Negative Charge Neutralization in the Loops and Turns of Outer Membrane Phospholipase A Impacts Folding Hysteresis at Neutral pH

Factors That Control the Force Needed to Unfold a Membrane Protein in Silico Depend on the Mode of Denaturation

Single-molecule force spectroscopy methods, such as AFM and magnetic tweezers, have proved extremely beneficial in elucidating folding pathways for soluble and membrane proteins. To identify factors that determine the force rupture levels in force-induced membrane protein unfolding, we applied our near-atomic-level Upside molecular dynamics package to study the vertical and lateral pulling of bacteriorhodopsin (bR) and GlpG, respectively. With our algorithm, we were able to selectively alter the magnitudes of individual interaction terms and identify that, for vertical pulling, hydrogen bond strength had the strongest effect, whereas other non-bonded protein and membrane-protein interactions had only moderate influences, except for the extraction of the last helix where the membrane-protein interactions had a stronger influence. The up-down topology of the transmembrane helices caused helices to be pulled out as pairs. The rate-limiting rupture event often was the loss of H-bonds and the ejection of the first helix, which then propagated tension to the second helix, which rapidly exited the bilayer. The pulling of the charged linkers across the membrane had minimal influence, as did changing the bilayer thickness. For the lateral pulling of GlpG, the rate-limiting rupture corresponded to the separation of the helices within the membrane, with the H-bonds generally being broken only afterward. Beyond providing a detailed picture of the rupture events, our study emphasizes that the pulling mode greatly affects the factors that determine the forces needed to unfold a membrane protein.

Determining the Free Energies of Outer Membrane Proteins in Lipid Bilayers

The thermodynamic stabilities of membrane proteins are of fundamental interest to provide a biophysical description of their structure-function relationships because energy determines conformational populations. In addition, structure-energy relationships can be exploited in membrane protein design and in synthetic biology. To determine the thermodynamic stability of a membrane protein, it is not sufficient to be able to unfold and refold the molecule: establishing path independence of this reaction is essential. Here we describe the procedures required to measure and verify path independence for the folding of outer membrane proteins in large unilamellar vesicles.

Reversible folding energetics of Yersinia Ail barrel reveals a hyperfluorescent intermediate

Deducing the molecular details of membrane protein folding has lately become an important area of research in biology. Using Ail, an outer membrane protein (OMP) from Yersina pestis as our model, we explore details of β-barrel folding, stability, and unfolding. Ail displays a simple transmembrane β-barrel topology. Here, we find that Ail follows a simple two-state mechanism in its folding and unfolding thermodynamics. Interestingly, Ail displays multi-step folding kinetics. The early kinetic intermediates in the folding pathway populate near the unfolded state (β_T ≈ 0.20), and do not display detectable changes in the local environment of the two interface indoles. Interestingly, tryptophans regulate the late events of barrel rearrangement, and Ail thermodynamic stability. We show that W¹⁴⁹ → Y/F/A substitution destabilizes Ail by ~0.13-1.7 kcal mol^-1, but retains path-independent thermodynamic equilibrium of Ail. In surprising contrast, substituting W⁴² and retaining W¹⁴⁹ shifts the thermodynamic equilibrium to an apparent kinetic retardation of only the unfolding process, which gives rise to an associated increase in scaffold stability by ~0.3-1.1 kcal mol^-1. This is accompanied by the formation of an unusual hyperfluorescent state in the unfolding pathway that is more structured, and represents a conformationally dynamic unfolding intermediate with the interface W¹⁴⁹ now lipid solvated. The defined role of each tryptophan and poorer folding efficiency of Trp mutants together presents compelling evidence for the importance of interface aromatics in the unique (un)folding pathway of Ail, and offers interesting insight on alternative pathways in generalized OMP assembly and unfolding mechanisms.

Transmembrane β-barrels: Evolution, folding and energetics

The biogenesis of transmembrane β-barrels (outer membrane proteins, or OMPs) is an elaborate multistep orchestration of the nascent polypeptide with translocases, barrel assembly machinery, and helper chaperone proteins. Several theories exist that describe the mechanism of chaperone-assisted OMP assembly in vivo and unassisted (spontaneous) folding in vitro. Structurally, OMPs of bacterial origin possess even-numbered strands, while mitochondrial β-barrels are even- and odd-stranded. Several underlying similarities between prokaryotic and eukaryotic β-barrels and their folding machinery are known; yet, the link in their evolutionary origin is unclear. While OMPs exhibit diversity in sequence and function, they share similar biophysical attributes and structure. Similarly, it is important to understand the intricate OMP assembly mechanism, particularly in eukaryotic β-barrels that have evolved to perform more complex functions. Here, we deliberate known facets of β-barrel evolution, folding, and stability, and attempt to highlight outstanding questions in β-barrel biogenesis and proteostasis.

Energetics of side-chain partitioning of β-signal residues in unassisted folding of a transmembrane β-barrel protein

The free energy of water-to-interface amino acid partitioning is a major contributing factor in membrane protein folding and stability. The interface residues at the C terminus of transmembrane β-barrels form the β-signal motif required for assisted β-barrel assembly in vivo but are believed to be less important for β-barrel assembly in vitro. Here, we experimentally measured the thermodynamic contribution of all 20 amino acids at the β-signal motif to the unassisted folding of the model β-barrel protein PagP. We obtained the partitioning free energy for all 20 amino acids at the lipid-facing interface (ΔΔG⁰_w,i(φ)) and the protein-facing interface (ΔΔG⁰_w,i(π)) residues and found that hydrophobic amino acids are most favorably transferred to the lipid-facing interface, whereas charged and polar groups display the highest partitioning energy. Furthermore, the change in non-polar surface area correlated directly with the partitioning free energy for the lipid-facing residue and inversely with the protein-facing residue. We also demonstrate that the interface residues of the β-signal motif are vital for in vitro barrel assembly, because they exhibit a side chain–specific energetic contribution determined by the change in nonpolar accessible surface. We further establish that folding cooperativity and hydrophobic collapse are balanced at the membrane interface for optimal stability of the PagP β-barrel scaffold. We conclude that the PagP C-terminal β-signal motif influences the folding cooperativity and stability of the folded β-barrel and that the thermodynamic contributions of the lipid- and protein-facing residues in the transmembrane protein β-signal motif depend on the nature of the amino acid side chain.