Studies Of Membrane Protein Folding Research Articles

How bilayer properties influence membrane protein folding.

The question of how proteins manage to organize into a unique three-dimensional structure has been a major field of study since the first protein structures were determined. For membrane proteins, the question is made more complex because, unlike water-soluble proteins, the solvent is not homogenous or even unique. Each cell and organelle has a distinct lipid composition that can change in response to environmental stimuli. Thus, the study of membrane protein folding requires not only understanding how the unfolded chain navigates its way to the folded state, but also how changes in bilayer properties can affect that search. Here we review what we know so far about the impact of lipid composition on bilayer physical properties and how those properties can affect folding. A better understanding of the lipid bilayer and its effects on membrane protein folding is not only important for a theoretical understanding of the folding process, but can also have a practical impact on our ability to work with and design membrane proteins.

Accurate Determination of Membrane Penetration of Proteins Using Fluorescence Quenching and Molecular Dynamics Simulations

Determination of the depth of membrane penetration provides important information for studies of membrane protein folding and protein-lipid interactions [1,2]. Here we use a combination of molecular dynamics (MD) simulations and depth-dependent fluorescence quenching to calibrate the methodology for extracting quantitative information on membrane penetration. The knowledge of the immersion depth of fluorescence quenchers (e.g., Doxyl or TEMPO spin probe attached to lipid acyl chains or headgroup) is critical for the determination of the transverse location of fluorescence probes attached to proteins and peptides. The question of bilayer penetration of TEMPO moiety, attached to lipid headgroup in TEMPO-PC, has recently came into prominence in two studies of interfacial solvation [3,4]. Here, we re-examine the arguments on TEMPO penetration using the cross-validation of MD simulations and depth-dependent fluorescence-quenching experiments, which confirms that TEMPO in TEMPO-PC penetrates below the level of phosphate groups. The proper analysis of fluorescence quenching requires the use of Tempo position below the level of phosphate groups; and failure to do so will result in substantial systematic errors in determining the penetration of the labeled site on a membrane protein [5]. Finally, we illustrate the application of this methodology by determining membrane penetration of site-selectively labeled mutants of diphtheria toxin translocation domain [6] and apoptotic inhibitor Bcl-xL [7]. [1] A. S. Ladokhin (2014) Biochim. Biophys. Acta 1838, 2289. [2] A. Kyrychenko et al. (2017) Reviews in Fluorescence 2016: Springer, 243-274. [3] C.-Y. Cheng et al. (2015) Biophys J 109, 330. [4] Y. Lee et al. (2016) Biophys J 111, 2481. [5] A. Kyrychenko et al. (2019) J Membr Biol 252, doi:10.1007/s00232-019-00094-1. [6] A. Kyrychenko et al. (2018) J Membr Biol 251, 379. [7] V. Vasquez-Montes et al. (2019) Biochim Biophys Acta 1867, 691.

Characterisation of denatured states of sensory rhodopsin II by solution-state NMR

Sensory rhodopsin II (pSRII), a retinal-binding photophobic receptor from Natronomonas pharaonis, is a novel model system for membrane protein folding studies. Recently, the SDS-denatured states and the kinetics for reversible unfolding of pSRII have been investigated, opening the door to the first detailed characterisation of denatured states of a membrane protein by solution-state nuclear magnetic resonance (NMR) using uniformly 15N-labelled pSRII. SDS denaturation and acid denaturation of pSRII both lead to fraying of helix ends but otherwise small structural changes in the transmembrane domain, consistent with little changes in secondary structure and disruption of the retinal-binding pocket and tertiary structure. Widespread changes in the backbone amide dynamics are detected in the form of line broadening, indicative of μs-to-ms timescale conformational exchange in the transmembrane region. Detailed analysis of chemical shift and intensity changes lead to high-resolution molecular insights on structural and dynamics changes in SDS- and acid-denatured pSRII, thus highlighting differences in the unfolding pathways under the two different denaturing conditions. These results will form the foundation for furthering our understanding on the folding and unfolding pathways of retinal-binding proteins and membrane proteins in general, and also for investigating the importance of ligand-binding in the folding pathways of other ligand-binding membrane proteins, such as GPCRs.

