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Re-visiting protein-centric two-tier classification of existing DNA-protein complexes.

Malhotra S, Sowdhamini R - BMC Bioinformatics (2012)

Bottom Line: Our results suggest that with the increasing number of availability of DNA-protein complexes in Protein Data Bank, the number of families in the classification increased by approximately three fold.The proposed re-visited classification can be used to perform genome-wide surveys in the genomes of interest for the presence of DNA-binding proteins.Further analysis of these complexes can aid in developing algorithms for identifying DNA-binding proteins and their family members from mere sequence information.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Centre for Biological Sciences, UAS-GKVK Campus, Bangalore 560 065, India.

ABSTRACT

Background: Precise DNA-protein interactions play most important and vital role in maintaining the normal physiological functioning of the cell, as it controls many high fidelity cellular processes. Detailed study of the nature of these interactions has paved the way for understanding the mechanisms behind the biological processes in which they are involved. Earlier in 2000, a systematic classification of DNA-protein complexes based on the structural analysis of the proteins was proposed at two tiers, namely groups and families. With the advancement in the number and resolution of structures of DNA-protein complexes deposited in the Protein Data Bank, it is important to revisit the existing classification.

Results: On the basis of the sequence analysis of DNA binding proteins, we have built upon the protein centric, two-tier classification of DNA-protein complexes by adding new members to existing families and making new families and groups. While classifying the new complexes, we also realised the emergence of new groups and families. The new group observed was where β-propeller was seen to interact with DNA. There were 34 SCOP folds which were observed to be present in the complexes of both old and new classifications, whereas 28 folds are present exclusively in the new complexes. Some new families noticed were NarL transcription factor, Z-α DNA binding proteins, Forkhead transcription factor, AP2 protein, Methyl CpG binding protein etc.

Conclusions: Our results suggest that with the increasing number of availability of DNA-protein complexes in Protein Data Bank, the number of families in the classification increased by approximately three fold. The folds present exclusively in newly classified complexes is suggestive of inclusion of proteins with new function in new classification, the most populated of which are the folds responsible for DNA damage repair. The proposed re-visited classification can be used to perform genome-wide surveys in the genomes of interest for the presence of DNA-binding proteins. Further analysis of these complexes can aid in developing algorithms for identifying DNA-binding proteins and their family members from mere sequence information.

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Common SCOP folds in old and new classification34 common folds in both old and new classification complexes. Number of members possessing these folds expanded in new classification compared to old classification. The fold increase in the number of members with each of these 34 folds is plotted. Maximum fold increase of 27 was observed in Histone family
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Figure 8: Common SCOP folds in old and new classification34 common folds in both old and new classification complexes. Number of members possessing these folds expanded in new classification compared to old classification. The fold increase in the number of members with each of these 34 folds is plotted. Maximum fold increase of 27 was observed in Histone family

Mentions: The new families were also examined for their folds as ascribed to them by SCOP 1.75 [16], and the folds were recorded [see Additional file 1. Although SCOP is a highly updated database, we realised that ~30% of the entries (PDB IDs) were not included in SCOP 1.75 due to newer PDB entries. 34 SCOP folds were common to both new and old classification and they experienced an expansion in the number of complexes. The fold change in these 34 common folds is represented in Figure 8. The number of members, belonging to both old and new classification possessing each of the common 34 folds is summarised [see Additional file 4. The top three folds, experiencing maximum expansion in terms of members possessing them, were Histone, Homing endonuclease and DNA/RNA Polymerase - truly reflecting the maximum increase in the number of members and families in enzymes group. Therefore, expansion in the existing families was seen to a maximum extent in the families of enzyme group which have property to bind to DNA and then carry out an enzymatic activity.


Re-visiting protein-centric two-tier classification of existing DNA-protein complexes.

Malhotra S, Sowdhamini R - BMC Bioinformatics (2012)

Common SCOP folds in old and new classification34 common folds in both old and new classification complexes. Number of members possessing these folds expanded in new classification compared to old classification. The fold increase in the number of members with each of these 34 folds is plotted. Maximum fold increase of 27 was observed in Histone family
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3472317&req=5

Figure 8: Common SCOP folds in old and new classification34 common folds in both old and new classification complexes. Number of members possessing these folds expanded in new classification compared to old classification. The fold increase in the number of members with each of these 34 folds is plotted. Maximum fold increase of 27 was observed in Histone family
Mentions: The new families were also examined for their folds as ascribed to them by SCOP 1.75 [16], and the folds were recorded [see Additional file 1. Although SCOP is a highly updated database, we realised that ~30% of the entries (PDB IDs) were not included in SCOP 1.75 due to newer PDB entries. 34 SCOP folds were common to both new and old classification and they experienced an expansion in the number of complexes. The fold change in these 34 common folds is represented in Figure 8. The number of members, belonging to both old and new classification possessing each of the common 34 folds is summarised [see Additional file 4. The top three folds, experiencing maximum expansion in terms of members possessing them, were Histone, Homing endonuclease and DNA/RNA Polymerase - truly reflecting the maximum increase in the number of members and families in enzymes group. Therefore, expansion in the existing families was seen to a maximum extent in the families of enzyme group which have property to bind to DNA and then carry out an enzymatic activity.

Bottom Line: Our results suggest that with the increasing number of availability of DNA-protein complexes in Protein Data Bank, the number of families in the classification increased by approximately three fold.The proposed re-visited classification can be used to perform genome-wide surveys in the genomes of interest for the presence of DNA-binding proteins.Further analysis of these complexes can aid in developing algorithms for identifying DNA-binding proteins and their family members from mere sequence information.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Centre for Biological Sciences, UAS-GKVK Campus, Bangalore 560 065, India.

ABSTRACT

Background: Precise DNA-protein interactions play most important and vital role in maintaining the normal physiological functioning of the cell, as it controls many high fidelity cellular processes. Detailed study of the nature of these interactions has paved the way for understanding the mechanisms behind the biological processes in which they are involved. Earlier in 2000, a systematic classification of DNA-protein complexes based on the structural analysis of the proteins was proposed at two tiers, namely groups and families. With the advancement in the number and resolution of structures of DNA-protein complexes deposited in the Protein Data Bank, it is important to revisit the existing classification.

Results: On the basis of the sequence analysis of DNA binding proteins, we have built upon the protein centric, two-tier classification of DNA-protein complexes by adding new members to existing families and making new families and groups. While classifying the new complexes, we also realised the emergence of new groups and families. The new group observed was where β-propeller was seen to interact with DNA. There were 34 SCOP folds which were observed to be present in the complexes of both old and new classifications, whereas 28 folds are present exclusively in the new complexes. Some new families noticed were NarL transcription factor, Z-α DNA binding proteins, Forkhead transcription factor, AP2 protein, Methyl CpG binding protein etc.

Conclusions: Our results suggest that with the increasing number of availability of DNA-protein complexes in Protein Data Bank, the number of families in the classification increased by approximately three fold. The folds present exclusively in newly classified complexes is suggestive of inclusion of proteins with new function in new classification, the most populated of which are the folds responsible for DNA damage repair. The proposed re-visited classification can be used to perform genome-wide surveys in the genomes of interest for the presence of DNA-binding proteins. Further analysis of these complexes can aid in developing algorithms for identifying DNA-binding proteins and their family members from mere sequence information.

Show MeSH
Related in: MedlinePlus