Proteome-wide comparison between the amino acid composition of domains and linkers

Publikationstyp:
Zeitschriftenaufsatz
Metadaten:
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

Datenquelle: Crossref

Andere Metadatenquellen:
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

Datenquelle: 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

Datenquelle: 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

Datenquelle: OPENSCIENCE.UB

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