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BBA - Biomembranes (v.1818, #4)
Computational studies of membrane proteins: Models and predictions for biological understanding by Jie Liang; Hammad Naveed; David Jimenez-Morales; Larisa Adamian; Meishan Lin (pp. 927-941).
We discuss recent progresses in computational studies of membrane proteins based on physical models with parameters derived from bioinformatics analysis. We describe computational identification of membrane proteins and prediction of their topology from sequence, discovery of sequence and spatial motifs, and implications of these discoveries. The detection of evolutionary signal for understanding the substitution pattern of residues in the TM segments and for sequence alignment is also discussed. We further discuss empirical potential functions for energetics of inserting residues in the TM domain, for interactions between TM helices or strands, and their applications in predicting lipid-facing surfaces of the TM domain. Recent progresses in structure predictions of membrane proteins are also reviewed, with further discussions on calculation of ensemble properties such as melting temperature based on simplified state space model. Additional topics include prediction of oligomerization state of membrane proteins, identification of the interfaces for protein–protein interactions, and design of membrane proteins. This article is part of a Special Issue entitled: Protein Folding in Membranes.► Prediction of membrane proteins and topology. ► Discovery of sequence and spatial motifs, detection of evolutionary signal. ► Empirical potential functions. ► Structure predictions and ensemble properties. ► Prediction of protein–protein interactions.
Keywords: Membrane protein; Bioinformatics; Empirical potential function; Motif; Protein-protein interaction; Ensemble properties of membrane proteins
Hydrogen bond dynamics in membrane protein function by Ana-Nicoleta Bondar; Stephen H. White (pp. 942-950).
Changes in inter-helical hydrogen bonding are associated with the conformational dynamics of membrane proteins. The function of the protein depends on the surrounding lipid membrane. Here we review through specific examples how dynamical hydrogen bonds can ensure an elegant and efficient mechanism of long-distance intra-protein and protein–lipid coupling, contributing to the stability of discrete protein conformational substates and to rapid propagation of structural perturbations. This article is part of a Special Issue entitled: Protein Folding in Membranes.► Networks of inter-helical hydrogen bonds can be present in membrane proteins. ► These inter-helical hydrogen bonds have a complex dynamics. ► Lipid hydrogen bonding changes the local structure and dynamics of membrane proteins. ► Intra-protein and lipid:protein hydrogen bonding couple the protein to lipids.
Keywords: Membrane protein structure; Hydrogen bond; Membrane protein dynamics; Lipid–protein interactions
Progress in understanding the role of lipids in membrane protein folding by Drake C. Mitchell (pp. 951-956).
Detailed investigations of membrane protein folding present a number of serious technical challenges. Most studies addressing this subject have emphasized aspects of protein amino acid sequence and structure. While it is generally accepted that the interplay between proteins and lipids plays an important role in membrane protein folding, the role(s) played by membrane lipids in this process have only recently been explored in any detail. This review is intended to summarize recent studies in which particular lipids or membrane physical properties have been shown to play a role in the folding of intact, functionally competent integral membrane proteins. This article is part of a Special Issue entitled: Protein Folding in Membranes.► Works which specifically examine lipids in membrane folding are reviewed. ► Focus on alpha helical proteins, beta barrels and membrane protein topogenesis. ► Focus on folding of intact, functional membrane proteins.
Keywords: Phospholipid; Phosphatidylethanolamine; Curvature stress
Recognition of polyunsaturated acyl chains by enzymes acting on membrane lipids by Richard M. Epand (pp. 957-962).
Polyunsaturated acyl chains play an important role in human biology. These lipids cannot be synthesized de novo and they are selectively distributed to certain organs and are found predominantly only in certain lipid classes. Their selective distribution is a consequence of the specificity of the binding of these lipids by certain proteins. Lipoxygenases are a group of well studied enzymes that specifically oxidize polyunsaturated fatty acids. We propose that certain features of the interaction of lipoxygenases with polyunsaturated acyl chains are also found in other unrelated proteins that act on lipids with these moieties. The features common to several of the enzymes that specifically interact with polyunsaturated acyl chains include the fact that the polyunsaturated chain is drawn out of the membrane to bind to a hydrophobic channel within the protein and that a similar pattern of required amino acids residues comprises part of the binding site for the polyunsaturated chain. This article is part of a Special Issue entitled: Protein Folding in Membranes.► Polyunsaturated chains contribute to the interaction of certain proteins with lipids. ► Binding sites for polyunsaturated chains are hydrophobic channels in the protein. ► A similar pattern of residues is important for binding polyunsaturated acyl chains.
