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

Biophysical characterization of G-protein coupled receptor-peptide ligand binding

G-protein coupled receptors (GPCRs) are ubiquitous membrane proteins allowing intracellular responses to extracellular factors that range from photons of light to small molecules to proteins. Despite extensive exploitation of GPCRs as therapeutic targets, biophysical characterization of GPCR-ligand interactions remains challenging. In this minireview, we focus on techniques that have been successfully used for structural and biophysical characterization of peptide ligands binding to their cognate GPCRs. The techniques reviewed include solution-state nuclear magnetic resonance (NMR) spectroscopy, solid-state NMR, X-ray diffraction, fluorescence spectroscopy and single-molecule fluorescence methods, flow cytometry, surface plasmon resonance, isothermal titration calorimetry, and atomic force microscopy. The goal herein is to provide a cohesive starting point to allow selection of techniques appropriate to the elucidation of a given GPCR-peptide interaction.

Three powerful research tools from single cells into single molecules: AFM, laser tweezers, and Raman spectroscopy

By using three physical techniques (atomic force microscopy (AFM), laser tweezers, and Raman spectroscopy), many excellent works in single-cell/molecule research have been accomplished. In this review, we present a brief introduction to the principles of these three techniques, and their capabilities toward single-cell/molecule research are highlighted. Afterward, the advances in single-cell/molecule research that have been facilitated by these three techniques are described. Following this, their complementary assets for single-cell/molecule research are analyzed, and the necessity of integrating the functions of these three techniques into one instrument is proposed.

Drosophila photoreceptor cells exploited for the production of eukaryotic membrane proteins: receptors, transporters and channels

BACKGROUND

Membrane proteins (MPs) play key roles in signal transduction. However, understanding their function at a molecular level is mostly hampered by the lack of protein in suitable amount and quality. Despite impressive developments in the expression of prokaryotic MPs, eukaryotic MP production has lagged behind and there is a need for new expression strategies. In a pilot study, we produced a Drosophila glutamate receptor specifically in the eyes of transgenic flies, exploiting the naturally abundant membrane stacks in the photoreceptor cells (PRCs). Now we address the question whether the PRCs also process different classes of medically relevant target MPs which were so far notoriously difficult to handle with conventional expression strategies.

PRINCIPAL FINDINGS

We describe the homologous and heterologous expression of 10 different targets from the three major MP classes--G protein-coupled receptors (GPCRs), transporters and channels in Drosophila eyes. PRCs offered an extraordinary capacity to produce, fold and accommodate massive amounts of MPs. The expression of some MPs reached similar levels as the endogenous rhodopsin, indicating that the PRC membranes were almost unsaturable. Expression of endogenous rhodopsin was not affected by the target MPs and both could coexist in the membrane stacks. Heterologous expression levels reached about 270 to 500 pmol/mg total MP, resulting in 0.2-0.4 mg purified target MP from 1 g of fly heads. The metabotropic glutamate receptor and human serotonin transporter--both involved in synaptic transmission--showed native pharmacological characteristics and could be purified to homogeneity as a prerequisite for further studies.

SIGNIFICANCE

We demonstrate expression in Drosophila PRCs as an efficient and inexpensive tool for the large scale production of functional eukaryotic MPs. The fly eye system offers a number of advantages over conventional expression systems and paves the way for in-depth analyses of eukaryotic MPs that have so far not been accessible to biochemical and biophysical studies.

Role of membrane integrity on G protein-coupled receptors: Rhodopsin stability and function

Rhodopsin is a prototypical G protein-coupled receptor (GPCR) - a member of the superfamily that shares a similar structural architecture consisting of seven-transmembrane helices and propagates various signals across biological membranes. Rhodopsin is embedded in the lipid bilayer of specialized disk membranes in the outer segments of retinal rod photoreceptor cells where it transmits a light-stimulated signal. Photoactivated rhodopsin then activates a visual signaling cascade through its cognate G protein, transducin or Gt, that results in a neuronal response in the brain. Interestingly, the lipid composition of ROS membranes not only differs from that of the photoreceptor plasma membrane but is critical for visual transduction. Specifically, lipids can modulate structural changes in rhodopsin that occur after photoactivation and influence binding of transducin. Thus, altering the lipid organization of ROS membranes can result in visual dysfunction and blindness.