Array of Freestanding Planar Lipid Bilayers for Parallel Optical and Electrical Recordings

Here we report on the design and validation of an array platform for parallel high-resolution electrophysiological and optical recordings. The recording chip is based on a SU-8 coated glass slide (ca. 200 μm thickness) containing 4 cavities with individual ring-shaped Ag/AgCl-microelectrodes as well as a common ground electrode. Four suspended lipid bilayers can be self-assembled on the chip surface over the cavities. The electrodes are connected to a multichannel amplifier capable of simultaneous electrical recording with high-bandwidth and low noise (<1pA [email protected]). The ring shape of the electrodes creates an optical window allowing access with a high-NA oil or water-immersion objective on an inverted microscope. This allows for e.g. single-molecule fluorescence measurements from one of the four bilayers using time-correlated-single-photon-counting (TCSPC). Fluorescently labeled alpha-hemolysin for optical and electrical measurements was expressed in-vitro and purified. BODIPY at position 131 was incorporated during the translation in a site-directed manner via stop or four-base codon suppression using pre-charged tRNAs. A series of characterization and validation experiments performed with the system include: (1)Studies of diffusion rates of fluorescently labelled Hemolysin and lipid molecules in the bilayer using fluorescence correlation spectroscopy (FCS); (2)Monitoring of alpha-hemolysin membrane insertion using fluorescence lifetime imaging (FLIM) and (3)Visualization of fusion of labeled proteoliposomes resulting in membrane channel insertion. In the two latter cases, changes in fluorescence intensity were monitored simultaneously with alterations in membrane conductance. This system allows for rapid membrane array formation and by providing ready combination of fluorescence microscopy with high-resolution electrophysiology, enables correlated optical and electrical characterization and monitoring of the interactions of channel forming proteins in artificial lipid bilayers on a single-molecule level. The technology can be further implemented for studies of membrane protein folding and mobility as well as of membrane transport.

Characterization of Denatured States and Reversible Unfolding of Sensory Rhodopsin II

Our understanding on the folding of membrane proteins lags behind that of soluble proteins due to challenges posed by the exposure of hydrophobic regions during in vitro chemical denaturation and refolding experiments. While different folding models are accepted for soluble proteins, only the two-stage model and the long-range interactions model have been proposed so far for helical membrane proteins. To address our knowledge gap on how different membrane proteins traverse their folding pathways, we have systematically investigated the structural features of SDS-denatured states and the kinetics for reversible unfolding of sensory rhodopsin II (pSRII), a retinal-binding photophobic receptor from Natronomonas pharaonis. pSRII is difficult to denature, and only SDS can dislodge the retinal chromophore without rapid aggregation. Even in 30% SDS (0.998 ΧSDS), pSRII retains the equivalent of six out of seven transmembrane helices, while the retinal-binding pocket is disrupted, with transmembrane residues becoming more solvent exposed. Folding of pSRII from an SDS-denatured state harboring a covalently bound retinal chromophore shows deviations from an apparent two-state behavior. SDS denaturation to form the sensory opsin apo-protein is reversible. We report pSRII as a new model protein which is suitable for membrane protein folding studies and has a unique folding mechanism that differs from those of bacteriorhodopsin and bovine rhodopsin.

Segmental Deuteration of α-Synuclein for Neutron Reflectometry on Tethered Bilayers.

Neutron reflectometry (NR) is uniquely suited for studying protein interaction with phospholipid bilayers along the bilayer normal on an angstrom scale. However, NR on its own cannot discern specific membrane-bound regions due to a lack of scattering contrast within a protein. Here we report the successful coupling of native chemical ligation (NCL) and NR to study α-synuclein (α-syn), a membrane-binding neuronal protein central in Parkinson's disease. Two α-syn variants were generated where either the first 86 or last 54 residues are deuterated, allowing for region-specific contrast within the protein and the identification of membrane interacting residues by NR. Residues 1-86 are positioned at the hydrocarbon/headgroup interface of the outer leaflet, whereas the density distribution of the 54 C-terminal residues ranges from the hydrocarbon region to the aqueous environment. Coupling of NCL and NR should have broad utility in studies of membrane protein folding.

A growing toolbox of techniques for studying β-barrel outer membrane protein folding and biogenesis.

Great strides into understanding protein folding have been made since the seminal work of Anfinsen over 40 years ago, but progress in the study of membrane protein folding has lagged behind that of their water soluble counterparts. Researchers in these fields continue to turn to more advanced techniques such as NMR, mass spectrometry, molecular dynamics (MD) and single molecule methods to interrogate how proteins fold. Our understanding of β-barrel outer membrane protein (OMP) folding has benefited from these advances in the last decade. This class of proteins must traverse the periplasm and then insert into an asymmetric lipid membrane in the absence of a chemical energy source. In this review we discuss old, new and emerging techniques used to examine the process of OMP folding and biogenesis in vitro and describe some of the insights and new questions these techniques have revealed.

