Interacting amino acid preferences of 3D pattern pairs at the binding sites of transient and obligate protein complexes

Lukaman, Suryani, Sim, Kelvin, Li, Jinyan and Chen, Yi-Ping Phoebe 2008, Interacting amino acid preferences of 3D pattern pairs at the binding sites of transient and obligate protein complexes, in APBC 2008 : Proceedings of the Sixth Asia-Pacific Bioinformatics Conference., Imperial College Press, London, England, pp. 69-78.

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Title Interacting amino acid preferences of 3D pattern pairs at the binding sites of transient and obligate protein complexes
Author(s) Lukaman, Suryani
Sim, Kelvin
Li, Jinyan
Chen, Yi-Ping Phoebe
Conference name Asia-Pacific Bioinformatics Conference (6th : 2008 : Kyoto, Japan)
Conference location Kyoto, Japan
Conference dates 14 - 17 January 2008
Title of proceedings APBC 2008 : Proceedings of the Sixth Asia-Pacific Bioinformatics Conference.
Editor(s) Brazma, Alvis
Miyano, Satoru
Akutsu, Tatsuya
Publication date 2008
Conference series Asia-Pacific Bioinformatics Conference
Start page 69
End page 78
Publisher Imperial College Press
Place of publication London, England
Keyword(s) bipartite graph
amino acid preferences
pattern pairs
transient complexes
obligate complexes
Summary To assess the physico-chemical characteristics of protein-protein interactions, protein sequences and overall structural folds have been analyzed previously. To highlight this, discovery and examination of amino acid patterns at the binding sites defined by structural proximity in 3-dimensional (3D) space are essential. In this paper, we investigate the interacting preferences of 3D pattern pairs discovered separately in transient and obligate protein complexes. These 3D pattern pairs are not necessarily sequence-consecutive, but each residue in two groups of amino acids from two proteins in a complex is within certain °A threshold to most residues in the other group. We develop an algorithm called AA-pairs by which every pair of interacting proteins is represented as a bipartite graph, and it discovers all maximal quasi-bicliques from every bipartite graph to form our 3D pattern pairs. From 112 and 2533 highly conserved 3D pattern pairs discovered in the transient and obligate complexes respectively, we observe that Ala and Leu is the highest occuring amino acid in interacting 3D patterns of transient (20.91%) and obligate (33.82%) complexes respectively. From the study on the dipeptide composition on each side of interacting 3D pattern pairs, dipeptides Ala-Ala and Ala-Leu are popular in 3D patterns of both transient and obligate complexes. The interactions between amino acids with large hydrophobicity difference are present more in the transient than in the obligate complexes. On contrary, in obligate complexes, interactions between hydrophobic residues account for the top 5 most occuring amino acid pairings.
ISBN 9781848161085
1848161085
Language eng
Field of Research 080301 Bioinformatics Software
HERDC Research category E1 Full written paper - refereed
ERA Research output type E Conference publication
HERDC collection year 2008
Persistent URL http://hdl.handle.net/10536/DRO/DU:30018130

Document type: Conference Paper
Collection: School of Engineering and Information Technology
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