Impact of Detergents on Membrane Protein Complex Isolation

Enzyme variants in biosynthesis and biological assessment of different molecular weight hyaluronan

In the present study, low- and high-molecular-weight hyaluronic acids (LMW-HA and HMW-HA) were synthesized in vitro by truncated Streptococcus equisimilis hyaluronan synthases (SeHAS). The enzyme kinetic parameters were determined for each enzyme variant. The MW, structure, dispersity, and biological activity of polymers were determined by electrophoresis, FTIR spectroscopy, carbazole, cell proliferation, and cell migration assay, respectively. The specific activities were calculated as 7.5, 6.8, 4.9, and 2.8 µgHA µgenzyme-1 min-1 for SeHAS, HAS123, HAS23, and HASIntra, respectively. The results revealed SeHAS produced a polydisperse HMW-HA (268 kDa), while HAS123 and HAS23 produced a polydisperse LMW-HA (< 30 kDa). Interestingly, HASIntra produced a low-disperse LMW-HA. Kinetics studies revealed the truncated variants displayed increased Km values for two substrates when compared to the wild-type enzyme. Biological assessments indicated all LMW-HAs showed a dose-dependent proliferation activity on endothelial cells (ECs), whereas HMW-HAs exhibited an inhibitory effect. Also, LMW-HAs had the highest cell migration effect at 10 µg/mL, while at 200 µg/mL, both LMW- and HMW-HAs postponed the healing recovery rate. The study elucidated that the transmembrane domains (TMDs) of SeHAS affect the enzyme kinetics, HA-titer, HA-size, and HA-dispersity. These findings open new insight into the rational engineering of SeHAS to produce size-defined HA.

Co-fractionation-mass spectrometry to characterize native mitochondrial protein assemblies in mammalian neurons and brain

Human mitochondrial (mt) protein assemblies are vital for neuronal and brain function, and their alteration contributes to many human disorders, e.g., neurodegenerative diseases resulting from abnormal protein-protein interactions (PPIs). Knowledge of the composition of mt protein complexes is, however, still limited. Affinity purification mass spectrometry (MS) and proximity-dependent biotinylation MS have defined protein partners of some mt proteins, but are too technically challenging and laborious to be practical for analyzing large numbers of samples at the proteome level, e.g., for the study of neuronal or brain-specific mt assemblies, as well as altered mtPPIs on a proteome-wide scale for a disease of interest in brain regions, disease tissues or neurons derived from patients. To address this challenge, we adapted a co-fractionation-MS platform to survey native mt assemblies in adult mouse brain and in human NTERA-2 embryonal carcinoma stem cells or differentiated neuronal-like cells. The workflow consists of orthogonal separations of mt extracts isolated from chemically cross-linked samples to stabilize PPIs, data-dependent acquisition MS to identify co-eluted mt protein profiles from collected fractions and a computational scoring pipeline to predict mtPPIs, followed by network partitioning to define complexes linked to mt functions as well as those essential for neuronal and brain physiological homeostasis. We developed an R/CRAN software package, Macromolecular Assemblies from Co-elution Profiles for automated scoring of co-fractionation-MS data to define complexes from mtPPI networks. Presently, the co-fractionation-MS procedure takes 1.5-3.5 d of proteomic sample preparation, 31 d of MS data acquisition and 8.5 d of data analyses to produce meaningful biological insights.

Quantitation of strain-specific hemagglutinin trimers in mosaic quadrivalent influenza nanoparticle vaccine by ELISA

