A homology modeling method of an icosahedral viral capsid: inclusion of surrounding protein structures

A methodological development is presented for homology modeling of an icosahedrally symmetric assembly of proteins. In the method, a main-chain structure of an asymmetric unit of a protein assembly is constructed and structure refinement is performed, taking the surrounding symmetry-related proteins into consideration with rotational symmetry boundary conditions. To test the procedure, three models of a poliovirus capsid were constructed with different modeling conditions based on the X-ray structure of a rhinovirus capsid. Model S and model N were constructed with and without considering surrounding proteins, respectively. Model N2 was obtained by refinement in rotational symmetry boundary conditions of the structure of model N. The three models were compared with the X-ray structure of a poliovirus capsid. Root mean square deviations and C alpha distances indicate that model S is the most accurate. Examination of the intermolecular short contacts indicates that model S and model N2 are superior to model N, because they do not make severe intermolecular short contacts. Symmetric intermolecular interactions are important for both the structural fragment search and energy minimization to predict better loop structures. The programs developed in this study are thus valuable in homology modeling of an icosahedral viral capsid.