The nucleoprotein of measles virus consists of an Nterminal moiety, N CORE , resistant to proteolysis and a C-terminal moiety, N TAIL , hypersensitive to proteolysis and not visible as a distinct domain by electron microscopy. We report the bacterial expression, purification, and characterization of measles virus N TAIL . Using nuclear magnetic resonance, circular dichroism, gel filtration, dynamic light scattering, and small angle x-ray scattering, we show that N TAIL is not structured in solution. Its sequence and spectroscopic and hydrodynamic properties indicate that N TAIL belongs to the premolten globule subfamily within the class of intrinsically disordered proteins. The same epitopes are exposed in N TAIL and within the nucleoprotein, which rules out dramatic conformational changes in the isolated N TAIL domain compared with the full-length nucleoprotein. Most unstructured proteins undergo some degree of folding upon binding to their partners, a process termed "induced folding." We show that N TAIL is able to bind its physiological partner, the phosphoprotein, and that it undergoes such an unstructured-to-structured transition upon binding to the C-terminal moiety of the phosphoprotein. The presence of flexible regions at the surface of the viral nucleocapsid would enable plastic interactions with several partners, whereas the gain of structure arising from induced folding would lead to modulation of these interactions. These results contribute to the study of the emerging field of natively unfolded proteins.

It is widely assumed that new proteins are created by duplication, fusion, or fission of existing coding sequences. Another mechanism of protein birth is provided by overlapping genes. They are created de novo by mutations within a coding sequence that lead to the expression of a novel protein in another reading frame, a process called "overprinting." To investigate this mechanism, we have analyzed the sequences of the protein products of manually curated overlapping genes from 43 genera of unspliced RNA viruses infecting eukaryotes. Overlapping proteins have a sequence composition globally biased toward disorder-promoting amino acids and are predicted to contain significantly more structural disorder than nonoverlapping proteins. By analyzing the phylogenetic distribution of overlapping proteins, we were able to confirm that 17 of these had been created de novo and to study them individually. Most proteins created de novo are orphans (i.e., restricted to one species or genus). Almost all are accessory proteins that play a role in viral pathogenicity or spread, rather than proteins central to viral replication or structure. Most proteins created de novo are predicted to be fully disordered and have a highly unusual sequence composition. This suggests that some viral overlapping reading frames encoding hypothetical proteins with highly biased composition, often discarded as noncoding, might in fact encode proteins. Some proteins created de novo are predicted to be ordered, however, and whenever a three-dimensional structure of such a protein has been solved, it corresponds to a fold previously unobserved, suggesting that the study of these proteins could enhance our knowledge of protein space.

In the past few years there has been a growing awareness that a large number of proteins contain long disordered (unstructured) regions that often play a functional role. However, these disordered regions are still poorly detected. Recognition of disordered regions in a protein is important for two main reasons: reducing bias in sequence similarity analysis by avoiding alignment of disordered regions against ordered ones, and helping to delineate boundaries of protein domains to guide structural and functional studies. As none of the available method for disorder prediction can be taken as fully reliable on its own, we present an overview of the methods currently employed highlighting their advantages and drawbacks. We show a few practical examples of how they can be combined to avoid pitfalls and to achieve more reliable predictions.

The existence and extent of disorder within the replicative complex (N, P and the polymerase, L) of Paramyxovirinae were investigated, drawing on the discovery that the N-terminal moiety of the phosphoprotein (P) and the C-terminal moiety of the nucleoprotein (N) of measles virus are intrinsically unstructured. We show that intrinsic disorder is a widespread property within Paramyxovirinae N and P, using a combination of different computational approaches relying on different physico-chemical concepts. Notably, experimental support that has often gone unnoticed for most of the predictions has been found in the literature. Identification of disordered regions allows the unveiling of a common organization in all Paramyxovirinae P, which are composed of six modules defined on the basis of structure or sequence conservation. The possible functional significance of intrinsic disorder is discussed in the light of experimental data, which show that unstructured regions of P and N are involved in numerous interactions with several protein and protein-RNA partners. This study provides a contribution to the rather poorly investigated field of intrinsically disordered proteins and helps in targeting protein domains for structural studies. INTRODUCTIONParamyxovirinae, which include major human pathogens such as parainfluenza virus and measles virus (MV), are enveloped viruses with a non-segmented, negative, singlestranded RNA genome encapsidated by the nucleoprotein (N) within a helical nucleocapsid. Transcription and replication are carried out on this (N : RNA) template by a viral RNA-dependent RNA polymerase complex, made of the phosphoprotein (P) and the large protein (L) (reviewed by Lamb & Kolakofsky, 2001). Association of P with the soluble, monomeric form of N (N o ) prevents its illegitimate self-assembly onto cellular RNA. The assembled form of N (N NUC ) also forms complexes with P and P-L during transcription and replication (Lamb & Kolakofsky, 2001). N consists of two regions: an N-terminal moiety, well conserved in sequence, N CORE , and a hypervariable, Cterminal moiety, N TAIL . N CORE contains all the regions necessary for self-assembly and RNA binding. N TAIL binds P within both N NUC and N o and is required for N : RNA to act as a template for viral RNA synthesis (Bankamp et al., 1996;Buchholz et al., 1994; Curran et al., 1993;Harty & Palese, 1995;Nishio et al., 1999).From a structural point of view, P is the best-characterized protein of the replicative complex. P is organized into two moieties that are functionally and structurally distinct: a C-terminal moiety (PCT) and an N-terminal moiety (PNT).PCT is the most conserved in sequence and contains all regions required for virus transcription, whereas PNT, which is poorly conserved, provides several additional functions required for replication (Curran & Kolakofsky, 1999). P forms oligomers through a coiled-coil motif located within PCT. PCT also contains the region responsible for binding to L (Liston et al., 1995;Smallwood et al., 1994), as well as th...