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Protein-related information is more accumulated rather than reduced to a synthetic view. Itemising properties of protein sequences is informative, so is the list of ingredients to do some cooking, but without a recipe, that is, quantification and chronology, understanding is incomplete. If the goal of accumulating information is to discover or reveal the function and related biochemical mechanisms, information has to be weighed and ordered. As a guideline, the weight of a piece of information should reflect how often it consistently occurs in various contexts. We propose a common sense approach to quantify and put data and information into perspective. Complete bacterial proteomes are individually mapped with the Pfam-A database of domains and protein family signatures in an attempt to assess the modularity of proteins at the level of a single proteome and the implications of a modular description of proteins for a functional interpretation. Poorly annotated proteins in the most documented bacteria (E. coli and B. subtilis) were considered in an attempt to formulate hypothesis on the basis of domain/module content. [Copyright &y& Elsevier]

• Lectins utilize several strategies for multivalency, resulting in strong avidity for glycoconjugates. • Tandem repeat lectins can be searched for in the structural database UniLectin3D. • Tandem repeat lectins are of high interest for understanding protein evolution and for engineering of "neo-lectins". • β-propeller and β-trefoil lectins have great potential as bio-markers. Through their ability to bind complex glycoconjugates, lectins have unique specificity and potential for biomedical and biotechnological applications. In particular, lectins with short repeated peptides forming carbohydrate-binding domains are not only of high interest for understanding protein evolution but can also be used as scaffold for engineering novel receptors. Synthetic glycobiology now provides the tools for engineering the specificity of lectins as well as their structure, multivalency and topologies. This review focuses on the structure and diversity of two families of tandem-repeat lectins, that is, β-trefoils and β-propellers, demonstrated as the most promising scaffold for engineering novel lectins. [ABSTRACT FROM AUTHOR]

Summary: The aim of this study is to investigate the relationships between citations and the scientific argumentation found abstracts. We design a related article search task and observe how the argumentation can affect the search results. We extracted citation lists from a set of 3200 full-text papers originating from a narrow domain. In parallel, we recovered the corresponding MEDLINE records for analysis of the argumentative moves. Our argumentative model is founded on four classes: PURPOSE, METHODS, RESULTS and CONCLUSION. A Bayesian classifier trained on explicitly structured MEDLINE abstracts generates these argumentative categories. The categories are used to generate four different argumentative indexes. A fifth index contains the complete abstract, together with the title and the list of Medical Subject Headings (MeSH) terms. To appraise the relationship of the moves to the citations, the citation lists were used as the criteria for determining relatedness of articles, establishing a benchmark; it means that two articles are considered as “related” if they share a significant set of co-citations. Our results show that the average precision of queries with the PURPOSE and CONCLUSION features is the highest, while the precision of the RESULTS and METHODS features was relatively low. A linear weighting combination of the moves is proposed, which significantly improves retrieval of related articles. [Copyright &y& Elsevier]

Lectins with a β-propeller fold bind glycans on the cell surface through multivalent binding sites and appropriate directionality. These proteins are formed by repeats of short domains, raising questions about evolutionary duplication. However, these repeats are difficult to detect in translated genomes and seldom correctly annotated in sequence databases. To address these issues, we defined the blade signature of the five types of β-propellers using 3D-structural data. With these templates, we predicted 3,887 β-propeller lectins in 1,889 species and organized this information in a searchable online database. The data reveal a widespread distribution of β-propeller lectins across species. Prediction also emphasizes multiple architectures and led to the discovery of a β-propeller assembly scenario. This was confirmed by producing and characterizing a predicted protein coded in the genome of Kordia zhangzhouensis. The crystal structure uncovers an intermediate in the evolution of β-propeller assembly and demonstrates the power of our tools. • Five β-propeller lectin families are defined by the HMM profiles of their blade repeats • Roughly 4,000 sequences of β-propeller lectins are compiled • A novel β-propeller assembly mode, based on dimerization, is predicted • The crystal structure of Kordia zhangzhouensis lectin confirms the predicted fold Donut-shaped β-propeller lectins are made of repeated blades, each containing binding sites for carbohydrates. This scaffold is of high interest for protein evolution, biotechnology, and nanotechnology. An algorithm for screening sequence databases for such lectins was implemented. Some predicted sequences revealed an alternate scenario of β-propeller assembly that we experimentally validated. [ABSTRACT FROM AUTHOR]