Proteome-wide comparison between the amino acid composition of domains and linkers
- Publication type:
- Journal article
- Metadata:
-
- Autoren
- Daniel Brüne
- Miguel A Andrade-Navarro
- Pablo Mier
- DOI
- 10.1186/s13104-018-3221-0
- eISSN
- 1756-0500
- Ausgabe der Veröffentlichung
- 1
- Zeitschrift
- BMC Research Notes
- Sprache
- en
- Artikelnummer
- 117
- Online publication date
- 2018
- Datum der Veröffentlichung
- 2018
- Status
- Published
- Herausgeber
- Springer Science and Business Media LLC
- Herausgeber URL
- http://dx.doi.org/10.1186/s13104-018-3221-0
- Datum der Datenerfassung
- 2019
- Titel
- Proteome-wide comparison between the amino acid composition of domains and linkers
- Ausgabe der Zeitschrift
- 11
Data source: Crossref
- Other metadata sources:
-
- Abstract
- <h4>Objective</h4>Amino acid composition is a sequence feature that has been extensively used to characterize proteomes of many species and protein families. Yet the analysis of amino acid composition of protein domains and the linkers connecting them has received less attention. Here, we perform both a comprehensive full-proteome amino acid composition analysis and a similar analysis focusing on domains and linkers, to uncover domain- or linker-specific differential amino acid usage patterns.<h4>Results</h4>The amino acid composition in the 38 proteomes studied showcase the greater variability found in archaea and bacteria species compared to eukaryotes. When focusing on domains and linkers, we describe the preferential use of polar residues in linkers and hydrophobic residues in domains. To let any user perform this analysis on a given domain (or set of them), we developed a dedicated R script called RACCOON, which can be easily used and can provide interesting insights into the compositional differences between a domain and its surrounding linkers.
- Addresses
- Institute of Pharmacy and Molecular Biotechnology, Ruprecht Karls University Heidelberg, 69120, Heidelberg, Germany.
- Autoren
- Daniel Brüne
- Miguel A Andrade-Navarro
- Pablo Mier
- DOI
- 10.1186/s13104-018-3221-0
- eISSN
- 1756-0500
- Externe Identifier
- PubMed Identifier: 29426365
- PubMed Central ID: PMC5807739
- Open access
- true
- ISSN
- 1756-0500
- Ausgabe der Veröffentlichung
- 1
- Zeitschrift
- BMC research notes
- Schlüsselwörter
- Bacteria
- Archaea
- Proteome
- Sequence Analysis, Protein
- Proteomics
- Amino Acid Sequence
- Catalytic Domain
- Eukaryota
- Sprache
- eng
- Medium
- Electronic
- Online publication date
- 2018
- Open access status
- Open Access
- Paginierung
- 117
- Datum der Veröffentlichung
- 2018
- Status
- Published
- Publisher licence
- CC BY
- Datum der Datenerfassung
- 2018
- Titel
- Proteome-wide comparison between the amino acid composition of domains and linkers.
- Sub types
- Comparative Study
- brief-report
- Journal Article
- Ausgabe der Zeitschrift
- 11
Files
https://bmcresnotes.biomedcentral.com/track/pdf/10.1186/s13104-018-3221-0 https://europepmc.org/articles/PMC5807739?pdf=render
Data source: Europe PubMed Central
- Abstract
- OBJECTIVE: Amino acid composition is a sequence feature that has been extensively used to characterize proteomes of many species and protein families. Yet the analysis of amino acid composition of protein domains and the linkers connecting them has received less attention. Here, we perform both a comprehensive full-proteome amino acid composition analysis and a similar analysis focusing on domains and linkers, to uncover domain- or linker-specific differential amino acid usage patterns. RESULTS: The amino acid composition in the 38 proteomes studied showcase the greater variability found in archaea and bacteria species compared to eukaryotes. When focusing on domains and linkers, we describe the preferential use of polar residues in linkers and hydrophobic residues in domains. To let any user perform this analysis on a given domain (or set of them), we developed a dedicated R script called RACCOON, which can be easily used and can provide interesting insights into the compositional differences between a domain and its surrounding linkers.
- Date of acceptance
- 2018
- Autoren
- Daniel Brüne
- Miguel A Andrade-Navarro
- Pablo Mier
- Autoren-URL
- https://www.ncbi.nlm.nih.gov/pubmed/29426365
- DOI
- 10.1186/s13104-018-3221-0
- eISSN
- 1756-0500
- Externe Identifier
- PubMed Central ID: PMC5807739
- Ausgabe der Veröffentlichung
- 1
- Zeitschrift
- BMC Res Notes
- Schlüsselwörter
- Amino acid composition
- Domains
- Linkers
- Amino Acid Sequence
- Archaea
- Bacteria
- Catalytic Domain
- Eukaryota
- Proteome
- Proteomics
- Sequence Analysis, Protein
- Sprache
- eng
- Country
- England
- Paginierung
- 117
- PII
- 10.1186/s13104-018-3221-0
- Datum der Veröffentlichung
- 2018
- Status
- Published online
- Datum, an dem der Datensatz öffentlich gemacht wurde
- 2018
- Titel
- Proteome-wide comparison between the amino acid composition of domains and linkers.
- Sub types
- Comparative Study
- Journal Article
- Ausgabe der Zeitschrift
- 11
Data source: PubMed
- Author's licence
- CC-BY
- Autoren
- Daniel Brüne
- Miguel Andrade
- Pablo Mier
- Hosting institution
- Universitätsbibliothek Mainz
- Sammlungen
- JGU-Publikationen
- Resource version
- Published version
- DOI
- 10.1186/s13104-018-3221-0
- Funding acknowledgements
- DFG, Open Access-Publizieren Universität Mainz / Universitätsmedizin
- File(s) embargoed
- false
- Open access
- true
- ISSN
- 1756-0500
- Zeitschrift
- BMC Research Notes
- Schlüsselwörter
- 570 Biowissenschaften
- 570 Life sciences
- Sprache
- eng
- Notes
- Andrade, Miguel veröffentlicht unter: Andrade-Navarro, Miguel A.
- Open access status
- Open Access
- Paginierung
- Art. 117
- Datum der Veröffentlichung
- 2018
- Public URL
- https://openscience.ub.uni-mainz.de/handle/20.500.12030/281
- Herausgeber
- BioMed Central
- Herausgeber URL
- http://dx.doi.org/10.1186/s13104-018-3221-0
- Datum der Datenerfassung
- 2019
- Datum, an dem der Datensatz öffentlich gemacht wurde
- 2019
- Zugang
- Public
- Titel
- Proteome-wide comparison between the amino acid composition of domains and linkers
- Ausgabe der Zeitschrift
- 11
Files
58799.pdf
Data source: OPENSCIENCE.UB
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