82 research outputs found
Random Network Behaviour of Protein Structures
Geometric and structural constraints greatly restrict the selection of folds
adapted by protein backbones, and yet, folded proteins show an astounding
diversity in functionality. For structure to have any bearing on function, it
is thus imperative that, apart from the protein backbone, other tunable degrees
of freedom be accountable. Here, we focus on side-chain interactions, which
non-covalently link amino acids in folded proteins to form a network structure.
At a coarse-grained level, we show that the network conforms remarkably well to
realizations of random graphs and displays associated percolation behavior.
Thus, within the rigid framework of the protein backbone that restricts the
structure space, the side-chain interactions exhibit an element of randomness,
which account for the functional flexibility and diversity shown by proteins.
However, at a finer level, the network exhibits deviations from these random
graphs which, as we demonstrate for a few specific examples, reflect the
intrinsic uniqueness in the structure and stability, and perhaps specificity in
the functioning of biological proteins.Comment: Expanded version available in Molecular BioSystem
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