Summary: Protein disorder is characterized by a lack of a stable 3D structure, and is considered to be involved in a number of important protein functions such as regulatory and signalling events. We developed a web application, the POODLE-S, which predicts the disordered region from amino acid sequences by using physicochemical features and reduced amino acid set of a position-specific scoring matrix. Availability: POODLE-S is available from http://mbs.cbrc.jp/poodle/ poodle-s.html and can be used by both academic and commercial users.
Polyelectrolyte multilayer thin films were prepared by an alternate deposition of poly(allylamine hydrochloride) (PAH) and anionic polysaccharides {carboxymethylcellulose (CMC) and alginic acid (AGA)} on the surface of a gold (Au) disk electrode, and the binding of ferricyanide [Fe(CN)(6)](3)(-) and hexaammine ruthenium ions [Ru(NH(3))(6)](3+) to the films was evaluated. Poly(acrylic acid) (PAA) was also employed as a reference polyanion bearing carboxylate side chains. A quartz-crystal microbalance study showed that PAH-CMC and PAH-AGA multilayer films grow exponentially as the number of depositions increases. The thicknesses of five bilayers of (PAH-CMC)(5) and (PAH-AGA)(5) films were estimated to be 150 +/- 20 and 90 +/- 15 nm, respectively, in the dry state. The PAH/polysaccharide multilayer film-coated Au electrodes exhibited a redox response to the [Fe(CN)(6)](3)(-) ion dissolved in solution, irrespective of the sign of the surface charge of the film, suggesting the high permeability of the films to the [Fe(CN)(6)](3)(-) ion. In contrast, the PAH-PAA film-coated Au electrodes exhibited a redox response only when the outermost surface of the film was covered with a positively charged PAH layer. However, the permeation of the [Ru(NH(3))(6)](3+) cation was severely suppressed for all of the multilayer films. It was possible to confine the [Fe(CN)(6)](3)(-) ion in the films by immersing the film-coated electrodes in a 1 mM [Fe(CN)(6)](3)(-) solution for 15 min. Thus, the [Fe(CN)(6)](3)(-)-confined electrodes exhibited a cyclic voltammetric response in the [Fe(CN)(6)](3)(-) ion-free buffer solution. The loading of the [Fe(CN)(6)](3)(-) ion in the films was higher when the surface charge of the film was positive and increased with increasing film thickness. It was also found that the [Fe(CN)(6)](3)(-) ion confined in the films serves as an electrocatalyst that oxidizes ascorbic acid in solution.
Background: Predicting intrinsically disordered proteins is important in structural biology because they are thought to carry out various cellular functions even though they have no stable three-dimensional structure. We know the structures of far more ordered proteins than disordered proteins. The structural distribution of proteins in nature can therefore be inferred to differ from that of proteins whose structures have been determined experimentally. We know many more protein sequences than we do protein structures, and many of the known sequences can be expected to be those of disordered proteins. Thus it would be efficient to use the information of structure-unknown proteins in order to avoid training data sparseness. We propose a novel method for predicting which proteins are mostly disordered by using spectral graph transducer and training with a huge amount of structure-unknown sequences as well as structure-known sequences.
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