Single-Molecule Measurement of Membrane Protein Stability

Our understanding of membrane proteins has been severely hindered by a dearth of techniques to investigate membrane protein folding and stability in lipid bilayers. Our lab has developed a technique to drive membrane protein unfolding under native conditions called the steric trap method, which uses a protein that preferentially binds the unfolded state such that binding drives unfolding. Previously, this method has been reliant on the use of a functionally assayable protein, such as the chromophore-containing protein bacteriorhodopsin or the membrane enzyme diacylglycerol kinase. We propose generalizing the steric trap method using single-molecule fluorescence technology. By moving the system to infinite dilution in which there is only a single protein per vesicle we can eliminate aggregation problems that plague membrane protein studies. The sensitivity of single-molecule detection permits us to use much less protein and lipid material, and the minimal light scattering allows us to observe proteins in vesicles instead of using solubilizing agents required for bulk spectroscopic assays. By circumventing the requirement for a protein-specific functional assay, we hope to expand the reach of membrane protein folding studies.

Design and characterization of a membrane protein unfolding platform in lipid bilayers.

Accurate measurement of membrane protein stability—and particularly how it may vary as a result of disease-phenotypic mutations—ideally requires a denaturant that can unfold a membrane-embedded structure while leaving the solubilizing environment unaffected. The steric trap method fulfills this requirement by using monovalent streptavidin (mSA) molecules to unfold membrane proteins engineered with two spatially close biotin tags. Here we adapted this method to an 87-residue helix-loop-helix (hairpin) construct derived from helices 3 and 4 in the transmembrane domain of the human cystic fibrosis transmembrane conductance regulator (CFTR), wherein helix-helix tertiary interactions are anticipated to confer a portion of construct stability. The wild type CFTR TM3/4 hairpin construct was modified with two accessible biotin tags for mSA-induced unfolding, along with two helix-terminal pyrene labels to monitor loss of inter-helical contacts by pyrene excimer fluorescence. A series of eight constructs with biotin tags at varying distances from the helix-terminal pyrene labels were expressed, purified and labeled appropriately; all constructs exhibited largely helical circular dichroism spectra. We found that addition of mSA to an optimized construct in lipid vesicles led to a complete and reversible loss in pyrene excimer fluorescence and mSA binding, and hence hairpin unfolding—results further supported by SDS-PAGE visualization of mSA bound and unbound species. While some dimeric/oligomeric populations persist that may affect quantitation of the unfolding step, our characterization of the design yields a promising prototype of a future platform for the systematic study of membrane protein folding in a lipid bilayer environment.

Calibration of Distribution Analysis of the Depth of Membrane Penetration Using Simulations and Depth-Dependent Fluorescence Quenching.

Determination of the depth of membrane penetration provides important information for studies of membrane protein folding and protein-lipid interactions. Here, we use a combination of molecular dynamics (MD) simulations and depth-dependent fluorescence quenching to calibrate the methodology for extracting quantitative information on membrane penetration. In order to investigate the immersion depth of the fluorescent label in lipid bilayer, we studied 7-nitrobenz-2-oxa-1,3-diazole (NBD) attached to the lipid headgroup in NBD-PE incorporated into POPC bilayer. The immersion depth of NBD was estimated by measuring steady-state and time-resolved fluorescence quenching with spin-labeled lipids co-incorporated into lipid vesicles. Six different spin-labeled lipids were utilized: one with headgroup-attached Tempo probe (Tempo-PC) and five with acyl chain-labeled n-Doxyl moieties (n-Doxyl-PC where n is a chain labeling position equal to 5, 7, 10, 12, and 14, respectively). The Stern-Volmer analysis revealed that NBD quenching in membranes occurs by both static and dynamic collisional quenching processes. Using the methodology of Distribution Analysis, the immersion depth and the apparent half-width of the transversal distributions of the NBD moiety were estimated to be 14.7 and 6.7Å, respectively, from the bilayer center. This position is independently validated by atomistic MD simulations of NBD-PE lipids in a POPC bilayer (14.4Å). In addition, we demonstrate that MD simulations of the transverse overlap integrals between dye and quencher distributions can be used for proper analysis of the depth-dependent quenching profile. Finally, we illustrate the application of this methodology by determining membrane penetration of site selectively labeled mutants of diphtheria toxin T-domain.

