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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Rebelling for a reason: protein structural "outliers".
Gandhimathi Arumugam1, Anu G Nair, Sridhar Hariharaputran
1National Centre for Biological Sciences, Tata Institute of Fundamental Research, Gandhi Krishi Vigyana Kendra Campus, Bangalore, India.
Protein structural divergence can significantly impact function, even within the same superfamily. Careful consideration is needed when predicting protein function based solely on structural conservation, especially at low sequence identities.
Area of Science:
- Protein bioinformatics
- Structural biology
- Evolutionary biology
Background:
- Analysis of structural variation in protein domain superfamilies offers insights into evolutionary constraints.
- The PASS2 database organizes structure-based sequence alignments of distantly related proteins, highlighting structurally conserved regions.
Purpose of the Study:
- To analyze the impact of structural divergence on protein function within multi-member superfamilies.
- To investigate functional annotations of structural outliers ('rebels') in relation to structural variations.
Main Methods:
- Selection of multi-member superfamilies from the PASS2 superfamily alignment database.
- Analysis of functional annotations in the context of structural variations and outliers.
Main Results:
- Structural divergence within superfamilies can be functionally relevant.
- Functional similarities cannot always be extrapolated from structural conservation alone.
- Structural outliers ('rebels') exhibit distinct functional annotations.
Conclusions:
- Protein structure prediction and classification benefit from understanding evolutionary constraints.
- Functional annotations should be inherited with caution, particularly at low sequence identities, due to structural variations.
- Fold-function prediction requires careful consideration of structural divergence and its functional implications.
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