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A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
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Comparative functional analysis of proteins containing low-complexity predicted amyloid regions
Bandana Kumari1, Ravindra Kumar1, Vipin Chauhan2,3
1Department of Biophysics, University of Delhi South Campus, New Delhi, India.
Peerj
|November 7, 2018
Summary
Low complexity regions (LCRs) in proteins vary in composition and amyloid-forming potential. Hydrophobic residue-rich LCRs are more prone to amyloid formation, impacting protein function.
Area of Science:
- Protein biochemistry and bioinformatics.
- Investigating protein structure-function relationships.
Background:
- Proteins contain low complexity regions (LCRs) with biased amino acid composition.
- LCRs are linked to uncontrolled expansion and amyloid formation.
- Comparative analysis of LCR behavior and amyloidogenic propensity is lacking.
Purpose of the Study:
- To comparatively analyze LCR behavior based on amino acid composition.
- To assess the association between LCR composition and amyloidogenic propensity.
- To explore functional characteristics of proteins with different LCR types.
Main Methods:
- Categorized LCRs by amino acid composition (homopolymers, charged, polar, hydrophobic).
- Analyzed LCR compositional patterns and amyloid propensity.
- Utilized DAVID for functional analysis of proteins with LCRs.
- Examined human proteins with LCR-mediated amyloid formation.
Main Results:
- Gln repeats were the most common homopolymeric LCRs; Met and aromatic repeats were least common.
- Negatively charged and polar LCRs were more frequent than positively charged and hydrophobic LCRs.
- Proteins with LCRs are often involved in transcription; Gly repeats associate with translation.
- Hydrophobic residue-rich LCRs showed higher amyloid formation propensity.
- Human proteins with amyloid-forming LCRs were linked to binding and catalytic activities.
Conclusions:
- Summarized common and rare LCRs, noting Asn repeats form the longest stretches.
- Demonstrated that LCRs' amyloid-forming potential varies significantly with amino acid composition.
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