Spectroscopic Studies of Membrane Protein Folding: Changes in Hydration

We have investigated the folding reaction of a model beta-barrel membrane protein, OmpA, using vibrational and electronic spectroscopy. Our primary focus is to interrogate changes in hydration during insertion and folding of the protein into the bilayer. The results suggest that expulsion of water and residual denaturant from the bilayer and/or protein core may give rise to the long-time component in folding kinetics. This finding is discussed in the context of in vitro mechanisms for membrane protein folding.

Pulsed hydrogen/deuterium exchange mass spectrometry for time‐resolved membrane protein folding studies

Kinetic folding experiments by pulsed hydrogen/deuterium exchange (HDX) mass spectrometry (MS) are a well-established tool for water-soluble proteins. To the best of our knowledge, the current study is the first that applies this approach to an integral membrane protein. The native state of bacteriorhodopsin (BR) comprises seven transmembrane helices and a covalently bound retinal cofactor. BR exposure to sodium dodecyl sulfate (SDS) induces partial unfolding and retinal loss. We employ a custom-built three-stage mixing device for pulsed-HDX/MS investigations of BR refolding. The reaction is triggered by mixing SDS-denatured protein with bicelles. After a variable folding time (10 ms to 24 h), the protein is exposed to excess D(2) O buffer under rapid exchange conditions. The HDX pulse is terminated by acid quenching after 24 ms. Subsequent off-line analysis is performed by size exclusion chromatography and electrospray MS. These measurements yield the number of protected backbone N-H sites as a function of folding time, reflecting the recovery of secondary structure. Our results indicate that much of the BR secondary structure is formed quite late during the reaction, on a time scale of 10 s and beyond. It is hoped that in the future it will be possible to extend the pulsed-HDX/MS approach employed here to membrane proteins other than BR.

Mapping of unfolding states of integral helical membrane proteins by GPS-NMR and scattering techniques: TFE-induced unfolding of KcsA in DDM surfactant

Membrane proteins are vital for biological function, and their action is governed by structural properties critically depending on their interactions with the membranes. This has motivated considerable interest in studies of membrane protein folding and unfolding. Here the structural changes induced by unfolding of an integral membrane protein, namely TFE-induced unfolding of KcsA solubilized by the n-dodecyl β-d-maltoside (DDM) surfactant is investigated by the recently introduced GPS-NMR (Global Protein folding State mapping by multivariate NMR) (Malmendal et al., PlosONE 5, e10262 (2010)) along with dynamic light scattering (DLS) and small-angle X-ray scattering (SAXS). GPS-NMR is used as a tool for fast analysis of the protein unfolding processes upon external perturbation, and DLS and SAXS are used for further structural characterization of the unfolding states. The combination allows addressing detergent properties and protein conformations at the same time. The mapping of the states reveals that KcsA undergoes a series of rearrangements which include expansion of the tetramer in several steps followed by dissociation into monomers at 29% TFE. Supplementary studies of DDM and TFE in the absence of KcsA suggest that the disintegration of the tetramer at 29% TFE is caused by TFE dissolving the surrounding DDM rim. Above 34% TFE, KcsA collapses to a new structure that is fully formed at 44% TFE.

Rationale Membrane Protein Design of a Beta-Barrel

Bacterial outer membrane proteins have robust beta-barrel structures. Therefore, they are targeted for engineering biological nanopores as stochastic biosensing elements. We used membrane protein engineering and single-channel electrical recordings to explore the ferric hydroxamate uptake component A (FhuA) as a target for redesigning membrane proteins. FhuA is a monomeric 22-stranded beta-barrel protein from the outer membrane of Escherichia coli. FhuA has a lumen with cross section of 3.1 X 4.4 nm that is filled by a globular N-terminal cork domain. We investigated various redesigned FhuA proteins, which had either single, double, or multiple deletions of the large extracellular loops and the cork domain. Analysis of the electrical signatures of these initial exploratory redesigned FhuA proteins led to the identification of four large extracellular loops that partially occlude the lumen when the cork domain is removed. Accordingly, we removed the cork along with the extracellular loops, FhuA delta C/delta 4L, resulting in the deletion of almost one third of the total number of amino acids of the wild-type FhuA protein. Remarkably, the newly redesigned protein forms an open pore in planar lipid bilayers, with a measured unitary conductance of ∼4.8 nanosiemens in 1 M KCl at pH 7.4, a value that has not been recorded previously with other engineered FhuA protein channels. We show several advantages and prospects of using such an engineered outer membrane protein in fundamental studies of membrane protein folding and design, and the mechanisms of ion conductance and gating. Further, FhuA delta C/delta 4L can be a platform for customized engineering in applicative areas of single-molecule sensing and analysis of proteins, nucleic acids and their ensembles.

