標題: Sequence Conservation, Radial Distance and Packing Density in Spherical Viral Capsids
作者: Chang, Chih-Min
Huang, Yu-Wen
Lee, Chi-Wen
Huang, Tsun-Tsao
Shih, Chung-Shiuan
Hwang, Jenn-Kang
生物資訊及系統生物研究所
Institude of Bioinformatics and Systems Biology
公開日期: 1-Jul-2015
摘要: The conservation level of a residue is a useful measure about the importance of that residue in protein structure and function. Much information about sequence conservation comes from aligning homologous sequences. Profiles showing the variation of the conservation level along the sequence are usually interpreted in evolutionary terms and dictated by site similarities of a proper set of homologous sequences. Here, we report that, of the viral icosahedral capsids, the sequence conservation profile can be determined by variations in the distances between residues and the centroid of the capsid - with a direct inverse proportionality between the conservation level and the centroid distance - as well as by the spatial variations in local packing density. Examining both the centroid and the packing density models against a dataset of 51 crystal structures of nonhomologous icosahedral capsids, we found that many global patterns and minor features derived from the viral structures are consistent with those present in the sequence conservation profiles. The quantitative link between the level of conservation and structural features like centroid-distance or packing density allows us to look at residue conservation from a structural viewpoint as well as from an evolutionary viewpoint.
URI: http://dx.doi.org/10.1371/journal.pone.0132234
http://hdl.handle.net/11536/128064
ISSN: 1932-6203
DOI: 10.1371/journal.pone.0132234
期刊: PLOS ONE
Volume: 10
Appears in Collections:Articles