Cavities and Atomic Packing in Protein Structures and Interfaces
Author Information
Author(s): Sonavane Shrihari, Chakrabarti Pinak
Primary Institution: Department of Biochemistry, Bose Institute, Calcutta, India
Hypothesis
The study investigates the relationship between cavities in protein structures and their atomic packing.
Conclusion
The analysis reveals that interfaces in proteins contain about twice the number of cavities compared to their tertiary structures, and these cavities are generally larger.
Supporting Evidence
- The total volume of cavities increases with the size of the protein.
- Larger cavities tend to be less spherical and are more likely to be solvated.
- Residues in β-strands are more frequently found lining the cavities compared to other structures.
Takeaway
This study looks at holes in proteins and how they are packed together, finding that when proteins interact, they create more and bigger holes.
Methodology
The study used a comparative analysis of cavities in protein structures and interfaces, employing Voronoi volume calculations.
Limitations
The study may not account for all variations in protein structures due to the resolution limits of the data.
Digital Object Identifier (DOI)
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