Predicting secondary structures of membrane proteins with neural networks

Back-propagation, feed-forward neural networks are used to predict the secondary structures of membrane proteins whose structures are known to atomic resolution. These networks are trained on globular proteins and can predict globular protein structures having no homology to those of the training set with correlation coefficients (C) of 0.45, 0.32 and 0.43 for a-helix, -strand and random coil structures, respectively. When tested on membrane proteins, neural networks trained on globular proteins do, on average, correctly predict (Q_i) 62%, 38% and 69% of the residues in the -helix, -strand and random coil structures. These scores rank higher than those obtained with the currently used statistical methods and are comparable to those obtained with the joint approaches tested so far on membrane proteins. The lower success score for -strand as compared to the other structures suggests that the sample of -strand patterns contained in the training set is less representative than those of a-helix and random coil. Our analysis, which includes the effects of the network parameters and of the structural composition of the training set on the prediction, shows that regular patterns of secondary structures can be successfully extrapolated from globular to membrane proteins. Correspondence to: R. Casadio     

Targeting of the mitochondrial membrane proteins to the cell surface for functional studies

Studying mitochondrial membrane proteins for ion or substrate transport is technically difficult, as the organelles are hidden within the cell interior and thus inaccessible to many conventional nondisruptive techniques. This technical barrier can potentially be overcome if the mitochondrial membrane proteins are targeted to the cell surface, where they can be more readily studied. We undertook experiments presented here to target two related mitochondrial membrane proteins, mitochondrial ATP-binding cassette-1 and -2 protein (mABC1 and mABC2, respectively) to the cell surface for functional studies. These two proteins have an N-terminal mitochondrial targeting signal (MTS), and we hypothesized that removal of this sequence or addition of a cell surface targeting signal would lead to cell membrane targeting of these proteins. When the MTS was removed from mABC1, it localized to intracellular secretory compartments as well as the plasma membrane. However, truncated mABC2 lacking the MTS aggregated inside the cell. Addition of a cell membrane signal sequence or the transmembrane domain from CD8 to the N-terminus of mABC1 or mABC2 resulted in similar subcellular localizations. We then performed patch clamp on cells expressing mABC1 on their surface. These cells exhibited nonselective transport of K(+) and Na(+) ions and resulted in the loss of membrane potential. Our findings open new ways to study mitochondrial membrane proteins in established cell culture systems by targeting them to the cell surface, where they can more reliably be studied using various molecular and cellular techniques.     

Capillary gel electrophoresis: separation of major erythrocyte membrane proteins

A new separation method of human erythrocyte membrane proteins by sodium dodecyl sulfate capillary gel electrophoresis (SDS–CGE) is described. In this method, a replaceable gel matrix was used. Seven major erythrocyte membrane proteins, α-and β-spectrin, ankyrin 2.1, band 3 (anion-exchanger), 4.1a and b, and 4.2 (pallidin), were separated and identified by SDS–CGE method. High reproducible migration times of these proteins (inter-assay coefficients of variation less than 2%), as well as quantification (inter-assay coefficients of variation less than 11%) were obtained. This new SDS–CGE method may provide important diagnostic evidence for hereditary spherocytosis. It can be a powerful diagnostic tool in place of SDS polyacrylamide gel electrophoresis for erythrocyte membrane protein analysis.     

Strategies for crystallizing membrane proteins

Crystallizing membrane proteins remains a challenging endeavor despite the increasing number of membrane protein structures solved by X-ray crystallography. The critical factors in determining the success of the crystallization experiments are the purification and preparation of membrane protein samples. Moreover, there is the added complication that the crystallization conditions must be optimized for use in the presence of detergents although the methods used to crystallize most membrane proteins are, in essence, straightforward applications of standard methodologies for soluble protein crystallization. The roles that detergents play in the stability and aggregation of membrane proteins as well as the colloidal properties of the protein-detergent complexes need to be appreciated and controlledbefore and during the crystallization trials. All X-ray quality crystals of membrane proteins were grown from preparations of detergent-solubilized protein, where the heterogeneous natural lipids from the membrane have been replaced by ahomogeneous detergent environment. It is the preparation of such monodisperse, isotropic solutions of membrane proteins that has allowed the successful application of the standard crystallization methods routinely used on soluble proteins. In this review, the issues of protein purification and sample preparation are addressed as well as the new refinements in crystallization methodologies for membrane proteins. How the physical behavior of the detergent, in the form of micelles or protein-detergent aggregates, affects crystallization and the adaptation of published protocols to new membrane protein systems are also addressed. The general conclusion is that many integral membrane proteins could be crystallized if pure and monodisperse preparations in a suitable detergent system can be prepared.In memory of Glenn D. Garavito.     

