Forces and factors that contribute to the structural stability of membrane proteins

Formation of Amyloid-Like Conformational States of β-Structured Membrane Proteins on the Example of OMPF Porin from the Yersinia pseudotuberculosis Outer Membrane

The work presents results of the in vitro and in silico study of formation of amyloid-like structures under harsh denaturing conditions by non-specific OmpF porin of Yersinia pseudotuberculosis (YpOmpF), a membrane protein with β-barrel conformation. It has been shown that in order to obtain amyloid-like porin aggregates, preliminary destabilization of its structure in a buffer solution with acidic pH at elevated temperature followed by long-term incubation at room temperature is necessary. After heating at 95°C in a solution with pH 4.5, significant conformational rearrangements are observed in the porin molecule at the level of tertiary and secondary structure of the protein, which are accompanied by the increase in the content of total β-structure and sharp decrease in the value of characteristic viscosity of the protein solution. Subsequent long-term exposure of the resulting unstable intermediate YpOmpF at room temperature leads to formation of porin aggregates of various shapes and sizes that bind thioflavin T, a specific fluorescent dye for the detection of amyloid-like protein structures. Compared to the initial protein, early intermediates of the amyloidogenic porin pathway, oligomers, have been shown to have increased toxicity to the Neuro-2aCCL-131™ mouse neuroblastoma cells. The results of computer modeling and analysis of the changes in intrinsic fluorescence during protein aggregation suggest that during formation of amyloid-like aggregates, changes in the structure of YpOmpF affect not only the areas with an internally disordered structure corresponding to the external loops of the porin, but also main framework of the molecule, which has a rigid spatial structure inherent to β-barrel.

Unfolding Individual Domains of BmrA, a Bacterial ABC Transporter Involved in Multidrug Resistance

The folding and stability of proteins are often studied via unfolding (and refolding) a protein with urea. Yet, in the case of membrane integral protein domains, which are shielded by a membrane or a membrane mimetic, urea generally does not induce unfolding. However, the unfolding of α-helical membrane proteins may be induced by the addition of sodium dodecyl sulfate (SDS). When protein unfolding is followed via monitoring changes in Trp fluorescence characteristics, the contributions of individual Trp residues often cannot be disentangled, and, consequently, the folding and stability of the individual domains of a multi-domain membrane protein cannot be studied. In this study, the unfolding of the homodimeric bacterial ATP-binding cassette (ABC) transporter Bacillus multidrug resistance ATP (BmrA), which comprises a transmembrane domain and a cytosolic nucleotide-binding domain, was investigated. To study the stability of individual BmrA domains in the context of the full-length protein, the individual domains were silenced by mutating the existent Trps. The SDS-induced unfolding of the corresponding constructs was compared to the (un)folding characteristics of the wild-type (wt) protein and isolated domains. The full-length variants BmrA_W413Y and BmrA_W104YW164A were able to mirror the changes observed with the isolated domains; thus, these variants allowed for the study of the unfolding and thermodynamic stability of mutated domains in the context of full-length BmrA.

The Thermodynamic Stability of Membrane Proteins in Micelles and Lipid Bilayers Investigated with the Ferrichrom Receptor FhuA

Extraction of integral membrane proteins into detergents for structural and functional studies often leads to a strong loss in protein stability. The impact of the lipid bilayer on the thermodynamic stability of an integral membrane protein in comparison to its solubilized form in detergent was examined and compared for FhuA from Escherichia coli and for a mutant, FhuAΔ5-160, lacking the N-terminal cork domain. Urea-induced unfolding was monitored by fluorescence spectroscopy to determine the effective free energies \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \Delta G{^\text{o}_{\rm u}} $$\end{document}ΔGuo of unfolding. To obtain enthalpic and entropic contributions of unfolding of FhuA, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \Delta G{^\text{o}_{\rm u}} $$\end{document}ΔGuo were determined at various temperatures. When solubilized in LDAO detergent, wt-FhuA and FhuAΔ5-160 unfolded in a single step. The 155-residue cork domain stabilized wt-FhuA by \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \Delta\Delta G{^\text{o}_{\rm u}} $$\end{document}ΔΔGuo~ 40 kJ/mol. Reconstituted into lipid bilayers, wt-FhuA unfolded in two steps, while FhuAΔ5-160 unfolded in a single step, indicating an uncoupled unfolding of the cork domain. For FhuAΔ5-160 at 35 °C, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \Delta G{^\text{o}_{\rm u}} $$\end{document}ΔGuo increased from ~ 5 kJ/mol in LDAO micelles to about ~ 20 kJ/mol in lipid bilayers, while the temperature of unfolding increased from T_M ~ 49 °C in LDAO micelles to T_M ~ 75 °C in lipid bilayers. Enthalpies \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\Delta H{_{\rm M}^\text{o}}$$\end{document}ΔHMowere much larger than free energies \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \Delta G{^\text{o}_{\rm u}} $$\end{document}ΔGuo, for FhuAΔ5-160 and for wt-FhuA, and compensated by a large gain of entropy upon unfolding. The gain in conformational entropy is expected to be similar for unfolding of FhuA from micelles or bilayers. The strongly increased T_M and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\Delta H{_{\rm M}^\text{o}}$$\end{document}ΔHMo observed for the lipid bilayer-reconstituted FhuA in comparison to the LDAO-solubilized forms, therefore, very likely arise from a much-increased solvation entropy of FhuA in bilayers.

