Sphericity of a protein via the beta-complex
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- Sphericity of a protein via the beta-complex
- Kim, Deok-Soo; Kim, Jae-Kwan; Won, Chung-In; Kim, Chong-Min; Park, Joon Young; Bhak, Jong Hwa
- β-complex; β-shape; PDB; Protein structure; Sphericity; Voronoi diagram
- Issue Date
- ELSEVIER SCIENCE INC
- JOURNAL OF MOLECULAR GRAPHICS & MODELLING, v.28, no.7, pp.636 - 649
- Molecular shape is a fundamental factor in determining the function of a molecule. As proteins tend to fold into globular shapes, the shape descriptor for protein sphericity is important in understanding molecular functions. In this paper, a definition of protein sphericity is introduced based on the recently developed geometric constructs of the β-complex and β-shape of a protein. The β-complex represents the Euclidean proximity among all the atoms in a protein, and the β-shape is the polyhedron contained within the boundary of the corresponding β-complex. Hence, the β-shape determines the proximity among the atoms on the boundary of a protein. Given the volume of a β-shape, the ratio between the surface area of a sphere with this volume and the surface area of the β-shape itself is a good measure to classify the sphericity of a protein, especially when the radius of a probe is 3.0 A. The presented measure is invariant to translation and rotation.
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