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Mining the entire Protein DataBank for frequent spatially cohesive amino acid patterns.

ABSTRACT: BACKGROUND:The three-dimensional structure of a protein is an essential aspect of its functionality. Despite the large diversity in protein structures and functionality, it is known that there are common patterns and preferences in the contacts between amino acid residues, or between residues and other biomolecules, such as DNA. The discovery and characterization of these patterns is an important research topic within structural biology as it can give fundamental insight into protein structures and can aid in the prediction of unknown structures. RESULTS:Here we apply an efficient spatial pattern miner to search for sets of amino acids that occur frequently in close spatial proximity in the protein structures of the Protein DataBank. This allowed us to mine for a new class of amino acid patterns, that we term FreSCOs (Frequent Spatially Cohesive Component sets), which feature synergetic combinations. To demonstrate the relevance of these FreSCOs, they were compared in relation to the thermostability of the protein structure and the interaction preferences of DNA-protein complexes. In both cases, the results matched well with prior investigations using more complex methods on smaller data sets. CONCLUSIONS:The currently characterized protein structures feature a diverse set of frequent amino acid patterns that can be related to the stability of the protein molecular structure and that are independent from protein function or specific conserved domains.

SUBMITTER: Meysman P

PROVIDER: S-EPMC4318390 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Mining the entire Protein DataBank for frequent spatially cohesive amino acid patterns.

Meysman Pieter P Zhou Cheng C Cule Boris B Goethals Bart B Laukens Kris K

BioData mining 20150131

<h4>Background</h4>The three-dimensional structure of a protein is an essential aspect of its functionality. Despite the large diversity in protein structures and functionality, it is known that there are common patterns and preferences in the contacts between amino acid residues, or between residues and other biomolecules, such as DNA. The discovery and characterization of these patterns is an important research topic within structural biology as it can give fundamental insight into protein str ...[more]

PMID: 25657820

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Project description:Breeding efforts over the last decades altered markedly empty body (EB) composition of pigs. This study aimed to re-evaluate the dynamics of changes in the composition and deposition rate of fat, protein and amino acids (AA) in the EB from birth to 140 kg BW depending on the dietary CP and AA supply in a current pig genotype. In the experiment 66 entire male, 58 castrated and 66 female Swiss Large White pigs were used. From 20 kg BW onwards, they had either ad libitum access to a control (C) diet or a diet (LP) compared to diet C only 80% of CP, lysine, methione+cystine, threonine and tryptophan. The EB composition was determined at birth on eight boars and eight females, at 10 and 20 kg BW on two boars, two castrates and two females, and at 20 kg intervals from 40 to 140 kg BW, on four pigs per gender and dietary treatment. Each EB fraction was weighed and analysed for protein, fat and AA profile. The AA-to-lysine ratio was calculated and the different chemical component contents were fitted to allometric regressions. Overall, C-boars had the greatest EB protein and AA content and deposition rates, and lowest fat content and deposition rates. At the beginning of the grower period, LP-castrates and females displayed the lowest protein and AA and the highest fat deposition rates. However, compared with their counterparts in the C-group, in LP-castrates and females protein and AA deposition rates were greater above 64 and 40 kg EB weight, respectively, whereas fat deposition rates was lower above 80 kg EB weight. Thus, there seems a great potential to optimise protein and AA efficiency especially in the finisher period in castrates and females. Important individual variations were found in the essential AA-to-lysine ratio of the EB. Phenylalanine and threonine-to-lysine ratios decreased with increasing EB weight. Valine- and threonine-to-lysine ratios in C-castrates and C-females were 5% and 4% greater than recently reported by the National Research Council (NRC) whereas cysteine-, methionine- and tyrosine-to-lysine ratios were lower by 34%, 25% and 10%, respectively. The clear differences found between the EB AA-to-lysine ratios in the present study and the NRC might partly be explained by the genotype and the temporal changes in the relative weight of each EB fraction or changes in the AA profile. Nevertheless, these findings on changes in the essential AA profile of tissue protein warrant further studies.

Dataset Information

Mining the entire Protein DataBank for frequent spatially cohesive amino acid patterns.

Publications

Mining the entire Protein DataBank for frequent spatially cohesive amino acid patterns.

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