Cryo-electron microscopy (cryo-EM) has revolutionized structural biology, offering unprecedented capabilities to visualize biological macromolecules in close to their native state. This powerful technique is particularly impactful in the study of viruses and viral capsids, providing high-resolution insights crucial for understanding mechanisms of infection, guiding vaccine design, and developing antiviral therapies. As the first commercial platform in Asia offering cryo-EM structure determination, Shuimu BioSciences is at the forefront of applying these technologies to virus research.

Understanding the structure of viruses and their components, such as viral capsids, is fundamental to combating infectious diseases. Cryo-EM Single Particle Analysis (SPA) is a primary approach used for this purpose. SPA involves collecting extensive 2D images of purified macromolecular particles and employing computational algorithms to process and reconstruct a detailed 3D structural model. This method is highly effective for analyzing viruses and viral capsid protein–RNA complexes. For example, SPA has been used to resolve the detailed 3D structure of baculovirus AcMNPV viral capsid protein–RNA complexes. The advantages of using cryo-EM SPA for virus studies include preserving samples close to their native state, capturing diverse conformations, requiring minimal sample volume, and the ability to determine the structures of heterologous protein complexes. Shuimu BioSciences provides One-Stop SPA Solutions designed for various targets, including VLPs (Virus-Like Particles), peptides, and membrane proteins. Their SPA workflow encompasses steps from project consultation and feasibility evaluation through protein expression and purification, negative staining, sample freezing and data collection, 2D particle picking, 3D reconstruction, model refinement, and final data delivery. This comprehensive approach saves time and costs.

The application of cryo-EM extends significantly into the Vaccine Field, providing critical support for research and development, quality control, and rapid response to emerging threats.

1. Viral Structure Analysis in Vaccine R&D: Cryo-EM can resolve the 3D structures of viruses at near-atomic resolution, offering insights into viral entry mechanisms and guiding vaccine design.

o For SARS-CoV-2 (COVID-19), cryo-EM determined the full-length structure of the ACE2 receptor and the 3D structure of the SARS-CoV-2 spike protein in complex with ACE2, providing a crucial basis for understanding viral entry and vaccine design. The sources mention several publications featuring SARS-CoV-2 related structures resolved by Shuimu's platform or partners, including the spike protein in complex with the human ACE2 receptor, and structures of neutralizing antibodies against SARS-CoV-2 variants.

o For the Influenza Virus, cryo-EM studies have led to new strategies for creating attenuated live influenza vaccines and designing PROTAR vaccine strains. Examining how antibodies bind to influenza virus surface proteins via cryo-EM also helps scientists design more effective vaccines.

o For the Measles Virus, cryo-EM has been employed to investigate how neutralizing antibodies block infection, furnishing a structural foundation for new vaccines.

2. Vaccine Quality Control: Cryo-EM can examine key quality attributes across manufacturing stages, such as morphology, particle size, integrity, and aggregation.

o It provides direct visualization of particle shape and integrity, detecting issues that may surface during production.

o It accurately measures the level of aggregation in vaccine components, critical for enhancing immunogenicity.

3. Antibody–Vaccine Interaction Studies: Cryo-EM clarifies how antibodies bind to vaccine antigens, aiding the optimization of vaccine immunogenicity.

o In HIV Vaccine Research, cryo-EM has resolved the structure of vaccine-induced antibodies in complex with the HIV-1 Env protein, offering a structural basis for designing broadly neutralizing antibodies.

4. Responding to Viral Mutations: Cryo-EM enables rapid structural analysis of new viral variants, helping researchers quickly adjust vaccine designs. For example, cryo-EM was used during the COVID-19 pandemic to study multiple SARS-CoV-2 variants, supporting vaccines targeting emerging strains.

Beyond SPA, Shuimu BioSciences also offers Cryo Characterization and Negative Staining services highly relevant to analyzing viruses and viral components like VLPs and AAV (Adeno-Associated Viruses).

· Cryo Characterization uses ultra-low temperature technology to maintain samples in their natural state for high-resolution structural observation and analysis. It has significant advantages in observing the structure of VLPs, AAV, liposomes, and LNPs (Lipid Nanoparticles). Shuimu employs its self-developed AI cryo-EM system, NanoSMART, which automatically identifies nanoparticle features from electron microscope images, providing detailed reports with one-click operation. NanoSMART can identify features like Size Distribution, Roundness, and Layered Full/Empty Integrity. Case studies show NanoSMART's excellent performance in identifying VLP types and handling a large number of small targets under low magnification, achieving recognition rates close to 100%. The system also offers powerful data analysis functions and user-friendly data presentation for overall project data summaries and detailed information display for individual images, including particle size distribution tables.

