Using yeast as a model to study membrane proteins:

Improved Protein Coverage in Bottom-Up Proteomes Analysis Using Fluoroalcohol-Mediated Supramolecular Biphasic Systems With Mixed Amphiphiles for Sample Extraction, Fractionation, and Enrichment

A new class of supramolecular biphasic systems containing fluoroalcohol-induced coacervates (FAiC) provides concomitant fractionation of complex protein mixtures, high solubilizing power for extraction of various types of proteins, especially those with high hydrophobicity (such as membrane proteins), and enrichment of low-abundance proteins. Subsequently, the use of FAiC biphasic systems (BPS) in the bottom-up proteomics workflow resulted in significantly higher coverage for the whole proteome, various subproteomes, especially those embedded or associated with membranes, post-translationally modified proteins, and low-abundance proteins (LAPs) as compared to the conventional methodologies. In this work, we used a new type of FAiC-BPS composed of mixed amphiphiles, a zwitterionic surfactant 3-(N,N-dimethylmyristyl ammonia) propane sulfonate (DMMAPS), a quaternary ammonium salt (QUATS), and hexafluoroisopropanol (HFIP) as the coacervator for extraction, fractionation, and enrichment of yeast proteome in bottom-up proteomics. The coverage of the lower-abundance proteins (abundance below 2000 molecules/cell) improved by more than 100% using DMMAPS and DMMAPS + QUATS systems as compared to the conventional methods using urea or detergent solutions for protein solubilization. Additionally, these coacervate systems show increased coverage of integral membrane proteins and proteins with α-helices by up to 24 and 555%, respectively.

Yeast-based assays for detecting protein-protein/drug interactions and their inhibitors

Understanding cellular processes at molecular levels in health and disease requires the knowledge of protein-protein interactions (PPIs). In line with this, identification of PPIs at genome-wide scale is highly valuable to understand how different cellular pathways are interconnected, and it eventually facilitates designing effective drugs against certain PPIs. Furthermore, investigating PPIs at a small laboratory scale for deciphering certain biochemical pathways has been demanded for years. In this regard, yeast two hybrid system (Y2HS) has proven an extremely useful tool to discover novel PPIs, while Y2HS derivatives and novel yeast-based assays are contributing significantly to identification of protein-drug/inhibitor interaction at both large- and small-scale set-ups. These methods have been evolving over time to provide more accurate, reproducible and quantitative results. Here we briefly describe different yeast-based assays for identification of various protein-protein/drug/inhibitor interactions and their specific applications, advantages, shortcomings, and improvements. The broad range of yeast-based assays facilitates application of the most suitable method(s) for each specific need.

Role of GxxxG Motifs in Transmembrane Domain Interactions

Transmembrane (TM) helices of integral membrane proteins can facilitate strong and specific noncovalent protein-protein interactions. Mutagenesis and structural analyses have revealed numerous examples in which the interaction between TM helices of single-pass membrane proteins is dependent on a GxxxG or (small)xxx(small) motif. It is therefore tempting to use the presence of these simple motifs as an indicator of TM helix interactions. In this Current Topic review, we point out that these motifs are quite common, with more than 50% of single-pass TM domains containing a (small)xxx(small) motif. However, the actual interaction strength of motif-containing helices depends strongly on sequence context and membrane properties. In addition, recent studies have revealed several GxxxG-containing TM domains that interact via alternative interfaces involving hydrophobic, polar, aromatic, or even ionizable residues that do not form recognizable motifs. In multipass membrane proteins, GxxxG motifs can be important for protein folding, and not just oligomerization. Our current knowledge thus suggests that the presence of a GxxxG motif alone is a weak predictor of protein dimerization in the membrane.

[Biomimetic sensors in biomedical research]

The recent research on both the synthesis of membrane proteins by cell-free systems and the reconstruction of planar lipid membranes, has led to the development of a cross-technology to produce biosensors or filters. Numerous biomimetic membranes are currently being standardized and used by the industry, such as filters containing aquaporin for water desalination, or used in routine at the laboratory scale, for example the bacteriorhodopsin as a light sensor. In the medical area, several fields of application of these biomimetic membranes are under consideration today, particularly for the screening of therapeutic molecules and for the developing of new tools in diagnosis, patient monitoring and personalized medicine.