MEDELLER: homology-based coordinate generation for membrane proteins

MOTIVATION

Membrane proteins (MPs) are important drug targets but knowledge of their exact structure is limited to relatively few examples. Existing homology-based structure prediction methods are designed for globular, water-soluble proteins. However, we are now beginning to have enough MP structures to justify the development of a homology-based approach specifically for them.

RESULTS

We present a MP-specific homology-based coordinate generation method, MEDELLER, which is optimized to build highly reliable core models. The method outperforms the popular structure prediction programme Modeller on MPs. The comparison of the two methods was performed on 616 target-template pairs of MPs, which were classified into four test sets by their sequence identity. Across all targets, MEDELLER gave an average backbone root mean square deviation (RMSD) of 2.62 Å versus 3.16 Å for Modeller. On our 'easy' test set, MEDELLER achieves an average accuracy of 0.93 Å backbone RMSD versus 1.56 Å for Modeller.

AVAILABILITY AND IMPLEMENTATION

http://medeller.info; Implemented in Python, Bash and Perl CGI for use on Linux systems; Supplementary data are available at http://www.stats.ox.ac.uk/proteins/resources.

Optical imaging of nanoscale cellular structures

Visualization of subcellular structures and their temporal evolution is of utmost importance to understand a vast range of biological processes. Optical microscopy is the method of choice for imaging live cells and tissues; it is minimally invasive, so processes can be observed over extended periods of time without generating artifacts due to intense light irradiation. The use of fluorescence microscopy is advantageous because biomolecules or supramolecular structures of interest can be labeled specifically with fluorophores, so the images reveal information on processes involving only the labeled molecules. The key restriction of optical microscopy is its moderate resolution, which is limited to about half the wavelength of light (∼200 nm) due to fundamental physical laws governing wave optics. Consequently, molecular processes taking place at spatial scales between 1 and 100 nm cannot be studied by regular optical microscopy. In recent years, however, a variety of super-resolution fluorescence microscopy techniques have been developed that circumvent the resolution limitation. Here, we present a brief overview of these techniques and their application to cellular biophysics.

Oligomeric forms of G protein-coupled receptors (GPCRs)

Oligomerization is a general characteristic of cell membrane receptors that is shared by G protein-coupled receptors (GPCRs) together with their G protein partners. Recent studies of these complexes, both in vivo and in purified reconstituted forms, unequivocally support this contention for GPCRs, perhaps with only rare exceptions. As evidence has evolved from experimental cell lines to more relevant in vivo studies and from indirect biophysical approaches to well defined isolated complexes of dimeric receptors alone and complexed with G proteins, there is an expectation that the structural basis of oligomerization and the functional consequences for membrane signaling will be elucidated. Oligomerization of cell membrane receptors is fully supported by both thermodynamic calculations and the selectivity and duration of signaling required to reach targets located in various cellular compartments.

A single glutamate residue controls the oligomerization, function, and stability of the aquaglyceroporin GlpF

Like many other alpha-helical membrane proteins, the monomeric Escherichia coli aquaglyceroporin GlpF associates within cellular membranes and forms higher-order oligomeric structures. A potential impact of the oligomeric state on the protein function remains enigmatic. We have analyzed the role of residues W42 and E43 in the oligomerization of the E. coli GlpF protein in vitro and in vivo. In contrast to W42, the polar glutamate residue at position 43 appears to be critical for oligomerization. While other polar residues can substitute for the function of E43, replacement of E43 with alanine results in a greatly reduced GlpF oligomerization propensity. The reduced interaction propensity of GlpF E43A correlates with an impaired in vivo function as well as a decreased in vivo stability. Therefore, E43 is critical for the proper oligomerization of GlpF, and protein oligomerization appears to be crucial for the channel function as well as for the in vivo stability of the protein.

Phototransduction motifs and variations

Seeing begins in the photoreceptors, where light is absorbed and signaled to the nervous system. Throughout the animal kingdom, photoreceptors are diverse in design and purpose. Nonetheless, phototransduction-the mechanism by which absorbed photons are converted into an electrical response-is highly conserved and based almost exclusively on a single class of photoproteins, the opsins. In this Review, we survey the G protein-coupled signaling cascades downstream from opsins in photoreceptors across vertebrate and invertebrate species, noting their similarities as well as differences.