Clustering and visualizing similarity networks of membrane proteins

We proposed a fast and unsupervised clustering method, minimum span clustering (MSC), for analyzing the sequence–structure–function relationship of biological networks, and demonstrated its validity in clustering the sequence/structure similarity networks (SSN) of 682 membrane protein (MP) chains. The MSC clustering of MPs based on their sequence information was found to be consistent with their tertiary structures and functions. For the largest seven clusters predicted by MSC, the consistency in chain function within the same cluster is found to be 100%. From analyzing the edge distribution of SSN for MPs, we found a characteristic threshold distance for the boundary between clusters, over which SSN of MPs could be properly clustered by an unsupervised sparsification of the network distance matrix. The clustering results of MPs from both MSC and the unsupervised sparsification methods are consistent with each other, and have high intracluster similarity and low intercluster similarity in sequence, structure, and function. Our study showed a strong sequence–structure–function relationship of MPs. We discussed evidence of convergent evolution of MPs and suggested applications in finding structural similarities and predicting biological functions of MP chains based on their sequence information. Proteins 2015; 83:1450–1461. © 2015 Wiley Periodicals, Inc.     

Functional and topological characterization of protein interaction networks

The elucidation of the cell's large-scale organization is a primary challenge for post-genomic biology, and understanding the structure of protein interaction networks offers an important starting point for such studies. We compare four available databases that approximate the protein interaction network of the yeast, Saccharomyces cerevisiae, aiming to uncover the network's generic large-scale properties and the impact of the proteins' function and cellular localization on the network topology. We show how each database supports a scale-free, topology with hierarchical modularity, indicating that these features represent a robust and generic property of the protein interactions network. We also find strong correlations between the network's structure and the functional role and subcellular localization of its protein constituents, concluding that most functional and/or localization classes appear as relatively segregated subnetworks of the full protein interaction network. The uncovered systematic differences between the four protein interaction databases reflect their relative coverage for different functional and localization classes and provide a guide for their utility in various bioinformatics studies.     

Sorting and function of peroxisomal membrane proteins

Peroxisomes are subcellular organelles and are present in virtually all eukaryotic cells. Characteristic features of these organelles are their inducibility and their functional versatility. Their importance in the intermediary metabolism of cells is exemplified by the discovery of several inborn, fatal peroxisomal errors in man, the so-called peroxisomal disorders. Recent findings in research on peroxisome biogenesis and function have demonstrated that peroxisomal matrix proteins and peroxisomal membrane proteins (PMPs) follow separate pathways to reach their target organelle. This paper addresses the principles of PMP sorting and summarizes the current knowledge of the role of these proteins in organelle biogenesis and function.     

Detergents for the stabilization and crystallization of membrane proteins

The use of detergents for the structural study of membrane proteins is discussed with an emphasis on practical issues relating to membrane solubilization, protein aggregation, detergent purity and detergent quantitation. Detergents are useful reagents as mimics of lipid bilayers because of their self-assembling properties, but as a result, they have complex properties in solution. It can be difficult to maintain a solubilized membrane protein in a native conformational state, and the non-specific aggregation of detergent-solubilized proteins is a common problem. Empirical "stability screens" can be helpful in choosing which detergents, and which detergent concentrations, may be optimal for a given system.     

Release of membrane proteins in relation to heat injury of spinach chloroplasts

Thylakoids isolated from spinach leaves ( Spinacia oleracea L. cvs. Monatol and Montako) were exposed to supraoptimal temperatures that inactivated their photochemical reactions. Membrane injury was accompanied by release of a small amount of membrane proteins. When sucrose was present during high-temperature treatment, thylakoids were partially protected and release of membrane proteins was less pronounced than in the absence of sugar. From thylakoids, which were isolated from heat-damaged spinach leaves, less protein was released when heated again after the isolation procedure, indicating that protein release also takes place during heat inactivation in vivo . Sodium dodecyl sulfate gel electropherograms of thylakoids demonstrated that heat inactivation of the lamellae was not accompanied by significant changes in the pattern of the proteins, which remained in the membranes. The same was found when thylakoids were solubilized with Triton X-100 before and after heat damage. It is suggested that the protein release that occurs during heat treatment is a consequence of irreversible alterations in the membrane structure; these changes may be responsible for thermal damage of chloroplast membranes.     

Multiple mechanisms of membrane anchoring of Escherichia coli penicillin-binding proteins

Abstract: The major penicillin-binding proteins (PBPs) of Escherichia coli play vital roles in cell wall biosynthesis and are located in the inner membrane. The high M _r PBPs 1A, 1B, 2 and 3 are essential bifunctional transglycosylases/transpeptidases which are thought to be type II integral inner membrane proteins with their C-terminal enzymatic domains projecting into the periplasm. The low M _r PBP4 is a DD-carboxypeptidase/endopeptidase, whereas PBPs 5 and are DD-carboxypeptidases. All three low M _r , PBPs act in the modification of peptidoglycan to allow expansion of the sacculus and are thought to be periplasmic proteins attached with varying affinities to the inner membrane via C-terminal amphiphilic α-helices. It is possible that the PBPs and other inner membrane proteins form a peptidoglycan synthesizing complex to coordinate their activities.     