Molecular Insight into the High Thermal Stability of Metalloprotein Azurin

We investigate the events characterizing the steps of the unfolding pathway of blue copper metalloprotein azurin using replica exchange molecular dynamics (REMD). Our studies show that the unfolding of azurin begins with the melting of α-helix and β-sheets II and V. This is followed by the melting of other β-sheets and the exposure of hydrophobic protein core to the solvent, resulting in disruptions of its tertiary structure. Free energy surfaces constructed at different temperatures portray different basins that signify the stability of different melted structures in the unfolding process. The contact maps at different temperatures reveal that the strong hydrophobic interaction within the core of the protein is the vital force that renders high stability to this protein. Analysis of the individual β-sheets by looking into their amino acid sequence shows that β-sheets with charged side chains on the surface melt fast compared to others. The β-barrel of azurin is able to dynamically rearrange, and it helps the protein to preserve its hydrophobic core, holding back the native topology from melting fast. B-factor analysis shows that residues of β-sheets III, IV, and VII deviate less from their initial structure at the transition temperature.

X-ray structure of the Rhodobacter sphaeroides reaction center with an M197 Phe→His substitution clarifies the properties of the mutant complex

The first steps of the global process of photosynthesis take place in specialized membrane pigment-protein complexes called photosynthetic reaction centers (RCs). The RC of the photosynthetic purple bacterium Rhodobacter sphaeroides, a relatively simple analog of the more complexly organized photosystem II in plants, algae and cyanobacteria, serves as a convenient model for studying pigment-protein interactions that affect photochemical processes. In bacterial RCs the bacteriochlorophyll (BChl) dimer P serves as the primary electron donor, and its redox potential is a critical factor in the efficient functioning of the RC. It has previously been shown that the replacement of Phe M197 by His strongly affects the oxidation potential of P (E _m P/P⁺), increasing its value by 125 mV, as well as increasing the thermal stability of RC and its stability in response to external pressure. The crystal structures of F(M197)H RC at high resolution obtained using various techniques presented in this report clarify the optical and electrochemical properties of the primary electron donor and the increased resistance of the mutant complex to denaturation. The electron-density maps are consistent with the donation of a hydrogen bond from the imidazole group of His M197 to the C2-acetyl carbonyl group of BChl P_B. The formation of this hydrogen bond leads to a considerable out-of-plane rotation of the acetyl carbonyl group and results in a 1.2 Å shift of the O atom of this group relative to the wild-type structure. Besides, the distance between BChl P_A and P_B in the area of pyrrole ring I was found to be increased by up to 0.17 Å. These structural changes are discussed in association with the spectral properties of BChl dimer P. The electron-density maps strongly suggest that the imidazole group of His M197 accepts another hydrogen bond from the nearest water molecule, which in turn appears to form two more hydrogen bonds to Asn M195 and Asp L155. As a result of the F(M197)H mutation, BChl P_B finds itself connected to the extensive hydrogen-bonding network that pre-existed in wild-type RC. Dissimilarities in the two hydrogen-bonding networks near the M197 and L168 sites may account for the different changes of the E _m P/P⁺ in F(M197)H and H(L168)F RCs. The involvement of His M197 in the hydrogen-bonding network also appears to be related to stabilization of the F(M197)H RC structure. Analysis of the experimental data presented here and of the data available in the literature points to the fact that the hydrogen-bonding networks in the vicinity of BChl dimer P may play an important role in fine-tuning the redox properties of the primary electron donor.

Recent Insights into the Structure and Function of Mycobacterial Membrane Proteins Facilitated by Cryo-EM

Mycobacterium tuberculosis (Mtb) is one of the deadliest pathogens encountered by humanity. Over the decades, its characteristic membrane organization and composition have been understood. However, there is still limited structural information and mechanistic understanding of the constituent membrane proteins critical for drug discovery pipelines. Recent advances in single-particle cryo-electron microscopy and cryo-electron tomography have provided the much-needed impetus towards structure determination of several vital Mtb membrane proteins whose structures were inaccessible via X-ray crystallography and NMR. Important insights into membrane composition and organization have been gained via a combination of electron tomography and biochemical and biophysical assays. In addition, till the time of writing this review, 75 new structures of various Mtb proteins have been reported via single-particle cryo-EM. The information obtained from these structures has improved our understanding of the mechanisms of action of these proteins and the physiological pathways they are associated with. These structures have opened avenues for structure-based drug design and vaccine discovery programs that might help achieve global-TB control. This review describes the structural features of selected membrane proteins (type VII secretion systems, Rv1819c, Arabinosyltransferase, Fatty Acid Synthase, F-type ATP synthase, respiratory supercomplex, ClpP1P2 protease, ClpB disaggregase and SAM riboswitch), their involvement in physiological pathways, and possible use as a drug target. Tuberculosis is a deadly disease caused by Mycobacterium tuberculosis. The Cryo-EM and tomography have simplified the understanding of the mycobacterial membrane organization. Some proteins are located in the plasma membrane; some span the entire envelope, while some, like MspA, are located in the mycomembrane. Cryo-EM has made the study of such membrane proteins feasible.

