Protein-fragment complementation assays for large-scale analysis of protein-protein interactions

Decoding the functional impact of the cancer genome through protein-protein interactions

Acquisition of genomic mutations enables cancer cells to gain fitness advantages under selective pressure and, ultimately, leads to oncogenic transformation. Interestingly, driver mutations, even within the same gene, can yield distinct phenotypes and clinical outcomes, necessitating a mutation-focused approach. Conversely, cellular functions are governed by molecular machines and signalling networks that are mostly controlled by protein-protein interactions (PPIs). The functional impact of individual genomic alterations could be transmitted through regulated nodes and hubs of PPIs. Oncogenic mutations may lead to modified residues of proteins, enabling interactions with other proteins that the wild-type protein does not typically interact with, or preventing interactions with proteins that the wild-type protein usually interacts with. This can result in the rewiring of molecular signalling cascades and the acquisition of an oncogenic phenotype. Here, we review the altered PPIs driven by oncogenic mutations, discuss technologies for monitoring PPIs and provide a functional analysis of mutation-directed PPIs. These driver mutation-enabled PPIs and mutation-perturbed PPIs present a new paradigm for the development of tumour-specific therapeutics. The intersection of cancer variants and altered PPI interfaces represents a new frontier for understanding oncogenic rewiring and developing tumour-selective therapeutic strategies.

Humanized Candida and NanoBiT Assays Expedite Discovery of Bdf1 Bromodomain Inhibitors With Antifungal Potential

The fungal Bromodomain and Extra-Terminal (BET) protein Bdf1 is a potential antifungal target against invasive fungal infections. However, the need to selectively inhibit both Bdf1 bromodomains (BDs) over human orthologs and the lack of molecular tools to assess on-target antifungal efficacy hamper efforts to develop Bdf1 BD inhibitors as antifungal therapeutics. This study reports a phenyltriazine compound that inhibits both Bdf1 BDs from the human fungal pathogen Candida glabrata with selectivity over the orthologous BDs from the human BET protein Brd4. On-target antifungal activity is established by devising two yeast-based inhibition assays: a growth assay using humanized Candida strains in which the Bdf1 BDs are replaced by their Brd4 counterparts, and a NanoBiT assay that evaluates the BD-mediated association of Bdf1 with chromatin. These assays additionally enable the discovery that BET inhibitor I-BET726 targets both Bdf1 BDs, inhibits the growth of a broad spectrum of Candida species, including antifungal-resistant clinical isolates, and displays efficacy in an invertebrate animal model of infection. These collective findings highlight the promising potential of Bdf1 BD inhibitors as an innovative class of antifungal therapeutics and the pivotal role of yeast-based assay development toward achieving this end.

Accurate and sensitive interactome profiling using a quantitative protein-fragment complementation assay

An accurate description of protein-protein interaction (PPI) networks is key to understanding the molecular mechanisms underlying cellular systems. Here, we constructed genome-wide libraries of yeast strains to systematically probe protein-protein interactions using NanoLuc Binary Technology (NanoBiT), a quantitative protein-fragment complementation assay (PCA) based on the NanoLuc luciferase. By investigating an array of well-documented PPIs as well as the interactome of four proteins with varying levels of characterization-including the well-studied nonsense-mediated mRNA decay (NMD) regulator Upf1 and the SCF complex subunits Cdc53 and Met30-we demonstrate that ratiometric NanoBiT measurements enable highly precise and sensitive mapping of PPIs. This work provides a foundation for employing NanoBiT in the assembly of more comprehensive and accurate protein interaction maps as well as in their functional investigation.

ReLo is a simple and rapid colocalization assay to identify and characterize direct protein-protein interactions

The characterization of protein-protein interactions (PPIs) is fundamental to the understanding of biochemical processes. Many methods have been established to identify and study direct PPIs; however, screening and investigating PPIs involving large or poorly soluble proteins remains challenging. Here, we introduce ReLo, a simple, rapid, and versatile cell culture-based method for detecting and investigating interactions in a cellular context. Our experiments demonstrate that ReLo specifically detects direct binary PPIs. Furthermore, we show that ReLo bridging experiments can also be used to determine the binding topology of subunits within multiprotein complexes. In addition, ReLo facilitates the identification of protein domains that mediate complex formation, allows screening for interfering point mutations, and it is sensitive to drugs that mediate or disrupt an interaction. In summary, ReLo is a simple and rapid alternative for the study of PPIs, especially when studying structurally complex proteins or when established methods fail.

