DOI: 10.1002/cphc.200900205 Limitations of Induced Folding in Molecular Recognition by Intrinsically Disordered Proteins Eszter Hazy and Peter Tompa* [a] 1. Introduction The traditional structure–func- tion paradigm equated protein function with a well-defined 3D structure, thought to be re- quired for the appropriate spa- tial arrangement of residues critical for molecular recognition and/or catalysis. This model has been instrumental in under- standing the molecular mecha- nism of the function of a wide array of enzymes, receptors, structural proteins and many more. It has recently been recognized, however, that the un- derlying structural view portrays too simple a picture, as many proteins and protein domains exist and function in an intrinsi- cally disordered (also termed intrinsically unstructured) state. [1–4] In structural terms, intrinsically disordered proteins (IDPs) resem- ble the denatured states of ordered proteins, characterized by an ensemble of rapidly interconverting alternative confor- ACHTUNGTRENNUNGmations. Many well-known proteins involved in key cellular processes and/or in diseases, such as casein, the prion protein and p53 (cf. Table 1) are either fully (IDP) or partially (intrinsically disordered region, IDR) disordered. IDPs/IDRs are common in proteomes and their frequency increases with increasing com- plexity of the organisms. Structural disorder is more than a mere curiosity, as underlined by its increased frequency in com- plex organisms and prevalence in proteins associated with signal transduction, cell-cycle regulation, gene expression and chaperone action. [5–7] Structural disorder confers many advan- tages on proteins, such as an increased speed of interaction, specificity without excessive binding strength and adaptability in binding. [1, 3, 8] As discussed in detail herein, IDPs often carry out their function by molecular recognition, when their short segment (recognition element) undergoes induced folding upon contacting the partner. We elucidate on the limitations of this emerging model by discussing recent results, which show that IDPs often use disordered domains for recognition, [9] part of their structure remains disordered even in the bound state [10] and due to their structural adaptability they can carry out differ- ent, sometimes disparate functions. [11] [a] E. Hazy, P. Tompa Institute of Enzymology, Biological Research Center Hungarian Academy of Sciences, P.O. Box 7, 1518 Budapest (Hungary) Fax: (+ 36) 1-466-5465 E-mail : tompa@enzim.hu Intrinsically disordered proteins (IDPs) exist and function with- out well-defined three-dimensional structures, thus they defy the classical structure–function paradigm. These proteins are common in proteomes, and they carry out essential functions often related to signalling and regulation of transcription. Herein, the experimental evidence for their lack of structure and the major functional benefits that structural disorder con- fers, are surveyed. It is shown that IDPs often function by mo- lecular recognition, in which either short motifs, or domain- sized disordered segments are used for partner recognition. In both cases, the binding segment undergoes induced folding and it attains an ordered structure. This folding-upon-binding scenario suggests that the function of IDPs can be interpreted in terms of the static structural view of the classical paradigm. New developments in the field, however, suggest that folding upon binding is limited, and many IDPs preserve a significant level of disorder in the bound state, a phenomenon termed fuzziness. In addition, IDPs may structurally adapt to different partners with different functional outcomes, resulting in pro- miscuity in function termed moonlighting. It is suggested that a new model describing the structure–function relationship of IDPs has to encompass such structural and functional promis- cuity inherent in the disordered state of IDPs. Table 1. Examples of IDPs: IDPs can be classified into six broad categories in terms of their functional modes. Here one representative of each category, with reference to its experimentally demonstrated disorder (DisProt database number [47] ) and function is given. Protein DisProt number Function titin DP00072 Entropic chain, (PEVK domain) elasticity in muscle CREB DP00080 Display site, (KID domain) transcription regulation upon PKA activation LEA protein DP00185 Chaperone, prevention of protein aggregation in dehydrated plant securin DP00521 Effector , inhibitor of separase in cell-cycle regulation p53 DP00086 Assembler , (trans-activator domain) transcription regulation in DNA repair and apoptosis casein DP00330 Scavenger , prevention of calcium-phosphate precipitation in milk ChemPhysChem 2009, 10, 1415 – 1419  2009 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim 1415