Protein Interaction Studies

Background & Overview

The exertion of protein function is not performed independently by a single protein, but by protein-protein interaction (PPI) to perform its function. Therefore, studying the interactions between proteins is of great significance to gain a deep understanding of many life processes. Protein interactions also open up new avenues for exploring the mechanisms of disease occurrence and development. Through the specific inhibition of protein interactions, new ideas have been opened for the search for new drug targets, the development of new drugs and the treatment of diseases. Hydrogen/deuterium exchange mass spectrometry from BOC Sciences provides a fast and efficient method for protein interaction studies.

Our Services

Protein interaction studies are an important tool for understanding protein function and disease-related states. BOC Sciences provides technical support in this regard. Our services include the following parts:

Epitope Mapping

Epitope mapping is a critical step in the design of therapeutic antibodies and vaccines. We probe epitopes with HDX MS, quickly providing near-complete information on epitope structure. Our technique, either without or in combination with X-ray structures, can focus attention on regions involved in interactions and inform other experiments to test these regions.

Protein/Large Molecule Interactions

Many proteins exert their functional roles by binding to other biological macromolecules, including nucleic acids, peptides, or other proteins. Our HDX MS has been applied to study protein/macromolecular complexes from all types of organisms including humans, yeast, E. coli, cyanobacteria or other microorganisms, specific complexes including proteins/peptides or small polypeptides, protein/nucleic acid, etc.

Protein/Small Molecule Interactions

Protein/small molecule interactions are also included in our scope. Small molecules referred to here are usually therapeutic drugs, natural substrates, regulatory molecules, metal ions or antibiotics, but can also be lipids, glycans, aromatic contaminants, metabolites, etc. In particular, our technology can be used to better characterize the effect of small molecules on target proteins in cancer small molecule therapy.

Fig.1 Small molecule interactions with a protein.^[1]

Technical Features

To improve the quality of data and gain more meaningful scientific insights from research findings, we have upgraded our HDX MS experimental technology, which include:

• Perform sample quality assessments prior to HDX experiments. Evaluations include denaturing electrophoresis (SDS-PAGE) analysis and intact protein mass spectrometry to confirm sample purity and confirm expected sequence and post-translational modifications.
• Size exclusion chromatography analysis was performed to determine the monomeric/oligomeric state of the studied samples.
• The composition of the buffer used in the labeling reaction as well as the temperature and pH were precisely recorded, and the labeling buffer and protein solution were pre-equilibrated at the HDX experimental temperature.
• Precisely maintain and clearly report the concentration of D₂O (%, v/v) present during the labeling reaction.
• Repeated measurements of deuterium incorporation were performed to ensure repeatability and provide an estimate of measurement accuracy.
• Make a "maximum label" control sample (also called a 100% exchange control) of the protein of interest, especially if absolute exchange amounts are required.
• Use a wide range of D₂O labeling times to interrogate all possible rates of amide exchange.
• For longer labeling times, if the physical stability of the protein studied under labeling conditions is unknown, first perform a quality control "deuterium pulse" experiment.

If you are interested in our services, please contact us immediately, then fill in the complete inquiry form, and we will reply to you as soon as possible.

References

1. Pirrone G F, et al. Applications of hydrogen/deuterium exchange MS from 2012 to 2014. Analytical chemistry. 2015, 87(1): 99-118.
2. Masson G R, et al. Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments. Nature methods. 2019, 16(7): 595-602.