Nanobody engineering for SARS-CoV-2 neutralization and detection

In response to the ongoing COVID-19 pandemic, the quest for coronavirus inhibitors has inspired research on a variety of small proteins beyond conventional antibodies, including robust single-domain antibody fragments, i.e., "nanobodies." Here, we explore the potential of nanobody engineering in the development of antivirals and diagnostic tools. Through fusion of nanobody domains that target distinct binding sites, we engineered multimodular nanobody constructs that neutralize wild-type SARS-CoV-2 and the Alpha and Delta variants at high potency, with IC50 values as low as 50 pM. Despite simultaneous binding to distinct epitopes, Beta and Omicron variants were more resistant to neutralization by the multimodular nanobodies, which highlights the importance of accounting for antigenic drift in the design of biologics. To further explore the applications of nanobody engineering in outbreak management, we present an assay based on fusions of nanobodies with fragments of NanoLuc luciferase that can detect sub-nanomolar quantities of the SARS-CoV-2 spike protein in a single step. Our work showcases the potential of nanobody engineering to combat emerging infectious diseases.

IMPORTANCE

Nanobodies, small protein binders derived from the camelid antibody, are highly potent inhibitors of respiratory viruses that offer several advantages over conventional antibodies as candidates for specific therapies, including high stability and low production costs. In this work, we leverage the unique properties of nanobodies and apply them as building blocks for new therapeutic and diagnostic tools. We report ultra-potent SARS-CoV-2 inhibition by engineered nanobodies comprising multiple modules in structure-guided combinations and develop nanobodies that carry signal molecules, allowing rapid detection of the SARS-CoV-2 spike protein. Our results highlight the potential of engineered nanobodies in the development of effective countermeasures, both therapeutic and diagnostic, to manage outbreaks of emerging viruses.

Multiparameter screen optimizes immunoprecipitation

Immunoprecipitation (IP) coupled with mass spectrometry effectively maps protein-protein interactions when genome-wide, affinity-tagged cell collections are used. Such studies have recorded significant portions of the compositions of physiological protein complexes, providing draft 'interactomes'; yet many constituents of protein complexes still remain uncharted. This gap exists partly because high-throughput approaches cannot optimize each IP. A key challenge for IP optimization is stabilizing in vivo interactions during the transfer from cells to test tubes; failure to do so leads to the loss of genuine interactions during the IP and subsequent failure to detect. Our high-content screening method explores the relationship between in vitro chemical conditions and IP outcomes, enabling rapid empirical optimization of conditions for capturing target macromolecular assemblies.

Screening for molecular glues - Challenges and opportunities

Molecular glues are small molecules, typically smaller than PROTACs, and usually with improved physicochemical properties that aim to stabilise the interaction between two proteins. Most often this approach is used to improve or induce an interaction between the target and an E3 ligase, but other interactions which stabilise interactions to increase activity or to inhibit binding to a natural effector have also been demonstrated. This review will describe the effects of induced proximity, discuss current methods used to identify molecular glues and introduce approaches that could be adapted for molecular glue screening.

A fluorescence-based binding assay for proteins using the cell surface as a sensing platform

Protein-protein interaction (PPI) analysis is very important for elucidating the functions of proteins because many proteins execute their functions in living cells by interacting with one another. In PPI analysis, methods using the sensor chips are widely employed to obtain quantitative data. However, these methods require that the target proteins be immobilized on the sensor chips, and the immobilization processes can affect the binding of the target proteins to their binding partners. In the present work, we propose a PPI analysis system in which the surface of the living cells is utilized as a sensing platform. In our approach, the target protein is displayed on the cell surface by expressing it as a fusion protein with a membrane protein, and the PPI analysis is then conducted by applying its binding partner labeled with a fluorescent dye to the cell surface. We have constructed a model of this binding analysis system using the interaction between biotin protein ligase (BPL) and biotin carboxyl carrier protein (BCCP), where BCCP was displayed on the cell surface and BPL labeled with fluorescein was applied to the cell surface. Here, a red fluorescent protein, mApple, was attached to the C-terminus of the fusion protein of BCCP with a membrane protein. We evaluated the binding level of the labeled BPL by using the intensity ratios of fluorescence from fluorescein to that from mApple. We found that the binding level of the labeled BPL was stably evaluated at least across 60 min observation period and estimated the binding dissociation constant between BPL and BCCP by equilibrium analysis to be 0.33 ± 0.05 μM.

Tri-part NanoLuc as a new split technology with potential applications in chemical biology: a mini-review

For several decades, researchers have been using protein-fragment complementation assay (PCA) approaches for biosensing to study protein-protein interaction for a variety of aims, including viral infection, cellular apoptosis, G protein coupled receptor (GPCR) signaling, drug and substrate screening, and protein aggregation and protein editing by CRISPR/Cas9. As a reporter, NanoLuc (NLuc), a smaller and the brightest engineered luciferase derived from deep-sea shrimp Oplophorus gracilirostris, has been found to have many benefits over other luminescent enzymes in PCA. Inspired by the split green fluorescent protein (GFP) and its β-barrel structure, two split NLuc consisting of peptide fragments have been reported including the binary and ternary NLuc systems. NanoBiT® (large fragment + peptide) has been used extensively. In contrast, tripart split NLuc (large fragment + 2 peptides) has been applied and hardly used, while it has some advantages over NanoBiT in some studies. Nevertheless, tripart NLuc has some drawbacks and challenges to overcome but has several potential characteristics to become a multifunctional and powerful tool. In this review, several aspects of tripart NLuc are studied and a brief comparison with NanoBiT® is given.