Incomplete distal renal tubular acidosis from a heterozygous mutation of the V-ATPase B1 subunit

Congenital distal renal tubular acidosis (RTA) from mutations of the B1 subunit of V-ATPase is considered an autosomal recessive disease. We analyzed a distal RTA kindred with a truncation mutation of B1 (p.Phe468fsX487) previously shown to have failure of assembly into the V1 domain of V-ATPase. All heterozygous carriers in this kindred have normal plasma HCO3- concentrations and thus evaded the diagnosis of RTA. However, inappropriately high urine pH, hypocitraturia, and hypercalciuria were present either individually or in combination in the heterozygotes at baseline. Two of the heterozygotes studied also had inappropriate urinary acidification with acute ammonium chloride loading and an impaired urine-blood Pco2 gradient during bicarbonaturia, indicating the presence of a H+ gradient and flux defects. In normal human renal papillae, wild-type B1 is located primarily on the plasma membrane, but papilla from one of the heterozygote who had kidney stones but not nephrocalcinosis showed B1 in both the plasma membrane as well as diffuse intracellular staining. Titration of increasing amounts of the mutant B1 subunit did not exhibit negative dominance over the expression, cellular distribution, or H+ pump activity of wild-type B1 in mammalian human embryonic kidney-293 cells and in V-ATPase-deficient Saccharomyces cerevisiae. This is the first demonstration of renal acidification defects and nephrolithiasis in heterozygous carriers of a mutant B1 subunit that cannot be attributable to negative dominance. We propose that heterozygosity may lead to mild real acidification defects due to haploinsufficiency. B1 heterozygosity should be considered in patients with calcium nephrolithiasis and urinary abnormalities such as alkalinuria or hypocitraturia.

Overexpression of membrane proteins from higher eukaryotes in yeasts

Heterologous expression and characterisation of the membrane proteins of higher eukaryotes is of paramount interest in fundamental and applied research. Due to the rather simple and well-established methods for their genetic modification and cultivation, yeast cells are attractive host systems for recombinant protein production. This review provides an overview on the remarkable progress, and discusses pitfalls, in applying various yeast host strains for high-level expression of eukaryotic membrane proteins. In contrast to the cell lines of higher eukaryotes, yeasts permit efficient library screening methods. Modified yeasts are used as high-throughput screening tools for heterologous membrane protein functions or as benchmark for analysing drug-target relationships, e.g., by using yeasts as sensors. Furthermore, yeasts are powerful hosts for revealing interactions stabilising and/or activating membrane proteins. We also discuss the stress responses of yeasts upon heterologous expression of membrane proteins. Through co-expression of chaperones and/or optimising yeast cultivation and expression strategies, yield-optimised hosts have been created for membrane protein crystallography or efficient whole-cell production of fine chemicals.

Liposomes physically coated with peptides: preparation and characterization

Physically coating liposomes with peptides of desirable functions is an economic, versatile, and less time-consuming approach to prepare drug delivery vehicles. In this work, we designed three peptides-Ac-WWKKKGGNNN-NH2 (W2K3), Ac-WWRRRGGNNN-NH2(W2R3), Ac-WWGGGGGNNN-NH2(W2G3)-and studied their coating ability on negatively charged liposomes. It was found that the coating was mainly driven by the electrostatic interaction between the peptides' cationic side groups and the acidic lipids, which also mediated the "anchoring " of Trp residuals in the interfacial region of lipid bilayers. At the same conditions, the amount of the coated W2R3 was more than that of W2K3, but the stability of the liposome coated with W2R3 was deteriorated. This was caused by the delocalized charge of the guanidinium group of arginine. The coating of the peptide rendered the liposome pH-responsive behavior but did not prominently change the phase transition temperature. The liposome coated with peptides displayed appropriate pH/temperature dual responsive characteristics and was able to release the content in a controlled manner.

