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A structure-based classification and analysis of protein domain family binding sites and their interactions.

Ghoorah AW, Devignes MD, Alborzi SZ, Smaïl-Tabbone M, Ritchie DW - Biology (Basel) (2015)

Bottom Line: Our results show that β elements are not highly represented in DFBSs compared to α and γ elements.At the DDI level, all classes of binding sites tend to preferentially bind to the same class of binding sites and α/β contacts are significantly disfavored.Conversely, promiscuous Pfam domains bear several DFBSs among which one or two are promiscuous, thereby multiplying the promiscuity of the concerned protein.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science and Engineering, University of Mauritius, 80837 Reduit, Mauritius. a.ghoorah@uom.ac.mu.

ABSTRACT
While the number of solved 3D protein structures continues to grow rapidly, the structural rules that distinguish protein-protein interactions between different structural families are still not clear. Here, we classify and analyse the secondary structural features and promiscuity of a comprehensive non-redundant set of domain family binding sites (DFBSs) and hetero domain-domain interactions (DDIs) extracted from our updated KBDOCK resource. We have partitioned 4001 DFBSs into five classes using their propensities for three types of secondary structural elements ("α" for helices, "β" for strands, and "γ" for irregular structure) and we have analysed how frequently these classes occur in DDIs. Our results show that β elements are not highly represented in DFBSs compared to α and γ elements. At the DDI level, all classes of binding sites tend to preferentially bind to the same class of binding sites and α/β contacts are significantly disfavored. Very few DFBSs are promiscuous: 80% of them interact with just one Pfam domain. About 50% of our Pfam domains bear only one single-partner DFBS and are therefore monogamous in their interactions with other domains. Conversely, promiscuous Pfam domains bear several DFBSs among which one or two are promiscuous, thereby multiplying the promiscuity of the concerned protein.

No MeSH data available.


Examples of DDIs involving various SSE class pairs: (a) α-rich with α-rich (PDB code 1VRC, chains A, C); (b) α-rich with α + γ (PDB code 2CG5, chains A, B); (c) α + β + γ with α + β + γ (PDB code 2YIB, chains F, B); (d) γ-rich with β + γ (PDB code 1TE1, chains A, B). Binding site SSEs are shown in red. This figure was drawn using the VMD program (http://www.ks.uiuc.edu/Research/vmd/).
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biology-04-00327-f003: Examples of DDIs involving various SSE class pairs: (a) α-rich with α-rich (PDB code 1VRC, chains A, C); (b) α-rich with α + γ (PDB code 2CG5, chains A, B); (c) α + β + γ with α + β + γ (PDB code 2YIB, chains F, B); (d) γ-rich with β + γ (PDB code 1TE1, chains A, B). Binding site SSEs are shown in red. This figure was drawn using the VMD program (http://www.ks.uiuc.edu/Research/vmd/).

Mentions: Figure 3 shows some examples of protein complexes with particular SSE class pairs at the domain interface.


A structure-based classification and analysis of protein domain family binding sites and their interactions.

Ghoorah AW, Devignes MD, Alborzi SZ, Smaïl-Tabbone M, Ritchie DW - Biology (Basel) (2015)

Examples of DDIs involving various SSE class pairs: (a) α-rich with α-rich (PDB code 1VRC, chains A, C); (b) α-rich with α + γ (PDB code 2CG5, chains A, B); (c) α + β + γ with α + β + γ (PDB code 2YIB, chains F, B); (d) γ-rich with β + γ (PDB code 1TE1, chains A, B). Binding site SSEs are shown in red. This figure was drawn using the VMD program (http://www.ks.uiuc.edu/Research/vmd/).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4498303&req=5

biology-04-00327-f003: Examples of DDIs involving various SSE class pairs: (a) α-rich with α-rich (PDB code 1VRC, chains A, C); (b) α-rich with α + γ (PDB code 2CG5, chains A, B); (c) α + β + γ with α + β + γ (PDB code 2YIB, chains F, B); (d) γ-rich with β + γ (PDB code 1TE1, chains A, B). Binding site SSEs are shown in red. This figure was drawn using the VMD program (http://www.ks.uiuc.edu/Research/vmd/).
Mentions: Figure 3 shows some examples of protein complexes with particular SSE class pairs at the domain interface.

Bottom Line: Our results show that β elements are not highly represented in DFBSs compared to α and γ elements.At the DDI level, all classes of binding sites tend to preferentially bind to the same class of binding sites and α/β contacts are significantly disfavored.Conversely, promiscuous Pfam domains bear several DFBSs among which one or two are promiscuous, thereby multiplying the promiscuity of the concerned protein.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science and Engineering, University of Mauritius, 80837 Reduit, Mauritius. a.ghoorah@uom.ac.mu.

ABSTRACT
While the number of solved 3D protein structures continues to grow rapidly, the structural rules that distinguish protein-protein interactions between different structural families are still not clear. Here, we classify and analyse the secondary structural features and promiscuity of a comprehensive non-redundant set of domain family binding sites (DFBSs) and hetero domain-domain interactions (DDIs) extracted from our updated KBDOCK resource. We have partitioned 4001 DFBSs into five classes using their propensities for three types of secondary structural elements ("α" for helices, "β" for strands, and "γ" for irregular structure) and we have analysed how frequently these classes occur in DDIs. Our results show that β elements are not highly represented in DFBSs compared to α and γ elements. At the DDI level, all classes of binding sites tend to preferentially bind to the same class of binding sites and α/β contacts are significantly disfavored. Very few DFBSs are promiscuous: 80% of them interact with just one Pfam domain. About 50% of our Pfam domains bear only one single-partner DFBS and are therefore monogamous in their interactions with other domains. Conversely, promiscuous Pfam domains bear several DFBSs among which one or two are promiscuous, thereby multiplying the promiscuity of the concerned protein.

No MeSH data available.