Cryo-electron microscopy (cryo-EM) has revolutionized structural biology, enabling researchers to determine the high-resolution 3D structures of biological macromolecules that were previously challenging or impossible to study using traditional methods like X-ray crystallography or NMR. This powerful technique is vital for life sciences and drug development, providing insights into both the structure and functional roles of biomolecules, ranging from single proteins to complex viruses. However, unlocking the full potential of cryo-EM requires sophisticated cryo-EM platforms equipped with cutting-edge hardware, intelligent software, and streamlined, integrated workflows.

Complex challenges such as low protein molecular weight, low concentration, high background noise, air-water interface disruption, and preferential orientation can hinder successful structure determination. Addressing these bottlenecks necessitates not just advanced microscopes but also robust sample preparation, efficient data collection, and powerful data analysis capabilities working together seamlessly.

Shuimu BioSciences, founded in 2017 at Tsinghua University, emerged as the first commercial cryo-EM platform in Asia, built upon deep research and technical heritage in structural biology. Led by a core team of world-class experts, Shuimu has established efficient, advanced integrated workflows for both experimental procedures and data analysis, aiming to provide "One-Stop" solutions from gene sequences to high-resolution 3D structures.

To explore how a comprehensive cryo-EM platform and integrated workflow can accelerate your research, visit https://shuimubio.com/.

The Foundation: State-of-the-Art Cryo-EM Hardware

A robust cryo-EM platform begins with powerful instrumentation. Shuimu BioSciences operates one of the world's largest commercial cryo-EM platforms. Their facilities include 300 kV instruments strategically located in both Beijing and Hangzhou. The platform boasts eight electron microscopes specifically dedicated to structural analysis, including G3i, G4, and Totem models. While the core strength is noted as having 2 × 300 kV instruments in Beijing and 6 × 300 kV instruments in Hangzhou, their 24-hour instrument access service mentions a total of 12 instruments in Beijing and 6 in Hangzhou available for 300 kV data acquisition under that specific offering. This extensive capacity underscores the platform's ability to handle a large volume of projects.

Ensuring optimal performance requires dedicated support. A dedicated team of EM engineers oversees daily operations and maintenance of the cryo-EM facilities. The platform emphasizes daily maintenance and upkeep, guaranteeing equipment is always in optimal condition. Through regular, high-frequency maintenance, Shuimu ensures the efficiency and quality of data collection, providing stable and reliable service support. Instruments are inspected and maintained regularly to ensure they are in optimal operating condition, with each electron microscope maintaining over 330 days of available machine time annually and an annual fault-free operation rate greater than 97%.

The Electron Microscopy Center Hardware Configuration highlights that Shuimu fully owns the world's most advanced biomolecular imaging equipment. These instruments are equipped with high-performance detectors, energy filters, spherical aberration, and phase plates, maximizing imaging quality. The provision of 24-hour, round-the-clock instrument time allows for convenient and efficient microscope-time reservation and data-collection services, underpinned by a commitment to quality and enabling faster structural determination.

This combination of extensive instrument capacity, cutting-edge technology, and rigorous maintenance is fundamental to a high-performance cryo-EM platform.

Discover the power of advanced hardware on the Shuimu BioSciences cryo-EM platform at https://shuimubio.com/.

Intelligent Analysis: Software and AI

Hardware is only part of the equation; intelligent software is crucial for processing the vast amounts of data generated by modern cryo-EM. Shuimu BioSciences leverages proprietary AI algorithms and software to enhance efficiency and accuracy in structure determination.

Key software components mentioned include:

· SMART Software Suite: This independently developed suite utilizes AI to streamline cryo-EM data analysis. It also reduces machine runtime and required data volume, improving the efficiency of the entire cryo-EM data analysis process.

· NanoSMART: A self-developed AI cryo-EM system specifically designed to automatically identify nanoparticle features from electron microscope images. Used in Cryo-Characterization, NanoSMART allows users to obtain detailed reports with one-click operation. It can analyze nanoparticle features such as Size Distribution, Roundness, and Layered Full/Empty Integrity. NanoSMART enhances the clarity of low-quality images to optimize recognition results and performs excellently in identifying ultra-small targets like VLPs. Its powerful data analysis functions and user-friendly data presentation features include project data summaries with histograms and tables, offering comprehensive insights.

· eTasED: Proprietary software that seamlessly integrates micro-electron diffraction (MicroED) technology into conventional cryo-EM systems without additional modifications. This significantly enhances research efficiency and accuracy for MicroED applications.

These software solutions are integral to the cryo-EM platform, automating and accelerating data processing and analysis, from initial particle picking to final model refinement. The AI-driven capabilities contribute to the platform's ability to achieve high resolutions and handle complex samples efficiently.

Learn how AI-driven software powers the Shuimu BioSciences cryo-EM platform at https://shuimubio.com/.

