Article

A knowledge-based potential highlights unique features of membrane α-helical and β-barrel protein insertion and folding.

BioMaPS Institute and the Graduate Program in Computational Biology and Molecular Biophysics, Rutgers University, Piscataway, NJ 08854, USA.
Protein Science (impact factor: 2.8). 01/2012; 21(1):50-62. DOI:10.1002/pro.758 pp.50-62
Source: PubMed

ABSTRACT 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.

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Keywords

functional residues
 
lipid environment
 
outer membrane proteins
 
Outer membrane β-barrel proteins
 
primary sequence information specific
 
secondary structure
 
similarities
 
TM β-barrel proteins
 
two potentials
 
unique aspects
 
α-helical inner membrane proteins
 
β-barrel membrane proteins
 

Daniel Hsieh