Uncovering Network Systems Within Protein Structures

Traditionally, proteins have been viewed as a construct based on elements of secondary structure and their arrangement in three-dimensional space. In a departure from this perspective we show that protein structures can be modelled as network systems that exhibit small-world, single-scale, and to so...

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Bibliographic Details
Published in:Journal of molecular biology 2003-12, Vol.334 (4), p.781-791
Main Authors: Greene, Lesley H., Higman, Victoria A.
Format: Article
Language:English
Subjects:
Models, Molecular
Models, Theoretical
networks
Protein Folding
protein structure
Protein Structure, Secondary
Protein Structure, Tertiary
scale-free
small-world
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Summary:Traditionally, proteins have been viewed as a construct based on elements of secondary structure and their arrangement in three-dimensional space. In a departure from this perspective we show that protein structures can be modelled as network systems that exhibit small-world, single-scale, and to some degree, scale-free properties. The phenomenological network concept of degrees of separation is applied to three-dimensional protein structure networks and reveals how amino acid residues can be connected to each other within six degrees of separation. This work also illuminates the unique features of protein networks in comparison to other networks currently studied. Recognising that proteins are networks provides a means of rationalising the robustness in the overall three-dimensional fold of a protein against random mutations and suggests an alternative avenue to investigate the determinants of protein structure, function and folding.
ISSN:0022-2836
1089-8638
DOI:10.1016/j.jmb.2003.08.061