Optimization of Short-Term Hot-Water Treatment of Apples for Fruit Salad Production by Non-Invasive Chlorophyll-Fluorescence Imaging

For fresh-cut salad production, hot-water treatment (HWT) needs optimization in terms of temperature and duration to guarantee a gentle and non-stressing processing to fully retain product quality besides an effective sanitation. One major initial target of heat treatment is photosynthesis, making it a suitable and sensitive marker for HWT effects. Chlorophyll fluorescence imaging (CFI) is a rapid and non-invasive tool to evaluate respective plant responses. Following practical applications in fruit salad production, apples of colored and of green-ripe cultivars ('Braeburn', 'Fuji', 'Greenstar', 'Granny Smith'), obtained from a local fruit salad producer, were hot-water treated from 44 to 70 °C for 30 to 300 s. One day after HWT and after 7 days of storage at 4 °C, CFI and remission spectroscopy were applied to evaluating temperature effects on photosynthetic activity, on contents of fruit pigments (chlorophylls, anthocyanins), and on various relevant quality parameters of intact apples. In 'Braeburn' apples, short-term HWT at 55 °C for 30 to 120 s avoided any heat injuries and quality losses. The samples of the other three cultivars turned out to be less sensitive and may be short-term heat-treated at temperatures of up to 60 °C for the same time. CFI proved to be a rapid, sensitive, and effective tool for process optimization of apples, closely reflecting the cultivar- or batch-specificity of heat effects on produce photosynthesis.

Native State Organization of Outer Membrane Porins Unraveled by HDx-MS

Hydrogen-deuterium exchange (HDx) associated with mass spectrometry (MS) is emerging as a powerful tool to provide conformational information about membrane proteins. Unfortunately, as for X-ray diffraction and NMR, HDx performed on reconstituted in vitro systems might not always reflect the in vivo environment. Outer-membrane vesicles naturally released by Escherichia coli were used to carry out analysis of native OmpF through HDx-MS. A new protocol compatible with HDx analysis that avoids hindrance from the lipid contents was setup. The extent of deuterium incorporation was in good agreement with the X-ray diffraction data of OmpF as the buried β-barrels incorporated a low amount of deuterium, whereas the internal loop L3 and the external loops incorporated a higher amount of deuterium. Moreover, the kinetics of incorporation clearly highlights that peptides segregate well in two distinct groups based exclusively on a trimeric organization of OmpF in the membrane: peptides presenting fast kinetics of labeling are facing the complex surrounding environment, whereas those presenting slow kinetics are located in the buried core of the trimer. The data show that HDx-MS applied to a complex biological system is able to reveal solvent accessibility and spatial arrangement of an integral outer-membrane protein complex.

Structural stability of purified human CFTR is systematically improved by mutations in nucleotide binding domain 1

The Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) is an ABC transporter containing two transmembrane domains forming a chloride ion channel, and two nucleotide binding domains (NBD1 and NBD2). CFTR has presented a formidable challenge to obtain monodisperse, biophysically stable protein. Here we report a comprehensive study comparing effects of single and multiple NBD1 mutations on stability of both the NBD1 domain alone and on purified full length human CFTR. Single mutations S492P, A534P, I539T acted additively, and when combined with M470V, S495P, and R555K cumulatively yielded an NBD1 with highly improved structural stability. Strategic combinations of these mutations strongly stabilized the domain to attain a calorimetric T_m > 70 °C. Replica exchange molecular dynamics simulations on the most stable 6SS-NBD1 variant implicated fluctuations, electrostatic interactions and side chain packing as potential contributors to improved stability. Progressive stabilization of NBD1 directly correlated with enhanced structural stability of full-length CFTR protein. Thermal unfolding of the stabilized CFTR mutants, monitored by changes in intrinsic fluorescence, demonstrated that Tm could be shifted as high as 67.4 °C in 6SS-CFTR, more than 20 °C higher than wild-type. H1402S, an NBD2 mutation, conferred CFTR with additional thermal stability, possibly by stabilizing an NBD-dimerized conformation. CFTR variants with NBD1-stabilizing mutations were expressed at the cell surface in mammalian cells, exhibited ATPase and channel activity, and retained these functions to higher temperatures. The capability to produce enzymatically active CFTR with improved structural stability amenable to biophysical and structural studies will advance mechanistic investigations and future cystic fibrosis drug development.

Unexpected Effects of K+ and Adenosine Triphosphate on the Thermal Stability of Na+,K+-ATPase

Na⁺,K⁺-ATPase is an integral membrane protein which couples ATP hydrolysis to the transport of three Na⁺ out and two K⁺ into the cell. The aim of this work is to characterize the effect of K⁺, ATP, and Mg²⁺ (essential activator) on the Na⁺,K⁺-ATPase thermal stability. Under all conditions tested, thermal inactivation of the enzyme is concomitant with a structural change involving the ATP binding site and membrane-associated regions. Both ligands exert a clear stabilizing effect due to both enthalpic and entropic contributions. Competition experiments between ATP and K⁺ showed that, when ATP is present, the inactivation rate coefficient exhibits a biphasic dependence on K⁺ concentration. At low [K⁺], destabilization of the enzyme is observed, while stabilization occurred at larger cation concentrations. This is not expected for a simple competition between the enzyme and two ligands that individually protect the enzyme. A model that includes enzyme species with none, one, or two K⁺ and/or one molecule of ATP bound explains the experimental data. We concluded that, despite both ligands stabilizing the enzyme, the species with one K⁺ and one ATP simultaneously bound is unstable.