Keywords: Abbreviations; PUFA; polyunsaturated fatty acids; PE; phosphatidylethanolamine; PI; phosphatidylinositol; PS; phosphatidylserine; PI4P; phosphatidylinositol-4-phosphate; PIP; 2; phosphatidylinositol-(4,5)-bisphosphate; DGK; diacylglycerol kinase; PI4P5K; phosphatidylinositol-4-phosphate-5-kinaseArachidonoyl; Linoleoyl; Docosahexanoyl; Lipoxygenase; Diacylglycerol kinase
Transmembrane helix–helix interactions are modulated by the sequence context and by lipid bilayer properties by Florian Cymer; Anbazhagan Veerappan; Dirk Schneider (pp. 963-973).
Folding of polytopic transmembrane proteins involves interactions of individual transmembrane helices, and multiple TM helix–helix interactions need to be controlled and aligned to result in the final TM protein structure. While defined interaction motifs, such as the GxxxG motif, might be critically involved in transmembrane helix–helix interactions, the sequence context as well as lipid bilayer properties significantly modulate the strength of a sequence specific transmembrane helix–helix interaction. Structures of 11 transmembrane helix dimers have been described today, and the influence of the sequence context as well as of the detergent and lipid environment on a sequence specific dimerization is discussed in light of the available structural information. This article is part of a Special Issue entitled: Protein Folding in Membranes.Display Omitted► Transmembrane helices specifically interact. ► GxxxG-like motifs might be involved in helix dimerization. ► The sequence context highly modulated the structure and stability of a helix dimer. ► The lipid bilayer properties might influence structure and stability of a helix dimer.
Keywords: Abbreviations; GpA; glycophorin A; TM; transmembrane; NMR; nuclear magnetic resonance spectroscopy; DMPC; Dimyristoylphosphatidylcholine; DOPC; 1,2-Dioleoyl-sn-glycero-3-phosphocholineMembrane protein; Helix dimer; GxxxG; Hydrogen bond; Lateral pressure; Hydrophobic thickness
Transmembrane domains interactions within the membrane milieu: Principles, advances and challenges by Avner Fink; Neta Sal-Man; Doron Gerber; Yechiel Shai (pp. 974-983).
Protein–protein interactions within the membrane are involved in many vital cellular processes. Consequently, deficient oligomerization is associated with known diseases. The interactions can be partially or fully mediated by transmembrane domains (TMD). However, in contrast to soluble regions, our knowledge of the factors that control oligomerization and recognition between the membrane–embedded domains is very limited. Due to the unique chemical and physical properties of the membrane environment, rules that apply to interactions between soluble segments are not necessarily valid within the membrane. This review summarizes our knowledge on the sequences mediating TMD–TMD interactions which include conserved motifs such as the GxxxG, QxxS, glycine and leucine zippers, and others. The review discusses the specific role of polar, charged and aromatic amino acids in the interface of the interacting TMD helices. Strategies to determine the strength, dynamics and specificities of these interactions by experimental (ToxR, TOXCAT, GALLEX and FRET) or various computational approaches (molecular dynamic simulation and bioinformatics) are summarized. Importantly, the contribution of the membrane environment to the TMD–TMD interaction is also presented. Studies utilizing exogenously added TMD peptides have been shown to influence in vivo the dimerization of intact membrane proteins involved in various diseases. The chirality independent TMD–TMD interactions allows for the design of novel shortd- andl-amino acids containing TMD peptides with advanced properties. Overall these studies shed light on the role of specific amino acids in mediating the assembly of the TMDs within the membrane environment and their contribution to protein function. This article is part of a Special Issue entitled: Protein Folding in Membranes.► An updated review on protein–protein interactions within the membrane milieu. ► Summary of our knowledge on the sequences mediating the interaction between transmembrane domains. ► Role of amino acids in TMDs assembly and contribution to protein function.
Keywords: Helix–helix interaction; Transmembrane domain; ToxR; TOXCAT; GALEX; Recognition within the membrane
Transmembrane helices can induce domain formation in crowded model membranes by Jan Domański; Siewert J. Marrink; Schafer Lars V. Schäfer (pp. 984-994).
