![]() The Half-Sphere Exposure (HSE) adds directionality to this measurement by splitting the spherical distance cutoff into two halves ( Hamelryck, 2005). Another such metric is the Contact Number (CN) of a residue in a protein, which is the count of spatially close residues within a distance cutoff to a target residue. The solvent-Accessible Surface Area (ASA) is one such descriptor which measures the exposure of a residue to solvent (water) in its folded state. low and high solvent accessibility, respectively) residues is important as active sites are typically located on the surface of a protein. The distinction between buried and exposed (i.e. In addition to local backbone structural properties, global three-dimensional structures of proteins can be characterized by the residue solvent accessibility. These angles all form a complementary basis for local backbone structure, and have been predicted as both discrete states ( Kang et al., 1993) and continuous values ( Faraggi et al., 2012 Heffernan et al., 2015, 2017 Lyons et al., 2014 Xue et al., 2008). Backbone angles ϕ and ψ are measurements of the residue-wise torsion ( Ramachandran et al., 1963), whereas angles θ and τ are spread over 3 (dihedral about C α i − 1-C α i-C α i + 1) and 4 (torsion about the C α i-C α i + 1 bond) residues, respectively ( Korkut and Hendrickson, 2009). Recognizing secondary structure as a coarse-grained description of protein backbone, more recent efforts have been shifted to the prediction of continuously valued backbone torsion angles. The accuracy of secondary structure prediction has risen from 70% ( Rost and Sander, 1993) to the latest 85% ( Fang et al., 2018a), approaching the theoretical upper bounds of effective prediction accuracy of 88–90% ( Rost, 2001 Yang et al., 2018). This has been refined into either 3 or 8 local conformational states ( Kabsch and Sander, 1983). (1951) in their findings of helical and sheet hydrogen bonding patterns in a protein backbone. As a result, it is necessary to address simpler problems in both the prediction of one-dimensional structural properties, such as backbone secondary structure and sidechain solvent accessibility, and two-dimensional structural properties, such as residue-residue contact maps.īackbone secondary structure was first described by Pauling et al. The main challenge stems from the exorbitantly large conformational space of a protein chain and the lack of an accurate energy function to model the folding process ( Zhou et al., 2011). Deriving a protein’s structure from its sequence alone remains an unsolved problem since its inception over 50 years ago ( Gibson and Scheraga, 1967 Yang et al., 2018).
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |