Light Color-Controlled pH-Adjustment of Aqueous Solutions Using Engineered Proteoliposomes.

Controlling the pH at the microliter scale can be useful for applications in research, medicine, and industry, and therefore represents a valuable application for synthetic biology and microfluidics. The presented vesicular system translates light of different colors into specific pH changes in the surrounding solution. It works with the two light-driven proton pumps bacteriorhodopsin and blue light-absorbing proteorhodopsin Med12, that are oriented in opposite directions in the lipid membrane. A computer-controlled measuring device implements a feedback loop for automatic adjustment and maintenance of a selected pH value. A pH range spanning more than two units can be established, providing fine temporal and pH resolution. As an application example, a pH-sensitive enzyme reaction is presented where the light color controls the reaction progress. In summary, light color-controlled pH-adjustment using engineered proteoliposomes opens new possibilities to control processes at the microliter scale in different contexts, such as in synthetic biology applications.

Antibiotic polymyxin arranges lipopolysaccharide into crystalline structures to solidify the bacterial membrane.

Polymyxins are last-resort antibiotics with potent activity against multi-drug resistant pathogens. They interact with lipopolysaccharide (LPS) in bacterial membranes, but mechanistic details at the molecular level remain unclear. Here, we characterize the interaction of polymyxins with native, LPS-containing outer membrane patches of Escherichia coli by high-resolution atomic force microscopy imaging, along with structural and biochemical assays. We find that polymyxins arrange LPS into hexagonal assemblies to form crystalline structures. Formation of the crystalline structures is correlated with the antibiotic activity, and absent in polymyxin-resistant strains. Crystal lattice parameters alter with variations of the LPS and polymyxin molecules. Quantitative measurements show that the crystalline structures decrease membrane thickness and increase membrane area as well as stiffness. Together, these findings suggest the formation of rigid LPS-polymyxin crystals and subsequent membrane disruption as the mechanism of polymyxin action and provide a benchmark for optimization and de novo design of LPS-targeting antimicrobials.

Monitoring the antibiotic darobactin modulating the ß-barrel assembly factor BamA.

The ß-barrel assembly machinery (BAM) complex is an essential component of Escherichia coli that inserts and folds outer membrane proteins (OMPs). The natural antibiotic compound darobactin inhibits BamA, the central unit of BAM. Here, we employ dynamic single-molecule force spectroscopy (SMFS) to better understand the structure-function relationship of BamA and its inhibition by darobactin. The five N-terminal polypeptide transport (POTRA) domains show low mechanical, kinetic, and energetic stabilities. In contrast, the structural region linking the POTRA domains to the transmembrane ß-barrel exposes the highest mechanical stiffness and lowest kinetic stability within BamA, thus indicating a mechano-functional role. Within the ß-barrel, the four N-terminal ß-hairpins H1-H4 expose the highest mechanical stabilities and stiffnesses, while the four C-terminal ß-hairpins H5-H6 show lower stabilities and higher flexibilities. This asymmetry within the ß-barrel suggests that substrates funneling into the lateral gate formed by ß-hairpins H1 and H8 can force the flexible C-terminal ß-hairpins to change conformations.

Proton gradients from light-harvesting E. coli control DNA assemblies for synthetic cells.

Bottom-up and top-down approaches to synthetic biology each employ distinct methodologies with the common aim to harness living systems. Here, we realize a strategic merger of both approaches to convert light into proton gradients for the actuation of synthetic cellular systems. We genetically engineer E. coli to overexpress the light-driven inward-directed proton pump xenorhodopsin and encapsulate them in artificial cell-sized compartments. Exposing the compartments to light-dark cycles, we reversibly switch the pH by almost one pH unit and employ these pH gradients to trigger the attachment of DNA structures to the compartment periphery. For this purpose, a DNA triplex motif serves as a nanomechanical switch responding to the pH-trigger of the E. coli. When DNA origami plates are modified with the pH-sensitive triplex motif, the proton-pumping E. coli can trigger their attachment to giant unilamellar lipid vesicles (GUVs) upon illumination. A DNA cortex is formed upon DNA origami polymerization, which sculpts and deforms the GUVs. We foresee that the combination of bottom-up and top down approaches is an efficient way to engineer synthetic cells.

Mechanical Unfolding and Refolding of Single Membrane Proteins by Atomic Force Microscopy.