A survey of computational methods for protein complex prediction from protein interaction networks

Complexes of physically interacting proteins are one of the fundamental functional units responsible for driving key biological mechanisms within the cell. Their identification is therefore necessary to understand not only complex formation but also the higher level organization of the cell. With the advent of "high-throughput" techniques in molecular biology, significant amount of physical interaction data has been cataloged from organisms such as yeast, which has in turn fueled computational approaches to systematically mine complexes from the network of physical interactions among proteins (PPI network). In this survey, we review, classify and evaluate some of the key computational methods developed till date for the identification of protein complexes from PPI networks. We present two insightful taxonomies that reflect how these methods have evolved over the years toward improving automated complex prediction. We also discuss some open challenges facing accurate reconstruction of complexes, the crucial ones being the presence of high proportion of errors and noise in current high-throughput datasets and some key aspects overlooked by current complex detection methods. We hope this review will not only help to condense the history of computational complex detection for easy reference but also provide valuable insights to drive further research in this area.

Biological function through network topology: a survey of the human diseasome

Molecular network data are increasingly becoming available, necessitating the development of well performing computational tools for their analyses. Such tools enabled conceptually different approaches for exploring human diseases to be undertaken, in particular, those that study the relationship between a multitude of biomolecules within a cell. Hence, a new field of network biology has emerged as part of systems biology, aiming to untangle the complexity of cellular network organization. We survey current network analysis methods that aim to give insight into human disease.

Interactome mapping for analysis of complex phenotypes: insights from benchmarking binary interaction assays

Protein interactions mediate essentially all biological processes and analysis of protein-protein interactions using both large-scale and small-scale approaches has contributed fundamental insights to the understanding of biological systems. In recent years, interactome network maps have emerged as an important tool for analyzing and interpreting genetic data of complex phenotypes. Complementary experimental approaches to test for binary, direct interactions, and for membership in protein complexes are used to explore the interactome. The two approaches are not redundant but yield orthogonal perspectives onto the complex network of physical interactions by which proteins mediate biological processes. In recent years, several publications have demonstrated that interactions from high-throughput experiments can be equally reliable as the high quality subset of interactions identified in small-scale studies. Critical for this insight was the introduction of standardized experimental benchmarking of interaction and validation assays using reference sets. The data obtained in these benchmarking experiments have resulted in greater appreciation of the limitations and the complementary strengths of different assays. Moreover, benchmarking is a central element of a conceptual framework to estimate interactome sizes and thereby measure progress toward near complete network maps. These estimates have revealed that current large-scale data sets, although often of high quality, cover only a small fraction of a given interactome. Here, I review the findings of assay benchmarking and discuss implications for quality control, and for strategies toward obtaining a near-complete map of the interactome of an organism.

A modification of the split-tobacco etch virus method for monitoring interactions between membrane proteins in mammalian cells

Despite progress in the development of methods to monitor protein interactions, studies of interactions between membrane proteins in mammalian cells remain challenging. Protein complementation assays (PCAs) are commonly used to study interactions between proteins due to their simplicity. They are based on interaction-mediated reconstitution of a reporter protein, which can be easily monitored. Recently, a protein complementation method named split-TEV (tobacco etch virus) has been developed and is based on the functional reconstitution of TEV protease and subsequent proteolytic-mediated activation of reporters. In this work, we have developed a modification of the split-TEV method to study the interactions between membrane proteins with increased specificity. This assay was validated by addressing the interactions between different membrane proteins, including G protein-coupled receptors (GPCRs) and ion channels. By comparing it with another PCA, we found that this new method showed a higher sensitivity.

Molecular tools to characterize adiponectin activity

Within the past years, numerous hormones were found to be secreted by adipose tissue. As these adipokines exert different physiological effects with great importance in obesity, they provide new strategies for the treatment of obesity associated disorders. Adiponectin is one of the most promising targets due to its protective properties in glucose and lipid metabolism, which are mediated by the adiponectin receptor 1 and 2. Within the past decades, substantial progress in understanding the molecular function of this unique ligand-receptor system could be achieved. This review summarizes the most important approaches for the investigation of adiponectin activity. Even though many insights into adipokine function could be achieved, clarification of the detailed mode of action is still challenging. For this reason, this review gives an overview of frequently used methods, which led to the molecular characterization of adiponectin and might help to get more detailed insights into the broad aspects of obesity.