Unique Advantages & Insights of Fox Radical Protein Footprinting
Fox Radical Protein Footprinting (FRPF) reveals how a protein’s structure responds when something binds it—across a wide range of protein classes and systems. These discoveries have the potential to greatly influence decision-making at every stage of the drug discovery and development journey, all leading to safer, more effective, and stable therapeutics.
Discover the cutting-edge advantages and new insights enabled by FRPF Systems & Services.
UNIQUE ADVANTAGES
FRPF directly measures the solvent accessibility of most amino acid side chains within a protein. When hydroxyl radicals (•OH) react with amino acid side chains, FRPF can identify individual residues that are exposed to the solvent and those that are shielded within the protein structure. This information is critical for understanding protein folding, dynamics, and interactions.
FRPF can validate the higher order structure of complex biologics, such as mAbs, by confirming the correct folding and assembly of the protein. By comparing the experimental FRPF data with the expected solvent accessibility based on the known protein structure, researchers can assess the structural integrity and accuracy of the higher-order structure of the biologic.
FRPF produces high spatial resolution information about protein structure, such as pinpointing specific amino acids and regions within a protein that are solvent-accessible or buried. This level of detail allows researchers to map protein surfaces and identify regions involved in protein-protein or protein-ligand interactions accurately.
FRPF handles a wide range of protein classes, including ones that are soluble, within the membrane, or form complexes. Not limited by size, type, or structure, FRPF enables researchers to study diverse protein systems. Able to handle very large and heterogeneous systems, insights generated by FRPF contribute to a better understanding of protein function and communication.
FRPF complements other structural biology techniques, such as X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, Hydrogen/Deuterium eXchange (HDX), cryo-electron microscopy (cryo-EM), and molecular modeling. FRPF provides information about proteins in a native solution state that may not be usable with other research methods. By combining FRPF with other techniques, researchers can obtain a more comprehensive understanding of protein structure and function.
NOVEL INSIGHTS
FRPF identifies protein-protein interaction sites and interfaces. By measuring how protein-protein interactions change the solvent accessibility of residues at the interaction interface, Fox Systems can pinpoint the regions or domains responsible for binding. This information helps researchers understand the structural basis of protein interactions, including those involving mAbs and their target antigens or other interacting proteins.
FRPF generates valuable information about the solvent accessibility of residues involved in antibody-antigen interactions and can rapidly identify changes that occur upon binding. This approach allows for the identification and mapping of the mAb’s epitopes and paratopes, providing insights into the binding interfaces and the regions responsible for antibody-antigen recognition. This knowledge is crucial for the design and optimization of therapeutic antibodies and diagnostic reagents.
FRPF uncovers valuable information about protein-ligand interactions. By assessing changes in solvent accessibility upon ligand binding, Fox Technology can identify residues involved in the binding site and reveal the conformational changes induced by the ligand. This information aids in understanding the binding mechanism and guiding drug discovery efforts.
FRPF detects conformational changes and dynamics within a protein. By comparing FRPF data across different conditions or time points, researchers can identify regions or domains that undergo structural rearrangements, exposing or shielding certain residues. This capability allows for the study of conformational dynamics, such as ligand-induced conformational changes or structural responses to environmental factors.
FRPF identifies regions influenced by allostery, which are critical for understanding how proteins transmit signals and undergo functional changes. By uncovering the regions impacted by allostery, the FRPF method helps elucidate the underlying mechanisms of protein function and assists in drug discovery efforts targeting allosteric sites.
FRPF reveals the solvent accessibility of glycoproteins. Glycans shield certain amino acids from oxidation, allowing researchers to understand glycan-protein interactions. Additionally, the approach helps analyze glycoprotein conformational changes and glycoprotein-protein interactions under various conditions, providing a more comprehensive understanding of glycoprotein structure and function.
To rapidly test structural models, FRPF data can be compared to the predicted solvent accessibility and flexibility from the structural model of the protein. Areas of the protein that are more susceptible to hydroxyl radical modification correspond to regions that are flexible in the model. Conversely, regions that are protected from modification correspond to buried or rigid regions. Discrepancies between the experimental data and the structural model can indicate potential structural inaccuracies. This information can be used to refine or validate the structural model.
