Clemaps: Multiple Alignment Of Protein Structures Based On Conformational Letters

CLEMAPS is a tool for multiple alignment of protein structures. It distinguishes itself from other existing algorithms for multiple structure alignment by the use of conformational letters, which are discretized states of 3D segmental structural states. A letter corresponds to a cluster of combinations of three angles formed by C-alpha pseudobonds of four contiguous residues. A substitution matrix called CLESUM is available to measure the similarity between any two such letters. The input 3D structures are first converted to sequences of conformational letters. Each string of a fixed length is then taken as the center seed to search other sequences for neighbors of the seed, which are strings similar to the seed. A seed and its neighbors form a center-star, which corresponds to a fragment set of local structural similarity shared by many proteins. The detection of center-stars using CLESUM is extremely efficient. Local similarity is a necessary, but insufficient, condition for structural alignment. Once center-stars are found, the spatial consistency between any two stars are examined to find consistent star duads using atomic coordinates. Consistent duads are later joined to create a core for multiple alignment, which is further polished to produce the final alignment. The utility of CLEMAPS is tested on various protein structure ensembles.

Growth response of Heterobranchus longifilis (Valenciennes, 1840) fingerlings fed raw and boiled Mucuna cochinchinensis seed meal

Feeding trial was conducted in static water to assess the growth of H. longifilis fingerlings fed different I inclusion levels of mucuna seed meal (MSM). Raw and boiled MSM were used in the diets at 10%, 20%, 30% and 40% inclusion levels and the performance of fish fed these diets was compared with fish fed a fishmeal-based diet which contained 40% protein. All diets were prepared to be isonitrogenous and isocaloric A two by five factorial experiment with three replicates using ten fish of average initial weight 1 .46g was carried out. Daily fish ration of five percent body weight was administered two times for eight weeks. The specific growth rate in diets 1 (control) and 6(10% boiled MSM) were similar and significantly (P<0.05) higher than the other dietary groups. The significantly lower growth performance of fish fed diets containing higher inclusion levels of both raw and boiled MSM might be due to incomplete elimination of the antinutritional factors present in MSM by boiling. Other methods of processing MSM to improve its nutritive value should be investigated. (7 page document)

Investigation of Interactions between Two Monoclonal Antibodies and SARS Virus with a Label-Free Protein Array

The investigation of interactions between two kinds of monoclonal antibodies and SARS virus with a label-free protein array technique were presented in this paper. The performance consists of three parts: a surface modification for ligand immobilization/surface, a protein array fabrication with an integrated microfluidic system for patterning, packaging and liquid handling, and a protein array reader of imaging ellipsometer. This revealed the technique could be used as an immunoassay for qualitative and quantitative detection as wen as kinetic analysis of biomolecule interaction.

The frequency of muscle protein polymorphism in Menidia menidia (Atherinidae) along the Atlantic coast

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