We studied compositionally heterogeneous multi-component model membranes comprised of saturated lipids, unsaturated lipids, cholesterol, and α-helical TM protein models using coarse-grained molecular dynamics simulations. Reducing the mismatch between the length of the saturated and unsaturated lipid tails reduced the driving force for segregation into liquid-ordered ( l o) and liquid-disordered ( l d) lipid domains. Cholesterol depletion had a similar effect, and binary lipid mixtures without cholesterol did not undergo large-scale phase separation under the simulation conditions. The phase-separating ternary dipalmitoyl-phosphatidylcholine (DPPC)/dilinoleoyl-PC (DLiPC)/cholesterol bilayer was found to segregate into l o and l d domains also in the presence of a high concentration of ΤΜ helices. The l d domain was highly crowded with TM helices (protein-to-lipid ratio ~1:5), slowing down lateral diffusion by a factor of 5–10 as compared to the dilute case, with anomalous (sub)-diffusion on the μs time scale. The membrane with the less strongly unsaturated palmitoyl-linoleoyl-PC instead of DLiPC, which in the absence of TM α-helices less strongly deviated from ideal mixing, could be brought closer to a miscibility critical point by introducing a high concentration of TM helices. Finally, the 7-TM protein bacteriorhodopsin was found to partition into the l d domains irrespective of hydrophobic matching. These results show that it is possible to directly study the lateral reorganization of lipids and proteins in compositionally heterogeneous and crowded model biomembranes with coarse-grained molecular dynamics simulations, a step toward simulations of realistic, compositionally complex cellular membranes. This article is part of a Special Issue entitled: Protein Folding in Membranes.Display Omitted► Saturated/unsaturated lipid/cholesterol mixtures can segregate in MD simulations. ►A high concentration of TM helices in the membrane slows down diffusion. ► TM helices can amplify non-ideal lipid mixing. ► Bacteriorhodopsin partitions into liquid-disordered lipid domains.
Keywords: Membrane protein; Lipid raft; Crowding; Molecular dynamics; Coarse grained
Physical–chemical principles underlying RTK activation, and their implications for human disease by Lijuan He; Kalina Hristova (pp. 995-1005).
RTKs, the second largest family of membrane receptors, exert control over cell proliferation, differentiation and migration. In recent years, our understanding of RTK structure and activation in health and disease has skyrocketed. Here we describe experimental approaches used to interrogate RTKs, and we review the quantitative biophysical frameworks and structural considerations that shape our understanding of RTK function. We discuss current knowledge about RTK interactions, focusing on the role of different domains in RTK homodimerization, and on the importance and challenges in RTK heterodimerization studies. We also review our understanding of pathogenic RTK mutations, and the underlying physical–chemical causes for the pathologies. This article is part of a Special Issue entitled: Protein Folding in Membranes.► Physical–chemical models provide an adequate description of RTK activation. ► Quantitative experimental methods shed new light on RTK function. ► Methods are available to characterize RTK homo and heterodimerization.
Keywords: Membrane receptors; Cell signaling; Dimerization thermodynamics; Experimental methods
Folding of diphtheria toxin T-domain in the presence of amphipols and fluorinated surfactants: Toward thermodynamic measurements of membrane protein folding by Alexander Kyrychenko; Mykola V. Rodnin; Mauricio Vargas-Uribe; Shivaji K. Sharma; Grégory Durand; Bernard Pucci; Jean-Luc Popot; Alexey S. Ladokhin (pp. 1006-1012).
Solubilizing membrane proteins for functional, structural and thermodynamic studies is usually achieved with the help of detergents, which, however, tend to destabilize them. Several classes of non-detergent surfactants have been designed as milder substitutes for detergents, most prominently amphipathic polymers called 'amphipols' and fluorinated surfactants. Here we test the potential usefulness of these compounds for thermodynamic studies by examining their effect on conformational transitions of the diphtheria toxin T-domain. The advantage of the T-domain as a model system is that it exists as a soluble globular protein at neutral pH yet is converted into a membrane-competent form by acidification and inserts into the lipid bilayer as part of its physiological action. We have examined the effects of various surfactants on two conformational transitions of the T-domain, thermal unfolding and pH-induced transition to a membrane-competent form. All tested detergent and non-detergent surfactants lowered the cooperativity of the thermal unfolding of the T-domain. The dependence of enthalpy of unfolding on surfactant concentration was found to be least for fluorinated surfactants, thus making them useful candidates for thermodynamic studies. Circular dichroism measurements demonstrate that non-ionic homopolymeric amphipols (NAhPols), unlike any other surfactants, can actively cause a conformational change of the T-domain. NAhPol-induced structural rearrangements are different from those observed during thermal denaturation and are suggested to be related to the formation of the membrane-competent form of the T-domain. Measurements of leakage of vesicle content indicate that interaction with NAhPols not only does not prevent the T-domain from inserting into the bilayer, but it can make bilayer permeabilization even more efficient, whereas the pH-dependence of membrane permeabilization becomes more cooperative. This article is part of a Special Issue entitled: Protein Folding in Membranes.► Amphipols and fluorinated surfactants are tested for thermodynamic studies. ► Two conformational transitions of the diphtheria toxin T-domain are examined. ► Unfolding enthalpy is least affected by fluorinated surfactants. ► Non-ionic amphipols can actively cause a conformational change. ► This change does not affect membrane activity of the T-domain.
