A knowledge-based potential highlights unique features of membrane α-helical and β-barrel protein insertion and folding.
Outer membrane β-barrel proteins differ from α-helical inner membrane proteins in lipid environment, secondary structure, and the proposed processes of folding and insertion. It is reasonable to expect that outer membrane proteins may contain primary sequence information specific for their folding and insertion behavior. In previous work, a depth-dependent insertion potential, E(z) , was derived for α-helical inner membrane proteins. We have generated an equivalent potential for TM β-barrel proteins. The similarities and differences between these two potentials provide insight into unique aspects of the folding and insertion of β-barrel membrane proteins. This potential can predict orientation within the membrane and identify functional residues involved in intermolecular interactions.
BioMaPS Institute and the Graduate Program in Computational Biology and Molecular Biophysics, Rutgers University, Piscataway, NJ 08854, USA.
Daniel
D
Hsieh
Alexander
A
Davis
Vikas
V
Nanda
D000596:Amino Acids / Q000737:chemistry; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry* / Q000378:metabolism; D057927:Hydrophobic and Hydrophilic Interactions; D008055:Lipids / Q000737:chemistry; D008956:Models, Chemical; D008958:Models, Molecular; D017510:Protein Folding; D054730:Protein Interaction Domains and Motifs; D017433:Protein Structure, Secondary; D013816:Thermodynamics
D000596:Amino Acids; D001425:Bacterial Outer Membrane Proteins; D008055:Lipids