An enzyme linked immunosorbent assay (ELISA) method was developed to analyze the assembly of a tetravalent mosaic influenza nanoparticle (NP) vaccine, Flumos-v1, consisting of hemagglutinin trimers (HAT) from H1 (A/Idaho/07/2018), H3 (A/Perth/1008/2019), HBV (Vic-B/Colorado/06/2017) and HBY (Yam-B/Phuket/3073/2013) strains. The sandwich ELISA assay used lectin from Galanthus nivalis as a universal capture reagent for all HAT strains and specific monoclonal antibody (mAb) to detect corresponding hemagglutinin antigen. The mAb binding of HATs incorporated into NPs diverged from those for single HAT solutions, resulting in inaccurate quantitation of assembled HATs. An optimized zwittergent treatment was used to fully dissociate the influenza NP and aligned binding activities in each pair of single HAT and dissociated HAT from NP. The dissociated HATs were then quantified against their corresponding HAT standard solutions for three development lots of FluMos-v1 vaccine and the assembly ratio of all four HATs was calculated. The molar ratio of different HATs incorporated into this quadrivalent NP vaccine was consistent and determined as H3:H1: HBV: HBY ∼ 1.00:0.92:0.96:0.87, which was close the expected 1:1:1:1 ratio and confirmed a proper assembling of multivalent NP.

Development of Cell-Derived Plasma Membrane Vesicles as a Nanoparticle Encapsulation and Delivery System

Background

Developing non-invasive delivery platforms with a high level of structural and/or functional similarity to biological membranes is highly desirable to reduce toxicity and improve targeting capacity of nanoparticles. Numerous studies have investigated the impacts of physicochemical properties of engineered biomimetic nanoparticles on their interaction with cells, yet technical difficulties have led to the search for better biomimetics, including vesicles isolated directly from live cells. Cell-derived giant plasma membrane vesicles (GPMVs), in particular, offer a close approximation of the intact cell plasma membrane by maintaining the latter's compositional complexity, protein positioning in a fluid-mosaic pattern, and physical and mechanical properties. Thus, to overcome technical barriers of prior nanoparticle delivery approaches, we aimed to develop a novel method using GPMVs to encapsulate a variety of engineered nanoparticles, then use these core-shell, nanoparticle-GPMV vesicle structures to deliver cargo to other cells.

Results

The GPMV system in this study was generated by chemically inducing vesiculation in A549 cells, a model human alveolar epithelial line. These cell-derived GPMVs retained encapsulated silica nanoparticles (50 nm diameter) for at least 48 hours at 37 °C. GPMVs showed nearly identical lipid and protein membrane profiles as the parental cell plasma membrane, with or without encapsulation of nanoparticles. Notably, GPMVs were readily endocytosed in the parental A549 cell line as well as the human monocytic THP-1 cell line. Higher cellular uptake levels were observed for GPMV-encapsulated nanoparticles compared to control groups, including free nanoparticles. Further, GPMVs delivered a variety of nanoparticles to parental cells with reduced cytotoxicity compared to free nanoparticles at concentrations that were otherwise significantly toxic.

Conclusions

We have introduced a novel technique to load nanoparticles within the cell plasma membrane during the GPMV vesiculation process. These GPMVs are capable of (a) encapsulating different types of nanoparticles (including larger and not highly-positively charged bodies that have been technically challenging cargoes) using a parental cell uptake technique, and (b) improving delivery of nanoparticles to cells without significant cytotoxicity. Ultimately, endogenous surface membrane proteins and lipids can optimize the physicochemical properties of cell membrane-derived vesicles, which could lead to highly effective cell membrane-based nanoparticle/drug delivery systems.

Blocking bacterial appendage attachment to wastewater treatment membranes using anti-adhesins

Membrane bioreactors (MBRs) suffer from high operational and cleaning costs due to biofouling. The biofouling begins when the adhesins (an anchor-type epitope made up of polar and charged amino acids) on microbial appendages bind to the surface. Two different compounds-dodecyl-β-D-maltoside (DDM) and methyl α-d-mannopyranoside (MeαMan)-were investigated as possible biofilm mitigation tools due to their documented anti-adhesin properties in the biomedical field. DDM prevented up to 56.3, 87.0, and 67.6% of the formation of Pseudomonas putida, Escherichia coli and wastewater culture biofilms, respectively, in microplate experiments. MeαMan increased biofilm in the microplates. In a biofilm reactor setting, DDM was then applied on typical membrane materials, polyvinylidene fluoride, polyamide, polyether-sulfone, and polyacrylonitrile and prevented 79.4, 62.5, 81.3, and 68.2% of the detectable wastewater culture biofilm formation, respectively. The mechanism of anti-adhesion was the binding of the polar head of the DDM to the polar amino acids of the microbial appendages in conjunction with the orientation of the DDM as it binds different membrane materials. If the anti-adhesins are effective at increasing the distance of the bacteria from the membrane materials, they will serve as a new method for delaying biofouling.