Redesign of a Plugged β-Barrel Membrane Protein

The redesign of biological nanopores is focused on bacterial outer membrane proteins and pore-forming toxins, because their robust β-barrel structure makes them the best choice for developing stochastic biosensing elements. Using membrane protein engineering and single-channel electrical recordings, we explored the ferric hydroxamate uptake component A (FhuA), a monomeric 22-stranded β-barrel protein from the outer membrane of Escherichia coli. FhuA has a luminal cross-section of 3.1 × 4.4 nm and is filled by a globular N-terminal cork domain. Various redesigned FhuA proteins were investigated, including single, double, and multiple deletions of the large extracellular loops and the cork domain. We identified four large extracellular loops that partially occlude the lumen when the cork domain is removed. The newly engineered protein, FhuAΔC/Δ4L, was the result of a removal of almost one-third of the total number of amino acids of the wild-type FhuA (WT-FhuA) protein. This extensive protein engineering encompassed the entire cork domain and four extracellular loops. Remarkably, FhuAΔC/Δ4L forms a functional open pore in planar lipid bilayers, with a measured unitary conductance of ∼4.8 nanosiemens, which is much greater than the values recorded previously with other engineered FhuA protein channels. There are numerous advantages and prospects of using such an engineered outer membrane protein not only in fundamental studies of membrane protein folding and design, and the mechanisms of ion conductance and gating, but also in more applicative areas of stochastic single-molecule sensing of proteins and nucleic acids.

Effects of Urea on the Microstructure and Phase Behavior of Aqueous Solutions of Poly(oxyethylene) Surfactants

Membrane proteins are made soluble in aqueous buffers by the addition of various surfactants (detergents) to form so-called protein-detergent complexes (PDCs). Properties of membrane proteins are commonly assessed by unfolding the protein in the presence of surfactant in a buffer solution by adding urea. The stability of the protein under these conditions is then monitored by biophysical methods such as fluorescence or circular dichroism spectroscopy. Often overlooked in these experiments is the effect of urea on the phase behavior and micellar microstructure of the different surfactants used to form the PDCs. Here the effect of urea on five polyoxyethylene surfactants - n-octylytetraoxyethylene (C(8)E(4)), n-octylpentaoxyethylene (C(8)E(5)), n-decylhexaoxyethylene (C(10)E(6)), n-dodecylhexaoxyethylene (C(12)E(6)) and n-dodecyloctaoxylethylene (C(12)E(8)) - is explored. The presence of urea increases the critical micelle concentration (CMC) of all surfactants studied, indicating that the concentration of both the surfactant and urea should be considered in membrane protein folding studies. The cloud point temperature of all surfactants studied also increases with increasing urea concentration. Small-angle neutron scattering shows a urea-induced transition from an elongated to a globular shape for micelles of C(8)E(4) and C(12)E(6). In contrast, C(8)E(5) and C(12)E(8) form more globular micelles at room temperature and the micelles remain globular as the urea concentration is increased. The effects of increasing urea concentration on micelle structure are analogous to those of decreasing the temperature. The large changes in micelle structure observed here could also affect membrane protein unfolding studies by changing the structure of the PDC.

