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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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Related in: MedlinePlus

Schematic of the Classification. The circles represent the entire pool of DNA-protein complexes. Within the circles, ovals are the different groups of DBP; orange stars are the existing families within groups. These groups vary in their size in terms of number of families present and also the number of members within each family. After our classification, one new group was realized (red oval), also the new members were added to existing families (shaded orange ovals) and also new families were realized as represented by blue stars.
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Figure 6: Schematic of the Classification. The circles represent the entire pool of DNA-protein complexes. Within the circles, ovals are the different groups of DBP; orange stars are the existing families within groups. These groups vary in their size in terms of number of families present and also the number of members within each family. After our classification, one new group was realized (red oval), also the new members were added to existing families (shaded orange ovals) and also new families were realized as represented by blue stars.

Mentions: The schematic of the classification represented in Figure 6 highlights the different ways adopted to classify DNA-protein complexes. Table 2 summarizes the modifications performed in Thornton’s families after association of new members. The listed families have been marked up appropriately as renamed or split or merged, as the case may be.


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

Malhotra S, Sowdhamini R - BMC Bioinformatics (2012)

Schematic of the Classification. The circles represent the entire pool of DNA-protein complexes. Within the circles, ovals are the different groups of DBP; orange stars are the existing families within groups. These groups vary in their size in terms of number of families present and also the number of members within each family. After our classification, one new group was realized (red oval), also the new members were added to existing families (shaded orange ovals) and also new families were realized as represented by blue stars.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Schematic of the Classification. The circles represent the entire pool of DNA-protein complexes. Within the circles, ovals are the different groups of DBP; orange stars are the existing families within groups. These groups vary in their size in terms of number of families present and also the number of members within each family. After our classification, one new group was realized (red oval), also the new members were added to existing families (shaded orange ovals) and also new families were realized as represented by blue stars.
Mentions: The schematic of the classification represented in Figure 6 highlights the different ways adopted to classify DNA-protein complexes. Table 2 summarizes the modifications performed in Thornton’s families after association of new members. The listed families have been marked up appropriately as renamed or split or merged, as the case may be.

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