Protein-protein interactions

Proteins facilitate most biological processes in a cell. This includes gene expression, cell growth, proliferation, nutrient uptake, morphology, motility, intercellular communication, and apoptosis.

Protein expression is a dynamic process that responds to various stimuli. Specific proteins may not always be expressed or activated for certain tasks. Cells also vary in their protein expression, which can complicate the study of protein function in the appropriate biological context. However, with careful investigation and analysis, these challenges can be overcome.

Before the late 1990s, protein function analyses primarily focused on individual proteins. However, since most proteins must interact with other proteins to function, they should be studied in the context of their interacting partners. The publication of the human genome and the development of proteomics have made it essential to understand protein interactions and identify biological networks to understand their function within the cell.

Important types of protein interactions include:

• Protein-ligand interactions
• Protein-DNA interactions
• Protein-protein interactions (PPIs)

In protein-protein interactions, proteins interact with each other to carry out specific functions in cells.

Since nearly all biological processes involve one or more PPIs, studying these interactions helps us understand the molecular mechanisms interactions within these processes, including: 

Cell signaling

Many biological processes, such as cell growth, differentiation, and apoptosis are regulated by intricate signaling networks involving protein-protein interactions. By studying these interactions, researchers can understand the signaling pathways involved in diseases like cancer and develop targeted therapies that disrupt or modulate these pathways.

Enzymatic activity

Enzymes often function in complexes with other proteins, where protein-protein interactions are essential for catalytic activity. Understanding these interactions can shed light on enzyme regulation, substrate specificity, and metabolic pathways, aiding in drug discovery and metabolic engineering.

Gene regulation

Transcription factors and regulatory proteins often form complexes to control gene expression. Studying protein-protein interactions involved in gene regulation can reveal key players in transcriptional control and provide insights into diseases linked to dysregulated gene expression, such as diabetes and neurodegenerative disorders.

Protein trafficking and localization

Protein-protein interactions govern the intracellular trafficking and localization of proteins within cells. By deciphering these interactions, researchers can uncover the mechanisms underlying organelle targeting, vesicular transport, and protein sorting, which are crucial for cellular homeostasis and function.

Structural biology

Protein-protein interactions contribute to the assembly of macromolecular complexes with specific architectures and functions. Using techniques like X-ray crystallography and cryo-electron microscopy, it is possible to determine the structures of these complexes. These analyses provide atomic-level insights into their mechanisms of action and support rational drug design.

Disease mechanisms

Malfunctioning protein-protein interactions are implicated in numerous diseases, including neurodegenerative disorders, autoimmune diseases, and infectious diseases. By studying these interactions, researchers can identify potential therapeutic targets and develop drugs that disrupt harmful interactions or stabilize beneficial ones.

Protein-protein interactions can be studied with several experimental techniques, each with unique advantages and limitations. The insights that these studies provide depend on the selected analysis method. 

Some (but not all) of the most widely used PPI analysis methods include:

Malvern Panalytical instruments have been used in several studies that analyze PPIs. A few examples are below: 

Plant membrane receptor kinases

Grating-coupled interferometry (GCI) with the WAVEsystem was used to explore the binding between several plant receptors and their ligands, and the role of a coreceptor (SERK3). Where the individual receptors have significantly different binding affinities for their respective ligands, the SERK3 ectodomain binds to the ligand-associated receptors with similar binding kinetics. 

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Cytokines and their mimics

GCI with the WAVEsystem was used to analyze interactions with synthetically produced ‘receptor mimics’ of cell surface receptors, which are often of interest as drug targets. 

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Voltage-gated calcium channel (Ca_v) interactions

Isothermal Titration Calorimetry (ITC) on the MicroCal demonstrated that changing the backbone of the protein can change the protein-protein interaction in voltage-gated calcium channels. 

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Peptide-based inhibitors of protein-protein interactions (ITC)

This paper reviewed the uses of ITC alongside other technologies to investigate the characteristics of constrained peptides that inhibit protein-protein interactions. 

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