Intrinsically disordered

I. Testing Whether Intrinsic Disorder Is Encoded by the Amino... 

Intrinsic disorder might not be encoded by the sequence, but rather might be the result of the absence of suitable tertiary interactions. If this were the general cause of intrinsic disorder, any subset of ordered sequences and any subset of disordered sequences would likely be the same within the statistical uncertainty of the sampling. On the other hand, if intrinsic disorder were encoded by the amino acid sequence, any subset of disordered sequences would likely differ significantly from samples of ordered protein sequences. Thus, to test the hypothesis that disorder is encoded by the sequence, we collected examples of intrinsically ordered and intrinsically disordered proteins, then determined whether and how their sequences were distinguishable. 

Once sufficient numbers of intrinsically disordered and ordered protein sequences were collected, it became possible to compare them directly. The sequences in these databases were examined for dilferences in amino acid composition, sequence attributes, and evolutionary characteristics. 

Number of Proteins and Residues in Databases of Intrinsically Disordered Protein Characterized by Various Methods... 

The enrichments and depletions displayed in Figure 1 are concordant with what would be expected if disorder were encoded by the sequence (Williams et al., 2001). Disordered regions are depleted in the hydrophobic amino acids, which tend to be buried, and enriched in the hydrophilic amino acids, which tend to be exposed. Such sequences would be expected to lack the ability to form the hydrophobic cores that stabilize ordered protein structure. Thus, these data strongly support the conjecture that intrinsic disorder is encoded by local amino acid sequence information, and not by a more complex code involving, for example, lack of suitable tertiary interactions. 

III. PONDR Estimations of the Commonness of Intrinsically Disordered Proteins... 

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. 

There are now numerous examples of proteins that are unstructured or only partially structured under physiological conditions yet are nevertheless functional (Dunker and Obradovic, 2001 Wright and Dyson, 1999). In many cases, such intrinsically disordered proteins adopt folded structures upon binding to their biological targets. As the proteins that constitute the transcriptional machinery have become... 

The region at the surface of membranes and the underlying phospholipid head-group region are of particular interest since these regions can vary considerably with variations in the membrane phospholipid composition and under the influence of external molecules such as ions and hydrophobic molecules. The fluorescence anisotropy parameter tends to be less useful for examining this region since it is already intrinsically disordered and the... 

Intrinsic disorder is observed in conditions of perfect stoichiometry of the crystal. It is related to two main defect equilibria Schottky defects and Frenkel defects. 

Equation 4.75 finds its application in the region of intrinsic disorder (a similar equation can be developed for Frenkel defects), where Schottky and Frenkel defects are dominant with respect to point impurities and nonstoichiometry. 

Although MC is an underutilized tool in the field of computational molecular biophysics, there are beneficial features that can be exploited, especially in conjunction with implicit solvent models. Specifically, MC has the potential of accessing length scales that are inaccessible to MD in complex phenomena like peptide aggregation or conformational sampling of intrinsically disordered proteins. 

Vitalis, A., Wang, X., Pappu, R.V. Quantitative characterization of intrinsic disorder in polyglutamine insights from analysis based on polymer theories. Biophys. J. 2007, 93, 1923-37. 

The optical properties of amorphous solids are interesting. These solids are optically isotropic. Furthermore, the sharp features present in crystal spectra are absent in the spectra of amorphous solids even at low temperatures. The overall features in the electronic spectra of amorphous solids (broad band maxima) are, however, not unlike those of crystals, reflecting the importance of short-range order in determining these characteristics. The optical absorption edges of amorphous materials are not sharp and there is an exponential tail in the absorption coefficient (Fig. 7.13) associated with the intrinsic disorder. 

Comparing this with eqn (1.57), it immediately follows that Na = Nj, eV + eV = fip. An intrinsic disorder parameter C , as a measure of the disorder of metal atoms at the stoichiometric composition, is defined as (by use of... 

---