Investigation of hydrophobic moment and hydrophobicity properties for transmembrane alpha-helices.

ABSTRACT: Integral membrane proteins are the primary targets of novel drugs but are largely without solved structures. As a consequence, hydrophobic moment plot methodology is often used to identify putative transmembrane alpha-helices of integral membrane proteins, based on their local maximum mean hydrophobic moment () and the corresponding mean hydrophobicity (). To calculate these properties, the methodology identifies an optimal eleven residue window (L = 11), assuming an amino acid angular frequency, theta, fixed at 100 degrees. Using a data set of 403 transmembrane alpha-helix forming sequences, the relationship between and , and the effect of varying of L and / or theta on this relationship, was investigated. Confidence intervals for correlations between and <

SUBMITTER: Wallace J 

PROVIDER: S-EPMC516255 | biostudies-literature | 2004 Aug

REPOSITORIES: biostudies-literature