Using the Proteomics Toolbox to Resolve Topology and Dynamics of Compartmentalized cAMP Signaling

cAMP is a second messenger that regulates a myriad of cellular functions in response to multiple extracellular stimuli. New developments in the field have provided exciting insights into how cAMP utilizes compartmentalization to ensure specificity when the message conveyed to the cell by an extracellular stimulus is translated into the appropriate functional outcome. cAMP compartmentalization relies on the formation of local signaling domains where the subset of cAMP signaling effectors, regulators and targets involved in a specific cellular response cluster together. These domains are dynamic in nature and underpin the exacting spatiotemporal regulation of cAMP signaling. In this review, we focus on how the proteomics toolbox can be utilized to identify the molecular components of these domains and to define the dynamic cellular cAMP signaling landscape. From a therapeutic perspective, compiling data on compartmentalized cAMP signaling in physiological and pathological conditions will help define the signaling events underlying disease and may reveal domain-specific targets for the development of precision medicine interventions.

Human Serum Mediated Bacteriophage Life Cycle Switch in Aggregatibacter actinomycetemcomitans Is Linked to Pyruvate Dehydrogenase Complex

Antimicrobial resistance is rising as a major global public health threat and antibiotic resistance genes are widely spread among species, including human oral pathogens, e.g., Aggregatibacter actinomycetemcomitans. This Gram-negative, capnophilic, facultative anaerobe is well recognized as a causative agent leading to periodontal diseases, as well as seriously systemic infections including endocarditis. A. actinomycetemcomitans has also evolved mechanisms against complement-mediated phagocytosis and resiliently survives in serum-rich in vivo environments, i.e., inflamed periodontal pockets and blood circulations. This bacterium, however, demonstrated increasing sensitivity to human serum, when being infected by a pseudolysogenic bacteriophage S1249, which switched to the lytic state as a response to human serum. Concomitantly, the pyruvate dehydrogenase complex (PDHc), which is composed of multiple copies of three enzymes (E1, E2, and E3) and oxidatively decarboxylates pyruvate to acetyl-CoA available for tricarboxylic acid (TCA) cycle, was found up-regulated 10-fold in the bacterial lysogen after human serum exposure. The data clearly indicated that certain human serum components induced phage virion replication and egress, resulting in bacterial lysis. Phage manipulation of bacterial ATP production through regulation of PDHc, a gatekeeper linking glycolysis to TCA cycle through aerobic respiration, suggests that a more efficient energy production and delivery system is required for phage progeny replication and release in this in vivo environment. Insights into bacteriophage regulation of bacterial fitness in a mimic in vivo condition will provide alternative strategies to control bacterial infection, in addition to antibiotics.

Transition-Linker Containing Detergents for Membrane Protein Studies

It is a pressing need, but still challenging to explore the structure and function of membrane proteins (MPs). One of the main obstacles is the limited availability of matched detergents for the handling of specific MPs. We describe herein the design of new detergents by incorporation of a transition linker between the hydrophilic head and the hydrophobic tail. This design allows a gradual change of hydrophobicity between the outside and inside of micelles, in contrast to the abrupt switch in conventional detergents. Notably, many of these detergents assembled into micelles in while retaining low critical micelle concentrations. Meanwhile, thermal stabilizing evaluation identified superior detergents for representative MPs, including G protein-coupled receptors and a transporter protein. Among them, further improved the NMR study of MPs. We anticipate these that results will encourage future detergent expansion through new remodeling on the traditional detergent scaffold.