On transversal hydrophobicity of some proteins and their modules

Hydrophobicity of proteins encoded in the genomes of diverse organisms was quantified using two novel concepts: (A) amino acid (AA) bulkiness-dependent hydrophobicity profiles and (B) spatial context of hydrophobicity distribution in AA triads. Both concepts were introduced into an algorithm that was used for extracting protein clusters from diverse genomic databases whose sequence attributes were similar to those in the multiple sequence alignment (MSA) of a given family of proteins. The sequences of the G protein-coupled receptors (GPCRs) encoded in different genomes were used as templates for testing the above concepts. The following sequence attributes were used for protein clustering: (A) sequence similarity scores (IDs); (B) amino acid composition (AAC); (C) hydrophobicity; (D) AA-bulkiness; and (E) alpha-helical propensity potentials. Diverse GPCRs display variable distributions of AA bulkiness-dependent buildups and declines in the hydrophobicity profiles that may be related to their function-dependent way of packing and allostery in the membrane. It is shown that intramolecular transversal nonbonded interactions between the TM segments in diverse GPCRs involve about 50% of hydrophobic atoms. Similar interaction networks exist between alpha-helices of tetratricopeptide (TPR) motifs-containing immunophilins and other proteins containing alpha-helical bundles.

Lateral diffusion of rhodopsin in photoreceptor membrane: a reappraisal

PURPOSE

In a series of works between 1972 and 1984, it was established that rhodopsin undergoes rotational and lateral Brownian motion in the plane of photoreceptor membrane. The concept of free movement of proteins of phototransduction cascade is an essential principle of the present scheme of vertebrate phototransduction. This has recently been challenged by findings that show that in certain conditions rhodopsin in the membrane may be dimeric and form extended areas of paracrystalline organization. Such organization seems incompatible with earlier data on free rhodopsin diffusion. Thus we decided to reinvestigate lateral diffusion of rhodopsin and products of its photolysis in photoreceptor membrane specifically looking for indications of possible oligomeric organization.

METHODS

Diffusion exchange by rhodopsin and its photoproducts between bleached and unbleached halves of rod outer segment was traced using high-speed dichroic microspectrophotometer. Measurements were conducted on amphibian (frog, toad, and salamander) and gecko rods.

RESULTS

We found that the curves that are supposed to reflect the process of diffusion equilibration of rhodopsin in nonuniformly bleached outer segment largely show production of long-lived bleaching intermediate, metarhodopsin III (Meta III). After experimental elimination of Meta III contribution, we observed rhodopsin equilibration time constant was threefold to tenfold longer than estimated previously. However, after proper correction for the geometry of rod discs, it translates into generally accepted value of diffusion constant of approximately 5 x 10(-9) cm(2) s(-1). Yet, we found that there exists an immobile rhodopsin fraction whose size can vary from virtually zero to 100%, depending on poorly defined factors. Controls suggest that the formation of the immobile fraction is not due to fragmentation of rod outer segment discs but supposedly reflects oligomerization of rhodopsin.

CONCLUSIONS

Implications of the new findings for the present model of phototransduction are discussed. We hypothesize that formation of paracrystalline areas, if controlled physiologically, could be an extra mechanism of cascade regulation.

Structural waters define a functional channel mediating activation of the GPCR, rhodopsin

Structural water molecules may act as prosthetic groups indispensable for proper protein function. In the case of allosteric activation of G protein-coupled receptors (GPCRs), water likely imparts structural plasticity required for agonist-induced signal transmission. Inspection of structures of GPCR superfamily members reveals the presence of conserved embedded water molecules likely important to GPCR function. Coupling radiolytic hydroxyl radical labeling with rapid H(2)O(18) solvent mixing, we observed no exchange of these structural waters with bulk solvent in either ground state or for the Meta II or opsin states. However, the radiolysis approach permitted labeling of selected side chain residues within the transmembrane helices and revealed activation-induced changes in local structural constraints likely mediated by dynamics of both water and protein. These results suggest both a possible general mechanism for water-dependent communication in family A GPCRs based on structural conservation, and a strategy for probing membrane protein structure.

