Complete and accurate 3D structural determination when one technique is not enough

To understand protein function within the cellular environment, it is essential to determine protein complex assembly and structure beyond just individual proteins. Solving the structure of large dynamic complexes often requires integrating several complementary techniques, such as biomolecular mass spectrometry (MS) and cryo-electron microscopy (cryo-EM) – an approach known as integrative structural biology.

MS has made significant advances in the field of structural biology, enabled by increased speed, sensitivity, selectivity, and a variety of MS fragmentation techniques. Similarly, recent developments in cryo-EM sample preparation, microscope and detector technology, automation in data collection, and image processing make it possible to reproducibly reach near-atomic resolution. Combined, a reliable and complete structure can be solved for macromolecular complexes composed of components like proteins, post-translational protein modifications, DNA, RNA, and lipids.

Integrative structural biology process (mass spec and electron microscopy).
Schematic of the integrative structural biology process including mass spec and cryo-EM data.
Electron Microscopy

Integrative Structural Biology

Mass spectrometry for 3D structural determination with cryo-electron microscopy.


Integrative structural biology workflow

Native mass spectrum showing protein complex and complex subunits.
Native MS can reveal if the intact complex matches the mass of the protein subunits, if it might exist as an oligomer, if a subunit is present in multiple copies, or if a small molecule might be binding to the complex.

Sample screening and optimization

A sample that is likely to result in a high-resolution cryo-EM structure must consist of biomolecules that are intact, stable and compositionally homogeneous. Native MS can quickly, easily, and quantitatively check these parameters.

Identification of structural components

Mass spec can provide the subunit composition of a protein complex via denaturing MS and reveal interaction partners in the cellular environment (interactomics) as well as subunit stoichiometry. This information gives structural identity, which aids in later interpretation and modeling.

 

Native mass spectrum showing folded, denatured and misfolded protein. Native mass spectrometry provides a fast and accurate readout of protein integrity and stability. Three preparations of the same protein are shown; correctly folded native state (top), denatured during preparation (middle) and misfolded (bottom). The state relates directly to the number of charges the protein complex acquires during ionization.

CryoEM structure of the KaiCBA protein complex that regulates the cyanobacterial circadian clock.

Cryo-electron microscopy imaging

Cryo-EM, particularly single particle analysis (SPA), is becoming an essential technique for structural determination of viruses and protein complexes. With SPA, 2D transmission electron micrographs of individual, randomly orientated viruses/protein complexes can be computationally aligned to generate a 3D volume of the specimen. This has allowed cryo-EM to emerge as an alternative to traditional techniques, such as X-ray crystallography and nuclear magnetic resonance (NMR), and it can even visualize complete macromolecular complexes rather than simply selected parts.

Building a 3D model

Chemical crosslinking, followed by mass spec, provides information on the global protein subunit topology within a large complex. This topology helps locate the subunits within the large cryo-EM density map. Beyond global subunit topology, the same crosslinks also allow de novo atomic model building within the EM density map when combined with the amino acid sequence. Lastly, facilitated by the spatial constraints of the crosslinks, an atomic model can be validated and refined.

28S subunit protein structure generated by cryo electron microscopy. Proteins of the 28S subunit. CX-MS crosslinking was used to identify mitochondrial-specific ribosomal proteins and confirm their locations (Cα of crosslinked residues shown as spheres).
KaiCBA protein complex imaged with cryo electron microscopy. Structure of the KaiCBA circadian clock protein complex at 4.7 Å resolution obtained by cryo electron microscopy after native MS screening for optimal sample conditions.

RNA, post-translational modifications and lipids

For further refinement and a complete atomic model, MS can localize flexible domains and weak densities within a macromolecular complex. Post-translational modifications, structural lipids and ribonucleic acids like RNA and DNA can all be identified and localized, aiding in the modeling of less defined areas of the EM density map.

When information from different sources and methods is integrated, an atomic model becomes much more reliable. With continued advancements in both MS and cryo-EM, and further application of these synergistic approaches, integrative structural biology will continue to produce more reliable, more complete and higher precision 3D structures.


Media Gallery

Studying small viral glycoproteins using an integrative structural biology approach

Recent advances in single-particle cryo-electron microscopy (cryo-EM) have enabled structure determination of small (<200 kDa) biological complexes, allowing researchers to study proteins that resist crystallization. Dr. Joost Snijder, Assistant Professor, Utrecht University, and Dr. Ieva Drulyte, Cryo-EM Application Specialist, Thermo Fisher Scientific, present the cryo-EM structure of the ~80 kDa heavily glycosylated human coronavirus HKU1 hemagglutinin esterase (HE) at a global resolution of 3.4 Å.

Watch on-demand

Native mass spectrometry-based screening for optimal sample preparation in single particle cryo-EM

In this webinar, Dr. Dom Olinares discusses recent advances in single particle cryogenic electron microscopy (cryo-EM) have enabled the structural determination of numerous flexible and conformationally heterogeneous protein assemblies at high resolution, yielding unprecedented insights into their function. However, despite its extraordinary capabilities, cryo-EM remains extremely resource-intensive and time-consuming. It is therefore beneficial to have a means for rapidly assessing and optimizing the quality of samples prior to lengthy cryo-EM analyses.