Surfactant-Mediated Solubilization of Myelin Figures: A Multistep Morphological Cascade

Lamellar mesophases of insoluble lipids are readily solubilized by the micellar mesophases of soluble surfactants. This simple process underscores a broad array of biochemical methodologies, including purification, reconstitution, and crystallization of membrane proteins, as well as the isolation of detergent-resistant membrane fractions. Although much is now known about the thermodynamic driving forces of membrane solubilization, the kinetic pathways by which the surfactant alters vesicular mesophases are only beginning to be appreciated. Little is known about how these interactions affect the solubilization of more complex, multilamellar mesophases. Here, we investigate how a common zwitterionic detergent affects the solubilization of a smectic, multilamellar, cylindrical mesophase of lipids, called the myelin figure. Our results reveal that myelin solubilization occurs in a multistep manner, producing a well-defined sequence of morphologically distinct intermediates en route to complete solubilization. The kinetic processes producing these intermediates include (1) coiling, which encompasses the formation, propagation, and tightening of extended helices; (2) thinning, which reflects the unbinding of lamellae in the smectic stacks; and (3) detachment or retraction, which either dissociates the myelinic protrusion from the source lipid mass or returns the myelinic protrusion to the source lipid mass─all in transit toward complete solubilization. These occasionally overlapping steps are most pronounced in single-lipid component myelins, while compositionally graded multicomponent myelins inhibit the coiling step and detach more frequently. Taken together, the appearance of these intermediates during the solubilization of myelins suggests a complex free-energy landscape characterizing myelin solubilization populated by metastable, morphological intermediates correlated with locally minimized changes in energy dependent upon the mesophase's composition. This then predicts the accessibility of structurally distinct, kinetic intermediates─such as loose and tight coiled helices, peeled myelins, retracted tubes, and detached protrusions─before reaching the stable ground state corresponding to a dissolved suspension of mixed surfactant-lipid micelles.

Prostate tumor-induced stromal reprogramming generates Tenascin C that promotes prostate cancer metastasis through YAP/TAZ inhibition

Metastatic prostate cancer (PCa) in bone induces bone-forming lesions that enhance PCa progression. How tumor-induced bone formation enhances PCa progression is not known. We have previously shown that PCa-induced bone originates from endothelial cells (ECs) that have undergone endothelial-to-osteoblast (EC-to-OSB) transition by tumor-secreted bone morphogenetic protein 4 (BMP4). Here, we show that EC-to-OSB transition leads to changes in the tumor microenvironment that increases the metastatic potential of PCa cells. We found that conditioned medium (CM) from EC-OSB hybrid cells increases the migration, invasion, and survival of PC3-mm2 and C4-2B4 PCa cells. Quantitative mass spectrometry (Isobaric Tags for Relative and Absolute Quantitation) identified Tenascin C (TNC) as one of the major proteins secreted from EC-OSB hybrid cells. TNC expression in tumor-induced OSBs was confirmed by immunohistochemistry of MDA PCa-118b xenograft and human bone metastasis specimens. Mechanistically, BMP4 increases TNC expression in EC-OSB cells through the Smad1-Notch/Hey1 pathway. How TNC promotes PCa metastasis was next interrogated by in vitro and in vivo studies. In vitro studies showed that a TNC-neutralizing antibody inhibits EC-OSB-CM-mediated PCa cell migration and survival. TNC knockdown decreased, while the addition of recombinant TNC or TNC overexpression increased migration and anchorage-independent growth of PC3 or C4-2b cells. When injected orthotopically, PC3-mm2-shTNC clones decreased metastasis to bone, while C4-2b-TNC-overexpressing cells increased metastasis to lymph nodes. TNC enhances PCa cell migration through α5β1 integrin-mediated YAP/TAZ inhibition. These studies elucidate that tumor-induced stromal reprogramming generates TNC that enhances PCa metastasis and suggest that TNC may be a target for PCa therapy.