Mapping the ATP binding site in the plasma membrane H(+)-ATPase from Kluyveromyces lactis

The plasma membrane H(+)-ATPase from Kluyveromyces lactis contains 14 tryptophan residues. Binding a nucleotide or unfolding with Gnd-HCl quenched intrinsic fluorescence by ≈60% suggesting that in the H(+)-ATPase-Nucleotide complex there is solvent-mediated collisional quenching of W505 fluorescence. N-bromosuccinimide (NBS) treatment of H(+)-ATPase modified a single W residue in both native and Gnd-HCl-unfolded H(+)-ATPase. Denaturing the H(+)-ATPase with 1% SDS led to expose six tryptophan residues while requiring 17 NBS/H(+)-ATPase. The remaining eight tryptophan residues kept buried indicating a highly stable TM domain. Acrylamide generated static quenching of fluorescence; partial in the native enzyme (V = 0.43 M(-1)) and complete in the Gnd-HCl-unfolded H(+)-ATPase (V = 0.81 M(-1)). Collisional quenching (K sv) increased from 3.12 to 7.45 M(-1) upon H(+)-ATPase unfolding. W505 fluorescence titration with NBS yielded a molar ratio of 6 NBS/H(+)-ATPase and quenched ≈ 60% fluorescence. In the recombinant N-domain, the distance between W505 and MantATP was estimated to be 21 Å by FRET. The amino acid residues involved in nucleotide binding were identified by N-domain molecular modelling and docking with ATP. In the N-domain/ATP complex model, the distance between W505 and ATP was 20.5 Å. ATP binding leads to a conformational change in the N-domain of H(+)-ATPase that exposes W505 to the environment.

Life at the border: adaptation of proteins to anisotropic membrane environment

This review discusses main features of transmembrane (TM) proteins which distinguish them from water-soluble proteins and allow their adaptation to the anisotropic membrane environment. We overview the structural limitations on membrane protein architecture, spatial arrangement of proteins in membranes and their intrinsic hydrophobic thickness, co-translational and post-translational folding and insertion into lipid bilayers, topogenesis, high propensity to form oligomers, and large-scale conformational transitions during membrane insertion and transport function. Special attention is paid to the polarity of TM protein surfaces described by profiles of dipolarity/polarizability and hydrogen-bonding capacity parameters that match polarity of the lipid environment. Analysis of distributions of Trp resides on surfaces of TM proteins from different biological membranes indicates that interfacial membrane regions with preferential accumulation of Trp indole rings correspond to the outer part of the lipid acyl chain region-between double bonds and carbonyl groups of lipids. These "midpolar" regions are not always symmetric in proteins from natural membranes. We also examined the hydrophobic effect that drives insertion of proteins into lipid bilayer and different free energy contributions to TM protein stability, including attractive van der Waals forces and hydrogen bonds, side-chain conformational entropy, the hydrophobic mismatch, membrane deformations, and specific protein-lipid binding.

β-Barrel mobility underlies closure of the voltage-dependent anion channel

The voltage-dependent anion channel (VDAC) is the major protein in the outer mitochondrial membrane, where it mediates transport of ATP and ADP. Changes in its permeability, induced by voltage or apoptosis-related proteins, have been implicated in apoptotic pathways. The three-dimensional structure of VDAC has recently been determined as a 19-stranded β-barrel with an in-lying N-terminal helix. However, its gating mechanism is still unclear. Using solid-state NMR spectroscopy, molecular dynamics simulations, and electrophysiology, we show that deletion of the rigid N-terminal helix sharply increases overall motion in VDAC's β-barrel, resulting in elliptic, semicollapsed barrel shapes. These states quantitatively reproduce conductance and selectivity of the closed VDAC conformation. Mutation of the N-terminal helix leads to a phenotype intermediate to the open and closed states. These data suggest that the N-terminal helix controls entry into elliptic β-barrel states which underlie VDAC closure. Our results also indicate that β-barrel channels are intrinsically flexible.

Shifting hydrogen bonds may produce flexible transmembrane helices

The intricate functions of membrane proteins would not be possible without bends or breaks that are remarkably common in transmembrane helices. The frequent helix distortions are nevertheless surprising because backbone hydrogen bonds should be strong in an apolar membrane, potentially rigidifying helices. It is therefore mysterious how distortions can be generated by the evolutionary currency of random point mutations. Here we show that we can engineer a transition between distinct distorted helix conformations in bacteriorhodopsin with a single-point mutation. Moreover, we estimate the energetic cost of the conformational transitions to be smaller than 1 kcal/mol. We propose that the low energy of distortion is explained in part by the shifting of backbone hydrogen bonding partners. Consistent with this view, extensive backbone hydrogen bond shifts occur during helix conformational changes that accompany functional cycles. Our results explain how evolution has been able to liberally exploit transmembrane helix bending for the optimization of membrane protein structure, function, and dynamics.

First insights on organic cosolvent effects on FhuA wildtype and FhuA Δ1-159

Circular dichroism (CD) and deconvolution were used to study the structural integrity of a "plugged" and an "open" FhuA transmembrane channel protein in the presence of varied concentrations of tetrahydrofuran (THF), ethanol (EtOH) and chloroform/methanol (C/M). FhuA is an Escherichia coli outer membrane protein (78.9 kDa) consisting of 22 β-sheets and an internal globular cork domain which acts as an iron transporter. FhuA and the deletion variant FhuA Δ1-159 showed comparable and remarkable resistance in the presence of THF (≤40 vol%) and EtOH (≤10 vol%). In C/M, significant differences in structural resistance were observed (FhuA stable ≤10 vol%; FhuA Δ1-159 ≤1 vol%). Deconvolution of CD-spectra for FhuA and FhuA Δ1-159 yielded β-sheet contents of 61 % (FhuA) and 58% (FhuA Δ1-159). Interestingly, FhuA and FhuA Δ1-159 had comparable β-sheet contents in the presence and absence of all three organic cosolvents. Additionally, precipitated FhuA and FhuA Δ1-159 (in 40 vol% C/M or 65 vol% THF) redissolved by supplementing the detergent n-octyl-oligo-oxyethylene (oPOE).

