Protein-Fragment Complementation Assays for Large-Scale Analysis, Functional Dissection, and Spatiotemporal Dynamic Studies of Protein-Protein Interactions in Living Cells

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.

SUMO-ID: A Strategy for the Identification of SUMO-Dependent Proximal Interactors

Posttranslational modifications by the ubiquitin-like family (UbL) of proteins determine the biological fate of a substrate, including new interaction partners. In the case of the small ubiquitin-like modifier (SUMO), this is achieved in part through its non-covalent interaction with SUMO-interacting motifs (SIMs) found in some proteins. Investigating such partner-complex formation is particularly challenging due to the fast dynamics and reversibility of SUMO modifications and the low affinity of SUMO-SIM interactions. Here, we present a detailed protocol of SUMO-ID, a technology that merges promiscuous proximity biotinylation by TurboID enzyme and protein-fragment complementation strategy to specifically biotinylate SUMO-dependent interactors of particular substrates. When coupled to streptavidin-affinity purification and mass spectrometry, SUMO-ID efficiently identifies SUMO-dependent interactors of a given protein. The methodology describes all the steps from SUMO-ID cell line generation to LC-MS sample preparation to study SUMO-dependent interactors of a particular protein. The protocol is generic and therefore adaptable to study other UbL-dependent interactors, such as ubiquitin.

The Multifarious Role of 14-3-3 Family of Proteins in Viral Replication

The 14-3-3 proteins are a family of ubiquitous and exclusively eukaryotic proteins with an astoundingly significant number of binding partners. Their binding alters the activity, stability, localization, and phosphorylation state of a target protein. The association of 14-3-3 proteins with the regulation of a wide range of general and specific signaling pathways suggests their crucial role in health and disease. Recent studies have linked 14-3-3 to several RNA and DNA viruses that may contribute to the pathogenesis and progression of infections. Therefore, comprehensive knowledge of host-virus interactions is vital for understanding the viral life cycle and developing effective therapeutic strategies. Moreover, pharmaceutical research is already moving towards targeting host proteins in the control of virus pathogenesis. As such, targeting the right host protein to interrupt host-virus interactions could be an effective therapeutic strategy. In this review, we generated a 14-3-3 protein interactions roadmap in viruses, using the freely available Virusmentha network, an online virus-virus or virus-host interaction tool. Furthermore, we summarize the role of the 14-3-3 family in RNA and DNA viruses. The participation of 14-3-3 in viral infections underlines its significance as a key regulator for the expression of host and viral proteins.

Detecting Protein-Protein Interaction Based on Protein Fragment Complementation Assay

Proteins are the most critical executive molecules by responding to the instructions stored in the genetic materials in any form of life. More frequently, proteins do their jobs by acting as a roleplayer that interacts with other protein(s), which is more evident when the function of a protein is examined in the real context of a cell. Identifying the interactions between (or amongst) proteins is very crucial for the biochemistry investigation of an individual protein and for the attempts aiming to draw a holo-picture for the interacting members at the scale of proteomics (or protein-protein interactions mapping). Here, we introduced the currently available reporting systems that can be used to probe the interaction between candidate protein pairs based on the fragment complementation of some particular proteins. Emphasis was put on the principles and details of experimental design. These systems are dihydrofolate reductase (DHFR), β-lactamase, tobacco etch virus (TEV) protease, luciferase, β- galactosidase, GAL4, horseradish peroxidase (HRP), focal adhesion kinase (FAK), green fluorescent protein (GFP), and ubiquitin.

A Single Protein Disruption Site Results in Efficient Reassembly by Multiple Engineering Methods

Disrupting a protein's sequence by cleavage or insertion of a hinge domain forms the basis for protein engineering tools, including fragment complementation, circular permutation, and domain swapping. Despite the utility of these designs, their widespread implementation has been limited by the difficulty in choosing where to interrupt the protein sequence: the resulting fragments often aggregate or fail to reassemble. Here, we show that an optimal site exists within ribose binding protein (RBP) that, when disrupted, results in the most efficient formation of fragment-complemented and domain-swapped species. Cleaving RBP at this site also produces a highly stable, cooperatively folded circular permutant. This hot-spot site was identified by an experimental approach involving selection among competing folds. We find that efficiency in the case of RBP is determined by kinetic factors (survival of the first) rather than thermodynamics (survival of the fittest). Together with emerging computational tools, this limited data set defines a pathway for designing robust platforms for molecular switches and biosensors based on the aforementioned protein modifications.