Watch on-demand

Studying small viral glycoproteins using an integrative structural biology approach

Recent advances in single-particle cryo-electron microscopy (cryo-EM) have enabled structure determination of small (<200 kDa) biological complexes, allowing researchers to study proteins that resist crystallization. Dr. Joost Snijder, Assistant Professor, Utrecht University, and Dr. Ieva Drulyte, Cryo-EM Application Specialist, Thermo Fisher Scientific, present the cryo-EM structure of the ~80 kDa heavily glycosylated human coronavirus HKU1 hemagglutinin esterase (HE) at a global resolution of 3.4 Å.

Watch on-demand

Native mass spectrometry-based screening for optimal sample preparation in single particle cryo-EM

In this webinar, Dr. Dom Olinares discusses recent advances in single particle cryogenic electron microscopy (cryo-EM) have enabled the structural determination of numerous flexible and conformationally heterogeneous protein assemblies at high resolution, yielding unprecedented insights into their function. However, despite its extraordinary capabilities, cryo-EM remains extremely resource-intensive and time-consuming. It is therefore beneficial to have a means for rapidly assessing and optimizing the quality of samples prior to lengthy cryo-EM analyses.

Watch on-demand

Applications

Life_Sciences_Application_274x180_144DPI

Structural Biology Research

Cryo-electron microscopy enables the structural analysis of challenging biological targets such as large complexes, flexible species and membrane protein.

DrugDiscovery_Appl_274x180

Drug Discovery

Learn how to take advantage of rational drug design for many more major drug target classes, leading to best-in-class drugs.


Samples


Proteins Analysis

Cryo-electron microscopy provides near-atomic resolution 3D protein structure. It can determine structural information for complexes and crystallization-resistant samples, as well as vital cellular context.

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Biopharmaceutical Research

Structural drug discovery is enabled by cryo-electron microscopy, as the method provides near-atomic-resolution detail for small molecules and protein biologics in their fully hydrated state.

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Virus Analysis

Cryo-EM enables the 3D structural visualization of virus particles, and the antigen-antibody interface, at near-atomic resolutions. A virus’s inherent structural symmetry makes it the ideal target for cryo-EM analysis.

Learn more ›


Products

Style Sheet for Instrument Cards Original

Krios Rx Cryo-TEM

  • Industry leading productivity and ease of use
  • Fixed 300 kV voltage for SPA only
  • Pharma-dedicated service package for guaranteed reliability

Krios G4 Cryo-TEM

  • Improved ergonomics
  • Fits more easily into new and existing labs
  • Maximized productivity and automation
  • Best image quality for high-resolution 3D reconstruction

Glacios Cryo-TEM

  • Flexible Accelerating Voltage 80-200 kV
  • Industry-leading Autoloader for cryogenic sample manipulation
  • Small footprint
  • Enhanced ease-of-use

Tundra Cryo-TEM

  • Structural information at biologically relevant resolution
  • Space efficient and cost effective
  • Easy, iterative sample optimization
  • Unique AI algorithms for streamlined data collection

Talos Arctica TEM

  • Increased data acquisition speed
  • High data with robotic sample handling & automated loading
  • Unattended platform operation and automated data acquisition
  • Low cost of ownership with remote diagnostics and preventive service

Talos F200C TEM

  • Flexible EDS analysis reveals chemical information
  • High-contrast, high-quality TEM and STEM imaging
  • Ceta 16 Mpixel CMOS camera provides large field of view and high read-out speed

Talos L120C TEM

  • Increased stability
  • 4k × 4K Ceta CMOS camera
  • TEM magnification range from 25–650 kX
  • Flexible EDS analysis reveals chemical information

Aquilos 2 Cryo-FIB

  • Automation enables production of multiple lamellas
  • Target and extract your structure of interest with lift-out nano-manipulator
  • 3D visualization for high-resolution tomography

Vitrobot System

  • Fully Automated Sample vitrification
  • Blotting Device
  • Semi-Automated Grid Transfer
  • High Sample Throughput

Selectris and Selectris X Imaging Filters

  • Designed for high stability and atomic resolution imaging
  • Straightforward operation
  • Paired with the latest generation Thermo Scientific Falcon 4 Direct Electron Detector

Ceta-D Camera

  • Optimum performance at any high tension (20–300 kV)
  • Compatible with post-column filters and spectrometers
  • Movie acquisition for dynamic studies

Falcon 4 Detector

  • Leading detective quantum efficiency
  • 10x shorter exposure time than its predecessor
  • Fully embedded in Thermo Scientific software
  • Built in data management

Tomography 5
Software

  • Automated multi-site batch tomography
  • Automatic cassette mapping
  • Dose symmetric tilt scheme for optimal electron dose
  • Fully integrated with Selectris Imaging Filters

Maps Software

  • Acquire high resolution images over large areas
  • Easily find regions of interest
  • Automate image acquisition process
  • Correlate data from different sources

Auto Slice and View 4.0 Software

  • Automated serial sectioning for DualBeam
  • Multi-modal data acquisition (SEM, EDS, EBSD)
  • On-the-fly editing capabilities
  • Edge based cut placement

Inspect 3D Software

  • Image processing tools and filters for cross-correlation
  • Feature tracking for image alignment
  • Algebraic reconstruction technique for iterative projection comparison

Amira Software
Life Sciences

  • Import and process image data
  • Auto-segmentation, object separation, labeling
  • Analyze and quantify with automated statistics
  • Create images, animations and videos

EPU 2 Software

  • Microscope-embedded solution for single particle acquisition
  • Optimized for high-throughput particle collection
  • Compatible with film, CCD cameras, and direct electron detectors


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