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  1. Using dynamics-based comparisons to predict nucleic acid binding sites in proteins: An application to OB-fold domains
    Author: Zen A.; De Chiara C.; Pastore A.; Micheletti C.
    Published: 2009

    Motivation: We have previously demonstrated that proteins may be aligned not only by sequence or structural homology, but also using their dynamical properties. Dynamics-based alignments are sensitive and powerful tools to compare even structurally... more

     

    Motivation: We have previously demonstrated that proteins may be aligned not only by sequence or structural homology, but also using their dynamical properties. Dynamics-based alignments are sensitive and powerful tools to compare even structurally dissimilar protein families. Here, we propose to use this method to predict protein regions involved in the binding of nucleic acids. We have used the OB-fold, a motif known to promote protein-nucleic acid interactions, to validate our approach. Results: We have tested the method using this well-characterized nucleic acid binding family. Protein regions consensually involved in statistically significant dynamics-based alignments were found to correlate with nucleic acid binding regions. The validated scheme was next used as a tool to predict which regions of the AXH-domain representatives (a sub-family of the OB-fold for which no DNA/RNA complex is yet available) are putatively involved in binding nucleic acids. The method, therefore, is a promising general approach for predicting functional regions in protein families on the basis of comparative large-scale dynamics. © The Author 2009. Published by Oxford University Press. All rights reserved.

     
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    Source: BASE Selection for Comparative Literature
    Language: English
    Media type: Article (journal)
    Format: Online
    Subjects: Amino Acid Motif; Binding Site; DNA; DNA-Binding Protein; Nucleic Acid Conformation; Protein Folding; RNA; RNA-Binding Protein; Sequence Alignment; Sequence Analysis; Protein; Software
  2. Modification and editing of RNA
    Published: ©1998
    Publisher:  ASM Press, Washington, DC

    Historical perspectives on RNA nucleoside modifications-- RNA-modifying and RNA-editing enzymes: methods for their identification-- Detection and structure analysis of modified nucleosides in RNA by mass spectrometry-- Incorporation of modified... more

    Access:
    Verlag (lizenzpflichtig)

    Location:
    Universität Potsdam, Universitätsbibliothek
    Inter-library loan:
    Unlimited inter-library loan, copies and loan

     

    Historical perspectives on RNA nucleoside modifications-- RNA-modifying and RNA-editing enzymes: methods for their identification-- Detection and structure analysis of modified nucleosides in RNA by mass spectrometry-- Incorporation of modified nucleotides into RNA for studies on RNA structure, function, and intermolecular interactions-- Biophysical and conformational properties of modified nucleosides in RNA (nuclear magnetic resonance studies)-- Effects of pseudouridylation on tRNA hydration and dynamics: a theoretical approach. Modulation role of modified nucleotides in RNA loop-loop interaction-- Mechanisms of RNA-modifying and -editing enzymes-- Structural basis of base exchange by tRNA guanine transglycosylases-- Biosynthesis and functions of modified nucleosides in eukaryotic mRNA-- Posttranscriptional modifications in the U small nuclear RNAs-- The pseudouridine residues of rRNA: number, location, biosynthesis, and function-- Small nucleolar RNAs guide the ribose methylations of eukaryotic rRNAs-- Fuctional aspects of the three modified nucleotides in yeast mitochondrial large-subunit rRNA. Regulatory aspects of rRNA modifications and pre-tRNA processing-- Editing of tRNA-- RNA editing by base conversion in plant organellar RNAs-- Apolipoprotein B mRNA editing-- Adenosine-to-inosine conversion in mRNA-- Nucleoside deaminases for cytidine and adenosine: comparison with deaminases acting on RNA-- Mitochondrial mRNA editing in kinetoplastid protozoa-- RNA editing in physarum mitochondria-- Contrascriptional paramyxovirus mRNA editing: a contradiction in trems?-- Intracellular locations of RNA-modifying enzymes. Genetics and regulation of base modification in the tRNA and rRNA of prokaryotes and eukaryotes-- Links between tRNA modification and metabolism and modified nucleosides as tumor markers-- Modified nucleosides in translation-- Importance of modified nucleotides in replication of retroviruses, plant pararetroviruses, and retrotransposons-- Modified nucleotides always were: an evolutionary model-- Chemical structures and classification of postranscriptionally modified nucleosides in RNA-- RNA editing types and characteristics. General properties of RNA-modifying and -editing enzymes-- Location and distribution of modified nucleotides in tRNA-- Modified nucleosides at positions 34 and 37 of tRNAs and their predicted coding capacities. This Comprehensive, current text explores the manifold ways in which living cells respond to genomic injury and alterations, including both spontaneous and environmentally induced DNA damage. With more than 4,000 complete references to primary research literature and over 380 color figures throughout, this book is an important text for all courses in DNA repair and mutagenesis. It will also serve as a major reference for all molecular biologists working in cancer biology, recombination, transcription and gene regulation, DNA replication, environmental studies, and biological evolution