The Spontaneous Refolding of Opacity-Associated Proteins into Lipid Membranes

The spontaneous folding of outer membrane proteins (OMPs) into lipid vesicles provides a means to study the determinants, kinetics, and thermodynamics of membrane protein folding in manipulatable systems modeling the native lipid environment. This information increases our ability to understand and utilize membrane proteins, but it remains sparse, with direct lipid refolding reported for fewer than a dozen unique OMPs. We present the spontaneous refolding of recombinant Opa proteins into lipid vesicles, with a systematic investigation of the impact protein and lipid bilayer variables have on the folding. Opa proteins are eight-stranded β-barreled monomeric integral outer membrane proteins found in the bacterial pathogens N. gonorrhoeae and N. meningitides. There are at least 26 characterized Opa proteins, nearly identical in sequence, but varying in three extracellular loops. In vivo, these proteins interact with specific human host cell receptors to breach the plasma membrane and gain entry to targeted human cells. The basis for host-receptor specificity is not well understood but is determined by the variable extracellular loops. These loops also play a role in folding. The β-sheets of Opa variants OpaI and OpaA are nearly identical in sequence, but OpaI refolds in DMPC vesicles while OpaA does not. These variants therefore provide a natural system to probe protein folding determinants. The effects of lipid composition (in particular both head group and chain length), buffer pH, ionic strength, and temperature on refolding have been characterized for these Opa variants. Ultimately, reconstitution into lipid bilayers required the matching of hydrophobic thicknesses as well as optimization of parameters mediating electrostatic interactions between the protein and lipids used. The reconstituted systems provide a new model in the study of membrane protein folding, with an exploration of refolding parameters that may be applicable to additional OMP-lipid systems.

Polar residues in transmembrane helices can decrease electrophoretic mobility in polyacrylamide gels without causing helix dimerization

There are only a few available methods to study lateral interactions and self assembly of transmembrane helices. One of the most frequently used methods is sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE) which can report on strong interactions between peptides in SDS solution. Here we offer a cautionary tale about studying the folding and assembly of membrane proteins using peptides and SDS-PAGE experiments as a membrane mimetic system. At least for the specific peptide and detergent systems studied here, we show that a polar asparagine residue in the 12th position of an otherwise hydrophobic helical segment of 20 amino acids causes a peptide to migrate on SDS-PAGE gels with an apparent molecular weight that is twice its true molecular weight, suggesting dimerization. However when examined carefully in SDS solutions and in situ in the polyacrylamide gel itself using Forster resonance energy transfer no interaction can be detected. Instead we show evidence suggesting that differential interactions between peptide and detergent drive the differences in electrophoretic mobility without any interaction between peptides. These results emphasize the need to apply multiple independent techniques to the study of membrane protein folding, and they highlight the usefulness of studying folding and structure of membrane proteins in lipid membranes rather than in detergents.

Energetics Of Peptide (pHLIP) Binding To And Folding Across A Lipid Bilayer Membrane

The pHLIP peptide (pH Low Insertion Peptide) serves as a model system for peptide insertion and folding across a lipid bilayer. It has three general states: (I) soluble in water or (II) bound to the surface of a lipid bilayer as an unstructured monomer, and (III) inserted across the bilayer as a monomeric α-helix. We used fluorescence spectroscopy and isothermal titration calorimetry to study the interactions of pHLIP with a POPC lipid bilayer and to calculate the transition energies between states. We found that the Gibbs Free Energy of binding to a POPC surface at low pHLIP concentration (state I - state II transition) at 37°C is about -7 kcal/mol near neutral pH and that the free energy of insertion and folding across a lipid bilayer at low pH (state II - state III transition) is nearly -2 kcal/mol. We plan to discuss a number of related thermodynamic parameters from our measurements. Besides its fundamental interest as a model system for the study of membrane protein folding, pHLIP has utility as an agent to target diseased tissues and translocate molecules through the membrane into the cytoplasm of cells in environments with elevated levels of extracellular acidity, as in cancer and inflammation. The results give the amount of energy that might be used to move cargo molecules across a membrane.

Energetics of peptide (pHLIP) binding to and folding across a lipid bilayer membrane

The pH low-insertion peptide (pHLIP) serves as a model system for peptide insertion and folding across a lipid bilayer. It has three general states: (I) soluble in water or (II) bound to the surface of a lipid bilayer as an unstructured monomer, and (III) inserted across the bilayer as a monomeric alpha-helix. We used fluorescence spectroscopy and isothermal titration calorimetry to study the interactions of pHLIP with a palmitoyloleoylphosphatidylcholine (POPC) lipid bilayer and to calculate the transition energies between states. We found that the Gibbs free energy of binding to a POPC surface at low pHLIP concentration (state I-state II transition) at 37 degrees C is approximately -7 kcal/mol near neutral pH and that the free energy of insertion and folding across a lipid bilayer at low pH (state II-state III transition) is nearly -2 kcal/mol. We discuss a number of related thermodynamic parameters from our measurements. Besides its fundamental interest as a model system for the study of membrane protein folding, pHLIP has utility as an agent to target diseased tissues and translocate molecules through the membrane into the cytoplasm of cells in environments with elevated levels of extracellular acidity, as in cancer and inflammation. The results give the amount of energy that might be used to move cargo molecules across a membrane.