Transbilayer mapping of membrane proteins using membranes isolated on polylysine-coated polyacrylamide beads

Erythrocyte and HeLa cell plasma membranes were isolated on polylysinecoated polyacrylamide beads and the transbilayer disposition of their proteins was investigated.When membranes of intact erythrocytes were isolated on beads and then labelled by lactoperoxidase-catalysed iodination, their labelling pattern was similar to that of inside-out vesicles in solution.When the membranes of intact HeLa cells were isolated on beads and then labelled by galactose oxidase-[³H]borohydride treatment, no glycoprotein or glycolipid sugars were accessible. On the other hand, when the HeLa cell membranes were isolated on beads and then labelled by the lactoperoxidase-catalysed iodination, all of the major membrane proteins were iodinated. These experiments confirmed for HeLa cell membranes what had previously been shown for erythrocyte membranes: when the membranes of intact cells are isolated on beads, the accessibility of their surfaces to enzymatic probes is the same as would be expected of inside-out vesicles in suspension. Double-label experiments, in which the HeLa cell membranes were labelled first on the intact HeLa cells and again after isolation on beads, identified several     

Phylogenetic classification of transporters and other membrane proteins from Saccharomyces cerevisiae

On the basis of functional and phylogenetic criteria, we have identified a total of 229 subfamilies and 111 singletons predicted to carry out transport or other membrane functions in Saccharomyces cerevisiae. We have extended the Transporter Classification (TC) and created a Membrane Classification (MC) for non-transporter membrane proteins. Using the preliminary phylogenetic digits X, Y, Z (for new families, subfamilies, and clusters, respectively), we allocated a five-digit number to 850 proteins predicted to contain more than two transmembrane domains. Compared with a previous TC of the yeast genome, we classified an additional set of 538 membrane proteins (transporters and non-transporters) and identified 111 novel phylogenetic subfamilies. Electronic Publication     

Design of recombinant antibody microarrays for membrane protein profiling of cell lysates and tissue extracts

Generating global protein expression profiles, including also membrane proteins, will be crucial for our understanding of biological processes in health and disease. In this study, we have expanded our antibody microarray technology platform and designed the first human recombinant antibody microarray for membrane proteins targeting crude cell lysates and tissue extracts. We have optimized all key technological parameters and successfully developed a setup for extracting, labeling and analyzing non-fractionated membrane proteomes under non-denaturing conditions. Finally, the platform was also extended and shown to be compatible with simultaneous profiling of both membrane proteins and water-soluble proteins.     

Identification and relative quantification of membrane proteins by surface biotinylation and two-dimensional peptide mapping

Membrane proteins play a central role in biological processes, but their separation and quantification using two-dimensional gel electrophoresis is often limited by their poor solubility and relatively low abundance. We now present a method for the simultaneous recovery, separation, identification, and relative quantification of membrane proteins, following their selective covalent modification with a cleavable biotin derivative. After cell lysis, biotinylated proteins are purified on streptavidin-coated resin and proteolytically digested. The resulting peptides are analyzed by high-pressure liquid chromatography and mass spectrometry, thus yielding a two-dimensional peptide map. Matrix assisted laser desorption/ionization-time of flight signal intensity of peptides, in the presence of internal standards, is used to quantify the relative abundance of membrane proteins from cells treated in different experimental conditions. As experimental examples, we present (i) an analysis of a BSA-spiked human embryonic kidney membrane protein extract, and (ii) an analysis of membrane proteins of human umbilical vein endothelial cells cultured in normoxic and hypoxic conditions. This last study allowed the recovery of the vascular endothelial-cadherin/actin/catenin complex, revealing an increased accumulation of beta-catenin at 2% O(2) concentration.     

ExoCarta: A compendium of exosomal proteins and RNA

Exosomes, membrane microvesicles (40–100 nm) secreted by most cell types, can be isolated in several ways while characterizing them is heavily based on electron microscopy and, most importantly, the identification of exosome marker proteins. Researchers rely on the identification of certain exosomal marker proteins including Alix, CD9 and CD63 to confirm the presence of exosomes in their preparations. An evolutionary‐conserved set of protein molecules have been identified in most exosomes studied to date. However, with the complexity of tissue/cell type‐specific proteins being incorporated in the exosomes, some of these so‐called exosomal markers are not always present in all the exosomes. The presence of tissue/cell type‐specific proteins in exosomes allows researchers to isolate them using immunoaffinity capture methods. A compendium for exosomal proteomes will aid researchers in identifying proteins that were more commonly found in various exosomes (exosome markers) and those that are specific to certain tissue/cell type‐derived exosomes. Here, we describe ExoCarta, a compendium for proteins and RNA molecules identified in exosomes. ExoCarta is first of its kind and the resource is freely available to the scientific community through the web ( http://exocarta.ludwig.edu.au ). We believe that this community resource will be of great biological importance for any future exosome analyses.     

