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09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Length variations amongst protein domain superfamilies and consequences on structure and function
Sankaran Sandhya1, Saane Sudha Rani, Barah Pankaj
1National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, India.
Plos One
|April 1, 2009
Summary
Insertions and deletions (indels) play diverse roles in protein domain superfamilies, influencing structural repeats, function, and interactions. Understanding indel impact is crucial for modeling new protein family members and refining sequence analysis filters.
Area of Science:
- Protein Bioinformatics
- Structural Biology
- Computational Biology
Background:
- Protein domains within superfamilies exhibit variable lengths.
- The structural and functional consequences of insertions and deletions (indels) within domain scaffolds are under investigation.
Purpose of the Study:
- To analyze the functional impact of length variations in protein domain superfamilies.
- To investigate the roles of indels in proteins with significant length differences.
Main Methods:
- Categorized domain superfamilies into 'length-deviant' (>30% length variation) and 'length-rigid' (<10% variation).
- Utilized an objective algorithm to delineate datasets for analyzing indel roles, structural repeats, functional variation, and protein-protein interactions.
- Examined 'domain contexts' in proteins tolerant to large length variations.
Main Results:
- 80% of top length-deviant superfamilies showed internal structural repeats; nearly half had diverse biological functions.
- Length-deviant superfamilies were more likely than length-rigid ones to feature internal structural repeats.
- Approximately 40% of length-deviant domains were part of multi-domain proteins involved in interactions.
Conclusions:
- Indels have specialized, superfamily-specific roles, influencing structural and functional feature accretion.
- Observed length variation trends and limits can guide the modeling of new superfamily members.
- Superfamily-specific length variation limits are relevant for selecting alignment length search filters in protein sequence analysis.
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