Beyond the Microscope: The Integrated Workflow

One of the key strengths of an advanced cryo-EM platform is its ability to offer an integrated workflow, often described as a "One-Stop" solution. This means handling the entire process, from initial sample preparation to final structure determination and analysis. This comprehensive approach minimizes variability, standardizes the pipeline, and successfully addresses challenges posed by difficult-to-express proteins.

The integrated workflow typically encompasses several critical stages:

1. Protein Preparation and Analysis: High-quality protein is fundamental for cryo-EM. Shuimu's platform includes a complete protein expression and purification platform featuring molecular cloning, protein expression, purification, and characterization.

o Protein Expression Systems: Offering flexibility based on protein type and desired modifications, systems include E. coli, mammalian cells, insect cells, and cell-free expression. E. coli is economical and fast, suitable for prokaryotic or simple eukaryotic proteins. Mammalian cells produce proteins closest to their natural state, preferred for therapeutics. Insect cells are good for high expression efficiency and post-translational modifications. Cell-free systems offer rapid synthesis.

o Purification Processes: Various chromatography methods are employed, such as Affinity chromatography, Ion-exchange chromatography, Gel filtration, and Reverse-phase HPLC (RP-HPLC), selected based on separation mechanism and target protein properties. Complex incubation and size-exclusion chromatography or gel filtration are used for higher purity.

o Protein Characterization and Assays: Quality control is rigorous. Techniques include SDS-PAGE, BN-PAGE, HPLC for purity and homogeneity, Mass Spectrometry for verification and modification analysis, and binding analysis techniques like SPR, BLI, MST, and ITC. Shuimu offers dedicated SPR, BLI, and ELISA services.

o Off-the-Shelf Proteins: A list of important drug targets, including membrane proteins like GPCRs, ion channels, and transporters, is available, along with customized protein target services.

2. Initial Sample Assessment: Before proceeding to cryo-EM, samples can be assessed.

o Negative Staining & 2D Negative Staining: This technique quickly provides low-resolution 2D projection images of macromolecules and complexes. It helps assess particle size, uniformity, morphology, density, flexibility, and integrity at a lower cost. It's used for proteins, AAV, exosomes, membrane proteins, viruses, soluble proteins, and even plant and animal tissue sections. Resolution typically reaches 2-5 nanometers.

o Cryo Characterization: Using ultra-low temperature to preserve the native state, this is particularly advantageous for observing liposomes, LNPs, AAV, VLPs, and proteins. Utilizing NanoSMART, it provides efficient and precise characterization services focusing on nanoparticle features.

3. Cryo-EM Data Collection (SPA): For high-resolution 3D structures, Single Particle Analysis (SPA) is the core method. After sample preparation and freezing (often requiring careful sample handling and specific requirements like purity, concentration, buffer composition, and avoiding freeze-thaw cycles), extensive 2D images of purified macromolecular particles are collected, often through 24-hour instrument access.

4. Computational Processing and Structure Determination: Computational algorithms are essential for processing the collected 2D images and reconstructing a detailed 3D structural model. This includes steps like 2D particle picking, 3D reconstruction, and model refinement. Shuimu utilizes its AI-driven platforms like SMART to streamline this data analysis. The proprietary graphene support grids (GraFuture™ GO, GraFuture™ RGO) can help overcome challenges like preferred orientation and air-water interface damage, suitable for small or low-concentration proteins.

5. Complementary Structural Techniques: The platform also integrates other structural methods:

o MicroED Solutions: A cutting-edge technology for resolving high-resolution structures from microcrystals and nanocrystals, particularly suitable for small molecule drugs, peptides, and protein crystals. Utilizing eTasED software, it provides accurate insights, achieving resolutions as high as 0.6-1.0Å in some cases.

o One-Stop Crystallographic Analysis: Provides comprehensive structural analysis using X-ray crystallography, covering protein expression, purification, crystallization, data collection, and structure analysis. This is used for antigen-antibody complexes, small molecule drugs, and peptides, gaining insights into interactions and optimizing drug design. Shuimu has successfully completed over 200 structural analysis projects using this method.

This comprehensive suite of services, integrated into a coherent workflow, allows researchers to access all necessary steps for structural determination and related analyses from a single provider.

Explore the benefits of an integrated workflow for your structural biology projects at https://shuimubio.com/.

Applications and Impact

The capabilities of an advanced cryo-EM platform with an integrated workflow have significant applications across various fields:

· Analyzing Biomacromolecules: SPA can reveal high-resolution 3D structures of proteins (membrane proteins, enzymes, ribosomes), DNA and RNA structures, protein-nucleic acid complexes, and viral particles (SARS-CoV-2, Influenza, ASFV, HHV-6B, VSV-GP). Specific examples include structures of GPCRs like GPR75 and TRPV4 ion channels.

