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Novel feature for catalytic protein residues reflecting interactions with other residues.

Li Y, Li G, Wen Z, Yin H, Hu M, Xiao J, Li M - PLoS ONE (2011)

Bottom Line: In an original attempt to quantify the effects of several key residues on catalytic residues, a power function was used to model interactions between residues.The results indicate that focusing on a few residues is a feasible approach to identifying catalytic residues.Values of 88.6 for sensitivity and 88.4 for specificity were obtained by 10-fold cross-validation.

View Article: PubMed Central - PubMed

Affiliation: College of Chemistry and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Peoples Republic of China.

ABSTRACT
Owing to their potential for systematic analysis, complex networks have been widely used in proteomics. Representing a protein structure as a topology network provides novel insight into understanding protein folding mechanisms, stability and function. Here, we develop a new feature to reveal correlations between residues using a protein structure network. In an original attempt to quantify the effects of several key residues on catalytic residues, a power function was used to model interactions between residues. The results indicate that focusing on a few residues is a feasible approach to identifying catalytic residues. The spatial environment surrounding a catalytic residue was analyzed in a layered manner. We present evidence that correlation between residues is related to their distance apart most environmental parameters of the outer layer make a smaller contribution to prediction and ii catalytic residues tend to be located near key positions in enzyme folds. Feature analysis revealed satisfactory performance for our features, which were combined with several conventional features in a prediction model for catalytic residues using a comprehensive data set from the Catalytic Site Atlas. Values of 88.6 for sensitivity and 88.4 for specificity were obtained by 10-fold cross-validation. These results suggest that these features reveal the mutual dependence of residues and are promising for further study of structure-function relationship.

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Observed frequency distribution of the shortest path between                                keyAAs and catalytic and non-catalytic                            residues.
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pone-0016932-g001: Observed frequency distribution of the shortest path between keyAAs and catalytic and non-catalytic residues.

Mentions: First, we analyzed the interactions between keyAAs central amino acids in a protein structure network see Materials and Methods and catalytic and noncatalytic residues. The five highestranked keyAAs were investigated for each enzyme. Interactions with a distance of 5 were considered, whereas those 5 were regarded as uninformative and were not used. The suitability of this approach was confirmed by analysis. Fig. 1 shows that catalytic residues exhibited a strong tendency to approach keyAAs, especially with direct contact or is the keyAA itself or at an interval of one residue. The rates for these two cases were significantly lower for noncatalytic residues, at only 15 and 12 of the rates for catalytic residues, respectively. However, the opposite was true when the interaction distance increased. It was found that the length of the shortest path between noncatalytic residues and keyAAs was usually 2. These results are in accord with our hypothesis that keyAAs are vital for catalytic activity and their effect on catalytic residues decreases as the interaction distance increases. Each keyAA was the subject of detailed investigation in Fig S1. Interestingly, the difference of distribution for each keyAA was quite small suggesting that several residues play key roles during protein folding and more than one position participates in formation of the exquisite scaffold for effective activity, some of which have a direct and others an indirect effect.


Novel feature for catalytic protein residues reflecting interactions with other residues.

Li Y, Li G, Wen Z, Yin H, Hu M, Xiao J, Li M - PLoS ONE (2011)

Observed frequency distribution of the shortest path between                                keyAAs and catalytic and non-catalytic                            residues.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3066176&req=5

pone-0016932-g001: Observed frequency distribution of the shortest path between keyAAs and catalytic and non-catalytic residues.
Mentions: First, we analyzed the interactions between keyAAs central amino acids in a protein structure network see Materials and Methods and catalytic and noncatalytic residues. The five highestranked keyAAs were investigated for each enzyme. Interactions with a distance of 5 were considered, whereas those 5 were regarded as uninformative and were not used. The suitability of this approach was confirmed by analysis. Fig. 1 shows that catalytic residues exhibited a strong tendency to approach keyAAs, especially with direct contact or is the keyAA itself or at an interval of one residue. The rates for these two cases were significantly lower for noncatalytic residues, at only 15 and 12 of the rates for catalytic residues, respectively. However, the opposite was true when the interaction distance increased. It was found that the length of the shortest path between noncatalytic residues and keyAAs was usually 2. These results are in accord with our hypothesis that keyAAs are vital for catalytic activity and their effect on catalytic residues decreases as the interaction distance increases. Each keyAA was the subject of detailed investigation in Fig S1. Interestingly, the difference of distribution for each keyAA was quite small suggesting that several residues play key roles during protein folding and more than one position participates in formation of the exquisite scaffold for effective activity, some of which have a direct and others an indirect effect.

Bottom Line: In an original attempt to quantify the effects of several key residues on catalytic residues, a power function was used to model interactions between residues.The results indicate that focusing on a few residues is a feasible approach to identifying catalytic residues.Values of 88.6 for sensitivity and 88.4 for specificity were obtained by 10-fold cross-validation.

View Article: PubMed Central - PubMed

Affiliation: College of Chemistry and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Peoples Republic of China.

ABSTRACT
Owing to their potential for systematic analysis, complex networks have been widely used in proteomics. Representing a protein structure as a topology network provides novel insight into understanding protein folding mechanisms, stability and function. Here, we develop a new feature to reveal correlations between residues using a protein structure network. In an original attempt to quantify the effects of several key residues on catalytic residues, a power function was used to model interactions between residues. The results indicate that focusing on a few residues is a feasible approach to identifying catalytic residues. The spatial environment surrounding a catalytic residue was analyzed in a layered manner. We present evidence that correlation between residues is related to their distance apart most environmental parameters of the outer layer make a smaller contribution to prediction and ii catalytic residues tend to be located near key positions in enzyme folds. Feature analysis revealed satisfactory performance for our features, which were combined with several conventional features in a prediction model for catalytic residues using a comprehensive data set from the Catalytic Site Atlas. Values of 88.6 for sensitivity and 88.4 for specificity were obtained by 10-fold cross-validation. These results suggest that these features reveal the mutual dependence of residues and are promising for further study of structure-function relationship.

Show MeSH
Related in: MedlinePlus