title: Prediction of lipid-binding regions in cytoplasmic and extracellular loops of membrane proteins as exemplified by protein translocation membrane proteins.
abstract: The presence of possible lipid-binding regions in the cytoplasmic or extracellular loops of membrane proteins with an emphasis on protein translocation membrane proteins was investigated in this study using bioinformatics. Recent developments in approaches recognizing lipid-binding regions in proteins were found to be promising. In this study a total bioinformatics approach specialized in identifying lipid-binding helical regions in proteins was explored. Two features of the protein translocation membrane proteins, the position of the transmembrane regions and the identification of additional lipid-binding regions, were analyzed. A number of well-studied protein translocation membrane protein structures were checked in order to demonstrate the predictive value of the bioinformatics approach. Furthermore, the results demonstrated that lipid-binding regions in the cytoplasmic and extracellular loops in protein translocation membrane proteins can be predicted, and it is proposed that the interaction of these regions with phospholipids is important for proper functioning during protein translocation.
authors.affiliation: Section of Chemistry, Charlemagne College, Wilhelminastraat 13-15, 6524 AJ Nijmegen, The Netherlands. rcakeller@kpnmail.nl
authors.forename: Rob C A
authors.initials: RC
authors.lastname: Keller
mesh_terms: D000595:Amino Acid Sequence; D008055:Lipids / Q000737:chemistry*; D008565:Membrane Proteins / Q000737:chemistry* / Q000378:metabolism*; D008954:Models, Biological; D008969:Molecular Sequence Data; D011485:Protein Binding; D021381:Protein Transport / Q000502:physiology; D017386:Sequence Homology, Amino Acid
chemical_list: D008055:Lipids; D008565:Membrane Proteins