title: Topological constraints and modular structure in the folding and functional motions of GlpG, an intramembrane protease.
abstract: We investigate the folding of GlpG, an intramembrane protease, using perfectly funneled structure-based models that implicitly account for the absence or presence of the membrane. These two models are used to describe, respectively, folding in detergent micelles and folding within a bilayer, which effectively constrains GlpG's topology in unfolded and partially folded states. Structural free-energy landscape analysis shows that although the presence of multiple folding pathways is an intrinsic property of GlpG's modular functional architecture, the large entropic cost of organizing helical bundles in the absence of the constraining bilayer leads to pathways that backtrack (i.e., local unfolding of previously folded substructures is required when moving from the unfolded to the folded state along the minimum free-energy pathway). This backtracking explains the experimental observation of thermodynamically destabilizing mutations that accelerate GlpG's folding in detergent micelles. In contrast, backtracking is absent from the model when folding is constrained within a bilayer, the environment in which GlpG has evolved to fold. We also characterize a near-native state with a highly mobile transmembrane helix 5 (TM5) that is significantly populated under folding conditions when GlpG is embedded in a bilayer. Unbinding of TM5 from the rest of the structure exposes GlpG's active site, consistent with studies of the catalytic mechanism of GlpG that suggest that TM5 serves as a substrate gate to the active site.
authors: Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark;
authors: Nicholas P
authors: NP
authors: Schafer
authors: Department of Chemistry, Center for Theoretical Biological Physics, Rice University, Houston, TX 77005;
authors: Ha H
authors: HH
authors: Truong
authors: Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark;
authors: Daniel E
authors: DE
authors: Otzen
authors: The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark lindorff@bio.ku.dk pwolynes@rice.edu.
authors: Kresten
authors: K
authors: Lindorff-Larsen
authors: Department of Chemistry, Center for Theoretical Biological Physics, Rice University, Houston, TX 77005; lindorff@bio.ku.dk pwolynes@rice.edu.
authors: Peter G
authors: PG
authors: Wolynes
mesh_terms: D004268:DNA-Binding Proteins / Q000737:chemistry*; D010450:Endopeptidases / Q000737:chemistry*; D004926:Escherichia coli / Q000201:enzymology*; D029968:Escherichia coli Proteins / Q000737:chemistry*; D008051:Lipid Bilayers / Q000737:chemistry*; D008565:Membrane Proteins / Q000737:chemistry*; D008958:Models, Molecular; D017510:Protein Folding
chemical_list: D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; C102898:GlpG protein, E coli; D008051:Lipid Bilayers; D008565:Membrane Proteins; D010450:Endopeptidases
keywords: bilayer folding; folding mechanism; intramembrane proteolysis; membrane proteins; micelle folding