Transmembrane and extramembrane contributions to membrane protein thermal stability: studies with the NaChBac sodium channel

The thermal stabilities of the extramembranous and transmembranous regions of the bacterial voltage-gated sodium channel NaChBac have been characterised using thermal-melt synchrotron radiation circular dichroism (SRCD) spectroscopy. A series of constructs, ranging from the full-length protein containing both the C-terminal cytoplasmic and the transmembranous domains, to proteins with decreasing amounts of the cytoplasmic domain, were examined in order to separately define the roles of these two types of domains in the stability and processes of unfolding of a membrane protein. The sensitivity of the SRCD measurements over a wide range of wavelengths and temperatures has meant that subtle but reproducible conformational changes could be detected with accuracy. The residues in the C-terminal extramembranous domain were highly susceptible to thermal denaturation, but for the most part the transmembrane residues were not thermally-labile and retained their helical character even at very elevated temperatures. The process of thermal unfolding involved an initial irreversible unfolding of the highly labile distal extramembranous C-terminal helical region, which was accompanied by a reversible unfolding of a small number of helical residues in the transmembrane domain. This was then followed by the irreversible unfolding of a limited number of additional transmembrane helical residues at greatly elevated temperatures. Hence this study has been able to determine the different contributions and roles of the transmembrane and extramembrane residues in the processes of thermal denaturation of this multipass integral membrane protein.

Folding and stability of membrane transport proteins in vitro

Transmembrane transporters are responsible for maintaining a correct internal cellular environment. The inherent flexibility of transporters together with their hydrophobic environment means that they are challenging to study in vitro, but recently significant progress been made. This review will focus on in vitro stability and folding studies of transmembrane alpha helical transporters, including reversible folding systems and thermal denaturation. The successful re-assembly of a small number of ATP binding cassette transporters is also described as this is a significant step forward in terms of understanding the folding and assembly of these more complex, multi-subunit proteins. The studies on transporters discussed here represent substantial advances for membrane protein studies as well as for research into protein folding. The work demonstrates that large flexible hydrophobic proteins are within reach of in vitro folding studies, thus holding promise for furthering knowledge on the structure, function and biogenesis of ubiquitous membrane transporter families. This article is part of a Special Issue entitled: Protein Folding in Membranes.

Thermodynamic stability of bacteriorhodopsin mutants measured relative to the bacterioopsin unfolded state

The stability of bacteriorhodopsin (bR) has often been assessed using SDS unfolding assays that monitor the transition of folded bR (bR(f)) to unfolded (bR(u)). While many criteria suggest that the unfolding curves reflect thermodynamic stability, slow retinal (RET) hydrolysis during refolding makes it impossible to perform the most rigorous test for equilibrium, i.e., superimposable unfolding and refolding curves. Here we made a new equilibrium test by asking whether the refolding rate in the transition zone is faster than RET hydrolysis. We find that under conditions we have used previously, refolding is in fact slower than hydrolysis, strongly suggesting that equilibrium is not achieved. Instead, the apparent free energy values reported previously are dominated by unfolding rates. To assess how different the true equilibrium values are, we employed an alternative method by measuring the transition of bR(f) to unfolded bacterioopsin (bO(u)), the RET-free form of unfolded protein. The bR(f)-to-bO(u) transition is fully reversible, particular when we add excess RET. We compared the difference in unfolding free energies for 13 bR mutants measured by both assays. For 12 of the 13 mutants with a wide range of stabilities, the results are essentially the same within experimental error. The congruence of the results is fortuitous and suggests the energetic effects of most mutations may be focused on the folded state. The bR(f)-to-bO(u) reaction is inconvenient because many days are required to reach equilibrium, but it is the preferable measure of thermodynamic stability. This article is part of a Special Issue entitled: Protein Folding in Membranes.

Horizontal gene transfer and assortative recombination within the Acinetobacter baumannii clinical population provide genetic diversity at the single carO gene, encoding a major outer membrane protein channel

We described previously the presence in Acinetobacter baumannii of a novel outer membrane (OM) protein, CarO, which functions as an L-ornithine OM channel and whose loss was concomitant with increased carbapenem resistance among clonally related nosocomial isolates of this opportunistic pathogen. Here, we describe the existence of extensive genetic diversity at the carO gene within the A. baumannii clinical population. The systematic analysis of carO sequences from A. baumannii isolates obtained from public hospitals in Argentina revealed the existence of four highly polymorphic carO variants among them. Sequence polymorphism between the different A. baumannii CarO variants was concentrated in three well-defined protein regions that superimposed mostly to predicted surface-exposed loops. Polymorphism among A. baumannii CarO variants was manifested in differential electrophoretic mobilities, antigenic properties, abilities to form stable oligomeric structures, and l-ornithine influx abilities through the A. baumannii OM under in vivo conditions. Incongruence between the phylogenies of the clinical A. baumannii isolates analyzed and those of the carO variants they harbor suggests the existence of assortative (entire-gene) carO recombinational exchange within the A. baumannii population. Exchange of carO variants possessing differential characteristics mediated by horizontal gene transfer may constitute an A. baumannii population strategy to survive radically changing environmental conditions, such as the leap from inanimate sources to human hosts and vice versa, persistence in a compromised host, and/or survival in health care facilities.