Keywords: Abbreviations; APols (amphipols); a class of amphipathic polymers designed for handling membrane proteins in aqueous solutions; NAhPols; Non-ionic homopolymeric amphipols (Fig. 1); A8-35; an anionic, polyacrylate-based APol (Fig. 1); F; 6; TAC (or FTAC) (6 refers to the number of fluorinated carbons); fluorinated surfactants 4-thia-7,7,8,8,9,9,10,10,11,11,12,12,12-tridecafluorododecanamyl; -poly-Tris; -(hydroxymethyl)acrylamidomethane (the same compound was called FTAC-C6 in some of our previous publications [1, 2]); F; 6; -Diglu (6 refers to the number of fluorinated carbons); fluorinated surfactant; N; -1,1-di[(; β; -D-glucopyranosyl)oxymethyl]hydroxyethyl-4-thia-7,7,8,8,9,9,10,10,11,11,12,12,12-tridecafluorododecanamide; OG; n; -octyl-α-; d; -glucopyranoside; DDM; n; -dodecyl-α-; d; -maltopyranoside; CMC; critical micelle concentration; DTT (or T-domain); diphtheria toxin T-domain; ANTS; 8-aminonapthalene-1,3,6 trisulfonic acid; DPX; p; -xylene-; bis; -pyridinium bromide; LUV; extruded large unilamellar vesicles of 100; nm diameter; POPC; palmitoyloleoylphosphatidylcholine; POPG; palmitoyloleoylphosphatidylglycerol; CD; circular dichroismMembrane protein solubilization; Thermodynamic stability; Bilayer insertion; pH-dependent conformational change; Circular dichroism
Folding and misfolding of alpha-synuclein on membranes by Igor Dikiy; David Eliezer (pp. 1013-1018).
The protein alpha-synuclein is considered to play a major role in the etiology of Parkinson's disease. Because it is found in a classic amyloid fibril form within the characteristic intra-neuronal Lewy body deposits of the disease, aggregation of the protein is thought to be of critical importance, but the context in which the protein undergoes aggregation within cells remains unknown. The normal function of synucleins is poorly understood, but appears to involve membrane interactions, and in particular reversible binding to synaptic vesicle membranes. Structural studies of different states of alpha-synuclein, in the absence and presence of membranes or membrane mimetics, have led to models of how membrane-bound forms of the protein may contribute both to functional properties of the protein, as well as to membrane-induced self-assembly and aggregation. This article reviews this area, with a focus on a particular model that has emerged in the past few years. This article is part of a Special Issue entitled: Protein Folding in Membranes.► Membrane binding by synuclein is associated with normal function. ► Membrane binding by synuclein is associated with aggregation. ► Membranes induce both broken- and extended-helix states and both may be functional. ► Membranes may induce partially helical intermediates that drive aggregation.
Keywords: Alpha-synuclein; Parkinson's; Amyloid; Membrane; Aggregation
Lactadherin binds to phosphatidylserine-containing vesicles in a two-step mechanism sensitive to vesicle size and composition by Daniel E. Otzen; Kristine Blans; Huabing Wang; Gary E. Gilbert; Jan T. Rasmussen (pp. 1019-1027).
