ABSTRACT
Protein sequence world is considerably larger than structure world. In consequence, numerous non-related sequences may adopt similar 3D folds and different kinds of amino acids may thus be found in similar 3D structures. By grouping together the 20 amino acids into a smaller number of representative residues with similar features, sequence world simplification may be achieved. This clustering hence defines a reduced amino acid alphabet (reduced AAA). Numerous works have shown that protein 3D structures are composed of a limited number of building blocks, defining a structural alphabet. We previously identified such an alphabet composed of 16 representative structural motifs (5-residues length) called Protein Blocks (PBs). This alphabet permits to translate the structure (3D) in sequence of PBs (1D). Based on these two concepts, reduced AAA and PBs, we analyzed the distributions of the different kinds of amino acids and their equivalences in the structural context. Different reduced sets were considered. Recurrent amino acid associations were found in all the local structures while other were specific of some local structures (PBs) (e.g Cysteine, Histidine, Threonine and Serine for the alpha-helix Ncap). Some similar associations are found in other reduced AAAs, e.g Ile with Val, or hydrophobic aromatic residues Trp with Phe and Tyr. We put into evidence interesting alternative associations. This highlights the dependence on the information considered (sequence or structure). This approach, equivalent to a substitution matrix, could be useful for designing protein sequence with different features (for instance adaptation to environment) while preserving mainly the 3D fold.
Subject(s)
Amino Acids/chemistry , Mutation/physiology , Proteins/chemistry , Proteins/genetics , Algorithms , Amino Acid Sequence , Models, Molecular , Models, Statistical , Molecular Sequence DataABSTRACT
Twenty four patients, consecutively hospitalized in the "Dr. Carlos J. Finlay" Military Hospital, Pediatric Intensive Care Unit, Havana City, were evaluated by the therapeutic intervention system (TISS), in order to extend knowledges on evaluative system. According to the clinic classification system, the cases were clustered into four classes. The most severe cases are included into class IV (higher score), while cases clustered into class I (lower score) are those under current surveillance. Ruling clinical classification corresponded to class II and IV, with seven cases in each group. Incidence of diagnosis of infection of the central nervous system, followed by intoxication, was observed. Mean index of patient/nurse score was 22.3 in the most severe cases. There was little difference between day shift (22.9 points) and night shift (24.1 points).
