of all porin isoforms. The GLK (and homologous or analogous motifs) and the eukaryotic porin motifs in the four representative Chordates tend to be in exons that appear to have changed little during the evolution of these metazoans. In fact there is phase correlation among the introns in these genes. Finally, our preliminary data support the notion that introns usually do not interrupt structural protein motifs, namely the predicted β-strands. These observations concur with the concept of exon shuffling, wherein exons encode structural modules of proteins and the loss and gain of introns and the shuffling of exons via recombination events contribute to the complexity of modern day proteomes.
    Type of Medium: Online Resource
    ISSN: 1471-2148
    URL: Article
    DOI: 10.1186/1471-2148-7-31
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2007
    detail.hit.zdb_id: 2041493-6
    detail.hit.zdb_id: 3053924-9
    SSG: 12
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