Prediction of buried helices in multispan alpha helical membrane proteins.
Analysis of a database of structures of membrane proteins shows that membrane proteins composed of 10 or more transmembrane (TM) helices often contain buried helices that are inaccessible to phospholipids. We introduce a method for identifying TM helices that are least phospholipid accessible and for prediction of fully buried TM helices in membrane proteins from sequence information alone. Our method is based on the calculation of residue lipophilicity and evolutionary conservation. Given that the number of buried helices in a membrane protein is known, our method achieves an accuracy of 78% and a Matthew's correlation coefficient of 0.68. A server for this tool (RANTS) is available online at http://gila.bioengr.uic.edu/lab/.
Adamian
Larisa
L
Department of Bioengineering, University of Illinois, Chicago, Illinois 60612-7340, USA.
Liang
Jie
J
D000465:Algorithms; D000818:Animals; D001426:Bacterial Proteins / Q000737:chemistry; D002462:Cell Membrane; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D019277:Entropy; D019143:Evolution, Molecular; D020407:Internet; D008055:Lipids / Q000737:chemistry; D008958:Models, Molecular; D015233:Models, Statistical; D010743:Phospholipids / Q000737:chemistry*; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D040901:Proteomics / Q000379:methods*; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein
D001426:Bacterial Proteins; D008055:Lipids; D010743:Phospholipids