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Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Repeatability in protein sequences.

Mohamed Kamel1, Pablo Mier2, Abdelkamel Tari1

  • 1Department of Computer Science, Faculty of Exact Sciences, University of Bejaia, 06000 Bejaia, Algeria.

Journal of Structural Biology
|August 14, 2019
PubMed
Summary
This summary is machine-generated.

Low complexity regions (LCRs) in proteins can form structures, especially short repeats. Our new algorithm identifies these repeats, revealing unique patterns in yeast, human, fish, and plant proteins.

Keywords:
Amino acid short tandem repeatsComputational detection of sequence repeatsHomorepeatsLow complexity regionsRepeatabilityWeb tool

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Area of Science:

  • * Bioinformatics
  • * Structural Biology
  • * Genomics

Background:

  • * Low complexity regions (LCRs) in proteins exhibit distinct properties compared to globular proteins.
  • * Standard secondary structure rules are often inapplicable in LCRs due to biased amino acid distribution.
  • * LCRs, particularly homorepeats, can adopt unpredictable, context-dependent structures, suggesting a role in protein interactions.

Purpose of the Study:

  • * To develop an efficient algorithm for analyzing local repeatability in protein sequences.
  • * To identify and characterize regions with approximate short repeats within LCRs.
  • * To investigate the prevalence of short repeats across different organisms.

Main Methods:

  • * Development of a novel algorithm, REpeatability Scanner (RES), to quantify local sequence repeatability.
  • * Application of the RES algorithm to analyze protein sequences from Saccharomyces cerevisiae, humans, Danio rerio, and Arabidopsis thaliana.
  • * Comparative analysis of repeat patterns, focusing on length and approximation.

Main Results:

  • * Yeast proteins show a depletion of short, odd-length repeats, unlike human proteins.
  • * Danio rerio proteins exhibit a high frequency of length-two repeats.
  • * Arabidopsis thaliana proteins display an unusual abundance of length-seven repeats.
  • * The RES algorithm effectively identifies regions with approximate short repeats.

Conclusions:

  • * Short repeats within LCRs can induce structure, explaining their prevalence and role in protein interactions.
  • * The RES algorithm provides a tool for characterizing compositional bias and LCR variability across species.
  • * Organism-specific patterns in short repeat distribution suggest diverse evolutionary strategies for LCR utilization.