     
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    Source: Union catalogues
    Language: English
    Media type: Ebook
    Format: Online
    ISBN: 9781683672685; 1683672682
    Other identifier:
    Subjects: RNA editing; RNA Editing; RNA Processing, Post-Transcriptional; 35.73 molecular genetics; RNA editing; RNS-Edierung; Aufsatzsammlung; RNA; Transcriptie (biochemie); Régulation génétique; ARN ; Édition; RNS
    Scope: 1 Online-Ressource (xiii, 596 pages), illustrations
    Notes:

    Includes bibliographical references and index
  3. RNA interference
    Published: 2005
    Publisher:  Elsevier Acad. Press, Amsterdam [u.a.]

    Location:
    Ostbayerische Technische Hochschule Amberg-Weiden / Hochschulbibliothek Amberg
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    Universitätsbibliothek Bayreuth
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    Universitätsbibliothek Erlangen-Nürnberg, Hauptbibliothek
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    Technische Universität München, Universitätsbibliothek
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    Universitätsbibliothek der LMU München
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    Universitätsbibliothek Regensburg
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    Universitätsbibliothek Würzburg
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    Content information
    Source: Union catalogues
    Language: English
    Media type: Ebook
    Format: Online
    ISBN: 0121827976; 9780121827977
    RVK Categories: WC 4355 ; WD 5355
    Series: Methods in enzymology ; 392
    Subjects: ARN; ARN - Édition; Inactivation génique; Petit ARN interférent; Gene silencing; RNA Interference; RNA editing; RNA; Small interfering RNA; Labortechnik; RNS-Interferenz
    Scope: 1 Online-Ressource
  4. RNA interference
    Contributor: Engelke, David R. (Komment.)
    Published: 2005
    Publisher:  Elsevier, Acad. Press, Amsterdam

    The newest volume in the critically acclaimed laboratory standard, Methods in Enzymology more

    Location:
    Technische Universität Bergakademie Freiberg, Bibliothek 'Georgius Agricola'
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    Universitätsbibliothek Freiburg
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    Universitätsbibliothek Heidelberg
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    Karlsruher Institut für Technologie, KIT-Bibliothek
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    Universitätsbibliothek Leipzig
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    The newest volume in the critically acclaimed laboratory standard, Methods in Enzymology

     
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    Content information
    Source: Union catalogues
    Contributor: Engelke, David R. (Komment.)
    Language: English
    Media type: Ebook
    Format: Online
    ISBN: 0121827976
    RVK Categories: WC 4355 ; WD 5355
    Edition: Online-Ausg.
    Series: Methods in enzymology ; 392
    Methods in enzymology 0076-6879 ; v. 392
    Subjects: RNA; RNA editing; Gene silencing; Small interfering RNA; ARN; ARN; Inactivation génique; Petit ARN interférent; RNA Interference; RNA; RNA editing; Gene silencing; Small interfering RNA
    Scope: Online-Ressource, illustrations (some color).
    Notes:

    Includes bibliographical references and indexes. - Made available through: Science Direct
  5. RNA interference
    Published: 2005
    Publisher:  Elsevier Acad. Press, Amsterdam [u.a.]

