Modelling Long Loops of Membrane Proteins using Pretzel

Abstract

Beta-barrel membrane proteins are found in the outer membrane of gram-negative bacteria, mitochondria, and chloroplasts. They play important roles in membrane anchoring, pore formation and enzyme activities. The extracellular loops (ECLs) of outer membrane proteins (OMPs) are highly variable, and often little is known about their functional roles. in this work, we study the extracellular loop regions of the protein LptD, an essential OMP that inserts lipopolysaccharide endotoxins into the outer membrane of Escherichia coli. LptD contains 26 strands and 13 loops. We model the longer loops of LptD using the Pretzel (Protein Topology of Zoetic Loops) method and generate a conformational ensemble of these loops which can help to understand their functionality. Pretzel provides a novel computational framework that combines Monte Carlo conformational sampling, structure clustering, and ensemble energy evaluation. It was developed to investigate gating behavior of OMPs under different pH conditions. While successfully applied to decipher the pH-regulated control mechanism of OmpG gating, our results show that Pretzel can be applied to broadly model the conformational ensembles of extracellular loops.