Residual structure, intrinsically disordered

Recently, there has been great interest in proteins that exhibit biological activity but lack a well-defined secondary or tertiary structure after purification (Dunker et al., 1998, 2001 Schweers et al., 1994 Uversky et al., 2000 Wright and Dyson, 1999). Such proteins are referred to as intrinsically disordered or unstructured. An analysis in 1998 of the Swiss Protein Database revealed that about 15,000 proteins in that database are likely to contain disordered segments at least 40 residues in length (Romero et al., 1998). Dyson and Wright (2002) review intrinsically disordered proteins in this volume. 

Millisecond Hydrogen Exchange 87 5.4.5 Residual Structure in Intrinsically Disordered Proteins... 

The topic of intrinsically disordered proteins is covered in detail in Chapter 17. It is also discussed briefly here, however, because the characterization of residual structure in the native conformational ensembles of intrinsically disordered proteins is an important application of millisecond HX. 

Intrinsically disordered proteins adopt a broad, but bounded distribution of structures under physiological conditions [59]. While much of the sequence is often fully disordered, there are also regions where the ensemble tends to transiently form specific secondary and/or tertiary stractures, known as residual structure. Residual structure is insufficient to attenuate HX to the point where it can be detected in conventional experiments however, it is easily detected with millisecond labeling. While a number of earlier studies hinted at the use of millisecond HX to examine residual structure (even if it was only to say that their earliest 10 s time point was inadequate to characterize disordered regions) [60, 61], the first direct reference was in a 2011 study by Keppel et al., in the investigation of the interaction between an intrinsically disordered domain and a molten globule domain to form a structured complex [4], However, this study used conventional labeling times. 

R97 M. Blackledge, P. Bernado and M. R. Jensen, Atomic-Level Characterization of Disordered Protein Ensembles Using NMR Residual Dipolar Couplings , in Instrumental Analysis of Intrinsically Disordered Proteins Assessing Structure and Conformation, eds. V. Uversky and S. Longhi, John Wiley Sons, Inc., Hoboken, N. J., 2010, p. 89. 

Keppel, T.R., Weis, DD. (2015) Mapping Residual Structure in Intrinsically Disordered Proteins at Residue Resolution Using Millisecond Hydrogen/Deuterium Exchange and Residue Averaging. J. Am. Soc. Mass Spectrom. 26 547-554. 

FIGURE 8.4 Intrinsically disordered proteins (IDPs). The balance between polar and apolar residues in a protein is a key parameter that controls the formation of a hydrophobic core in water. Proteins with too much polar versus apolar residues will not fold through an entropicaUy driven mechanism and will instead adopt a myriad of conformations in water (4 possible conformers of the same protein are shown from the top of the cartoon). These proteins, referred to as "intrinsically disordered proteins" (IDPs), lack a precise 3D structure in water. IDPs have a high level of conformational plasticity and they can adapt their conformation to various molecular partners, which can be either a protein or a membrane. In this example, the protein is acidic (red surface in the lower model). The sequence of the protein is shown at the bottom of the illustration (apolar residues in black, acidic in red, and polar but not acidic in green). 

Intrinsically disordered protein (IDP) A protein without a stable three-dimensional structure. IDPs oscillate between a wide range of extended conformations. In fact, these proteins do not have a sufficient proportion of apolar amino acid residues to adopt a globular structure in water. IDPs have a high conformational plasticity that allows them to recognize and adopt their shape to various Ugands. Amyloid proteins are generally IDPs. 

Residual dipolar couplings that reflect the mutual orientation of individual chemical bonds or larger structural fragments are veiy important parameters carrying information about the transient states populated by intrinsically disordered proteins. In two reviews, by Sklenaf and co-workers and by Konrat, the development and recently proposed NMR-based strategies including RDCs to characterize transient states have been discussed. 

Nuclease-(1-126) is inactive and appears to be disordered as judged by measurements of optical rotation, circular dichroism, and intrinsic viscosity 80). Nuclease-(127-149) is also inactive and does not bind to nuclease-(1-126) (80). Thus, the cleavage of the peptide bond between residues 126 and 127 destroys the functional structure of nuclease in contrast to the cleavage of bonds in the region of residues 48-50, which leaves the structure of nuclease essentially unchanged. 

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