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The majority of the proteins encoded in the genomes of eukaryotes containmore than one domain. Reasons for high prevalence of multi-domain proteins invarious organisms have been attributed to higher stability and functional andfolding advantages over single-domain proteins. Despite these advantages, manyproteins are composed of only one domain while their homologous domains arepart of multi-domain proteins. In the study presented here, differences in theproperties of protein domains in single-domain and multi-domain systems andtheir influence on functions are discussed. We studied 20 pairs of identicalprotein domains, which were crystallized in two forms (a) tethered to otherproteins domains and (b) tethered to fewer protein domains than (a) or nottethered to any protein domain. Results suggest that tethering of domains inmulti-domain proteins influences the structural, dynamic and energeticproperties of the constituent protein domains. 50% of the protein domain pairsshow significant structural deviations while 90% of the protein domain pairsshow differences in dynamics and 12% of the residues show differences in theenergetics. To gain further insights on the influence of tethering on thefunction of the domains, 4 pairs of homologous protein domains, where one ofthem is a full-length single-domain protein and the other protein domain is apart of a multi-domain protein, were studied. Analyses showed that identicaland structurally equivalent functional residues show differential dynamics inhomologous protein domains, though comparable dynamics between in-silicogenerated chimera protein and multi-domain proteins were observed. From theseobservations, the differences observed in the functions of homologous proteinscould be attributed to the presence of tethered domain. Overall, we concludethat tethered domains in multi-domain proteins not only provide stability orfolding advantages but also influence pathways resulting in differences infunction or regulatory properties.

Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains