More Than 1,001 Problems with Protein Domain Databases: Transmembrane Regions, Signal Peptides and the Issue of Sequence Homology

Large-scale genome sequencing gained general importance for life science because functional annotation of otherwise experimentally uncharacterized sequences is made possible by the theory of biomolecular sequence homology. Historically, the paradigm of similarity of protein sequences implying common structure, function and ancestry was generalized based on studies of globular domains. Having the same fold imposes strict conditions over the packing in the hydrophobic core requiring similarity of hydrophobic patterns. The implications of sequence similarity among non-globular protein segments have not been studied to the same extent; nevertheless, homology considerations are silently extended for them. This appears especially detrimental in the case of transmembrane helices (TMs) and signal peptides (SPs) where sequence similarity is necessarily a consequence of physical requirements rather than common ancestry. Thus, matching of SPs/TMs creates the illusion of matching hydrophobic cores. Therefore, inclusion of SPs/TMs into domain models can give rise to wrong annotations. More than 1001 domains among the 10,340 models of Pfam release 23 and 18 domains of SMART version 6 (out of 809) contain SP/TM regions. As expected, fragment-mode HMM searches generate promiscuous hits limited to solely the SP/TM part among clearly unrelated proteins. More worryingly, we show explicit examples that the scores of clearly false-positive hits, even in global-mode searches, can be elevated into the significance range just by matching the hydrophobic runs. In the PIR iProClass database v3.74 using conservative criteria, we find that at least between 2.1% and 13.6% of its annotated Pfam hits appear unjustified for a set of validated domain models. Thus, false-positive domain hits enforced by SP/TM regions can lead to dramatic annotation errors where the hit has nothing in common with the problematic domain model except the SP/TM region itself. We suggest a workflow of flagging problematic hits arising from SP/TM-containing models for critical reconsideration by annotation users

Fe-57 Mössbauer and Mo K-EXAFS Investigations of MoxFe3-xO4, an Interesting Mixed-Valent Oxide System

Ferrites of the formula MoxFe3-xO4, prepared by a soft-chemistry route, show mixed valence states of both iron and molybdenum cations. Mössbauer studies show that Fe2+ and Fe3+ ions are present on both the A and B sites, giving Fe an average oxidation state between 2+ and 3+. Molybdenum is present in the 3+ and the 4+ states on the B sites. The presence of Mo in the 3+ state has been established by determining the Mo3+-O distance (2.2 Å), for the first time, by Mo K-EXAFS. The mixed valence of Fe on both the A and B sites and of Mo on the B sites is responsible for the fast electron transfer between the cations. All the Mössbauer parameters including the line width show a marked change at a composition (x ? 0.3) above which the concentration of Fe2+A increases rapidly

Effects of silicon addition on the electrical and magnetic properties of copper-doped (La,Ca)MnO3 compounds

In this paper we report about the electrical properties of La0.7Ca0.3MnO3 compounds substituted by copper on the manganese site and/or deliberately contaminated by SiO2 in the reactant mixture. Several phenomena have been observed and discussed. SiO2 addition leads to the formation of an apatite-like secondary phase that affects the electrical conduction through the percolation of the charge carriers. On the other hand, depending on the relative amounts of copper and silicon, the temperature dependence of the electrical resistivity can be noticeably modified: our results enable us to compare the effects of crystallographic vacancies on the A and B sites of the perovskite with the influence of the copper ions substituted on the manganese site. The most original result occurs for the compounds with a small ratio Si/Cu, which display double-peaked resistivity vs. temperature curves. (C) 2003 Elsevier B.V. All rights reserved