Using linear algebra for protein structural comparison and classification.

In this article, we describe a novel methodology to extract semantic characteristics from protein structures using linear algebra in order to compose structural signature vectors which may be used efficiently to compare and classify protein structures into fold families. These signatures are built from the pattern of hydrophobic intrachain interactions using Singular Value Decomposition (SVD) and Latent Semantic Indexing (LSI) techniques. Considering proteins as documents and contacts as terms, we have built a retrieval system which is able to find conserved contacts in samples of myoglobin fold family and to retrieve these proteins among proteins of varied folds with precision of up to 80%. The classifier is a web tool available at our laboratory website. Users can search for similar chains from a specific PDB, view and compare their contact maps and browse their structures using a JMol plug-in.

Evaluation of double treated starches using thermal tools.

Starch is the main polysaccharide found in cereals, composed by amylose and amylopectin. Corn is the principal source of starches worldwide. Starches treatment, through physical, chemical and/or biological methods, can improve the applications range. Acid modification in alcoholic solution promotes minimally degradation in the granule. Ball mill is one physical method poorly explored. The aim was to treat the starches using HCl 0.5 mol L-1 for 1 hour in 100 ml of aqueous, ethanol or methanol solutions with subsequent ball milling processes. One sample was selected as native sample. The four others, one native sample and three acid modified samples, were treated by physical process with the oscillating ball mill. The DTG-60H equipment was used for the TG and DTA analysis. The TG curves showed three mass losses related to dehydration, decomposition and oxidation. The native sample without physical modification showed major resistance to total degradation. This occurs because the physical modification cleaves hydrogen bonds, leaving a weakened granule. The TGDTA results showed that the mass loss in the 2nd event was minor in the hydrolyzed samples compared with native samples. The acid modification can provide starch higher resistance to degradation up to 340 °C. These results showed that chemical and physical treatment changed the thermal behaviors of the starches.