Regions with two amino acids in protein sequences: A step forward from homorepeats into the low complexity landscape

Publication type:
Journal article
Metadata:
Autoren
  • Pablo Mier
  • Miguel A Andrade-Navarro
Autoren-URL
https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000874658200014&DestLinkType=FullRecord&DestApp=WOS_CPL
DOI
10.1016/j.csbj.2022.09.011
Externe Identifier
  • Clarivate Analytics Document Solution ID: 5R7AF
  • PubMed Identifier: 36249567
ISSN
2001-0370
Zeitschrift
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
Schlüsselwörter
  • Protein sequence analysis
  • Low complexity regions
  • Linear motifs
  • polyXY
Paginierung
5516 - 5523
Datum der Veröffentlichung
2022
Status
Published
Titel
Regions with two amino acids in protein sequences: A step forward from homorepeats into the low complexity landscape
Sub types
  • Article
Ausgabe der Zeitschrift
20

Data source: Web of Science (Lite)

Other metadata sources:
Autoren
  • Pablo Mier
  • Miguel A Andrade-Navarro
DOI
10.1016/j.csbj.2022.09.011
ISSN
2001-0370
Zeitschrift
Computational and Structural Biotechnology Journal
Sprache
en
Paginierung
5516 - 5523
Datum der Veröffentlichung
2022
Status
Published
Herausgeber
Elsevier BV
Herausgeber URL
http://dx.doi.org/10.1016/j.csbj.2022.09.011
Datum der Datenerfassung
2024
Titel
Regions with two amino acids in protein sequences: A step forward from homorepeats into the low complexity landscape
Ausgabe der Zeitschrift
20

Data source: Crossref

Abstract
Low complexity regions (LCRs) differ in amino acid composition from the background provided by the corresponding proteomes. The simplest LCRs are homorepeats (or polyX), regions composed of mostly-one amino acid type. Extensive research has been done to characterize homorepeats, and their taxonomic, functional and structural features depend on the amino acid type and sequence context. From them, the next step towards the study of LCRs are the regions composed of two types of amino acids, which we call polyXY. We classify polyXY in three categories based on the arrangement of the two amino acid types 'X' and 'Y': direpeats (e.g. 'XYXYXY'), joined (e.g. 'XXXYYY') and shuffled (e.g. 'XYYXXY'). We developed a script to search for polyXY, and located them in a comprehensive set of 20,340 reference proteomes. These results are available in a dedicated web server called XYs, in which the user can also submit their own protein datasets to detect polyXY. We studied the distribution of polyXY types by amino acid pair XY and category, and show that polyXY in Eukaryota are mainly located within intrinsically disordered regions. Our study provides a first step towards the characterization of polyXY as protein motifs.
Addresses
  • Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany.
Autoren
  • Pablo Mier
  • Miguel A Andrade-Navarro
DOI
10.1016/j.csbj.2022.09.011
eISSN
2001-0370
Externe Identifier
  • PubMed Identifier: 36249567
  • PubMed Central ID: PMC9550522
Open access
true
ISSN
2001-0370
Zeitschrift
Computational and structural biotechnology journal
Sprache
eng
Medium
Electronic-eCollection
Online publication date
2022
Open access status
Open Access
Paginierung
5516 - 5523
Datum der Veröffentlichung
2022
Status
Published
Publisher licence
CC BY
Datum der Datenerfassung
2022
Titel
Regions with two amino acids in protein sequences: A step forward from homorepeats into the low complexity landscape.
Sub types
  • research-article
  • Journal Article
Ausgabe der Zeitschrift
20

Files

https://europepmc.org/articles/PMC9550522?pdf=render

Data source: Europe PubMed Central

Abstract
Low complexity regions (LCRs) differ in amino acid composition from the background provided by the corresponding proteomes. The simplest LCRs are homorepeats (or polyX), regions composed of mostly-one amino acid type. Extensive research has been done to characterize homorepeats, and their taxonomic, functional and structural features depend on the amino acid type and sequence context. From them, the next step towards the study of LCRs are the regions composed of two types of amino acids, which we call polyXY. We classify polyXY in three categories based on the arrangement of the two amino acid types 'X' and 'Y': direpeats (e.g. 'XYXYXY'), joined (e.g. 'XXXYYY') and shuffled (e.g. 'XYYXXY'). We developed a script to search for polyXY, and located them in a comprehensive set of 20,340 reference proteomes. These results are available in a dedicated web server called XYs, in which the user can also submit their own protein datasets to detect polyXY. We studied the distribution of polyXY types by amino acid pair XY and category, and show that polyXY in Eukaryota are mainly located within intrinsically disordered regions. Our study provides a first step towards the characterization of polyXY as protein motifs.
Date of acceptance
2022
Autoren
  • Pablo Mier
  • Miguel A Andrade-Navarro
Autoren-URL
https://www.ncbi.nlm.nih.gov/pubmed/36249567
DOI
10.1016/j.csbj.2022.09.011
Externe Identifier
  • PubMed Central ID: PMC9550522
ISSN
2001-0370
Zeitschrift
Comput Struct Biotechnol J
Schlüsselwörter
  • Linear motifs
  • Low complexity regions
  • Protein sequence analysis
  • polyXY
Sprache
eng
Country
Netherlands
Paginierung
5516 - 5523
PII
S2001-0370(22)00416-0
Datum der Veröffentlichung
2022
Status
Published online
Titel
Regions with two amino acids in protein sequences: A step forward from homorepeats into the low complexity landscape.
Sub types
  • Journal Article
Ausgabe der Zeitschrift
20

Data source: PubMed

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