Discovering that two proteins interact is only the first step. To truly understand function, develop drugs, or engineer a biologic, you must know where they bind. Identifying the precise contact surface—the specific domain, motif, or amino acid residues—is a significant challenge in biological research. Creative Biolabs' interaction domain mapping service uses phage display to offer a fast, high-throughput, and robust solution. We pinpoint the exact structural components of any domain-domain interaction, enabling your research to move from simple observation to a high-resolution molecular map. This service uses advanced phage display to find the specific binding interface with amino-acid-level precision.
This high-resolution service is a crucial component of our comprehensive Phage Display Protein Interaction Mapping Service, which offers comprehensive solutions for understanding complex molecular interactions.
Fig.1 The phage display workflow for Creative Biolabs' interaction domain mapping by service.
Identifying a protein's binding partners is a discovery. Mapping the interface where they touch is a feat of engineering. This interaction domain mapping is the critical transition point for many research programs. Knowing the exact binding site allows you to:
For decades, this work was slow, complex, and had extremely low throughput.
Phage display overcomes all of these challenges. Instead of building mutants one by one, we can build a library of billions of different protein fragments displayed on phages. By screening this protein fragment library against your target, we can quickly identify the exact fragment that contains the binding site. It is a high-throughput, high-resolution, and highly efficient method for identifying binding sites.
We have developed a suite of specialized services to answer your specific questions about protein-protein interactions. Our platform is designed to deliver precise and actionable data.
This service is crucial for the development of therapeutic antibodies. We screen your antibody against a custom protein fragment library or a dense peptide library representing the antigen. The result is a high-resolution map of the specific amino acids that form the binding epitope. This is critical for patent protection, mechanism-of-action studies, and engineering antibodies with novel properties.
Large proteins are built from smaller, functional modules called domains (e.g., SH2, SH3, PDZ domains). This service identifies which specific domain is responsible for a known domain-domain interaction. We screen a library of structured domains against your protein partner to see which one is captured. This quickly defines the functional architecture of the interaction and is a key part of mapping cellular signaling networks.
This service is used to characterize panels of new antibodies. We use phage display in a competitive format to group, or "bin," antibodies based on their binding footprint. This epitope binning is vital for selecting antibody pairs for the research of therapeutic antibody cocktails.
This is a core service for drug discovery. By mapping the precise binding pocket, you uncover the "hotspot" on the receptor. This information is the foundation for the rational design of small molecules or peptide mimetics that can either block (antagonist) or mimic (agonist) the natural ligand's function.
We have streamlined the interaction domain mapping process into a five-stage approach. Each step is optimized for precision, speed, and clear, interpretable data.
The project begins with a deep dive with our Ph.D. scientific team. We help you define the exact question: are you performing high-resolution epitope mapping of a single antibody, or broad protein domain mapping of a new interaction? Based on this goal, we select the correct library strategy and confirm the preparation of your "bait" target protein, which you can provide or we can express for you.
This is the most critical step. Unlike discovery projects, mapping requires a specific type of library. We will select the best one from our extensive portfolio, such as a high-density peptide library for linear motifs or a protein fragment library (often custom-made from your protein of interest) for structured domains. We then perform 3-5 rounds of biopanning to enrich for the few phage particles that display the exact fragment or peptide that binds to your target.
After the final biopanning round, we have a highly enriched pool of phages with desired qualities. We extract the DNA from these phages and use next-generation sequencing (NGS) to read millions of individual sequences. This high-throughput data acquisition provides the raw sequence information that will be used to build the interaction map.
This is where the map is drawn. Our bioinformatics team takes the millions of NGS sequences and aligns them back to the known, full-length sequence of your protein. The result is a clear heat map, commonly shown as a graph where sequences cluster over a particular region. This statistical enrichment profile unambiguously identifies the binding site, often down to a handful of amino acids.
You receive a comprehensive final report. This includes all raw NGS data, the detailed bioinformatics analysis, and the final, high-resolution interaction map. The deliverable is typically a consensus sequence, a "sequence logo" for motifs, or a list of the minimal amino acid coordinates that define the binding site. As an optional service, we can validate these findings, for example, by synthesizing the identified peptide and confirming its binding activity via ELISA or SPR.
Our success is built on a foundation of three robust, interconnected technology pillars. This ecosystem ensures that every project, from simple epitope mapping to complex domain-domain interaction analysis, is executed at the highest standard.
We provide the flexibility to screen any target in its most relevant form. Our in vitro protein-based screening platform is ideal for purified proteins, providing clean, low-background results. For more complex targets, our In Vitro Cell-Based Screening Platform enables us to screen against proteins, such as receptors or ion channels, in their native, folded conformation on the surface of a living cell.
A successful mapping project relies on an appropriate library. We maintain a vast portfolio of world-class, high-complexity libraries. Our Phage Display Peptide Library Construction services serve as the engine for discovering linear motifs and epitopes. For mapping structured domains, we leverage our Phage Display cDNA Library Construction and Phage Display Scaffold Library Construction capabilities to create high-diversity protein fragment library collections. We also offer Custom Phage Display Library Construction from any species, tissue, or gene set to meet your exact needs.
You cannot map what you cannot see. Precision mapping requires deep data. Our Phage Display NGS Service is the high-fidelity readout that makes this possible. By sequencing millions of enriched phages, we generate the massive statistical power needed to build a high-resolution map of the binding site, distinguishing the proper signal from experimental noise with high confidence.
Precision is power. Understanding protein interactions is a crucial step in designing next-generation therapeutics, engineering novel proteins, and unraveling complex biological processes. Our interaction domain mapping service provides the high-resolution data you need to move from discovery to design. to discuss your mapping project and receive a custom quote.
Please kindly note that our services can only be used to support research purposes (Not for clinical use).
Creative Biolabs is a globally recognized phage company. Creative Biolabs is committed to providing researchers with the most reliable service and the most competitive price.