Database Study on the Expression and Purification of Membrane Proteins

Membrane proteins are crucial for biological processes, and many of them are important to drug targets. Understanding the three-dimensional structures of membrane proteins are essential to evaluate their bio function and drug design. High-purity membrane proteins are important for structural determination. Membrane proteins have low yields and are difficult to purify because they tend to aggregate. We summarized membrane protein expression systems, vectors, tags, and detergents, which have deposited in the Protein Data Bank (PDB) in recent four-and-a-half years. Escherichia coli is the most expression system for membrane proteins, and HEK293 cells are the most commonly cell lines for human membrane protein expression. The most frequently vectors are pFastBac1 for alpha-helical membrane proteins, pET28a for beta-barrel membrane proteins, and pTRC99a for monotopic membrane proteins. The most used tag for membrane proteins is the 6×His-tag. FLAG commonly used for alpha-helical membrane proteins, Strep and GST for beta-barrel and monotopic membrane proteins, respectively. The detergents and their concentrations used for alpha-helical, beta-barrel, and monotopic membrane proteins are different, and DDM is commonly used for membrane protein purification. It can guide the expression and purification of membrane proteins, thus contributing to their structure and bio function studying.

Development of Styrene Maleic Acid Lipid Particles as a Tool for Studies of Phage-Host Interactions

The infection of a bacterium by a phage starts with attachment to a receptor molecule on the host cell surface by the phage. Since receptor-phage interactions are crucial to successful infections, they are major determinants of phage host range and, by extension, of the broader effects that phages have on bacterial communities. Many receptor molecules, particularly membrane proteins, are difficult to isolate because their stability is supported by their native membrane environments. Styrene maleic acid lipid particles (SMALPs), a recent advance in membrane protein studies, are the result of membrane solubilizations by styrene maleic acid (SMA) copolymer chains. SMALPs thereby allow for isolation of membrane proteins while maintaining their native environment. Here, we explore SMALPs as a tool to isolate and study phage-receptor interactions. We show that SMALPs produced from taxonomically distant bacterial membranes allow for receptor-specific decrease of viable phage counts of several model phages that span the three largest phage families. After characterizing the effects of incubation time and SMALP concentration on the activity of three distinct phages, we present evidence that the interaction between two model phages and SMALPs is specific to bacterial species and the phage receptor molecule. These interactions additionally lead to DNA ejection by nearly all particles at high phage titers. We conclude that SMALPs are a potentially highly useful tool for phage-host interaction studies.IMPORTANCE Bacteriophages (viruses that infect bacteria or phages) impact every microbial community. All phage infections start with the binding of the viral particle to a specific receptor molecule on the host cell surface. Due to its importance in phage infections, this first step is of interest to many phage-related research and applications. However, many phage receptors are difficult to isolate. Styrene maleic acid lipid particles (SMALPs) are a recently developed approach to isolate membrane proteins in their native environment. In this study, we explore SMALPs as a tool to study phage-receptor interactions. We find that different phage species bind to SMALPs, while maintaining specificity to their receptor. We then characterize the time and concentration dependence of phage-SMALP interactions and furthermore show that they lead to genome ejection by the phage. The results presented here show that SMALPs are a useful tool for future studies of phage-receptor interactions.

From classical to new generation approaches: An excursus of -omics methods for investigation of protein-protein interaction networks

Functional Proteomics aims to the identification of in vivo protein-protein interaction (PPI) in order to piece together protein complexes, and therefore, cell pathways involved in biological processes of interest. Over the years, proteomic approaches used for protein-protein interaction investigation have relied on classical biochemical protocols adapted to a global overview of protein-protein interactions, within so-called "interactomics" investigation. In particular, their coupling with advanced mass spectrometry instruments and innovative analytical methods led to make great strides in the PPIs investigation in proteomics. In this review, an overview of protein complexes purification strategies, from affinity purification approaches, including proximity-dependent labeling techniques and cross-linking strategy for the identification of transient interactions, to Blue Native Gel Electrophoresis (BN-PAGE) and Size Exclusion Chromatography (SEC) employed in the "complexome profiling", has been reported, giving a look to their developments, strengths and weakness and providing to readers several recent applications of each strategy. Moreover, a section dedicated to bioinformatic databases and platforms employed for protein networks analyses was also included.