Lactadherin binds to phosphatidylserine (PS) in a stereospecific and calcium independent manner that is promoted by vesicle curvature. Because membrane binding of lactadherin is supported by a PS content of as little as 0.5%, lactadherin is a useful marker for cell stress where limited PS is exposed, as well as for apoptosis where PS freely traverses the plasma membrane. To gain further insight into the membrane-binding mechanism, we have utilized intrinsic lactadherin fluorescence. Our results indicate that intrinsic fluorescence increases and is blue-shifted upon membrane binding. Stopped-flow kinetic experiments confirm the specificity for PS and that the C2 domain contains a PS recognition motif. The stopped-flow kinetic data are consistent with a two-step binding mechanism, in which initial binding is followed by a slower step that involves either a conformational change or an altered degree of membrane insertion. Binding is detected at concentrations down to 0.03% PS and the capacity of binding reaches saturation around 1% PS (midpoint 0.15% PS). Higher concentrations of PS (and also to some extent PE) increase the association kinetics and the affinity. Increasing vesicle curvature promotes association. Remarkably, replacement of vesicles with micelles destroys the specificity for PS lipids. We conclude that the vesicular environment provides optimal conditions for presentation and recognition of PS by lactadherin in a simple binding mechanism. This article is part of a Special Issue entitled: Protein Folding in Membranes.Display Omitted► Lactadherin binds specifically to phosphatidylserine containing membranes. ► This process occurs as a rapid two-step binding mechanism. ► As little as 0.03% PS is detected in the membrane by the kinetic assay. ► Phospatidylserine and increased curvature both promote binding. ► Presentation of PS in surfactant micelles abolishes PS specificity.
Keywords: Abbreviations; DPC; dodecylphosphocholine; PC; phosphatidylcholine; PE; phosphatidyl ethanolamine; PS; phosphatidyl serineStopped-flow kinetic; Phosphatidylserine; Association and dissociation rate constant; Mixed micelle
Membrane assembly of the cholesterol-dependent cytolysin pore complex by Eileen M. Hotze; Rodney K. Tweten (pp. 1028-1038).
The cholesterol-dependent cytolysins (CDCs) are a large family of pore-forming toxins that are produced, secreted and contribute to the pathogenesis of many species of Gram-positive bacteria. The assembly of the CDC pore-forming complex has been under intense study for the past 20years. These studies have revealed a molecular mechanism of pore formation that exhibits many novel features. The CDCs form large β-barrel pore complexes that are assembled from 35 to 40 soluble CDC monomers. Pore formation is dependent on the presence of membrane cholesterol, which functions as the receptor for most CDCs. Cholesterol binding initiates significant secondary and tertiary structural changes in the monomers, which lead to the assembly of a large membrane embedded β-barrel pore complex. This review will focus on the molecular mechanism of assembly of the CDC membrane pore complex and how these studies have led to insights into the mechanism of pore formation for other pore-forming proteins. This article is part of a Special Issue entitled: Protein Folding in Membranes.► The cholesterol dependent cytolysins (CDCs) have a novel cholesterol-binding motif. ► The CDCs assemble oligomeric membrane complexes composed of 35–40 monomers. ► CDCs undergo major secondary and tertiary structural changes to form a β-barrel pore. ► Membrane attack complex/perforin immunity proteins may be related to the CDCs.
Keywords: Pore; Perfringolysin; CD59; Intermedilysin; Complement; Perforin
Structural and biophysical properties of a synthetic channel-forming peptide: Designing a clinically relevant anion selective pore by U. Bukovnik; J. Gao; G.A. Cook; L.P. Shank; M.B. Seabra; B.D. Schultz; T. Iwamoto; J. Chen; J.M. Tomich (pp. 1039-1048).
The design, synthesis, modeling and in vitro testing of channel-forming peptides derived from the cys-loop superfamily of ligand-gated ion channels are part of an ongoing research focus. Over 300 different sequences have been prepared based on the M2 transmembrane segment of the spinal cord glycine receptor α-subunit. A number of these sequences are water-soluble monomers that readily insert into biological membranes where they undergo supramolecular assembly, yielding channels with a range of selectivities and conductances. Selection of a sequence for further modifications to yield an optimal lead compound came down to a few key biophysical properties: low solution concentrations that yield channel activity, greater ensemble conductance, and enhanced ion selectivity. The sequence NK4-M2GlyR T19R, S22W (KKKKPARVGLGITTVLTMRTQW) addressed these criteria. The structure of this peptide has been analyzed by solution NMR as a monomer in detergent micelles, simulated as five-helix bundles in a membrane environment, modified by cysteine-scanning and studied for insertion efficiency in liposomes of selected lipid compositions. Taken together, these results define the structural and key biophysical properties of this sequence in a membrane. This model provides an initial scaffold from which rational substitutions can be proposed and tested to modulate anion selectivity. This article is part of a Special Issue entitled: Protein Folding in Membranes.► Channel-forming peptides undergo supramolecular assembly forming membrane pores. ► These peptides are able to accommodate amino acid replacements. ► The NMR-structure of the monomer peptide was determined in detergent micelles. ► Computer simulations of the pore indicate structures adopt a left-handed structure. ► The lipid composition of the bilayers affects peptide insertion.
