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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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Representative Selection. Schematic of the methodology for selecting reprsentatives of new families formed after classification. If the percentage identity plot is narrow, any member of the family is assessed for its coverage, but if the distribution of percent identity is wide, the decision of whether to perform Jack-knifing is dependent on the size of the family.
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Figure 2: Representative Selection. Schematic of the methodology for selecting reprsentatives of new families formed after classification. If the percentage identity plot is narrow, any member of the family is assessed for its coverage, but if the distribution of percent identity is wide, the decision of whether to perform Jack-knifing is dependent on the size of the family.

Mentions: The best representative of newly formed families was selected using Jack-knifing and phylogeny. The decision to choose either of the one techniques was based on the size of the family and also the distribution of the percent identity plot within the family (Figure 2 depicts the methodology of selecting the representatives). For two-member families, both the members are allowed to behave as a representative and then both are assessed in terms of their coverage for that particular family. If the old representative is able to have 100% coverage on the family, then it was retained as a new representative also.


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

Malhotra S, Sowdhamini R - BMC Bioinformatics (2012)

Representative Selection. Schematic of the methodology for selecting reprsentatives of new families formed after classification. If the percentage identity plot is narrow, any member of the family is assessed for its coverage, but if the distribution of percent identity is wide, the decision of whether to perform Jack-knifing is dependent on the size of the family.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Representative Selection. Schematic of the methodology for selecting reprsentatives of new families formed after classification. If the percentage identity plot is narrow, any member of the family is assessed for its coverage, but if the distribution of percent identity is wide, the decision of whether to perform Jack-knifing is dependent on the size of the family.
Mentions: The best representative of newly formed families was selected using Jack-knifing and phylogeny. The decision to choose either of the one techniques was based on the size of the family and also the distribution of the percent identity plot within the family (Figure 2 depicts the methodology of selecting the representatives). For two-member families, both the members are allowed to behave as a representative and then both are assessed in terms of their coverage for that particular family. If the old representative is able to have 100% coverage on the family, then it was retained as a new representative also.

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