Transcription Factors That Govern Development and Disease: An Achilles Heel in Cancer

Development requires the careful orchestration of several biological events in order to create any structure and, eventually, to build an entire organism. On the other hand, the fate transformation of terminally differentiated cells is a consequence of erroneous development, and ultimately leads to cancer. In this review, we elaborate how development and cancer share several biological processes, including molecular controls. Transcription factors (TF) are at the helm of both these processes, among many others, and are evolutionarily conserved, ranging from yeast to humans. Here, we discuss four families of TFs that play a pivotal role and have been studied extensively in both embryonic development and cancer-high mobility group box (HMG), GATA, paired box (PAX) and basic helix-loop-helix (bHLH) in the context of their role in development, cancer, and their conservation across several species. Finally, we review TFs as possible therapeutic targets for cancer and reflect on the importance of natural resistance against cancer in certain organisms, yielding knowledge regarding TF function and cancer biology.

EGF-activated PI3K/Akt signalling coordinates leucine uptake by regulating LAT3 expression in prostate cancer

Background

Growth factors, such as EGF, activate the PI3K/Akt/mTORC1 signalling pathway, which regulates a distinct program of protein synthesis leading to cell growth. This pathway relies on mTORC1 sensing sufficient levels of intracellular amino acids, such as leucine, which are required for mTORC1 activation. However, it is currently unknown whether there is a direct link between these external growth signals and intracellular amino acid levels. In primary prostate cancer cells, intracellular leucine levels are regulated by L-type amino acid transporter 3 (LAT3/SLC43A1), and we therefore investigated whether LAT3 is regulated by growth factor signalling.

Methods

To investigate how PI3K/Akt signalling regulates leucine transport, prostate cancer cells were treated with different PI3K/Akt inhibitors, or stable knock down of LAT3 by shRNA, followed by analysis of leucine uptake, western blotting, immunofluorescent staining and proximity ligation assay.

Results

Inhibition of PI3K/Akt signalling significantly reduced leucine transport in LNCaP and PC-3 human prostate cancer cell lines, while growth factor addition significantly increased leucine uptake. These effects appeared to be mediated by LAT3 transport, as LAT3 knockdown blocked leucine uptake, and was not rescued by growth factor activation or further inhibited by signalling pathway inhibition. We further demonstrated that EGF significantly increased LAT3 protein levels when Akt was phosphorylated, and that Akt and LAT3 co-localised on the plasma membrane in EGF-activated LNCaP cells. These effects were likely due to stabilisation of LAT3 protein levels on the plasma membrane, with EGF treatment preventing ubiquitin-mediated LAT3 degradation.

Conclusion

Growth factor-activated PI3K/Akt signalling pathway regulates leucine transport through LAT3 in prostate cancer cell lines. These data support a direct link between growth factor and amino acid uptake, providing a mechanism by which the cells rapidly coordinate amino acid uptake for cell growth.

Electronic supplementary material

The online version of this article (10.1186/s12964-019-0400-0) contains supplementary material, which is available to authorized users.

Amino acid substitution in the C-terminal domain of collagen XVII reduces laminin-332 interaction causing mild skin fragility with atrophic scarring

The behavior of a cell depends on how its adhesion molecules interact with the cellular microenvironment. Hemidesmosomal collagen XVII essentially contributes to cell adhesion and modulates keratinocyte directionality and proliferation during skin regeneration, however only little is known about the involved interactions. Here, we used keratinocytes from patients with junctional epidermolysis bullosa with late onset, which exclusively produce a collagen XVII mutant with the p.R1303Q mutation within its extracellular C-terminus. Although this mutant was normally expressed and targeted to the membrane and the expression of integrins α3β1, α6β4 and of laminin-332 was unchanged, the keratinocytes were less adhesive, showed migratory defects and decreased clonogenic growth. Since the p.R1303Q substitution is located within the predicted laminin-332 binding site of collagen XVII, we anticipated an altered collagen XVII-laminin-332 interaction. Indeed, the pR1303Q collagen XVII ectodomain showed decreased binding capability to laminin-332 and was less co-localized with pericellular laminin-332 molecules in cell culture. Thus, aberrant collagen XVII-laminin-332 interaction results in reduced cell adhesion, destabilized cell motility and decreased clonogenicity, which in turn lead to blister formation, delayed wound healing and skin atrophy.