· Negative Staining & 2D Negative Staining is a widely used technique for quick, low-resolution structural study of macromolecules and complexes. Shuimu's negative staining service helps clients quickly obtain 2D projection images as a basis for further cryo-EM research. This method can initially reveal sample particle size, uniformity, oligomeric state, morphology, particle density, protein structure, flexibility, sample integrity, conformation, and compositional heterogeneity at a lower cost. It is commonly used for observing viruses, nanoparticles, organelles, and protein complexes. For viruses and protein complexes arranged on a 2D plane, Negative Staining 2D is used. Shuimu utilizes Transmission Electron Microscopy (TEM), which can generally provide resolutions up to 2-5 nanometers with Negative Staining 2D, suitable for observing molecular-level structures. It is commonly used for detailed observation of protein complexes, viral particles, and extracellular vesicles in two-dimensional space. Negative staining is also used for assessing particle homogeneity in proteins, including AAV, exosomes, membrane proteins, viruses, and soluble proteins.

Shuimu BioSciences possesses core strengths that make it a compelling choice for cryo em virus and viral capsid analysis. They operate one of the world’s largest commercial cryo-EM platforms, equipped with eight electron microscopes, including 300 kV instruments. This infrastructure supports 24-hour data acquisition services. The team is composed of PhD-level experts specializing in structural biology, protein science, and computational biology from preeminent institutions. They have extensive experience, having completed over 400 cryo-EM projects and resolved more than 150 structures. This includes elucidating protein structures as small as 51 kDa and achieving resolutions down to 1.8 Å, with a groundbreaking resolution of 1.4 Å mentioned in case sharing. Shuimu leverages proprietary AI algorithms and graphene-based grids (GraFuture™, GO, RGO) to significantly enhance the efficiency and accuracy of structure determination. GraFuture™ grids specifically offer potential solutions to challenges in sample preparation, such as preferred orientation, and are suitable for applications involving small protein molecular weight, low concentration, high background noise, and air-water interface damage. Their independently developed SMART software suite utilizes AI to streamline cryo-EM data analysis.

Analyzing viral structures often requires high-quality protein samples, particularly the viral proteins that form the capsid or spikes. Shuimu supports cryo-EM services with comprehensive Protein Preparation and Analysis Services. This includes Protein Expression Systems (E. coli, mammalian cells, insect cells, cell-free expression), Protein Purification Processes (Affinity, Ion-exchange, Gel filtration, RP-HPLC), and Protein Quality Control (SDS-PAGE, Western blot, Mass spectrometry, thermal stability, solubility testing). They also offer Protein Assays like SPR, BLI, and ELISA, which can be useful for studying interactions involving viral proteins or antibodies against them. Shuimu's Off-the-Shelf Protein List includes relevant targets such as Spike protein and 3CL. Their expertise includes extensive experience in the production and purification of membrane proteins, which is relevant for studying viral membrane proteins. Shuimu aims to provide "One-Stop" solutions from gene sequences to high-resolution 3D structures by enhancing these upstream capabilities.

Sample submission requirements for cryo-EM SPA and Negative Staining services for protein samples involve specific criteria for protein concentration, volume, purity, and buffer composition. For Cryo Characterization of viruses (like AAV) and VLPs, specific concentration/power recommendations are provided. For all services, clear labeling and appropriate storage/transportation are crucial.

Numerous research results supported by Shuimu's platform have been published in top international journals, resolving atomic-level resolution structures covering various biological samples, including antigen-antibody complexes, which are highly relevant to virus research and vaccine/antibody development. Specific case examples mentioned in the sources highlight the successful resolution of SARS-CoV-2 related structures, and applications of negative staining for protein particle uniformity detection in viruses and VLPs.

In conclusion, cryo-EM is an indispensable tool for gaining high-resolution structural insights into viruses and viral capsids, supporting fundamental research, vaccine development, and the fight against infectious diseases. Shuimu BioSciences offers comprehensive, one-stop cryo-EM services, leveraging cutting-edge equipment, an elite scientist team, extensive experience, and advanced AI platforms to accelerate and enhance cryo em virus and viral capsid analysis. From initial sample preparation and characterization using techniques like Negative Staining and Cryo Characterization to high-resolution SPA for detailed 3D structures, Shuimu is equipped to handle challenging viral projects. Their commitment to pushing the boundaries of resolution and efficiency makes them a valuable partner in virology research.

For more detailed information on cryo-EM services for virus structure analysis and other structural biology applications, or to discuss your specific research needs, please visit https://shuimubio.com/.