title: Uncover the conserved property underlying sequence-distant and structure-similar proteins.
abstract: It is widely accepted that a protein's sequence determines its structure. The surprising finding that proteins of distant sequence can adopt similar 3D structures has raised interesting questions regarding underlying conserved properties that are essential for protein folding and stability. Uncovering the conserved properties may shed light on the folding mechanism of proteins and help with the development of computational tools for protein structure prediction. We compiled and analyzed a structure pair dataset of 66 high-resolution and low sequence identity (16-38%) soluble proteins. Structure deviation for each pair was confirmed by calculating its C(alpha) SiMax value and comparing its potential energy per residue. Analysis of favorable inter-residue interactions for each structure pair indicated that the average number of inter-residue interactions within each structure represents a conserved feature of homologous structures of distant sequence. Detailed comparison of individual types of interactions showed that the average number of either hydrophobic or hydrogen bonding interactions remains unchanged for each structure pair. These findings should be of help to improving the quality of homology models based on templates of low sequence identity, thus broadening the application of homology modeling techniques for protein studies.
authors.affiliation: Department of Bioinformatics and Computer Science, University of the Sciences in Philadelphia, Philadelphia, PA 19104, USA.
authors.forename: Jun
authors.initials: J
authors.lastname: Gao
authors.forename: Zhijun
authors.initials: Z
authors.lastname: Li
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D008956:Models, Chemical; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D012995:Solubility; D013816:Thermodynamics
chemical_list: D011506:Proteins