CRISPR-Cas9 a boon or bane: the bumpy road ahead to cancer therapeutics

Genome editing allows for the precise manipulation of DNA sequences in a cell making this technology essential for understanding gene function. CRISPR/Cas9 is a targeted genome-editing platform derived from bacterial adaptive immune system and has been repurposed into a genome-editing tool. The RNA-guided DNA endonuclease, Cas9 can be easily programmed to target new sites by altering its guide RNA sequence, making this technology easier, more efficient, scalable and an indispensable tool in biological research. This technology has helped genetically engineer animal models to understand disease mechanisms and elucidate molecular details that can be exploited for improved therapeutic outcomes. In this review, we describe the CRISPR-Cas9 gene-editing mechanism, CRISPR-screening methods, therapeutic targeting of CRISPR in animal models and in cancer immunotherapy. We also discuss the ongoing clinical trials using this tool, limitations of this tool that might impede the clinical applicability of CRISPR-Cas9 and future directions for developing effective CRISPR-Cas9 delivery systems that may improve cancer therapeutics.

Global Identification of Protein Complexes within the Membrane Proteome of Arabidopsis Roots Using a SEC-MS Approach

Biological processes consist of several consecutive and interacting steps as, for example, in signal transduction cascades or metabolic reaction chains. These processes are regulated by protein-protein interactions and the formation of larger protein complexes, which also occur within biological membranes. To gain a large-scale overview of complex-forming proteins and the composition of such complexes within the cellular membranes of Arabidopsis roots, we use the combination of size-exclusion chromatography and mass spectrometry. First, we identified complex-forming proteins by a retention shift analysis relative to expected retention times of monomeric proteins during size-exclusion chromatography. In a second step we predicted complex composition through pairwise correlation of elution profiles. As result we present an interactome of 963 proteins within cellular membranes of Arabidopsis roots. Identification of complex-forming proteins was highly robust between two independently grown root proteomes. The protein complex composition derived from pairwise correlations of coeluting proteins reproducibly identified stable protein complexes (ribosomes, proteasome, mitochondrial respiratory chain supercomplexes) but showed higher variance between replicates regarding transient interactions (e.g., interactions with kinases) within membrane protein complexes.

Partition of Glutamic Acid-Based Single-Chain and Gemini Amphiphiles into Phospholipid Membranes

Understanding the interactions of amphiphile molecules with biological membranes is very important to many practical applications. Amino acid amphiphiles are a kind of mild surfactants and have many unique performances. However, their interactions with phospholipid membranes have scarcely been studied. This work has studied the interactions of glutamic acid-based gemini amphiphile C₁₂(Glu)₂C₁₂ and single-chain amphiphile C₁₂Glu with the model biomembrane formed by the phospholipid 1,2-dioleoyl- sn-glycero-3-phosphocholine (DOPC). The partition coefficients of C₁₂(Glu)₂C₁₂ and C₁₂Glu into the DOPC vesicles were derived from the observed enthalpy curves obtained by isothermal titration calorimetry at temperatures of 25.0 and 37.0 °C, and pHs of 5.6 and 7.4, corresponding to the skin surface and human physiological conditions. The results from cryogenic transmission electron microscopy, dynamic light scattering, and zeta potential measurements show that the amphiphile molecules form different aggregates, which make the amphiphile molecules exhibit different partition abilities to the DOPC vesicles. For C₁₂Glu, the molecules form shorter wormlike micelles with a lower surface charge at all the pHs and temperatures used, and the partition coefficient of C₁₂Glu into the DOPC vesicles does not change with temperature and pH. Differently, the C₁₂(Glu)₂C₁₂ molecules form fibers with a larger negative charge and belts with a smaller negative charge at pHs 7.4 and 5.6, respectively, no matter what temperature is used. As a result, the partitions of C₁₂(Glu)₂C₁₂ into the DOPC vesicles are markedly different at these two pH values, and the belts at pH 7.4 exhibit a stronger partition ability than the fibrils at pH 5.6. Moreover, at any temperature and pH, C₁₂(Glu)₂C₁₂ shows a stronger partition ability than C₁₂Glu. This work can help to understand the relationship between the molecular structure and aggregate structure of amino acid amphiphiles and their partition abilities into the biomembranes.