The use of the condensed single protein production system for isotope-labeled outer membrane proteins, OmpA and OmpX in E. coli

Gram-negative bacteria consist of two independent membranes, the inner cytoplasmic membrane and the outer membrane. The outer membrane contains a number of β-barrel proteins such as OmpF, OmpC, OmpA, and OmpX. In this article, we explored to use the condensed Single Protein Production (cSPP) system for isotope labelling of OmpA and OmpX for NMR structural study, both of which are known to consist of eight β-strands forming a barrel in the outer membrane. Using a deletion strain lacking all major outer membrane proteins, both OmpA and OmpX were expressed well in a 20-fold cSPP system. We demonstrated that outer membrane fractions prepared from the cSPP system in M9 medium containing ¹⁵N-NH₄Cl can be directly used for NMR structural study of the outer mebrane proteins without any further purification to get excellent [¹H-¹⁵N]-TROSY spectra. This method would be quite valuable for the study of pure proteins in their native membrane environment without the need of purification and reconstitution.

Membrane protein folding: how important are hydrogen bonds?

Water is an inhospitable environment for protein hydrogen bonds because it is polarizable and capable of forming competitive hydrogen bonds. In contrast, the apolar core of a biological membrane seems like an ideal environment for hydrogen bonds, and it has long been assumed that hydrogen bonding should be a powerful force driving membrane protein folding. Nevertheless, while backbone hydrogen bonds may be much stronger in membrane proteins, experimental measurements indicate that side chain hydrogen bond strengths are not strikingly different in membrane and water soluble proteins. How is this possible? I argue that model compounds in apolar solvents do not adequately describe the system because the protein itself is ignored. The protein chain provides a rich source of competitive hydrogen bonds and a polarizable environment that can weaken hydrogen bonds. Thus, just like water soluble proteins, evolution can drive the creation of potent hydrogen bonds in membrane proteins where necessary, but mitigating forces in their environment must still be overcome.

Comparison of the thermodynamic landscapes of unfolding and formation of the energy dissipative state in the isolated light harvesting complex II

In biochemistry and cell biology, understanding the molecular mechanisms by which physiological processes are regulated is regarded as an ultimate goal. In higher plants, one of the most widely investigated regulatory processes occurs in the light harvesting complexes (LHCII) of the chloroplast thylakoid membranes. Under limiting photon flux densities, LHCII harvests sunlight with high efficiency. When the intensity of incident radiation reaches levels close to the saturation of the photosynthesis, the efficiency of light harvesting is decreased by a process referred to as nonphotochemical quenching (NPQ), which enhances the singlet-excited state deactivation via nonradiative dissipative processes. Conformational rearrangements in LHCII are known to be crucial in promoting and controlling NPQ in vitro and in vivo. In this article, we address the thermodynamic nature of the conformational rearrangements promoting and controlling NPQ in isolated LHCII. A combined, linear reaction scheme in which the folded, quenched state represents a stable intermediate on the unfolding pathway was employed to describe the temperature dependence of the spectroscopic signatures associated with the chlorophyll fluorescence quenching and the loss of secondary structure motifs in LHCII. The thermodynamic model requires considering the temperature dependence of Gibbs free energy difference between the quenched and the unquenched states, as well as the unfolded and quenched states, of LHCII. Even though the same reaction scheme is adequate to describe the quenching and the unfolding processes in LHCII monomers and trimers, their thermodynamic characteristics were found to be markedly different. The results of the thermodynamic analysis shed light on the physiological importance of the trimeric state of LHCII in stabilizing the efficient light harvesting mode as well as preventing the quenched conformation of the protein from unfolding. Moreover, the transition to the quenched conformation in trimers reveals a larger degree of cooperativity than in monomers, explained by a small characteristic entropy (DeltaH(q) = 85 +/- 3 kJ mol(-1) compared to 125 +/- 5 kJ mol(-1) in monomers), which enables the fine-tuning of nonphotochemical quenching in vivo.

Biogenesis of mitochondrial outer membrane proteins

Mitochondria are surrounded by two distinct membranes: the outer and the inner membrane. The mitochondrial outer membrane mediates numerous interactions between the mitochondrial metabolic and genetic systems and the rest of the eukaryotic cell. Proteins of this membrane are nuclear-encoded and synthesized as precursor proteins in the cytosol. They are targeted to the mitochondria and inserted into their target membrane via various pathways. This review summarizes our current knowledge of the sorting signals for this specific targeting and describes the mechanisms by which the mitochondrial import machineries recognize precursor proteins, mediate their membrane integration and facilitate assembly into functional complexes.

