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Bhak, Jong
KOrean GenomIcs Center(KOGIC)
Research Interests
  • Geromics, genomics, bioinformatics, protein Engineering, OMICS

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Visualisation and graph-theoretic analysis of a large-scale protein structural interactome

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Title
Visualisation and graph-theoretic analysis of a large-scale protein structural interactome
Other Titles
Visualisation and Graph-theoretic Analysis of a Large-scale Protein Structural Interactome.
Author
Bolser, DDafas, PHarrington, RBhak, Jong HwaSchroeder, M
Keywords
INTERACTION NETWORKS; INTERACTION MAP; MOLECULAR-COMPLEXES; GENOME SEQUENCES; SMALL-WORLD; YEAST; CLASSIFICATION; INTERFACES; FAMILIES; DATABASE
Issue Date
2003-10
Publisher
BIOMED CENTRAL LTD
Citation
BMC BIOINFORMATICS, v.4, no.45, pp.22 -
Abstract
Background: Large-scale protein interaction maps provide a new, global perspective with which to analyse protein function. PSIMAP, the Protein Structural Interactome Map, is a database of all the structurally observed interactions between superfamilies of protein domains with known three-dimensional structure in the PDB. PSIMAP incorporates both functional and evolutionary information into a single network. Results: We present a global analysis of PSIMAP using several distinct network measures relating to centrality, interactivity, fault-tolerance, and taxonomic diversity. We found the following results: Centrality: we show that the center and barycenter of PSIMAP do not coincide, and that the superfamilies forming the barycenter relate to very general functions, while those constituting the center relate to enzymatic activity. Interactivity: we identify the P-loop and immunoglobulin superfamilies as the most highly interactive. We successfully use connectivity and cluster index, which characterise the connectivity of a superfamily's neighbourhood, to discover superfamilies of complex I and II. This is particularly significant as the structure of complex I is not yet solved. Taxonomic diversity: we found that highly interactive superfamilies are in general taxonomically very diverse and are thus amongst the oldest. Fault-tolerance: we found that the network is very robust as for the majority of superfamilies removal from the network will not break up the network. Conclusions: Overall, we can single out the P-loop containing nucleotide triphosphate hydrolases superfamily as it is the most highly connected and has the highest taxonomic diversity. In addition, this superfamily has the highest interaction rank, is the barycenter of the network (it has the shortest average path to every other superfamily in the network), and is an articulation vertex, whose removal will disconnect the network. More generally, we conclude that the graph-theoretic and taxonomic analysis of PSIMAP is an important step towards the understanding of protein function and could be an important tool for tracing the evolution of life at the molecular level
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DOI
10.1186/1471-2105-4-45
ISSN
1471-2105
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BME_Journal Papers
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