Epitope Mapping Service | Cryo-EM

Epitope mapping is the process of precisely identifying antibody-antigen binding regions. This is crucial for understanding immune mechanisms, guiding therapeutic antibody development, optimizing vaccine design, and supporting intellectual property protection. High-resolution epitope mapping reveals atomic-level interactions and conformational dynamics between antibodies and antigens, providing a solid structural foundation for rational drug development.

Various technologies offer different strengths and limitations for epitope mapping:

Platform	Advantages	Limitations
Cryo-EM	No need for crystallization; supports large, flexible, heterogeneous complexes; near-atomic resolution	Requires rigorous sample preparation and image processing
X-ray Crystallography	Atomic resolution structures	Requires crystallization; unsuitable for flexible or unstable complexes
HDX-MS	Detects conformational changes; suitable for rapid screening	Limited resolution; does not provide direct 3D structure
Negative Stain TEM	Rapid screening; assesses complex integrity	Low resolution; dehydration and artifacts possible

 

Among these, cryo-electron microscopy (Cryo-EM) has emerged as a preferred technology for high-resolution epitope mapping due to its ability to operate under near-native conditions without crystallization and its compatibility with a wide range of biomolecular complexes.

 

MtoZ Biolabs offers advanced Epitope Mapping Service that leverages a robust cryo-EM platform and deep experience in antibody–antigen complex analysis. Our service empowers therapeutic antibody discovery with precise epitope definition.

 

Services at MtoZ Biolabs

MtoZ Biolabs provides Epitope Mapping Service based on Cryo-EM using single particle analysis (SPA) to acquire thousands of 2D projections of antibody–antigen complexes. These projections are classified, aligned, and reconstructed into high-resolution 3D models that enable accurate mapping of epitopes and their corresponding paratopes. To enhance cryo-EM success rates, we also perform initial quality screening using Negative Stain TEM to evaluate sample integrity and homogeneity prior to vitrification.

 

Why Choose MtoZ Biolabs?

In the Epitope Mapping Service based on Cryo-EM, MtoZ Biolabs offers:

✅ Advanced Instrumentation: High-end Cryo-EM systems (e.g., Thermo Fisher Krios) with direct electron detectors and automated data acquisition.

✅ Skilled Team: Experts with deep experience in resolving antibody-antigen structures, including complex and flexible samples.

✅ Customized Workflows: Flexible protocols including SPA, negative stain TEM, crosslinking, and stabilization strategies tailored to sample characteristics.

✅ Fast Turnaround: Preliminary 3D reconstruction within 2–4 weeks post-QC.

✅ End-to-End Support: From project design to data delivery, full-cycle support with scientific consultation.

 

Applications

The Epitope Mapping Service based on Cryo-EM is widely applicable to a variety of research and development scenarios that require detailed structural insights into antibody–antigen interactions, including but not limited to:

· Therapeutic Antibody Discovery: Identify functional epitopes to optimize binding affinity and specificity.

· Vaccine Design: Define protective epitopes to guide antigen engineering.

· Immune Mechanism Research: Understand the action of neutralizing or autoantibodies.

· Conformation-Dependent Antibody Development: Reveal conformational epitopes relevant to dynamic targets.

 

Case Study

Case 1: Cryo-EM-Based Epitope Mapping for Broad-Spectrum Antibody Discovery

In a 2024 study on porcine delta-coronavirus (PDCoV), researchers used Cryo-EM to determine the structures of two broadly neutralizing monoclonal antibodies (PD33 and PD41) bound to the spike protein’s receptor-binding domain (RBD) and trimeric form. High-resolution Cryo-EM maps precisely defined the epitopes and clarified the neutralization mechanism. Coupled with deep-mutational scanning, the study established links between RBD antigenicity and neutralization potency, offering new insights into immune escape and epitope function.

 



Rexhepaj, M. et al. Immunity. 2024.

 

This work demonstrates the critical role of Epitope Mapping Service based on Cryo-EM in therapeutic antibody development. MtoZ Biolabs provides expert support for epitope definition, antibody screening, and mechanistic elucidation.

 

FAQ

Q1: Does the Epitope Mapping Service based on Cryo-EM require full-length mAbs, or are Fab fragments acceptable?

Full-length antibodies are not mandatory. Fab fragments are often preferred due to reduced flexibility and improved particle orientation, which enhance high-resolution reconstruction. MtoZ Biolabs has extensive experience with both formats and will tailor protocols accordingly.

 

Q2: Can Cryo-EM resolve epitopes on flexible antigens?

Yes, though it presents challenges. For highly flexible targets, MtoZ Biolabs applies stabilization strategies such as optimized freezing conditions, focused classification, and chemical crosslinking to improve reconstruction outcomes.

 

Q3: Is there a minimum complex size for successful Cryo-EM epitope mapping?

We recommend complexes of ≥100 kDa to ensure sufficient contrast in SPA. For smaller systems, we enhance data acquisition density and apply advanced particle picking and processing techniques to support high-resolution mapping.

 

With the Epitope Mapping Service based on Cryo-EM, MtoZ Biolabs helps researchers pinpoint critical epitope-paratope interfaces and translate structural insights into therapeutic breakthroughs. Contact us today to discuss a tailored solution for your antibody-antigen project.