Development of a biochemical and biophysical suite for integral membrane protein targets: A review

Evaluation of Membrane Mimetics for the Native Ion Mobility─Mass Spectrometry Analysis of Membrane Proteins

Membrane protein (MP) structures and functions are intricately linked to their surrounding membrane environments and their respective lipid compositions in addition to influences exerted by unique membrane microdomains (i.e., lipid rafts). Owing to the complexity of their native environments, MPs pose significant challenges to structural biology due to their intrinsic hydrophobic nature rendering them incompatible with aqueous conditions commonly deployed during sample preparation. To overcome these solubility issues, MP studies commonly utilize detergent micelles. In recent years, numerous efforts have been directed toward developing membrane mimetics to facilitate successful solubilization and stabilization of MPs. Collision-induced dissociation (CID) can be employed to remove surrounding molecules from MPs during native mass spectrometry (nMS) experiments, and such methods can be used to evaluate previously inaccessible MPs. However, the differential effects of various membrane mimetics on MP structure and stability remain largely unexplored. In this study, we evaluate a range of MPs, including both transmembrane and monotopic variants, solubilized in detergent micelles, mixed lipid bicelles, and nanodisc mimetics. Our findings reveal significant differences in collision induced unfolding (CIU) features, stabilities, collision cross sections (CCS), and RMSD comparisons with values exceeding 26%. These results underscore the importance of considering the choice of membrane mimetics when studying MP structure.

Discovery of Therapeutic Antibodies Targeting Complex Multi-Spanning Membrane Proteins

Complex integral membrane proteins, which are embedded in the cell surface lipid bilayer by multiple transmembrane spanning polypeptides, encompass families of proteins that are important target classes for drug discovery. These protein families include G protein-coupled receptors, ion channels, transporters, enzymes, and adhesion molecules. The high specificity of monoclonal antibodies and the ability to engineer their properties offers a significant opportunity to selectively bind these target proteins, allowing direct modulation of pharmacology or enabling other mechanisms of action such as cell killing. Isolation of antibodies that bind these types of membrane proteins and exhibit the desired pharmacological function has, however, remained challenging due to technical issues in preparing membrane protein antigens suitable for enabling and driving antibody drug discovery strategies. In this article, we review progress and emerging themes in defining discovery strategies for a generation of antibodies that target these complex membrane protein antigens. We also comment on how this field may develop with the emerging implementation of computational techniques, artificial intelligence, and machine learning.

Mass Spectrometry Methods for Measuring Protein Stability

Mass spectrometry is a central technology in the life sciences, providing our most comprehensive account of the molecular inventory of the cell. In parallel with developments in mass spectrometry technologies targeting such assessments of cellular composition, mass spectrometry tools have emerged as versatile probes of biomolecular stability. In this review, we cover recent advancements in this branch of mass spectrometry that target proteins, a centrally important class of macromolecules that accounts for most biochemical functions and drug targets. Our efforts cover tools such as hydrogen-deuterium exchange, chemical cross-linking, ion mobility, collision induced unfolding, and other techniques capable of stability assessments on a proteomic scale. In addition, we focus on a range of application areas where mass spectrometry-driven protein stability measurements have made notable impacts, including studies of membrane proteins, heat shock proteins, amyloidogenic proteins, and biotherapeutics. We conclude by briefly discussing the future of this vibrant and fast-moving area of research.

Biological Functions and Molecular Mechanisms of MiR-608 in Cancer

In recent years, microRNAs (miRNAs) have attracted much attention because of their prominent role in cancer. An increasing number of studies have shown that miRNAs play an important role in a variety of tumors. miR-608 has been reported to be decreased in cancers, especially in solid tumors. miR-608 is regarded as a tumor suppressor, which has been verified through a large number of experiments both in vivo and in vitro. miR-608 participates in many biological processes, including cell proliferation, invasion, migration, and apoptosis, by inhibiting transmembrane proteins and many signaling pathways. Here, we summarize the expression profile and biological functions and mechanism of miR-608, suggesting that miR-608 is an ideal diagnostic and prognostic biomarker and a treatment target for cancer.

Recent advances in polymeric nanostructured ion selective membranes for biomedical applications

Nano structured ion-selective membranes (ISMs) are very attractive materials for a wide range of sensing and ion separation applications. The present review focuses on the design principles of various ISMs; nanostructured and ionophore/ion acceptor doped ISMs, and their use in biomedical engineering. Applications of ISMs in the biomedical field have been well-known for more than half a century in potentiometric analysis of biological fluids and pharmaceutical products. However, the emergence of nanotechnology and sophisticated sensing methods assisted in miniaturising ion-selective electrodes to needle-like sensors that can be designed in the form of implantable or wearable devices (smartwatch, tattoo, sweatband, fabric patch) for health monitoring. This article provides a critical review of recent advances in miniaturization, sensing and construction of new devices over last decade (2011-2021). The designing of tunable ISM with biomimetic artificial ion channels offered intensive opportunities and innovative clinical analysis applications, including precise biosensing, controlled drug delivery and early disease diagnosis. This paper will also address the future perspective on potential applications and challenges in the widespread use of ISM for clinical use. Finally, this review details some recommendations and future directions to improve the accuracy and robustness of ISMs for biomedical applications.