Stable interactions between the transmembrane domains of the adenosine A2A receptor

G-protein-coupled receptors (GPCRs) must properly insert and fold in the membrane to adopt a stable native structure and become biologically active. The interactions between transmembrane (TM) helices are believed to play a major role in these processes. Previous studies in our group showed that specific interactions between TM helices occur, leading to an increase in helical content, especially in weakly helical TM domains, suggesting that helix-helix interactions in addition to helix-lipid interactions facilitate helix formation. They also demonstrated that TM peptides interact in a similar fashion in micelles and lipid vesicles, as they exhibit relatively similar thermal stability and alpha-helicity inserted in SDS micelles to that observed in liposomes. In this study, we perform an analysis of pairwise interactions between peptides corresponding to the seven TM domains of the human A(2A) receptor (A(2A)R). We used a combination of Förster resonance energy transfer (FRET) measurement and circular dichroism (CD) spectroscopy to detect and analyze these interactions in detergent micelles. We found that strong and specific interactions occur in only seven of the 28 possible peptide pairs. Furthermore, not all interactions, identified by FRET, lead to a change in helicity. Our results identify stabilizing contacts that are likely related to the stability of the receptor and that are consistent with what is known about the three-dimensional structure and stability of rhodopsin and the beta(2) adrenergic receptor.

Vertebrate membrane proteins: structure, function, and insights from biophysical approaches

Membrane proteins are key targets for pharmacological intervention because they are vital for cellular function. Here, we analyze recent progress made in the understanding of the structure and function of membrane proteins with a focus on rhodopsin and development of atomic force microscopy techniques to study biological membranes. Membrane proteins are compartmentalized to carry out extra- and intracellular processes. Biological membranes are densely populated with membrane proteins that occupy approximately 50% of their volume. In most cases membranes contain lipid rafts, protein patches, or paracrystalline formations that lack the higher-order symmetry that would allow them to be characterized by diffraction methods. Despite many technical difficulties, several crystal structures of membrane proteins that illustrate their internal structural organization have been determined. Moreover, high-resolution atomic force microscopy, near-field scanning optical microscopy, and other lower resolution techniques have been used to investigate these structures. Single-molecule force spectroscopy tracks interactions that stabilize membrane proteins and those that switch their functional state; this spectroscopy can be applied to locate a ligand-binding site. Recent development of this technique also reveals the energy landscape of a membrane protein, defining its folding, reaction pathways, and kinetics. Future development and application of novel approaches during the coming years should provide even greater insights to the understanding of biological membrane organization and function.

Prediction of membrane protein types in a hybrid space

Prediction of the types of membrane proteins is of great importance both for genome-wide annotation and for experimental researchers to understand proteins' functions. We describe a new strategy for the prediction of the types of membrane proteins using the Nearest Neighbor Algorithm. We introduced a bipartite feature space consisting of two kinds of disjoint vectors, proteins' domain profile and proteins' physiochemical characters. Jackknife cross validation test shows that a combination of both features greatly improves the prediction accuracy. Furthermore, the contribution of the physiochemical features to the classification of membrane proteins has also been explored using the feature selection method called "mRMR" (Minimum Redundancy, Maximum Relevance) ( IEEE Trans. Pattern Anal. Mach. Intell. 2005, 27 ( 8), 1226- 1238 ). A more compact set of features that are mostly contributive to membrane protein classification are obtained. The analyses highlighted both hydrophobicity and polarity as the most important features. The predictor with 56 most contributive features achieves an acceptable prediction accuracy of 87.02%. Online prediction service is available freely on our Web site http://pcal.biosino.org/TransmembraneProteinClassification.html.

The N-terminal helix is a post-assembly clamp in the bacterial outer membrane protein PagP

The Escherichia coli outer membrane beta-barrel enzyme PagP and its homologues are unique in that the eight-stranded barrel is tilted by about 25 degrees with respect to the membrane normal and is preceded by a 19-residue amphipathic alpha-helix. To investigate the role of this helix in the folding and stability of PagP, mutants were generated in which the helix was deleted (Delta(1-19)), or in which residues predicted to be involved in helix-barrel interactions were altered (W17A or R59L). The ability of the variants to insert into detergent micelles or liposomes was studied in vitro using circular dichroism, fluorescence, Fourier transform infrared spectroscopy, electrophoretic mobility and gain of enzyme activity. The data show that PagP, initially unfolded in 5% (w/v) perfluoro-octanoic acid or 6 M guanidinium chloride, inserts spontaneously and folds quantitatively to an active conformation into detergent micelles of cyclofos-7 or into large vesicles of diC(12:0)-phosphatidylcholine (diC(12:0)PC), respectively, the latter in the presence of 7 M urea. Successful refolding of all variants into both micelles and liposomes ruled out an essential role for the helix or helix-barrel interactions in folding and membrane insertion. Measurements of thermal stability indicated that the variants R59L, W17A/R59L and Delta(1-19) were destabilised substantially compared with wild-type PagP. However, in contrast to the other variants, destabilisation of the W17A variant relative to wild-type PagP was much greater in liposomes than in micelles. Analysis of the kinetics of folding and unfolding of all variants in diC(12:0)PC liposomes suggested that this destabilisation arises predominantly from an increased dissociation of the refolded variant proteins from the lipid-inserted state. The data support the view that the helix of PagP is not required for folding and assembly, but instead acts as a clamp, stabilising membrane-inserted PagP after folding and docking with the membrane are complete.