Atomic force microscopy (AFM)-based single-molecule force spectroscopy allows direct physical manipulation of single membrane proteins under near-physiological conditions. It can be applied to study mechanical properties and molecular interactions as well as unfolding and folding pathways of membrane proteins. Here, we describe the basic procedure to study membrane proteins by single-molecule force spectroscopy and discuss general requirements of the experimental setup as well as common pitfalls typically encountered when working with membrane proteins in AFM.

High-Resolution Imaging of Maltoporin LamB while Quantifying the Free-Energy Landscape and Asymmetry of Sugar Binding.

Maltoporins are a family of membrane proteins that facilitate the diffusion of hydrophilic molecules and maltosaccharides across the outer membrane of Gram-negative bacteria. Two contradicting models propose the sugar binding, uptake, and transport by maltoporins to be either symmetric or asymmetric. Here, we address this contradiction and introduce force-distance-based atomic force microscopy to image single maltoporin LamB trimers in the membrane at sub-nanometer resolution and simultaneously quantify the binding of different malto-oligosaccharides. We assay subtle differences of the binding free-energy landscape of maltotriose, maltotetraose, and maltopentaose, which quantifies how binding strength and affinity increase with the malto-oligosaccharide chain length. The ligand-binding parameters change considerably by mutating the extracellular loop 3, which folds into and constricts the transmembrane pore of LamB. By recording LamB topographs and structurally mapping binding events at sub-nanometer resolution, we observe LamB to preferentially bind maltodextrin from the periplasmic side, which shows sugar binding and uptake to be asymmetric. The study introduces atomic force microscopy as an analytical nanoscopic tool that can differentiate among the factors modulating and models describing the binding and uptake of substrates by membrane proteins.

POTRA Domains, Extracellular Lid, and Membrane Composition Modulate the Conformational Stability of the ß Barrel Assembly Factor BamA.

The core component BamA of the ß barrel assembly machinery (BAM) adopts several conformations, which are thought to facilitate the insertion and folding of ß barrel proteins into the bacterial outer membrane. Which factors alter the stability of these conformations remains to be quantified. Here, we apply single-molecule force spectroscopy to characterize the mechanical properties of BamA from Escherichia coli. In contrast to the N-terminal periplasmic polypeptide-transport-associated (POTRA) domains, the C-terminal transmembrane ß barrel domain of BamA is mechanically much more stable. Exposed to mechanical stress this ß barrel stepwise unfolds ß hairpins until unfolding has been completed. Thereby, the mechanical stabilities of ß barrel and ß hairpins are modulated by the POTRA domains, the membrane composition and the extracellular lid closing the ß barrel. We anticipate that these differences in stability, which are caused by factors contributing to BAM function, promote conformations of the BamA ß barrel required to insert and fold outer membrane proteins.

Fusion Domains Guide the Oriented Insertion of Light-Driven Proton Pumps into Liposomes.

One major objective of synthetic biology is the bottom-up assembly of minimalistic nanocells consisting of lipid or polymer vesicles as architectural scaffolds and of membrane and soluble proteins as functional elements. However, there is no reliable method to orient membrane proteins reconstituted into vesicles. Here, we introduce a simple approach to orient the insertion of the light-driven proton pump proteorhodopsin (PR) into liposomes. To this end, we engineered red or green fluorescent proteins to the N- or C-terminus of PR, respectively. The fluorescent proteins optically identified the PR constructs and guided the insertion of PR into liposomes with the unoccupied terminal end facing inward. Using the PR constructs, we generated proton gradients across the vesicle membrane along predefined directions such as are required to power (bio)chemical processes in nanocells. Our approach may be adapted to direct the insertion of other membrane proteins into vesicles.

Maltoporin LamB Unfolds ß Hairpins along Mechanical Stress-Dependent Unfolding Pathways.

Upon mechanical pulling at either terminal end, ß barrel outer membrane proteins stepwise unfold ß strands or ß hairpins until entirely extracted from the membrane. This unique unfolding pathway has been described for ß barrels comprising 8, 14, or 22 ß strands. Here we mechanically unfold the 18-stranded ß barrel outer membrane protein LamB from Escherichia coli. We find that its mechanical unfolding pathway is shaped by the stepwise unfolding of ß hairpins. However, we also observe that ß hairpins can unfold groupwise. Thereby, ß hairpins unfolding at higher pulling forces show a higher probability to unfold collectively, whereas ß hairpins unfolding at lower forces tend to unfold individually. This result suggests that the collective unfolding of ß hairpins resembles a far-from-equilibrium process, whereas the unfolding of individual ß hairpins describes a closer-to-equilibrium process. Our findings support a direct link between outer membrane protein structure and the unfolding pathway and contribute to a better understanding of their unfolding in response to mechanical stress.