title: Analysis of dihedral angle preferences for alanine and glycine residues in alpha and beta transmembrane regions.
abstract: For the past 50 years, the Ramachandran map has been used effectively to study the protein structure and folding. However, though extensive analysis has been done on dihedral angle preferences of residues in globular proteins, related studies and reports of membrane proteins are limited. It is of interest to explore the conformational preferences of residues in transmembrane regions of membrane proteins which are involved in several important and diverse biological processes. Hence, in the present work, a systematic comparative computational analysis has been made on dihedral angle preferences of alanine and glycine in alpha and beta transmembrane regions (the two major classes of transmembrane proteins) with the aid of the Ramachandran map. Further, the conformational preferences of residues in transmembrane regions were compared with the non-transmembrane regions. We have extracted cation-pi interacting residues present in transmembrane regions and explored the dihedral angle preferences. From our observations, we reveal the higher percentage of occurrences of glycine in alpha and beta transmembrane regions than other hydrophobic residues. Further, we noted a clear shift in ψ-angle preferences of glycine residues from negative bins in alpha transmembrane regions to positive bins in beta transmembrane regions. Also, cation-pi interacting residues in beta transmembrane regions avoid preferring ψ-angles in the range of -59° to -30°. In this article, we insist that the studies on preferences of dihedral angles in transmembrane regions, thorough understanding of structure and folding of transmembrane proteins, can lead to modeling of novel transmembrane regions towards designing membrane proteins.
authors.affiliation: a School of Biotechnology, Centre of Excellence in Bioinformatics , Madurai Kamaraj University , Palkalai Nagar, Madurai 625 021 , India.
authors.forename: K M
authors.initials: KM
authors.lastname: Saravanan
authors.forename: S
authors.initials: S
authors.lastname: Krishnaswamy
mesh_terms: D000409:Alanine / Q000737:chemistry*; D000595:Amino Acid Sequence; D005998:Glycine / Q000737:chemistry*; D008565:Membrane Proteins / Q000737:chemistry*; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D013816:Thermodynamics
chemical_list: D008565:Membrane Proteins; D000409:Alanine; D005998:Glycine
keywords: Ramachandran map; conformational space; dihedral angles; folding and stability; transmembrane proteins