A novel superfamily containing the β-grasp fold involved in binding diverse soluble ligands

BACKGROUND: Domains containing the β-grasp fold are utilized in a great diversity of physiological functions but their role, if any, in soluble or small molecule ligand recognition is poorly studied. RESULTS: Using sensitive sequence and structure similarity searches we identify a novel superfamily containing the β-grasp fold. They are found in a diverse set of proteins that include the animal vitamin B12 uptake proteins transcobalamin and intrinsic factor, the bacterial polysaccharide export proteins, the competence DNA receptor ComEA, the cob(I)alamin generating enzyme PduS and the Nqo1 subunit of the respiratory electron transport chain. We present evidence that members of this superfamily are likely to bind a range of soluble ligands, including B12. There are two major clades within this superfamily, namely the transcobalamin-like clade and the Nqo1-like clade. The former clade is typified by an insert of a β-hairpin after the helix of the β-grasp fold, whereas the latter clade is characterized by an insert between strands 4 and 5 of the core fold. CONCLUSION: Members of both clades within this superfamily are predicted to interact with ligands in a similar spatial location, with their specific inserts playing a role in the process. Both clades are widely represented in bacteria suggesting that this superfamily was derived early in bacterial evolution. The animal lineage appears to have acquired the transcobalamin-like proteins from low GC Gram-positive bacteria, and this might be correlated with the emergence of the ability to utilize B12 produced by gut bacteria. REVIEWERS: This article was reviewed by Andrei Osterman, Igor Zhulin, and Arcady Mushegian

Discovery of Novel Term Associations in a Document Collection

Non peer reviewe

A Comparison of Automatic Summarizers of Texts in Brazilian Portuguese

Automatic Summarization (AS) in Brazil has only recently become a significant research topic. When compared to other languages initiatives, such a delay can be explained by the lack of specific resources, such as expressive lexicons and corpora that could provide adequate foundations for deep or shallow approaches on AS. Taking advantage of having commonalities with respect to resources and a corpus of texts and summaries written in Brazilian Portuguese, two NLP research groups have decided to start a common task to assess and compare their AS systems. In the experiment five distinct extractive AS systems have been assessed. Some of them incorporate techniques that have been already used to summarize texts in English; others propose novel approaches to AS. Two baseline systems have also been considered. An overall performance comparison has been carried out, and its outcomes are discussed in this paper

Implicit Options in Life Insurance: Valuation and Risk Management

Participating life insurance contracts typically contain various types of implicit options. These implicit options can be very valuable and can thus represent a significant risk to insurance companies if they practice insufficient risk management. Options become especially risky through interaction with other options included in the contracts, which makes their evaluation even more complex. This article provides a comprehensive overview and classification of implicit options in participating life insurance contracts and discusses the relevant literature. It points out the potential problems particularly associated with the valuation of rights to early exercise due to policyholder exercise behavior. The risk potential of the interaction of implicit options is illustrated with numerical examples by means of a life insurance contract that includes common implicit options, i.e., a guaranteed interest rate, stochastic annual surplus participation, and paid-up and resumption options. Valuation is conducted using risk-neutral valuation, a concept that implicitly assumes the implementation of risk management measures such as hedging strategie

Topic-Focused Summarization of News Events Based on Biased Snippet Extraction and Selection

In this paper, we propose a framework to produce topic-focused summarization of news events, based on biased snippet extraction and selection. Through our approach, a summarization only retaining information related to a predefined topic (e.g. economy or politics) can be generated for a given news event to satisfy users with specific interests. To better balance coherence and coverage of the summarization, snippets rather than sentences or paragraphs are used as textual components. Topic signature is employed in snippet extraction and selection in order to emphasize the topic-biased information. Experiments conducted on real data demonstrate a good coverage, topic-relevancy, and content coherence of the summaries generated by our approach. ? Springer International Publishing Switzerland 2014.EI024-35887