Carbocation Footprinting of Soluble and Transmembrane Proteins

Here, we introduce carbocations (R3C+) as laser-initiated footprinting reagents for proteins. We screened seven candidates and selected trifluomethoxy benzyl bromide (TFBB) as an effective precursor for the electrophilic trifluomethoxy benzyl carbocation (TFB+) under laser (248 nm) irradiation on the fast photochemical oxidation of proteins (FPOP) platform. Initial results demonstrate that this electrophilic cation reagent affords residue coverage of nucleophilic amino acids including H, W, M, and S. Further, the addition of TFB+ increases the hydrophobicity of the peptides so that separation of isomeric peptide products by reversed-phase LC is improved, suggesting opportunities for subresidue footprinting. Comparison of apo- and holo-myoglobin footprints shows that the TFB+ footprinting is sensitive to protein conformational change and solvent accessibility. Interestingly, because the TFB+ is amphiphilic, the reagent can potentially footprint membrane proteins as demonstrated for vitamin K epoxide reductase (VKOR) stabilized in a micelle. Not only does footprinting of the extra-membrane domain occur, but also some footprinting of the hydrophobic transmembrane domain is achieved owing to the interaction of TFB+ with the micelle. Carbocation precursors are stable and amenable for tailoring their properties and those of the incipient carbocation, enabling targeting their soluble or membrane-associated or embedded regions and distinguishing between the extra- and trans-membrane domains of membrane proteins.

Cys-labeling kinetics of membrane protein GlpG: a role for specific SDS binding and micelle changes?

Empirically, α-helical membrane protein folding stability in surfactant micelles can be tuned by varying the mole fraction MF^SDS of anionic (sodium dodecyl sulfate (SDS)) relative to nonionic (e.g., dodecyl maltoside (DDM)) surfactant, but we lack a satisfying physical explanation of this phenomenon. Cysteine labeling (CL) has thus far only been used to study the topology of membrane proteins, not their stability or folding behavior. Here, we use CL to investigate membrane protein folding in mixed DDM-SDS micelles. Labeling kinetics of the intramembrane protease GlpG are consistent with simple two-state unfolding-and-exchange rates for seven single-Cys GlpG variants over most of the explored MF^SDS range, along with exchange from the native state at low MF^SDS (which inconveniently precludes measurement of unfolding kinetics under native conditions). However, for two mutants, labeling rates decline with MF^SDS at 0-0.2 MF^SDS (i.e., native conditions). Thus, an increase in MF^SDS seems to be a protective factor for these two positions, but not for the five others. We propose different scenarios to explain this and find the most plausible ones to involve preferential binding of SDS monomers to the site of CL (based on computational simulations) along with changes in size and shape of the mixed micelle with changing MF^SDS (based on SAXS studies). These nonlinear impacts on protein stability highlights a multifaceted role for SDS in membrane protein denaturation, involving both direct interactions of monomeric SDS and changes in micelle size and shape along with the general effects on protein stability of changes in micelle composition.

Neural network strategies for plasma membrane selection in fluorescence microscopy images

In recent years, there has been an explosion of fluorescence microscopy studies of live cells in the literature. The analysis of the images obtained in these studies often requires labor-intensive manual annotation to extract meaningful information. In this study, we explore the utility of a neural network approach to recognize, classify, and select plasma membranes in high-resolution images, thus greatly speeding up data analysis and reducing the need for personnel training for highly repetitive tasks. Two different strategies are tested: 1) a semantic segmentation strategy, and 2) a sequential application of an object detector followed by a semantic segmentation network. Multiple network architectures are evaluated for each strategy, and the best performing solutions are combined and implemented in the Recognition Of Cellular Membranes software. We show that images annotated manually and with the Recognition Of Cellular Membranes software yield identical results by comparing Förster resonance energy transfer binding curves for the membrane protein fibroblast growth factor receptor 3. The approach that we describe in this work can be applied to other image selection tasks in cell biology.

Generating therapeutic monoclonal antibodies to complex multi-spanning membrane targets: Overcoming the antigen challenge and enabling discovery strategies

Complex integral membrane proteins, which are embedded in the cell surface lipid bilayer by multiple transmembrane spanning helices, encompass families of proteins which are important target classes for drug discovery. These protein families include G protein-coupled receptors, ion channels and transporters. Although these proteins have typically been targeted by small molecule drugs and peptides, the high specificity of monoclonal antibodies offers a significant opportunity to selectively modulate these target proteins. However, it remains the case that isolation of antibodies with desired pharmacological function(s) has proven difficult due to technical challenges in preparing membrane protein antigens suitable to support antibody drug discovery. In this review recent progress in defining strategies for generation of membrane protein antigens is outlined. We also highlight antibody isolation strategies which have generated antibodies which bind the membrane protein and modulate the protein function.