Protein-Peptide Interaction Analysis

Why Analyze Protein-Peptide Interaction?

Protein-peptide interactions are defined as the association and communication between proteins and peptides, which are little chains of amino acids. Peptides can be made chemically or from larger proteins and typically range in size from 10 to 50 amino acids. These interactions participate in a variety of cellular processes, including signal transduction, protein regulation, and molecular recognition, and they are crucial to many biological processes.

Proteins are large, complex molecules composed of one or more polypeptide chains folded into specific three-dimensional structures. They carry out a variety of tasks in the cell, including catalyzing metabolic processes, moving molecules, and supporting structural integrity. On the other hand, peptides are shorter sequences of amino acids that have the ability to behave as signaling molecules, cellular process mediators, or protein function regulators.

For many biological processes, interactions between proteins and peptides are essential. They allow proteins to participate in cellular signaling networks, recognize specific target sequences, modify enzymatic activity, and control gene expression. These interactions frequently take place via certain binding interfaces, in which the peptide attaches to a particular area on the surface of the protein known as the binding site or domain. Depending on the affinities and kinetics of the interaction, the binding may be temporary or permanent.

In a number of disciplines, including molecular biology, biochemistry, drug discovery, and therapeutic development, it is crucial to comprehend protein-peptide interactions. Insight into the regulation of protein activity, networks of protein-protein interactions, and the development of therapeutic approaches that target certain protein activities can all be gained through studying these interactions and their effects on cellular processes.

Extending structure prediction networks for binder classificationExtending structure prediction networks for binder classification (Motmaen et al., 2023).

Protein-Peptide Interaction Assay in Creative Proteomics

Creative Proteomics provides protein-peptide interaction analysis services, including but not limited to:

Integration Assay:

Integration assays are used to detect and quantify protein-peptide interactions. One commonly employed method is the surface plasmon resonance (SPR) technique. In SPR, the protein of interest is immobilized on a sensor surface, and the peptide is passed over it. Binding events between the protein and peptide cause a change in the refractive index, which can be detected as a shift in the SPR signal. By measuring this shift, you can determine the binding kinetics and affinity of the interaction.

Affinity Determination:

The affinity of a protein-peptide interaction refers to the strength of the binding between the two molecules. Several methods can be employed to determine affinity, including:

a. Isothermal Titration Calorimetry (ITC): ITC measures the heat changes associated with binding events. It directly determines the binding affinity by measuring the heat released or absorbed during the interaction.

b. Fluorescence-based Assays: Fluorescent labeling of either the protein or peptide allows for the measurement of changes in fluorescence upon binding. Fluorescence polarization (FP), fluorescence resonance energy transfer (FRET), or fluorescence anisotropy are common fluorescence-based techniques used to determine affinity.

c. Microscale Thermophoresis (MST): MST measures changes in the movement of molecules in a temperature gradient. The binding of a labeled peptide to a protein alters its movement, providing information about the interaction and enabling affinity determination.

Dissociation Constant (Kd) Determination:

The dissociation constant (Kd) is a quantitative measure of the affinity between a protein and a peptide. It represents the concentration of the peptide at which half of the protein is bound. Kd can be calculated from the affinity data obtained using various methods, including those mentioned above. It is often determined by fitting the experimental data to appropriate binding models, such as the law of mass action or a specific binding isotherm.

In addition, structural biology techniques, such as X-ray crystallography, NMR spectroscopy and cryo-electron microscopy, provide atomic-level details of protein-peptide complexes and help to understand their interactions at the molecular level.


  1. Motmaen, Amir, et al. "Peptide-binding specificity prediction using fine-tuned protein structure prediction networks." Proceedings of the National Academy of Sciences 120.9 (2023): e2216697120.
* This service is for RESEARCH USE ONLY, not intended for any clinical use.