Prediction of membrane protein structures with complex topologies using limited constraints

TitlePrediction of membrane protein structures with complex topologies using limited constraints
Publication TypeJournal Article
Year of Publication2009
AuthorsBarth, P., Wallner B., & Baker D.
JournalProceedings of the National Academy of Sciences of the United States of America
Volume106
Issue5
Pagination1409-14
Date Published2009 Feb 3
ISSN1091-6490
KeywordsMembrane Proteins, Models, Molecular, Primary Publication, Protein Conformation, Protein Folding
Abstract

Reliable structure-prediction methods for membrane proteins are important because the experimental determination of high-resolution membrane protein structures remains very difficult, especially for eukaryotic proteins. However, membrane proteins are typically longer than 200 aa and represent a formidable challenge for structure prediction. We have developed a method for predicting the structures of large membrane proteins by constraining helix-helix packing arrangements at particular positions predicted from sequence or identified by experiments. We tested the method on 12 membrane proteins of diverse topologies and functions with lengths ranging between 190 and 300 residues. Enforcing a single constraint during the folding simulations enriched the population of near-native models for 9 proteins. In 4 of the cases in which the constraint was predicted from the sequence, 1 of the 5 lowest energy models was superimposable within 4 A on the native structure. Near-native structures could also be selected for heme-binding and pore-forming domains from simulations in which pairs of conserved histidine-chelating hemes and one experimentally determined salt bridge were constrained, respectively. These results suggest that models within 4 A of the native structure can be achieved for complex membrane proteins if even limited information on residue-residue interactions can be obtained from protein structure databases or experiments.

Alternate JournalProc. Natl. Acad. Sci. U.S.A.
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