An unfolding story of helical transmembrane proteins

Reversible unfolding of helical transmembrane proteins could provide valuable information about the free energy of interaction between transmembrane helices. Thermal unfolding experiments suggest that this process for integral membrane proteins is irreversible. Chemical unfolding has been accomplished with organic acids, but the unfolding or refolding pathways involve irreversible steps. Sodium dodecyl sulfate (SDS) has been used as a perturbant to study reversible unfolding and refolding kinetics. However, the interpretation of these experiments is not straightforward. It is shown that the results could be explained by SDS binding without substantial unfolding. Furthermore, the SDS-perturbed state is unlikely to include all of the entropy terms involved in an unfolding process. Alternative directions for future research are suggested: fluorinated alcohols in homogeneous solvent systems, inverse micelles, and fragment association studies.

Kinetic analysis of the thermal stability of the photosynthetic reaction center from Rhodobacter sphaeroides

The temperature-induced denaturation of the photosynthetic reaction center from Rhodobacter sphaeroides has been studied through the changes that occur in the absorption spectrum of the bound chromophores on heating. At elevated temperatures, the characteristic absorbance bands of the bacteriochlorins bound to the polypeptides within the reaction center are lost, and are replaced by features typical of unbound bacteriochlorophyll and bacteriopheophytin. The kinetics of the spectral changes cannot be explained by a direct conversion from the functional to the denatured form of the protein, and require the presence of at least one intermediate. Possible mechanisms for the transformation via an intermediate are examined using a global analysis of the kinetic data, and the most likely mechanism is shown to involve a reversible transformation between the native state and an off-pathway intermediate, coupled to an irreversible transformation to the denatured state. The activation energies for the transformations between the three components are calculated from the effect of temperature on the individual rate constants, and the likely structural changes of the protein during the temperature-induced transformation are discussed.

Observing Folding Pathways and Kinetics of a Single Sodium-proton Antiporter from Escherichia coli

Mechanisms of folding and misfolding of membrane proteins are of interest in cell biology. Recently, we have established single-molecule force spectroscopy to observe directly the stepwise folding of the Na+/H+ antiporter NhaA from Escherichia coli in vitro. Here, we improved this approach significantly to track the folding intermediates of a single NhaA polypeptide forming structural segments such as the Na+-binding site, transmembrane alpha-helices, and helical pairs. The folding rates of structural segments ranged from 0.31 s(-1) to 47 s(-1), providing detailed insight into a distinct folding hierarchy of an unfolded polypeptide into the native membrane protein structure. In some cases, however, the folding chain formed stable and kinetically trapped non-native structures, which could be assigned to misfolding events of the antiporter.

Thermal stability of outer membrane protein porin fromParacoccus denitrificans: FT-IR as a spectroscopic tool to study lipid-protein interaction

Lipid protein interactions play a key role in the stability and function of various membrane proteins. Earlier we have reported the extreme thermal stability of porin from Paracoccus denitrificans reconstituted into liposomes. Here, we used Fourier transform infrared spectroscopy for a label free analysis of the global secondary structural changes and local changes in the tyrosine microenvironment. Our results show that a mixed lipid system (non-uniform bilayer) optimizes the thermal stability of porin as compared to the porin in pure lipids (uniform bilayer) or detergent micelles. This is in line with the fact that the bacterial outer membrane is a dynamic system made up of lipids of varying chain lengths, head groups and the barrel wall height contacting the membrane is uneven.

Reversible unfolding of beta-sheets in membranes: a calorimetric study

The hexapeptide acetyl-Trp-Leu(5) (AcWL(5)) has the remarkable ability to assemble reversibly and spontaneously into beta-sheets on lipid membranes as a result of monomer partitioning followed by cooperative assembly. This system provides a unique opportunity to study the thermodynamics of protein folding in membranes, which we have done using isothermal titration calorimetry (ITC) and differential scanning calorimetry (DSC). The results, which may represent the first example of reversible thermal unfolding of peptides in membranes, help to define the contribution of hydrogen bonding to the extreme thermal stability of membrane proteins. ITC revealed that the enthalpy change for partitioning of monomeric, unstructured AcWL(5) from water into membranes was zero within experimental error over the temperature range of 5 degrees C to 75 degrees C. DSC showed that the beta-sheet aggregates underwent a reversible, endothermic, and very asymmetric thermal transition with a concentration-dependent transition temperature (T(m)) in the range of 60 degrees C to 80 degrees C. A numerical model of nucleation and growth-dependent assembly of oligomeric beta-sheets, proposed earlier to describe beta-sheet formation in membranes, recreated remarkably well the unusual shape and concentration-dependence of the transition peaks. The enthalpy for thermal unfolding of AcWL(5) beta-sheets in the membrane was found to be about 8(+/-1)kcal mol(-1), or about 1.3(+/-0.2)kcal mol(-1) per residue.

Probing the Energy Landscape of the Membrane Protein Bacteriorhodopsin

The folding and stability of transmembrane proteins is a fundamental and unsolved biological problem. Here, single bacteriorhodopsin molecules were mechanically unfolded from native purple membranes using atomic force microscopy and force spectroscopy. The energy landscape of individual transmembrane alpha helices and polypeptide loops was mapped by monitoring the pulling speed dependence of the unfolding forces and applying Monte Carlo simulations. Single helices formed independently stable units stabilized by a single potential barrier. Mechanical unfolding of the helices was triggered by 3.9-7.7 A extension, while natural unfolding rates were of the order of 10(-3) s(-1). Besides acting as individually stable units, helices associated pairwise, establishing a collective potential barrier. The unfolding pathways of individual proteins reflect distinct pulling speed-dependent unfolding routes in their energy landscapes. These observations support the two-stage model of membrane protein folding in which alpha helices insert into the membrane as stable units and then assemble into the functional protein.