Keywords: Channel-forming peptide; Self-assembly; Glycine receptor; Pore structure
Thermodynamic stability of bacteriorhodopsin mutants measured relative to the bacterioopsin unfolded state by Zheng Cao; Jonathan P. Schlebach; Chiwook Park; James U. Bowie (pp. 1049-1054).
The stability of bacteriorhodopsin (bR) has often been assessed using SDS unfolding assays that monitor the transition of folded bR (bRf) to unfolded (bRu). 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 bRf to unfolded bacterioopsin (bOu), the RET-free form of unfolded protein. The bRf-to-bOu 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 bRf-to-bOu 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.► We re-examine a commonly used assay for measuring how mutants alter bacteriorhodopsin stability. ► We find the assay measures kinetic rather than thermodynamic stability. ► Nevertheless, for 12 of 13 mutants tested, the error in the equilibrium assumption is small. ► Thus, the free energy effects of most mutants may be mostly on the folded state.
Keywords: Membrane protein; Protein folding; Folding kinetics; SDS
Folding and stability of membrane transport proteins in vitro by Nicola J. Harris; Paula J. Booth (pp. 1055-1066).
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.► Up to date review of membrane transporter folding ► Reversible re-folding and re-assembly of members of the major facilitator and ATP binding cassette transport families ► Determination of folding free energy for key membrane transport proteins
Keywords: Abbreviations; MFS; Major Facilitator Superfamily; GalP; Escherichia coli; galactose transporter; LacY; Lactose Permease; ABC; ATP Binding Cassette Protein; DDM; n; -dodecyl β-D-maltoside; DS; decanoylsucrose; LDAO; Lauryldimethyl-; N; -amineoxide; PE; phosphatidylserine; NBD; Nucleotide Binding Domain; TMD; Transmembrane domain; DOPE; L-α-1,2-dioleoylphospatidylethanolamine; DOPC; L-α-1,2-dioleoylphospatidylcholine; GuHCl; Guanidine Hydrochloride; SDS; Sodium Dodecyl Sulphate; CD; Circular Dichroism; ITC; Isothermal Titration Calorimetry; C12E10; Polyoxyethylene 10 Laurylether; SDS-PAGE; Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis; DSC; Differential Scanning Calorimetry; PTS; phosphotransferase system; PEP; phosphoenolpyruvate; DGK; diacylglycerol kinase; KcsA; potassium channel; DsbB; disulphide bond reducing protein; CopA; thermophilic copper transporter; EmrE; small multidrug transporter; CFTR; cystic fibrosis transmembrane conductance regulator; TDG; β,D-galactopyronosyl 1 -thio- β,D-galactopyranoside; POPG; 1-palmitoyl-2-oleoyl phosphatidylglycerol; POPE; 1-palmitoyl-2-oleoyl phosphatidylethanolamine; NhaA; Sodium proton antiporter; AFM; Atomic Force Microscopy; SMR; Small Multidrug ResistanceIntegral membrane protein; Membrane transport; Major Facilitator Superfamily; ABC transporter; Protein folding; Thermal stability
The Bam machine: A molecular cooper by Dante P. Ricci; Thomas J. Silhavy (pp. 1067-1084).
The bacterial outer membrane (OM) is an exceptional biological structure with a unique composition that contributes significantly to the resiliency of Gram-negative bacteria. Since all OM components are synthesized in the cytosol, the cell must efficiently transport OM-specific lipids and proteins across the cell envelope and stably integrate them into a growing membrane. In this review, we discuss the challenges associated with these processes and detail the elegant solutions that cells have evolved to address the topological problem of OM biogenesis. Special attention will be paid to the Bam machine, a highly conserved multiprotein complex that facilitates OM β-barrel folding. This article is part of a Special Issue entitled: Protein Folding in Membranes.► OM biogenesis requires exquisitely regulated and dedicated transport systems. ► OMP folding is catalyzed by a conserved multiprotein complex. ► Structural characterization of Bam has afforded significant insight into function.