A protein aggregation platform that distinguishes oligomers from amyloid fibrils

Deposition of aggregated proteins is a pathological feature in many neurodegenerative disorders such as Alzheimer's and Parkinson's. In addition to insoluble amyloid fibrils, protein aggregation leads to the formation of soluble oligomers, which are more toxic and pathogenic than fibrils. However, it is challenging to screen for inhibitors targeting oligomers due to the overlapping processes of oligomerization and fibrillization. Here we report a protein aggregation platform that uses intact and split TEM-1 β-lactamase proteins as reporters of protein aggregation. The intact β-lactamase fused with an amyloid protein can report the overall protein aggregation, which leads to loss of lactamase activity. On the other hand, reconstitution of active β-lactamase from the split lactamase construct requires the formation of amyloid oligomers, making the split lactamase system sensitive to oligomerization. Using Aβ, a protein that forms amyloid plaques in Alzheimer's disease, we show that the growth curves of bacterial cells expressing either intact or split lactamase-Aβ fusion proteins can report changes in the Aβ aggregation. The cell lysate lactamase activity assays show that the oligomer fraction accounts for 20% of total activity for the split lactamase-Aβ construct, but only 3% of total activity for the intact lactamase-Aβ construct, confirming the sensitivity of the split lactamase to oligomerization. The combination of the intact and split lactamase constructs allows the distinction of aggregation modulators targeting oligomerization from those targeting overall aggregation. These low-cost bacterial cell-based and biochemical assays are suitable for high-throughput screening of aggregation inhibitors targeting oligomers of various amyloid proteins.

Investigating the dynamics of protein-protein interactions in plants

Both stable and transient protein interactions play an important role in the complex assemblies required for the proper functioning of living cells. Several methods have been developed to monitor protein-protein interactions in plants. However, the detection of dynamic protein complexes is very challenging, with few technologies available for this purpose. Here, we developed a new platform using the plant UBIQUITIN promoter to drive transgene expression and thereby to detect protein interactions in planta. Typically, to decide which side of the protein to link the tags, the subcellular localization of the protein fused either N-terminal or C-terminal mCitrine was firstly confirmed by using eight different specific mCherry markers. Following stable or transient protein expression in plants, the protein interaction network was detected by affinity purification mass spectrometry. These interactions were subsequently confirmed by bimolecular fluorescence complementation (BiFC), bioluminescence resonance energy transfer and co-immunoprecipitation assays. The dynamics of these interactions were monitored by Förster resonance energy transfer (FRET) and split-nano luciferase, whilst the ternary protein complex association was monitored by BiFC-FRET. Using the canonical glycolytic metabolon as an example, the interaction between these enzymes was characterized under conditions that mimic physiologically relevant energy statuses.

New Dielis species and structural dichotomy of the mitochondrial cox2 gene in Scoliidae wasps

Some mitochondrial protein-coding genes of protists and land plants have split over the course of evolution into complementary genes whose products can form heteromeric complexes that likely substitute for the undivided proteins. One of these genes, cox2, has also been found to have split in animals, specifically in Scoliidae wasps (Hymenoptera: Apocrita) of the genus Dielis (Campsomerini), while maintaining the conventional structure in related Scolia (Scoliini). Here, a hitherto unrecognized Nearctic species of Dielis, D. tejensis, is described based on its phenotype and mtDNA. The mitogenome of D. tejensis sp. nov. differs from that of the sympatric sibling species Dielis plumipes fossulana by the reduced size of the cox2-dividing insert, which, however, still constitutes the fifth part of the mtDNA; an enlarged nad2-trnW intergenic region; the presence of two trnK^ttt paralogues; and other features. Both species of Dielis have a unique insertion of a threonine in COXIIA, predicted to be involved in COXIIA-COXIIB docking, and substitutions of two hydrophobic residues with redox-active cysteines around the Cu_A centre in COXIIB. Importantly, the analysis of mtDNA from another Campsomerini genus, Megacampsomeris, shows that its cox2 gene is also split. The presented data highlight evolutionary processes taking place in hymenopteran mitogenomes that do not fall within the mainstream of animal mitochondrion evolution.

