Protein–protein interaction
Protein–protein interactions are physical contacts of high specificity established between two or more protein molecules as a result of biochemical events steered by interactions that include electrostatic forces, hydrogen bonding and the hydrophobic effect. Many are physical contacts with molecular associations between chains that occur in a cell or in a living organism in a specific biomolecular context.
Proteins rarely act alone as their functions tend to be regulated. Many molecular processes within a cell are carried out by molecular machines that are built from numerous protein components organized by their PPIs. These physiological interactions make up the so-called interactomics of the organism, while aberrant PPIs are the basis of multiple aggregation-related diseases, such as Creutzfeldt–Jakob and Alzheimer's diseases.
PPIs have been studied with many methods and from different perspectives: biochemistry, quantum chemistry, molecular dynamics, signal transduction, among others. All this information enables the creation of large protein interaction networks – similar to metabolic or genetic/epigenetic networks – that empower the current knowledge on biochemical cascades and molecular etiology of disease, as well as the discovery of putative protein targets of therapeutic interest.
Examples
Electron transfer proteins
In many metabolic reactions, a protein that acts as an electron carrier binds to an enzyme that acts as its reductase. After it receives an electron, it dissociates and then binds to the next enzyme that acts as its oxidase. These interactions between proteins are dependent on highly specific binding between proteins to ensure efficient electron transfer. Examples: mitochondrial oxidative phosphorylation chain system components cytochrome c-reductase / cytochrome c / cytochrome c oxidase; microsomal and mitochondrial P450 systems.In the case of the mitochondrial P450 systems, the specific residues involved in the binding of the electron transfer protein adrenodoxin to its reductase were identified as two basic Arg residues on the surface of the reductase and two acidic Asp residues on the adrenodoxin.
More recent work on the phylogeny of the reductase has shown that these residues involved in protein–protein interactions have been conserved throughout the evolution of this enzyme.
Signal transduction
The activity of the cell is regulated by extracellular signals. Signal propagation inside and/or along the interior of cells depends on PPIs between the various signaling molecules. The recruitment of signaling pathways through PPIs is called signal transduction and plays a fundamental role in many biological processes and in many diseases including Parkinson's disease and cancer.Membrane transport
A protein may be carrying another protein.Cell metabolism
In many biosynthetic processes enzymes interact with each other to produce small compounds or other macromolecules.Muscle contraction
Physiology of muscle contraction involves several interactions. Myosin filaments act as molecular motors and by binding to actin enables filament sliding. Furthermore, members of the skeletal muscle lipid droplet-associated proteins family associate with other proteins, as activator of adipose triglyceride lipase and its coactivator comparative gene identification-58, to regulate lipolysis in skeletal muscleTypes
To describe the types of protein–protein interactions it is important to consider that proteins can interact in a "transient" way or to interact with other proteins in a "stable" way to form complexes that become molecular machines within the living systems. A protein complex assembly can result in the formation of homo-oligomeric or hetero-oligomeric complexes. In addition to the conventional complexes, as enzyme-inhibitor and antibody-antigen, interactions can also be established between domain-domain and domain-peptide. Another important distinction to identify protein–protein interactions is the way they have been determined, since there are techniques that measure direct physical interactions between protein pairs, named "binary" methods, while there are other techniques that measure physical interactions among groups of proteins, without pairwise determination of protein partners, named "co-complex" methods.Homo-oligomers vs. hetero-oligomers
Homo-oligomers are macromolecular complexes constituted by only one type of protein subunit. Protein subunits assembly is guided by the establishment of non-covalent interactions in the quaternary structure of the protein. Disruption of homo-oligomers in order to return to the initial individual monomers often requires denaturation of the complex. Several enzymes, carrier proteins, scaffolding proteins, and transcriptional regulatory factors carry out their functions as homo-oligomers.Distinct protein subunits interact in hetero-oligomers, which are essential to control several cellular functions. The importance of the communication between heterologous proteins is even more evident during cell signaling events and such interactions are only possible due to structural domains within the proteins.