Phospholipids are needed for the proper formation, stability, and function of the photoactivated rhodopsin-transducin complex

Heterotrimeric G proteins become activated after they form a catalytically active complex with activated G protein-coupled receptors (GPCRs) and GTP replaces GDP on the G protein alpha-subunit. This transient coupling can be stabilized by nucleotide depletion, resulting in an empty-nucleotide G protein-GPCR complex. Efficient and reproducible formation of conformationally homogeneous GPCR-Gt complexes is a prerequisite for structural studies. Herein, we report isolation conditions that enhance the stability and preserve the activity and proper stoichiometry of productive complexes between the purified prototypical GPCR, rhodopsin (Rho), and the rod cell-specific G protein, transducin (Gt). Binding of purified Gt to photoactivated Rho (Rho*) in n-dodecyl beta-D-maltoside (DDM) examined by gel filtration chromatography was generally modest, and purified complexes provided heterogeneous ratios of protein components, most likely because of excess detergent. Rho*-Gt complex stability and activity were greatly increased by addition of phospholipids such as DOPC, DOPE, and DOPS and asolectin to detergent-containing solutions of these proteins. In contrast, native Rho*-Gt complexes purified directly from light-exposed bovine ROS membranes by sucrose gradient centrifugation exhibited improved stability and the expected 2:1 stoichiometry between Rho* and Gt. These results strongly indicate a lipid requirement for stable complex formation in which the likely oligomeric structure of Rho provides a superior platform for coupling to Gt, and phospholipids likely form a matrix to which Gt can anchor through its myristoyl and farnesyl groups. Our findings also demonstrate that the choice of detergent and purification method is critical for obtaining highly purified, stable, and active complexes with appropriate stoichiometry between GPCRs and G proteins needed for structural studies.

Membrane rafts and caveolae in cardiovascular signaling

PURPOSE OF REVIEW

Substantial evidence documents the key role of lipid (membrane) rafts and caveolae as microdomains that concentrate a wide variety of receptors and postreceptor components regulated by hormones, neurotransmitters and growth factors.

RECENT FINDINGS

Recent data document that these microdomains are important in regulating vascular endothelial and smooth muscle cells and renal epithelial cells, and particularly in signal transduction across the plasma membrane.

SUMMARY

Raft/caveolae domains are cellular regions, including in cardiovascular and renal epithelial cells, which organize a large number of signal transduction components, thereby providing spatially and temporally efficient regulation of cell function.

iMembrane: homology-based membrane-insertion of proteins

iMembrane is a homology-based method, which predicts a membrane protein's position within a lipid bilayer. It projects the results of coarse-grained molecular dynamics simulations onto any membrane protein structure or sequence provided by the user. iMembrane is simple to use and is currently the only computational method allowing the rapid prediction of a membrane protein's lipid bilayer insertion. Bilayer insertion data are essential in the accurate structural modelling of membrane proteins or the design of drugs that target them.

Deciphering soluble and membrane protein function using yeast systems (Review)

Membrane protein-protein interactions are important for regulation, targeting, and activity of proteins in membranes but are difficult to detect and analyse. This review covers current approaches to studying membrane protein interactions. In addition to standard biochemical and genetic techniques, the classic yeast nuclear two-hybrid system has been highly successful in identification and characterization of soluble protein-protein interactions. However, classic yeast two-hybrid assays do not work for membrane proteins because such yeast-based interactions must occur in the nucleus. Here, we highlight recent advances in yeast systems for the detection and characterization of eukaryote membrane protein-protein interactions. We discuss these implications for drug screening and discovery.

Topology of class A G protein-coupled receptors: insights gained from crystal structures of rhodopsins, adrenergic and adenosine receptors

Biological membranes are densely packed with membrane proteins that occupy approximately half of their volume. In almost all cases, membrane proteins in the native state lack the higher-order symmetry required for their direct study by diffraction methods. Despite many technical difficulties, numerous crystal structures of detergent solubilized membrane proteins have been determined that illustrate their internal organization. Among such proteins, class A G protein-coupled receptors have become amenable to crystallization and high resolution X-ray diffraction analyses. The derived structures of native and engineered receptors not only provide insights into their molecular arrangements but also furnish a framework for designing and testing potential models of transformation from inactive to active receptor signaling states and for initiating rational drug design.

Enzymes without borders: mobilizing substrates, delivering products

Many cellular reactions involve both hydrophobic and hydrophilic molecules that reside within the chemically distinct environments defined by the phospholipid-based membranes and the aqueous lumens of cytoplasm and organelles. Enzymes performing this type of reaction are required to access a lipophilic substrate located in the membranes and to catalyze its reaction with a polar, water-soluble compound. Here, we explore the different binding strategies and chemical tricks that enzymes have developed to overcome this problem. These reactions can be catalyzed by integral membrane proteins that channel a hydrophilic molecule into their active site, as well as by water-soluble enzymes that are able to capture a lipophilic substrate from the phospholipid bilayer. Many chemical and biological aspects of this type of enzymology remain to be investigated and will require the integration of protein chemistry with membrane biology.