Relation between sequence and structure in membrane proteins

• DOI: 10.1093/bioinformatics/btt249
• Publication Date: 2013-05-16T01:00:44Z
• Authors: Mireia Olivella; Angel Gonzalez; Leonardo Pardo; Xavier Deupi
• Keywords: Sequence (biology)

Abstract Motivation: Integral polytopic membrane proteins contain only two types of folds in their transmembrane domains: α-helix bundles and β-barrels. The increasing number available crystal structures these permits an initial estimation how sequence variability affects the structure conservation domains. We, thus, aim to determine pairwise identity necessary maintain molecular architectures compatible with hydrophobic nature lipid bilayer. Results: Root-mean-square deviation (rmsd) were calculated from structural alignments pairs homologous sharing same fold. Analysis data reveals that segment so-called ‘twilight zone’ (20–35%) display high-structural similarity (rmsd < 1.5 Å). Moreover, a large group β-barrel low-sequence (<20%) still close 2.5 Thus, we conclude fold preservation regions requires less than for globular proteins. These findings have direct implications homology modeling evolutionary-related Contact: [e-mail] or [e-mail] Supplementary information: are at Bioinformatics online.