Graphene and graphene oxide as a solid matrix for extraction of membrane and membrane-associated proteins

Metal organic layers enabled cell surface engineering coupling biomembrane fusion for dynamic membrane proteome profiling

Systematically dissecting the highly dynamic and tightly communicating membrane proteome of living cells is essential for the system-level understanding of fundamental cellular processes and intricate relationship between membrane-bound organelles constructed through membrane traffic. While extensive efforts have been made to enrich membrane proteins, their comprehensive analysis with high selectivity and deep coverage remains a challenge, especially at the living cell state. To address this problem, we developed the cell surface engineering coupling biomembrane fusion method to map the whole membrane proteome from the plasma membrane to various organelle membranes taking advantage of the exquisite interaction between two-dimensional metal-organic layers and phospholipid bilayers on the membrane. This approach, which bypassed conventional biochemical fractionation and ultracentrifugation, facilitated the enrichment of membrane proteins in their native phospholipid bilayer environment, helping to map the membrane proteome with a specificity of 77% and realizing the deep coverage of the HeLa membrane proteome (5087 membrane proteins). Furthermore, membrane N-phosphoproteome was profiled by integrating the N-phosphoproteome analysis strategy, and the dynamic membrane proteome during apoptosis was deciphered in combination with quantitative proteomics. The features of membrane protein N-phosphorylation modifications and many differential proteins during apoptosis associated with mitochondrial dynamics and ER homeostasis were found. The method provided a simple and robust strategy for efficient analysis of membrane proteome, offered a reliable platform for research on membrane-related cell dynamic events and expanded the application of metal-organic layers.

Tailoring Oxygen-Containing Groups on Graphene for Ratiometric Electrochemical Measurements of Ascorbic Acid in Living Subacute Parkinson's Disease Mouse Brains

Ascorbic acid (AA), a major antioxidant in the central nervous system (CNS), is involved in withstanding oxidative stress that plays a significant role in the pathogenesis of Parkinson's disease (PD). Exploring the AA disturbance in the process of PD is of great value in understanding the molecular mechanism of PD. Herein, by virtue of a carbon fiber electrode (CFE) as a matric electrode, a three-step electrochemical process for tailoring oxygen-containing groups on graphene was well designed: potentiostatic deposition was carried out to fabricate graphene oxide on CFE, electrochemical reduction that assisted in removing the epoxy groups accelerated the electron transfer kinetics of AA oxidation, and electrochemical oxidation that increased the content of the carbonyl group (C═O) generated an inner-reference signal. The mechanism was solidified by ab initio calculations by comparing AA absorption on defected models of graphene functionalized with different oxygen groups including carboxyl, hydroxyl, epoxy, and carbonyl. It was found that epoxy groups would hinder the physical absorption of AA onto graphene, while other functional groups would be beneficial to it. Biocompatible polyethylenedioxythiophene (PEDOT) was further rationally assembled to improve the antifouling property of graphene. As a result, a new platform for ratiometric electrochemical measurements of AA with high sensitivity, excellent selectivity, and reproducibility was established. In vivo determination of AA levels in different regions of living mouse brains by the proposed method demonstrated that AA decreased remarkably in the hippocampus and cortex of a subacute PD mouse than those of a normal mouse.

Metal Organic Framework Nanomaterial-Based Extraction and Proteome Analysis of Membrane and Membrane-Associated Proteins

Membrane proteins (MPs) play a key role in various biological processes, while difficulties still exist in the extraction because of their inherent low abundance and poor solubility caused by high hydrophobicity. Metal organic framework (MOF) materials with good hydrophobic properties have the ability to absorb MPs, especially zeolitic imidazolate framework (ZIF) materials. Here, two MOF materials (ZIF-8 and ZIF-67) were compared for MP extraction, and our results revealed that higher yield was obtained with ZIF-67. After method development, the optimal enrichment effect was obtained when the mass ratio of proteins and ZIF-67 reached 1:20 with 100 mM NaCl in 20% ethanol at 4 °C and pH 9.0. When compared with a commercial kit, the extraction yield increased by 88.11% and the average number of identified MPs elevated by 29.17% with the developed ZIF method. Normal lung cell MRC5 was employed to verify the effectiveness of the ZIF method. Results showed 45.13% increase in yield and 22.88% increase in average number of identified MPs by the ZIF method. Our method was further applied to the enrichment of MPs for high-metastatic (95D) and low-metastatic (95C) human lung cancer cells. A total of 1732 (95D) and 1711 (95C) MPs were identified, among which 710 MPs were dysregulated significantly; 441 upregulated MPs in 95D cells were found to be closely related to the growth, proliferation, and migration of lung cancer cells. Our results collectively demonstrated that ZIF-67 was an ideal material for MP extraction, which might be helpful for analysis of cancer proteomics and discovery of cancer migration associated MPs.

Understanding the interactions between inorganic-based nanomaterials and biological membranes

The interactions between inorganic-based nanomaterials (NMs) and biological membranes are among the most important phenomena for developing NM-based therapeutics and resolving nanotoxicology. Herein, we introduce the structural and functional effects of inorganic-based NMs on biological membranes, mainly the plasma membrane and the endomembrane system, with an emphasis on the interface, which involves highly complex networks between NMs and biomolecules (such as membrane proteins and lipids). Significant efforts have been devoted to categorizing and analyzing the interaction mechanisms in terms of the physicochemical characteristics and biological effects of NMs, which can directly or indirectly influence the effects of NMs on membranes. Importantly, we summarize that the biological membranes act as platforms and thereby mediate NMs-immune system contacts. In this overview, the existing challenges and potential applications in the areas are addressed. A strong understanding of the discussed concepts will promote therapeutic NM designs for drug delivery systems by leveraging the NMs-membrane interactions and their functions.

