Sphericity of a protein via the beta-complex.
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 beta-complex and beta-shape of a protein. The beta-complex represents the Euclidean proximity among all the atoms in a protein, and the beta-shape is the polyhedron contained within the boundary of the corresponding beta-complex. Hence, the beta-shape determines the proximity among the atoms on the boundary of a protein. Given the volume of a beta-shape, the ratio between the surface area of a sphere with this volume and the surface area of the beta-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.
Kim
Deok-Soo
DS
Department of Industrial Engineering, Hanyang University, 17 Haengdang-dong, Seongdong-gu, Seoul 133-791, South Korea. dskim@hanyang.ac.kr
Kim
Jae-Kwan
JK
Won
Chung-In
CI
Kim
Chong-Min
CM
Park
Joon Young
JY
Bhak
Jong
J
D003198:Computer Simulation; D030562:Databases, Protein; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013997:Time Factors
D011506:Proteins