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Analyzing protein-protein interactions with mass photometry



Protein-protein interactions underpin virtually all cellular processes. Studying these interactions can be challenging however, since they often involve multiple components and complex, dynamic equilibria. Many of the resulting protein complexes appear at very low concentrations, making them difficult to detect and quantify with traditional analytical methods. 

Mass photometry is a powerful solution for analyzing protein-protein interactions. It rapidly provides detailed information on the mass distribution of protein samples at a single-molecule level, enabling the detection and quantification of trace protein complexes and transient interactions. 

A powerful technique for protein analytics 

Whether investigating the assembly of large, multimeric complexes or probing oligomerization behavior, mass photometry delivers rapid and accurate insights into the full range of species present in a sample.  

By measuring the mass of individual proteins and complexes in a sample, mass photometry quantifies the relative abundance of each species present in a protein-protein interaction at equilibrium. This enables users to identify the complexes formed, assess their stoichiometry, and evaluate the strength of the interactions by determining the dissociation constant (KD). The method is label-free and non-destructive – helping you to achieve optimal reproducibility in your results.  

Figure 1: Mass photometry reveals differences in complex formation between protein A and IgG antibodies of differing origin. When human IgG was mixed with protein A at a 1:1 ratio (blue line), several species could be resolved, including Protein A; IgG; and protein A: IgG complexes of stoichiometry ratios 1:1, 1:2, 2:3 and 2:4. When bovine IgG was mixed with protein A (orange line), Protein A, IgG, 1:1 protein A: IgG complex and IgG dimers could be resolved. 

Gain quantitative insights into protein-protein interactions 

The value of mass photometry for protein-protein interaction analysis lies in the rapid quantitative overview it provides of the biomolecular species and complexes present in a sample. In addition, its capability to perform measurements across a diverse array of buffer conditions makes the technology well-suited for evaluating protein interactions under a variety of physiologically relevant conditions. 

The TwoMP mass photometer delivers protein analytics results in minutes, enabling researchers to observe the evolution of protein interactions over time, and therefore characterize reaction equilibria and dynamics efficiently and effectively. 

A major advantage of mass photometry is its single-molecule resolution, which affords precise quantification of the relative amounts of molecular species in a sample. This is especially valuable when analyzing protein components present at low concentrations. 

Figure 2: KD values for interactions involving the IgG of human origin (blue) and of bovine origin (orange) are both shown. The KD calculation was not applicable for certain interactions (depicted as N/A). KD values were calculated for each of three repeated mass photometry measurements, and the mean ± standard deviation is given. 

A powerful technique for protein analytics
Gain quantitative insights into protein-protein interactions

Characterizing protein oligomerization
with mass photometry 

Oligomerization, the self-assembly of proteins into specific quaternary structures, plays a vital role in protein functionality. This self-assembly is essential for numerous proteins to perform their biological roles effectively. For example, oligomerization states can regulate the activity of enzymes by allosteric inhibition.  

Mass photometry characterizes these oligomeric behaviors with high precision. It can detect species that represent less than 1% of the molecules in a sample, providing insights into the diversity of oligomeric states and their role in protein function. This high-resolution capability ensures that you can identify and analyze even the most transient and low-abundance complexes, offering a comprehensive view of protein behaviors. 

Figure 3: A mass histogram of a protein-only sample, with monomers and dimers present. B: Calcium chloride (present in excess) induced the formation of tetramers and reduced the number of dimers. C: Adding a saturating concentration of EDTA reversed this effect, resulting in the disappearance of the tetrameric species. 

Delivering results swiftly, mass photometry is an ideal tool for screening protein variants for oligomerization behavior. With the TwoMP mass photometer, you can simultaneously evaluate protein oligomer variants under various conditions, revealing how environmental factors influence protein assembly. Since the concentrations used in mass photometry experiments are within the nanomolar range, similar to physiological conditions, the observed oligomeric states closely mirror the protein's behavior in vivo. 

Further enhancing its utility in protein oligomerization studies, the TwoMP Auto mass photometer can automate oligomerization analysis, allowing for repeated measurements and hands-free analysis of up to 24 samples. The addition of the MassFluidix HC microfluidics add-on supercharges the capability of the TwoMP Mass Photometer to characterize low-affinity interactions. Harnessing microfluidics to rapidly dilute samples prior to measurement, it uncovers complexes that would remain undetected at the nanomolar concentrations typically used in mass photometry. This opens novel avenues for the exploration of transient and weak interactions, offering a fuller picture of protein behavior in physiological and experimental conditions. 

Characterizing protein oligomerization with mass photometry

What mass photometry users are saying

"I feel that mass photometry is really reporting on my actual sample as I have it in my Eppendorf tube. That's a huge benefit. In particular, you can parse out compositional heterogeneity independent of conformational variability, which is a difficult thing to get with other techniques.  "

 John Zinder. Senior scientist at Odyssey Therapeutics. 

Mass photometry solutions for protein interaction analytics 

For molecular mass measurements with unmatched sensitivity, speed and simplicity of use, a TwoMP mass photometer offers wide mass range and single-molecule resolution. 

  • High-fidelity measurements of molecular mass 

  • Minimal quantities of sample required 

  • ​Intuitive acquisition and data analysis software  

  • ​Easy setup – a compact, benchtop instrument with minimum installation requirements 


Further resources on membrane protein analytics with mass photometry

To learn more about how mass photometry could elevate your protein-protein interaction analysis 

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