Virtual identification of essential proteins within the protein interaction network of yeast

Topological analysis of large scale protein-protein interaction networks (PINs) is important for understanding the organizational and functional principles of individual proteins. The number of interactions that a protein has in a PIN has been observed to be correlated with its indispensability. Essential proteins generally have more interactions than the nonessential ones. We show here that the lethality associated with removal of a protein from the yeast proteome correlates with different centrality measures of the nodes in the PIN, such as the closeness of a protein to many other proteins, or the number of pairs of proteins which need a specific protein as an intermediary in their communications, or the participation of a protein in different protein clusters in the PIN. These measures are significantly better than random selection in identifying essential proteins in a PIN. Centrality measures based on graph spectral properties of the network, in particular the subgraph centrality, show the best performance in identifying essential proteins in the yeast PIN. Subgraph centrality gives important structural information about the role of individual proteins, and permits the selection of possible targets for rational drug discovery through the identification of essential proteins in the PIN.     

Selective sorting of cargo proteins into bacterial membrane vesicles

In contrast to the well established multiple cellular roles of membrane vesicles in eukaryotic cell biology, outer membrane vesicles (OMV) produced via blebbing of prokaryotic membranes have frequently been regarded as cell debris or microscopy artifacts. Increasingly, however, bacterial membrane vesicles are thought to play a role in microbial virulence, although it remains to be determined whether OMV result from a directed process or from passive disintegration of the outer membrane. Here we establish that the human oral pathogen Porphyromonas gingivalis has a mechanism to selectively sort proteins into OMV, resulting in the preferential packaging of virulence factors into OMV and the exclusion of abundant outer membrane proteins from the protein cargo. Furthermore, we show a critical role for lipopolysaccharide in directing this sorting mechanism. The existence of a process to package specific virulence factors into OMV may significantly alter our current understanding of host-pathogen interactions.     

Differential dynamics of membrane proteins in yeast

Lateral diffusion of lipids and proteins in yeast plasma membranes has been reported to be anomalously slow, and implicated as a possible reason for polarization in yeast. In order to gain insight into the observed slow diffusion in yeast membranes, we explored lateral diffusion of two proteins of different origin. We compared lateral dynamics of the Candida drug resistance protein-1 (Cdr1p), and the human serotonin_1A receptor (5-HT_1AR) by fluorescence recovery after photobleaching (FRAP). Our results show that while Cdr1p-GFP displays slow diffusion, the diffusion of 5-HT_1AR-EYFP is significantly faster. Interestingly, upon ergosterol depletion, the mobility of Cdr1p-GFP did not exhibit appreciable change, while 5-HT_1AR-EYFP mobility showed an increase. On the other hand, upon actin cytoskeleton destabilization, the mobile fraction of 5-HT_1AR-EYFP showed considerable increase, while the mobility of Cdr1p-GFP was not altered. Our results represent the first report on the dynamics of the important drug resistance protein Cdr1p and provide novel insight on diffusion of membrane proteins in yeast membranes.     

Lifetime fluorescence method for determining membrane topology of proteins

Recently, we introduced a sensitive method for determining the bilayer topology (cis- or trans-leaflet location) of single-site cysteine-linked 7-nitrobenz-2-oxa-1,3-diazol-4-yl (NBD) fluorescent labels on membrane proteins. It uses a novel quencher, LysoUB, composed of a single acyl chain attached to a UniBlue chromophore. In its original version, the method relied on the comparison of steady-state fluorescence measurements of membrane-inserted proteins in samples with different distributions of the LysoUB in cis- and trans-leaflets of the lipid bilayer. Here we modify the method to take advantage of the fluorescence lifetime methodology, which allows us to simplify sample manipulation and, as a result, increase the reliability of topology determination. We tested the method using three model systems with artificially created all-cis, all-trans, and isotropic distribution of NBD. Because the quenching efficiency is higher when LysoUB and NBD are in the same leaflet, introduction of the quencher into the cis-leaflet results in a predictably different amount of quenching for these three model systems. Indeed, the addition of 2% LysoUB into the all-cis NBD model system causes strong reduction of the longest lifetime (from 8.1 to 4.9 ns), whereas the same addition of LysoUB results in marginal quenching (from 8.7 to 8.5 ns) in the case of all-trans NBD. This difference provides a good basis for topology determination using time-resolved fluorescence quenching.