    Location:
    TU Berlin, Universitätsbibliothek
    Inter-library loan:
    Unlimited inter-library loan, copies and loan

    Location:
    Universität Potsdam, Universitätsbibliothek
    Inter-library loan:
    Unlimited inter-library loan, copies and loan
    Export to reference management software   RIS file
      BibTeX file
    Content information
    Source: Union catalogues
    Language: English
    Media type: Ebook
    Format: Online
    ISBN: 0121827976; 9780121827977
    RVK Categories: WC 4355 ; WD 5355
    Series: Methods in enzymology ; 392
    Subjects: ARN; ARN - Édition; Inactivation génique; Petit ARN interférent; Gene silencing; RNA Interference; RNA editing; RNA; Small interfering RNA; Labortechnik; RNS-Interferenz
    Scope: 1 Online-Ressource
  6. Modification and editing of RNA
    Published: ©1998
    Publisher:  ASM Press, Washington, DC

    Historical perspectives on RNA nucleoside modifications-- RNA-modifying and RNA-editing enzymes: methods for their identification-- Detection and structure analysis of modified nucleosides in RNA by mass spectrometry-- Incorporation of modified... more

    Access:
    Verlag (lizenzpflichtig)

    Location:
    Hochschule Aalen, Bibliothek
    Signature:
    eBook Wiley
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    Technische Universität Chemnitz, Universitätsbibliothek
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    Bibliotheks-und Informationssystem der Carl von Ossietzky Universität Oldenburg (BIS)
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    Universitätsbibliothek der Eberhard Karls Universität
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    Historical perspectives on RNA nucleoside modifications-- RNA-modifying and RNA-editing enzymes: methods for their identification-- Detection and structure analysis of modified nucleosides in RNA by mass spectrometry-- Incorporation of modified nucleotides into RNA for studies on RNA structure, function, and intermolecular interactions-- Biophysical and conformational properties of modified nucleosides in RNA (nuclear magnetic resonance studies)-- Effects of pseudouridylation on tRNA hydration and dynamics: a theoretical approach. Modulation role of modified nucleotides in RNA loop-loop interaction-- Mechanisms of RNA-modifying and -editing enzymes-- Structural basis of base exchange by tRNA guanine transglycosylases-- Biosynthesis and functions of modified nucleosides in eukaryotic mRNA-- Posttranscriptional modifications in the U small nuclear RNAs-- The pseudouridine residues of rRNA: number, location, biosynthesis, and function-- Small nucleolar RNAs guide the ribose methylations of eukaryotic rRNAs-- Fuctional aspects of the three modified nucleotides in yeast mitochondrial large-subunit rRNA. Regulatory aspects of rRNA modifications and pre-tRNA processing-- Editing of tRNA-- RNA editing by base conversion in plant organellar RNAs-- Apolipoprotein B mRNA editing-- Adenosine-to-inosine conversion in mRNA-- Nucleoside deaminases for cytidine and adenosine: comparison with deaminases acting on RNA-- Mitochondrial mRNA editing in kinetoplastid protozoa-- RNA editing in physarum mitochondria-- Contrascriptional paramyxovirus mRNA editing: a contradiction in trems?-- Intracellular locations of RNA-modifying enzymes. Genetics and regulation of base modification in the tRNA and rRNA of prokaryotes and eukaryotes-- Links between tRNA modification and metabolism and modified nucleosides as tumor markers-- Modified nucleosides in translation-- Importance of modified nucleotides in replication of retroviruses, plant pararetroviruses, and retrotransposons-- Modified nucleotides always were: an evolutionary model-- Chemical structures and classification of postranscriptionally modified nucleosides in RNA-- RNA editing types and characteristics. General properties of RNA-modifying and -editing enzymes-- Location and distribution of modified nucleotides in tRNA-- Modified nucleosides at positions 34 and 37 of tRNAs and their predicted coding capacities. This Comprehensive, current text explores the manifold ways in which living cells respond to genomic injury and alterations, including both spontaneous and environmentally induced DNA damage. With more than 4,000 complete references to primary research literature and over 380 color figures throughout, this book is an important text for all courses in DNA repair and mutagenesis. It will also serve as a major reference for all molecular biologists working in cancer biology, recombination, transcription and gene regulation, DNA replication, environmental studies, and biological evolution

     
    Export to reference management software   RIS file
      BibTeX file
    Source: Union catalogues
    Language: English
    Media type: Ebook
    Format: Online
    ISBN: 9781683672685; 1683672682
    Other identifier:
    Subjects: RNA editing; RNA Editing; RNA Processing, Post-Transcriptional; 35.73 molecular genetics; RNA editing; RNS-Edierung; Aufsatzsammlung; RNA; Transcriptie (biochemie); Régulation génétique; ARN ; Édition; RNS
    Scope: 1 Online-Ressource (xiii, 596 pages), illustrations
    Notes:

    Includes bibliographical references and index