Week 8: Protein-Protein interactions (PPI) + Introduction to Protein Engineering Definitions in yellow Key words Examples (specific) Protein-Protein Interactions (PPI) -Huge variety of protein functions that depend on/ are being conveyed through PPI or protein networks -Huge protein networks (P networks) exist which play major roles in cellular and molecular biology -Diseases often caused by/ involve changes in PPI (Protein aggregation/ misfolding) -Protein interactome: a complete set of PPI in a particular cell -understanding PPI = insights into molecular machinery underlying complex phenotypes, protein function, functional and metabolic pathways -Protein-DNA + protein-RNA are other common biopolymer interactions PPI brief overview -DNA transcription: transcription factors interact with each other like RNA polymerase these are protein-protein (P-P)+ protein-DNA (P-DNA) -gene regulation achieved through protein-protein interactions Translation: protein accessory factors and rRNA interact to assist translation initiation, elongation + termination (P-P + P-rRNA) -Protein Processing: PPI involved in cleavage, PTMs, folding, targeting/trafficking - anchoring -Protein Function: often involve PPI+P networks + involved in protein segregation machinery PPI Definition -PPI: Specific physical contacts with molecular docking between proteins that occur in a cell/ living organisms in vivo (Not a functional contract like ribosomal proteins + newly synthesised proteins, these are functional but not specific for one type of protein) -a specific ribosomal contact is between the ribosomal proteins within the ribosomes or antibody-antigen interaction -the interaction between the proteins needs to be intentional and not accidental (unintentional is not a PPI) -The interaction interface must be non-generic (evolved for a specific purpose distinct from generic functions such as P folding, degradation, synthesis rather than a generic contact with ribosomes, chaperones, proteases) -PPI can be stable (multi- subunit complexes) or transient (occur under set conditions like in response to ligand binding, conformational changes etc) -PPI can be strong or weak -Contacts between subunits of HSP60 and HSP10 form a complex multi subunit barrel which is a specific interaction with a specific interface that has been developed to keep the subunits together so is PPI (barrel is required to help protein folding) -However interactions between the folded protein and HSP chaperones (HSP70 - they help maintain newly folded proteins) is not PPI as it doesn't interact with a specific interface on those proteins - it is generic and just sticks to hydrophobic parts of the protein
Summary: to be considered PPI you need; 1ffi Specific physical contacts (Not functional) 2ffi Intentional interface (not accidental) 3ffi Non generic interface (evolved for that purpose) Stable PPIs -some proteins assemblies are stable macromolecular protein complexes like multi subunit proteins such as: Glutamate receptors: usually 4 different subunits which are usually formed by two dimers coming together to form a tetramer Voltage dependent gated K+ channel: 8 subunits form one protein and although its stable it has flexible components ATP synthase: many subunits with a rotation of the transmembrane subunits -These don't usually dissociate from their quaternary structure Transient PPIs -some are built only for transient actions so can form and break down transiently like transcription factors · RNA polymerase