Stable interactions vs. transient interactions
Stable interactions involve proteins that interact for a long time, taking part of permanent complexes as subunits, in order to carry out functional roles. These are usually the case of homo-oligomers, and some hetero-oligomeric proteins, as the subunits of ATPase. On the other hand, a protein may interact briefly and in a reversible manner with other proteins in only certain cellular contexts – cell type, cell cycle stage, external factors, presence of other binding proteins, etc. – as it happens with most of the proteins involved in biochemical cascades. These are called transient interactions. For example, some G protein–coupled receptors only transiently bind to Gi/o proteins when they are activated by extracellular ligands, while some Gq-coupled receptors, such as muscarinic receptor M3, pre-couple with Gq proteins prior to the receptor-ligand binding. Interactions between intrinsically disordered protein regions to globular protein domains are transient interactions.Covalent vs. non-covalent
Covalent interactions are those with the strongest association and are formed by disulphide bonds or electron sharing. While rare, these interactions are determinant in some posttranslational modifications, as ubiquitination and SUMOylation. Non-covalent bonds are usually established during transient interactions by the combination of weaker bonds, such as hydrogen bonds, ionic interactions, Van der Waals forces, or hydrophobic bonds.Role of water
Water molecules play a significant role in the interactions between proteins. The crystal structures of complexes, obtained at high resolution from different but homologous proteins, have shown that some interface water molecules are conserved between homologous complexes. The majority of the interface water molecules make hydrogen bonds with both partners of each complex. Some interface amino acid residues or atomic groups of one protein partner engage in both direct and water mediated interactions with the other protein partner. Doubly indirect interactions, mediated by two water molecules, are more numerous in the homologous complexes of low affinity. Carefully conducted mutagenesis experiments, e.g. changing a tyrosine residue into a phenylalanine, have shown that water mediated interactions can contribute to the energy of interaction. Thus, water molecules may facilitate the interactions and cross-recognitions between proteins.Structure
The molecular structures of many protein complexes have been unlocked by the technique of X-ray crystallography. The first structure to be solved by this method was that of sperm whale myoglobin by Sir John Cowdery Kendrew. In this technique the angles and intensities of a beam of X-rays diffracted by crystalline atoms are detected in a film, thus producing a three-dimensional picture of the density of electrons within the crystal.Later, nuclear magnetic resonance also started to be applied with the aim of unravelling the molecular structure of protein complexes. One of the first examples was the structure of calmodulin-binding domains bound to calmodulin. This technique is based on the study of magnetic properties of atomic nuclei, thus determining physical and chemical properties of the correspondent atoms or the molecules. Nuclear magnetic resonance is advantageous for characterizing weak PPIs.
Protein-protein interaction domains
Some proteins have specific structural domains or sequence motifs that provide binding to other proteins. Here are some examples of such domains:- Src homology 2 domain
- Src homology 3 domain
- Phosphotyrosine-binding domain
- LIM domain
- Sterile alpha motif domain
- PDZ domain
- FERM domain
- Calponin homology domain
- Pleckstrin homology domain
- WW domain
- ''WSxWS motif ''
Properties of the interface
Parameters evaluated include size, shape, complementarity between surfaces, residue interface propensities, hydrophobicity, segmentation and secondary structure, and conformational changes on complex formation.
The great majority of PPI interfaces reflects the composition of protein surfaces, rather than the protein cores, in spite of being frequently enriched in hydrophobic residues, particularly in aromatic residues. PPI interfaces are dynamic and frequently planar, although they can be globular and protruding as well. Based on three structures – insulin dimer, trypsin-pancreatic trypsin inhibitor complex, and oxyhaemoglobin – Cyrus Chothia and Joel Janin found that between 1,130 and 1,720 Å2 of surface area was removed from contact with water indicating that hydrophobicity is a major factor of stabilization of PPIs. Later studies refined the buried surface area of the majority of interactions to 1,600±350 Å2. However, much larger interaction interfaces were also observed and were associated with significant changes in conformation of one of the interaction partners. PPIs interfaces exhibit both shape and electrostatic complementarity.