Identifying Local Similarity in Protein Structures
Author Information
Author(s): Agarwal Garima, Mahajan Swapnil, Srinivasan Narayanaswamy, de Brevern Alexandre G.
Primary Institution: Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
Hypothesis
Can local conformational similarities in structurally variable regions of homologous proteins be identified using Protein Blocks-based alignment?
Conclusion
The study successfully identified local structural similarities in a significant number of structurally variable regions of homologous proteins, improving alignment accuracy.
Supporting Evidence
- 74% of structurally variable regions showed local conformational similarity after realignment.
- An increase of 21% in identified local similarities compared to classical alignment methods.
- Improved alignment scores were observed for 56% of the structurally variable regions.
Takeaway
The researchers found that even if two proteins look different overall, they can still have similar parts when looked at closely.
Methodology
The study used Protein Blocks to realign structurally variable regions of proteins and compared the results with previous alignments.
Limitations
The approach may not perform well in cases where the segments are conformationally distinct despite high sequence similarity.
Statistical Information
P-Value
p<2.2e-16
Statistical Significance
p<2.2e-16
Digital Object Identifier (DOI)
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