Protein–Protein Interactions Essentials Key Concepts to Building and Analyzing Interactome Networks 英文参考文献.docVIP

Education Protein–ProteinInteractionsEssentials:KeyConceptsto BuildingandAnalyzingInteractomeNetworks JavierDeLasRivas*,CeliaFontanillo BioinformaticsFunctionalGenomicsResearchGroup,CancerResearchCenter(CiC-IBMCC,CSIC/USAL),Salamanca,Spain This PLoS Computational Biology tuto- To achieve appropriate understanding of PPIs and to design better ways for analyzing and interpreting them, this educational review presents several essen- tial concepts and definitions intended to facilitate the use of PPI information both by computational and experimental biologists. are. Commonly they are understood as physical contacts with molecular docking betweenproteinsthatoccurinacellorin a living organism in vivo. As discussed previously [5,6], the issue of whether two proteins share a ‘‘functional contact’’ is quitedistinctfromthequestionofwhether the same two proteins interact directly with each other. Any protein in the ribosome or in the basal transcriptional apparatussharesafunctionalcontactwith the other proteins in the complex, but certainly not all the proteins in the particular complex interact. Indubitably, the existence of many other types of rialwaspresentedatISMB2009 Decades of research into cell biology, molecular biology, biochemistry, structural biology, and biophysics have produced a remarkable compendium of knowledge on the function and molecular properties of individual proteins. This knowledge iswell recordedandmanuallycuratedintomajor proteindatabaseslikeUniProt[1,2].How- ever,proteinsrarelyactalone.Manytimes they team up into ‘‘molecular machines’’ andhaveintricatephysicochemicaldynamic connections to undertake biological func- tionsatbothcellular and systems levels.A criticalsteptowardsunravelingthecomplex molecular relationships in living systems is the mapping of protein-to-protein physical ‘‘interactions’’.Thecompletemapofprotein interactions that can occur in a living organism is called the interactome [3]. Interactome mapping has become one of