Magnetic cucurbit[6]uril-based hypercrosslinked polymers for efficient enrichment of ubiquitin

The design and preparation of magnetic cucurbit[6]uril hypercrosslinked with polymers are described. The materials have a large specific surface, abundant mesopores and cavities, and display superparamagnetism. They were applied to the enrichment of ubiquitinated peptides from standard protein digests. Following desorption with 0.15% TFA, the peptides were quantified by MALDI-TOF MS. The method has a detection limit of 2 fmol·μL^-1 and a mass ratio selectivity of 1:5000 as shown for ubiquitin and bovine serum albumin. The materials enable selective capture of ubiquitinated peptides from genuine samples comprising of oyster mushroom and human serum. This demonstrates their potential for the analysis of low-level ubiquitin in complex samples. Graphical abstract Schematic presentation for the synthesis of magnetic cucurbit[6]urils hypercrosslinked polymers (MagCB[6]-HCPs).

Thermoresponsive Amphiphilic Functionalization of Thermally Reduced Graphene Oxide to Study Graphene/Bacteria Hydrophobic Interactions

An understanding of the interactions of 2D nanomaterials with pathogens is of vital importance to developing and controlling their antimicrobial properties. In this work, the interaction of functionalized graphene with tunable hydrophobicity and bacteria is investigated. Poly(ethylene glycol)- block-(poly- N-isopropylacrylamide) copolymer (PEG- b-PNIPAM) with the triazine joint point was attached to the graphene surface by a nitrene [2 + 1] cycloaddition reaction. By thermally switching between hydrophobic and hydrophilic states, functionalized graphene sheets were able to bind to bacteria. Bacteria were eventually disrupted when the functionality was switched to the hydrophobic state. On the basis of measuring the different microscopy methods and a live/dead viability assay, it was found that Escherichia coli ( E. coli) bacteria are more susceptible to hydrophobic interactions than B. cereus bacteria, under the same conditions. Our investigations confirm that hydrophobic interaction is one of the main driving forces at the presented graphene/bacteria interfaces and promotes the antibacterial activity of graphene derivatives significantly.

Applications of three-dimensional graphenes for preconcentration, extraction, and sorption of chemical species: a review

This review (with 115 refs) summarizes applications of 3-dimensional graphene (3DGs) and its derivatives in the fields of preconcentration, extraction, and sorption. Following an introduction into the field (including a definition of the materials treated here), the properties and synthetic strategies for 3DGs are described. The next section covers applications of 3DG-based adsorbents in solid phase extraction of organic species including drugs, phthalate esters, chlorophenols, aflatoxins, insecticides, and pesticides. Another section treats applications of 3DGs in solid phase microextraction of species such as polycyclic aromatic hydrocarbons, alcohols, and pesticides. We also describe how the efficiency of assays may be improved by using these materials as a sorbent. A final section covers conclusions and perspectives. Graphical abstract Graphical abstract contains poor quality and small text inside the artwork. Please do not re-use the file that we have rejected or attempt to increase its resolution and re-save. It is originally poor, therefore, increasing the resolution will not solve the quality problem. We suggest that you provide us the original format. We prefer replacement figures containing vector/editable objects rather than embedded images. Preferred file formats are eps, ai, tiff and pdf.Tiff file of graphical abstract was attached. Schematic presentation of synthesis of three-dimensional graphene (3DG) from two-dimensional graphene (2DG) with self-assembly, template-assisted and direct deposition methods. Application of 3DG-based nanoadsorbents in direct immersion-solid phase microextraction (DI-SPME), headspace-SPME (HS-SPME), magnetic-solid phase extraction (Magnetic-SPE), dispersive-SPE, and magnetic sheet-SPE.

A porous graphene sorbent coated with titanium(IV)-functionalized polydopamine for selective lab-in-syringe extraction of phosphoproteins and phosphopeptides

A novel polydopamine coated three-dimensional porous graphene aerogel sorbent carrying immobilized titanium(IV) ions (denoted as Ti⁴⁺@PDA@GA) was fabricated without using an organic solvent. The material is shown to be a viable carbon foam type of monolithic sorbent for selective lab-in-syringe enrichment of phosphoproteins and phosphopeptides. The phosphoproteins can be separated from a sample by aspiration and then bind to the sorbent. The analytes then can be dispensed within 5 min. The weight percent of titanium in the monolith typically is 14%, and the absorption capacities for the model proteins β-casein and κ-casein are 1300 and 1345 mg g^-1, respectively. The absorption capacities for nonphosphoproteins are much smaller, typically 160 mg g^-1 for β-lactoglobulin, 125 mg g^-1 for bovine serum, and 4.8 mg g^-1 for lysozyme. The results demonstrate that the selectivity for phosphoproteins was excellent on multiple biological samples including standard protein mixtures, spiked human blood serum, and drinking milk. The selective enrichment of phosphopeptides also makes the method a promising tool in phosphoproteomics. Graphical abstract Schematic of a polydopamine coated three-dimensional porous graphene aerogel for immobilization of titanium(IV) ions. The material served as a monolithic sorbent for selective enrichment of phosphopeptides and phosphoproteins from biological samples. The enrichment process can be carried out conveniently using a lab-in-syringe way.