Keywords: Abbreviations; LPS; lipopolysaccharide; IM; inner membrane; OM; outer membrane; PE; phosphatidylethanolamine; PG; phosphatidylglycerol; OMP; OM β-barrel protein; GFP; green fluorescent protein; PMF; proton motive force; ATP; adenosine triphosphate; Psp; phage shock protein; NMR; nuclear magnetic resonance; PELDOR; pulsed-electro double resonance; SAXS; small-angle X-ray scattering; rmsd; root-mean-square deviation; AT; autotransporter; Bam; β-barrel assembly machine; POTRA; polypeptide translocation-associated; TPR; tetratricopeptide repeat; IL; interconnecting loop; EOM; ensemble optimization method; FHA; filamentous hemagglutinin; Mla; maintenance of lipid assymetryOuter membrane biogenesis; β-barrel; Bam complex; LPS
Unresolved mysteries in the biogenesis of mitochondrial membrane proteins by Kai Stefan Dimmer; Doron Rapaport (pp. 1085-1090).
Mitochondria are essential eukaryotic organelles that are surrounded by two membranes. Both membranes contain a variety of different integral membrane proteins. After three decades of research on mitochondrial biogenesis five major import complexes with more than 40 subunits altogether were identified and characterized. In the current contribution we want to draw attention to some unexplored issues regarding the integration of mitochondrial membrane proteins and to formulate crucial questions that remain unanswered. This article is part of a Special Issue entitled: Protein Folding in Membranes.► Discussion of open questions in the biogenesis of mitochondrial membrane proteins. ► Mechanisms of insertase activities. ► Importance of lipids in membrane integration of proteins.
Keywords: Mitochondrial import; Membrane protein; Mitochondrial translocase; Protein insertion into mitochondrial membrane
Manipulating the genetic code for membrane protein production: What have we learnt so far? by Norholm Morten H.H. Nørholm; Sara Light; Minttu T.I. Virkki; Arne Elofsson; Gunnar von Heijne; Daniel O. Daley (pp. 1091-1096).
With synthetic gene services, molecular cloning is as easy as ordering a pizza. However choosing the right RNA code for efficient protein production is less straightforward, more akin to deciding on the pizza toppings. The possibility to choose synonymous codons in the gene sequence has ignited a discussion that dates back 50years: Does synonymous codon use matter? Recent studies indicate that replacement of particular codons for synonymous codons can improve expression in homologous or heterologous hosts, however it is not always successful. Furthermore it is increasingly apparent that membrane protein biogenesis can be codon-sensitive. Single synonymous codon substitutions can influence mRNA stability, mRNA structure, translational initiation, translational elongation and even protein folding. Synonymous codon substitutions therefore need to be carefully evaluated when membrane proteins are engineered for higher production levels and further studies are needed to fully understand how to select the codons that are optimal for higher production. This article is part of a Special Issue entitled: Protein Folding in Membranes.► Codon use differs between membrane proteins and soluble proteins. ► The availability of synonymous codons means that a single protein can be encoded by a myriad of different DNA sequences. ► In some cases, manipulation of the genetic code can lead to higher overexpression levels of membrane proteins. ► In some cases, manipulation of the genetic code has no effect on overexpression levels, or leads to misfolded proteins.
Keywords: Membrane protein overexpression; Membrane protein folding; Codon use; Membrane protein engineering
Molecular genetic and biochemical approaches for defining lipid-dependent membrane protein folding by William Dowhan; Mikhail Bogdanov (pp. 1097-1107).