· Vaccine Field: Cryo-EM plays a crucial role in vaccine R&D, quality control, and interaction studies.

o Viral Structure Analysis: Resolving 3D viral structures at near-atomic resolution provides insights into viral entry mechanisms, crucial for vaccine design. Examples include studies on SARS-CoV-2 Spike protein-ACE2 complex, strategies for attenuated live influenza vaccines, and neutralizing antibody mechanisms against measles virus.

o Vaccine Quality Control: Used to examine morphology, particle size, integrity, and aggregation across manufacturing stages to optimize processes. Direct visualization helps detect production issues and accurately measure aggregation levels.

o Antibody–Vaccine Interaction Studies: Clarifies how antibodies bind to vaccine antigens, aiding immunogenicity optimization. Used in HIV vaccine research to resolve antibody-Env protein structures and in influenza vaccine studies.

o Responding to Viral Mutations: Enables rapid structural analysis of new viral variants to adjust vaccine designs quickly, as seen during the COVID-19 pandemic with SARS-CoV-2 variants.

· Antibody Drugs: Cryo-EM is crucial in antibody drug development.

o Antibody–Antigen Complex Analysis: Reveals high-resolution structures of interactions, helping understand recognition mechanisms and binding sites, vital for designing effective antibody drugs.

o Mechanism of Action Studies: Used to study how antibody drugs bind to targets and modulate pathways, aiding in developing new therapies targeting mutations.

o Optimization and Design: Analyzing existing drug structures helps identify improvements, revealing dynamic processes and conformational changes during binding to design antibodies with higher affinity and specificity. Assists in mapping conformational epitopes.

o Membrane Protein Targets: Resolving high-resolution structures of membrane protein targets like GPCRs sheds light on ligand binding and signal transduction, crucial for developing antibodies against them.

o Accelerating Development: High resolution and rapid data acquisition accelerate the optimization of antibody designs and overall drug development processes.

The success of the platform is demonstrated by numerous research results published in top international journals, resolving atomic-level resolution structures covering ion channels, GPCRs, antigen-antibody complexes, spliceosomes, and other biological samples. Specific published cases highlight structures of human GluN1-GluN2A NMDA receptor, histamine H1 receptor/Gq complex, bradykinin receptors, SARS-CoV-2 related structures, and many others listed in the source, covering a wide range of protein classes and complexes. Since 2017, Shuimu has provided structures for over 400 clients, completing over 400 cryo-EM projects and over 300 single particle projects, with more than 150 structures resolved. They have achieved resolutions as low as 1.4Å (with a best resolution of 1.8Å noted elsewhere) and elucidated structures as small as 51kDa.

Learn more about successful applications and case studies leveraging this cryo-EM platform and integrated workflow at https://shuimubio.com/.

Why Choose Shuimu BioSciences?

Choosing the right cryo-EM platform and partner is critical. Shuimu BioSciences distinguishes itself through:

· Extensive Experience: Over 400 completed cryo-EM projects, over 200 cryo-EM projects spanning various sample types like membrane proteins and antigen-antibody complexes, and over 200 structural analysis projects for crystallography.

· Elite Scientist Team: Composed of PhD-level experts from preeminent institutions specializing in structural biology, protein science, computational biology, and experienced EM scientists and technicians.

· Uncompromising Pursuit of Resolution: Achieved a groundbreaking resolution of 1.4Å, continuously pushing boundaries. More than 150 structures resolved with a best resolution of 1.8Å and down to a minimum molecular weight of 51 kDa. Dedicated pursuit of high-resolution structural analysis.

· AI-Driven Platform: Utilizing proprietary software like SMART and NanoSMART to streamline data analysis and enhance efficiency.

· Cost-Effectiveness: Offering competitive prices and ensuring rapid delivery, with prices lower than the industry average for crystallography while providing more comprehensive service.

· Strict Quality Control System: Protein quality control based on rigorous cryo-EM analysis and characterization to ensure samples meet requirements.

· Flexible Cooperation Models: Adjusting protein production scales and offering flexible models.

Shuimu's commitment to cutting-edge equipment, expert personnel, high resolution, and integrated services ensures a comprehensive and efficient pathway to structural determination.

To partner with a leading cryo-EM platform provider, visit https://shuimubio.com/.

Conclusion

Modern structural biology demands advanced tools and integrated approaches. A state-of-the-art cryo-EM platform, combining high-performance hardware, intelligent AI-driven software, and a seamless integrated workflow from sample preparation to final structure, is essential for tackling challenging biological questions and accelerating drug discovery. Shuimu BioSciences offers a comprehensive solution built on extensive experience, elite expertise, and a commitment to pushing the boundaries of resolution.

To learn more about how Shuimu BioSciences' cryo-EM platform and integrated workflow can support your research needs, visit https://shuimubio.com/.