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Interaction modes at protein hetero-dimer interfaces.

Vaishnavi A, Sowmya G, Kalaivanii J, Ilakya S, Kangueane U, Kangueane P - Bioinformation (2010)

Bottom Line: The size of protein subunits interacting are either small-small, largelarge, medium-medium, large-small, large-medium and small-medium.These features are believed to have application in the prediction of interaction partners and sites from sequences.However, the use of such features for interaction prediction from sequence is not currently clear.

View Article: PubMed Central - PubMed

Affiliation: Biomedical Informatics, Pondicherry 607 402, India; Equal contributions; Pandjassarame Kangueane.

ABSTRACT
Hetero dimer (different monomers) interfaces are involved in catalysis and regulation through the formation of interface active sites. This is critical in cell and molecular biology events. The physical and chemical factors determining the formation of the interface active sites is often large in numbers. The combined role of interacting features is frequently combinatorial and additive in nature. Therefore, it is important to determine the physical and chemical features of such interactions. A number of such features have been documented in literature since 1975. However, the use of such interaction features in the prediction of interaction partners and sites given their sequences is still a challenge. In a non-redundant dataset of 156 hetero-dimer structures determined by X-ray crystallography, the interacting partners are often varying in size and thus, size variation between subunits is an important factor in determining the mode of interface formation. The size of protein subunits interacting are either small-small, largelarge, medium-medium, large-small, large-medium and small-medium. It should also be noted that the interface formed between subunits have physical interactions at N terminal (N), C terminal (C) and middle (M) region of the protein with reference to their sequences in one dimension. These features are believed to have application in the prediction of interaction partners and sites from sequences. However, the use of such features for interaction prediction from sequence is not currently clear.

No MeSH data available.


Protein-protein interactions and protein size is illustrated using examples; (a) small protein ‐ small protein; (b) large protein ‐ largeprotein; (c) large protein ‐ small protein.
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Figure 1: Protein-protein interactions and protein size is illustrated using examples; (a) small protein ‐ small protein; (b) large protein ‐ largeprotein; (c) large protein ‐ small protein.

Mentions: Size variation between the interacting partners is an important factor indetermining the mode of interface formation. The size of proteinsubunits interacting are either small-small, large-large, mediummedium,large-small, large-medium and small-medium (Figure 1).Proteins of sizes 100-300 residues are most represented for subunit Aand 50-200 residues for subunit B in the dataset (Table 5 supplementary material).


Interaction modes at protein hetero-dimer interfaces.

Vaishnavi A, Sowmya G, Kalaivanii J, Ilakya S, Kangueane U, Kangueane P - Bioinformation (2010)

Protein-protein interactions and protein size is illustrated using examples; (a) small protein ‐ small protein; (b) large protein ‐ largeprotein; (c) large protein ‐ small protein.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2957768&req=5

Figure 1: Protein-protein interactions and protein size is illustrated using examples; (a) small protein ‐ small protein; (b) large protein ‐ largeprotein; (c) large protein ‐ small protein.
Mentions: Size variation between the interacting partners is an important factor indetermining the mode of interface formation. The size of proteinsubunits interacting are either small-small, large-large, mediummedium,large-small, large-medium and small-medium (Figure 1).Proteins of sizes 100-300 residues are most represented for subunit Aand 50-200 residues for subunit B in the dataset (Table 5 supplementary material).

Bottom Line: The size of protein subunits interacting are either small-small, largelarge, medium-medium, large-small, large-medium and small-medium.These features are believed to have application in the prediction of interaction partners and sites from sequences.However, the use of such features for interaction prediction from sequence is not currently clear.

View Article: PubMed Central - PubMed

Affiliation: Biomedical Informatics, Pondicherry 607 402, India; Equal contributions; Pandjassarame Kangueane.

ABSTRACT
Hetero dimer (different monomers) interfaces are involved in catalysis and regulation through the formation of interface active sites. This is critical in cell and molecular biology events. The physical and chemical factors determining the formation of the interface active sites is often large in numbers. The combined role of interacting features is frequently combinatorial and additive in nature. Therefore, it is important to determine the physical and chemical features of such interactions. A number of such features have been documented in literature since 1975. However, the use of such interaction features in the prediction of interaction partners and sites given their sequences is still a challenge. In a non-redundant dataset of 156 hetero-dimer structures determined by X-ray crystallography, the interacting partners are often varying in size and thus, size variation between subunits is an important factor in determining the mode of interface formation. The size of protein subunits interacting are either small-small, largelarge, medium-medium, large-small, large-medium and small-medium. It should also be noted that the interface formed between subunits have physical interactions at N terminal (N), C terminal (C) and middle (M) region of the protein with reference to their sequences in one dimension. These features are believed to have application in the prediction of interaction partners and sites from sequences. However, the use of such features for interaction prediction from sequence is not currently clear.

No MeSH data available.