Limits...
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.


Representation of protein-protein interfaces in 3D (structure complex in panel a), 2D (X-Y plots using X-Y plots in panel b) and 1D(sequence in panel c).
© Copyright Policy - open-access
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2957768&req=5

Figure 2: Representation of protein-protein interfaces in 3D (structure complex in panel a), 2D (X-Y plots using X-Y plots in panel b) and 1D(sequence in panel c).

Mentions: The interface formed between subunits A and B have physicalinteractions at N terminal (N), C terminal (C) and middle (M) region ofthe protein with reference to its sequence in one dimension (Figure 2).A representation of the protein ¯ protein interface in 3D, 2D and 1D isshown for chemo-taxis proteins chey and chea (PDB ID: 1FFG) inFigure 2. In this dataset, nearly 33% of interfaces have NMC - NMCmode of interactions ( Table 6). However, the dataset contains a wide type of interaction modes like N-N, C-C, NMC-NMC, M-M, NC-NC,NM-NM, and MC-MC (Table 4 in supplementary material).


Interaction modes at protein hetero-dimer interfaces.

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

Representation of protein-protein interfaces in 3D (structure complex in panel a), 2D (X-Y plots using X-Y plots in panel b) and 1D(sequence in panel c).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Representation of protein-protein interfaces in 3D (structure complex in panel a), 2D (X-Y plots using X-Y plots in panel b) and 1D(sequence in panel c).
Mentions: The interface formed between subunits A and B have physicalinteractions at N terminal (N), C terminal (C) and middle (M) region ofthe protein with reference to its sequence in one dimension (Figure 2).A representation of the protein ¯ protein interface in 3D, 2D and 1D isshown for chemo-taxis proteins chey and chea (PDB ID: 1FFG) inFigure 2. In this dataset, nearly 33% of interfaces have NMC - NMCmode of interactions ( Table 6). However, the dataset contains a wide type of interaction modes like N-N, C-C, NMC-NMC, M-M, NC-NC,NM-NM, and MC-MC (Table 4 in 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.