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CHAPTER VI: DETECTION OF PROTEIN-PROTEIN INTERACTIONS VI.1. INTRODUCTION Protein interaction is crucial for every organism. Most proteins function through interaction with other molecules, and often these are other proteins. Enzymes interact with their substrates, inhibitors interact with enzymes, transport proteins interact with structural proteins, hormones interact with receptors – and that’s just a few of the interactions that happen in a cell. Some proteins are made up of more than one polypeptide chain, and the interactions between the different peptides are necessary for the whole protein to function. Since they are so essential, protein-protein interactions ( PPI ) are an important topic for scientists to understand. Nowadays, one talks about “ functional proteomics ”. There are many different functional proteomics techniques, which can be subdivided into two major groups: the biochemical and the genetic approaches . In this chapter, we would like to address the different methods that are used to unravel and study protein-protein interactions (PPI), both on a single interaction and on whole protein- protein complexes. As stated above, proteins do not act in isolation but engage in complex and dynamic interactions with other proteins to fulfill their diverse cellular roles and are intrinsic to every cellular process such as c DNA replication e.g. DNA replication complex c Transcription/Translation e.g. RNA polymerase is a multi-subunit complex, ribonucleoprotein complexes such as the snRNPs of the spliceosome c Splicing c Secretion c Cell cycle control c Transport of proteins across membranes e.g. nuclear pore complex (contains about 100 different interacting proteins) c Signal transduction e.g. receptor complexes (signalosomes)
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When an interaction takes place between two or more proteins, this often results in a measurable or detectable effect such as c Alteration of the kinetic properties of proteins c Formation of new binding site c (In)activation of a protein c Change specificity of a protein for its substrate (e.g. interaction of transcription factors with RNA polymerase directs the polymerase to different promoters) c Modification of a protein (e.g. phosphorylation of a substrate by its kinase) c Translocation of a protein c Why study PPIs? If one can identify an interaction between an unknown protein and a well-characterized protein, this will give you information of the function of the former one, to place it in a signalling pathway, . .. On the other hand, interference with intermolecular interactions or with PPIs by drugs is of interest for pharmaceutical and biotech companies. In the past century, drug development has been focusing mainly on inhibition of enzymes such as kinases, proteases,… as well as on inhibition of G-protein coupled receptors, which represent the largest class of receptors (development of agonistic or antagonistic ligands). The contact surfaces involved in these protein – small molecule interactions
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This note was uploaded on 05/28/2010 for the course WE BIBI000000 taught by Professor Johangrooten during the Spring '10 term at Ghent University.

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