GPCRtm: An amino acid substitution matrix for the transmembrane region of class A G Protein-Coupled Receptors.

ABSTRACT:

Background

Protein sequence alignments and database search methods use standard scoring matrices calculated from amino acid substitution frequencies in general sets of proteins. These general-purpose matrices are not optimal to align accurately sequences with marked compositional biases, such as hydrophobic transmembrane regions found in membrane proteins. In this work, an amino acid substitution matrix (GPCRtm) is calculated for the membrane spanning segments of the G protein-coupled receptor (GPCR) rhodopsin family; one of the largest transmembrane protein family in humans with great importance in health and disease.

Results

The GPCRtm matrix reveals the amino acid compositional bias distinctive of the GPCR rhodopsin family and differs from other standard substitution matr

SUBMITTER: Rios S 

PROVIDER: S-EPMC4489126 | biostudies-literature | 2015 Jul

REPOSITORIES: biostudies-literature