title: A knowledge-based scale for amino acid membrane propensity.
abstract: In this article, a membrane-propensity scale for amino acids is derived using only two ingredients: (i) a set of transmembrane helices segments from membrane protein crystal structures and (ii) the request that each component of the set has a free energy lower than that of a typical soluble protein sequence of the same length. Although the most widely used hydropathy scales satisfy this request, we use an optimization procedure that allows for extraction of an optimal scale, which correlates equally well with those scales. We show that, if the choice of the sequence database is accurate, significant knowledge-based scales, which are robust with respect to changes in the learning set, can be easily derived. The obtained scales can be used for transmembrane helices prediction. The predictive power of one of these scales is tested on membrane proteins, soluble proteins, and signal peptides databases, finding that its performances is comparable with those of the hydropathy scales.
authors.affiliation: International School for Advanced Studies (SISSA), and Istituto Nazionale di Fisica della Materia, Via Beirut 2-4, 34014 Trieste, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Punta
authors.forename: Amos
authors.initials: A
authors.lastname: Maritan
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000032:analysis*; D057927:Hydrophobic and Hydrophilic Interactions; D008565:Membrane Proteins / Q000737:chemistry*; D021382:Protein Sorting Signals; D017433:Protein Structure, Secondary; D015203:Reproducibility of Results; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D000596:Amino Acids; D008565:Membrane Proteins; D021382:Protein Sorting Signals