A growth-based platform for detecting domain-peptide interactions in the cytoplasm of mammalian cells

Development of a method for detecting protein-protein interactions (PPIs) in living cells is important for therapeutic drug screening against various diseases including infectious diseases. We have recently developed a method named SOS localization-based interaction screening (SOLIS), in which we designed membrane-anchored and SOS-fused chimeric proteins, whose PPI-dependent association triggers membrane localization of the SOS-fused chimeric protein, activates the Ras/MAPK pathway, and induces cell growth. While SOLIS was able to detect relatively strong PPIs, further sensitivity was required for detecting intracellular endogenous PPIs typically having a micromolar order of dissociation constant (K_d). Here we develop high-sensitive SOLIS (H-SOLIS) that could universally detect PPIs with lower affinities. In order to improve the sensitivity, H-SOLIS introduces a heterodimeric helper interaction, in which addition of a small-molecule helper ligand could accommodate association of the two chimeric proteins and regulate the sensitivity. Four types of domain-peptide interactions having known K_d values are employed to examine the versatility and detection limit of H-SOLIS. Consequently, the heterodimer-inducible helper ligand dramatically enhances detection sensitivity, lowering the detection limit to a ten-micromolar order of K_d. Thus, H-SOLIS could be a platform to detect disease-related domain-peptide interactions for drug discovery screening.

CDNF Interacts with ER Chaperones and Requires UPR Sensors to Promote Neuronal Survival

Cerebral dopamine neurotrophic factor (CDNF) is a neurotrophic factor that has beneficial effects on dopamine neurons in both in vitro and in vivo models of Parkinson's disease (PD). CDNF was recently tested in phase I-II clinical trials for the treatment of PD, but the mechanisms underlying its neuroprotective properties are still poorly understood, although studies have suggested its role in the regulation of endoplasmic reticulum (ER) homeostasis and the unfolded protein response (UPR). The aim of this study was to investigate the mechanism of action of CDNF through analyzing the involvement of UPR signaling in its anti-apoptotic function. We used tunicamycin to induce ER stress in mice in vivo and used cultured primary neurons and found that CDNF expression is regulated by ER stress in vivo and that the involvement of UPR pathways is important for the neuroprotective function of CDNF. Moreover, we used AP-MS and BiFC to perform the first interactome screening for CDNF and report novel binding partners of CDNF. These findings allowed us to hypothesize that CDNF protects neurons from ER-stress-inducing agents by modulating UPR signaling towards cell survival outcomes.

Methods for the directed evolution of biomolecular interactions

Noncovalent interactions between biomolecules such as proteins and nucleic acids coordinate all cellular processes through changes in proximity. Tools that perturb these interactions are and will continue to be highly valuable for basic and translational scientific endeavors. By taking cues from natural systems, such as the adaptive immune system, we can design directed evolution platforms that can generate proteins that bind to biomolecules of interest. In recent years, the platforms used to direct the evolution of biomolecular binders have greatly expanded the range of types of interactions one can evolve. Herein, we review recent advances in methods to evolve protein-protein, protein-RNA, and protein-DNA interactions.

Split-enzyme immunoassay to monitor EGFR-HER2 heterodimerization on cell surfaces

Over 30,000 protein-protein interactions with pathological implications have been identified; yet, discovering and investigating drugs that target these specific interactions is greatly limited by the inability to monitor native protein-protein interactions (PPIs) efficiently. The two most frequently used tools to monitor PPIs, resonance-energy transfer (RET) assays and protein complementation assays (PCA), face significant limitations. RET assays have a narrow working range of 10 to 50 Å, while PCA require permanent attachment of a reporter probe to a protein of interest by chemical conjugation or genetic engineering. We developed a non-invasive assay platform to measure PPIs without modifications to the proteins of interest and is functional at a greater working range than RET assays. We demonstrate our approach by monitoring the EGFR-HER2 heterodimerization on relevant cell surfaces, utilizing various EGFR- and HER2-specific binders (e.g., Fab, DARPin, and VHH) fused with small fragments of a tri-part split-luciferase derived from NanoLuc®. Following independent binding of the binder fusions to their respective targets, the dimerization of EGFR and HER2 induces complementation of the luciferase fragments into a functional native structure, producing glow-type luminescence. We have confirmed the functionality of the platform to monitor EGFR-HER2 dimerization induction and inhibition. STATEMENT OF SIGNIFICANCE: We describe a platform technology for rapid monitoring of protein-protein interactions (PPIs). Our approach is uses a luciferase split into three parts - two short peptide "tags" and a large third fragment. Each of the short peptides can be fused to antibodies which bind to domains of a target antigens which orients the two tags and facilitates refolding of an active enzyme. To our knowledge this is the first example of a split-enzyme used to monitor PPIs without requiring any modification of the target proteins. We demonstrate our approach on the important PPI of HER2 and EGFR. Significantly, we quantify stimulation and inhibition of these partners, opening the possibility of using our approach to assess potential drugs without engineering cells.