Structurally, SH3 domains are constituted by a beta barrel formed by two orthogonal beta sheets and three anti-parallel beta strands.
Growth factor receptor binding proteins and phospholipase Cγ are examples of proteins that have SH2 domains. The existence of a deep binding pocket with high affinity for phosphotyrosine, but not for phosphoserine or phosphothreonine, is essential for the recognition of tyrosine phosphorylated proteins, mainly autophosphorylated growth factor receptors. SH2 domains are structurally composed by three-stranded twisted beta sheet sandwiched flanked by two alpha-helices. Proteins hold structural domains that allow their interaction with and bind to specific sequences on other proteins: Interactions between intrinsically disordered protein regions to globular protein domains (i.e. For example, some G protein-coupled receptors only transiently bind to G i/o proteins when they are activated by extracellular ligands, while some G q-coupled receptors, such as muscarinic receptor M3, pre-couple with G q proteins prior to the receptor-ligand binding. – as it happens with most of the proteins involved in biochemical cascades. 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. cytochrome c), and some hetero-oligomeric proteins, as the subunits of ATPase. These are usually the case of homo-oligomers (e.g. Stable interactions involve proteins that interact for a long time, taking part of permanent complexes as subunits, in order to carry out structural or functional roles. 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.
In addition to the conventional complexes, as enzyme-inhibitor and antibody-antigen, interactions can also be established between domain-domain and domain-peptide. A protein complex assembly can result in the formation of homo-oligomeric or hetero-oligomeric complexes. To describe the types of protein–protein interactions (PPIs) it is important to consider that proteins can interact in a 'transient' way (to produce some specific effect in a short time) or to interact with other proteins in a 'stable' way to build multiprotein complexes that are molecular machines within the living systems.
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