We provide an overview of lipid-dependent polytopic membrane protein folding and topogenesis. Lipid dependence of this process was determined by employing Escherichia coli cells in which specific lipids can be eliminated, substituted, tightly titrated or controlled temporally during membrane protein synthesis and assembly. The secondary transport protein lactose permease (LacY) was used to establish general principles underlying the molecular basis of lipid-dependent effects on protein domain folding, protein transmembrane domain (TM) orientation, and function. These principles were then extended to several other secondary transport proteins of E. coli. The methods used to follow proper conformational organization of protein domains and the topological organization of protein TMs in whole cells and membranes are described. The proper folding of an extramembrane domain of LacY that is crucial for energy dependent uphill transport function depends on specific lipids acting as non-protein molecular chaperones. Correct TM topogenesis is dependent on charge interactions between the cytoplasmic surface of membrane proteins and a proper balance of the membrane surface net charge defined by the lipid head groups. Short-range interactions between the nascent protein chain and the translocon are necessary but not sufficient for establishment of final topology. After release from the translocon short-range interactions between lipid head groups and the nascent protein chain, partitioning of protein hydrophobic domains into the membrane bilayer, and long-range interactions within the protein thermodynamically drive final membrane protein organization. Given the diversity of membrane lipid compositions throughout nature, it is tempting to speculate that during the course of evolution the physical and chemical properties of proteins and lipids have co-evolved in the context of the lipid environment of membrane systems in which both are mutually dependent on each other for functional organization of proteins. This article is part of a Special Issue entitled: Protein Folding in Membranes► E. coli strains in which membrane lipid composition can be systematically altered. ► Charge interactions with lipids are determinants of membrane protein topogenesis. ► Late folding events outside the translocon determine membrane protein structure. ► Lipids act as a molecular chaperone that assists in membrane protein folding. ► Membrane protein organization can change due to changes in the lipid environment.
Keywords: Abbreviations; TM; transmembrane domain; PE; phosphatidylethanolamine; PG; phosphatidylglycerol; CL; cardiolipin; PA; phosphatidic acid; PS; phosphatidylserine; lys; lysyl; PC; phosphatidylcholine; GlcDAG; monoglucosyl diacylglycerol; GlcGlcDAG; diglucosyl diacylglycerol; PI; phosphatidylinositol; LacY; lactose permease; CscB; sucrose permease; PheP; phenylalanine permease; GabP; γ-aminobutyrate permease; mAb; monoclonal antibody; SCAM™; substituted cysteine accessibility method as applied to TMsPhosphatidylethanolamine; Lactose permease; Protein topology; Lipochaperone; Positive-inside rule
Mechanisms for quality control of misfolded transmembrane proteins by Scott A. Houck; Douglas M. Cyr (pp. 1108-1114).
To prevent the accumulation of misfolded and aggregated proteins, the cell has developed a complex network of cellular quality control (QC) systems to recognize misfolded proteins and facilitate their refolding or degradation. The cell faces numerous obstacles when performing quality control on transmembrane proteins. Transmembrane proteins have domains on both sides of a membrane and QC systems in distinct compartments must coordinate to monitor the folding status of the protein. Additionally, transmembrane domains can have very complex organization and QC systems must be able to monitor the assembly of transmembrane domains in the membrane. In this review, we will discuss the QC systems involved in repair and degradation of misfolded transmembrane proteins. Also, we will elaborate on the factors that recognize folding defects of transmembrane domains and what happens when misfolded transmembrane proteins escape QC and aggregate. This article is part of a Special Issue entitled: Protein Folding in Membranes.► We discuss the basis for unfolding of transmembrane proteins. ► We discuss the quality control pathways responsible for recognition of misfolded transmembrane. ► We discuss what happens when transmembrane proteins aggregate.
Keywords: Transmembrane protein; Quality control; Autophagy; Membrane chaperone; Protein folding
Membrane protein misassembly in disease by Derek P. Ng; Bradley E. Poulsen; Charles M. Deber (pp. 1115-1122).
Helix–helix interactions play a central role in the folding and assembly of integral α-helical membrane proteins and are fundamentally dictated by the amino acid sequence of the TM domain. It is not surprising then that missense mutations that target these residues are often linked to disease. In this review, we focus on the molecular mechanisms through which missense mutations lead to aberrant folding and/or assembly of these proteins, and then discuss pharmacological approaches that may potentially mitigate or reverse the negative effects of these mutations. Improving our understanding of how missense mutations affect the interactions between TM α-helices will increase our capability to develop effective therapeutic approaches to counter the misassembly of these proteins and, ultimately, disease. This article is part of a Special Issue entitled: Protein Folding in Membranes.► Helix–helix interactions mediate membrane protein assembly in a sequence-dependent manner. ► Missense mutations that disrupt membrane protein assembly often lead to disease. ► A missense mutation can impair assembly by either disrupting or strengthening helix–helix interactions. ► Pharmacological approaches may alleviate membrane protein misassembly and disease.
Keywords: Disease; Missense mutation; Membrane protein misfolding; Helix–helix interaction; Pharmacoperone; Folding