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Computer experiments are performed to investigate why protein contactnetworks (networks induced by spatial contacts between amino acid residues of aprotein) do not have shorter average shortest path lengths in spite of theirimportance to protein folding. We find that shorter average inter-nodaldistances is no guarantee of finding a global optimum more easily. Results fromthe experiments also led to observations which parallel an existing view thatneither short-range nor long-range interactions dominate the protein foldingprocess. Nonetheless, runs where there was a slight delay in the use oflong-range interactions yielded the best search performance. We incorporatethis finding into the optimization function by giving more weight toshort-range links. This produced results showing that randomizing long-rangelinks does not yield better search performance than protein contact networks aunatural even though randomizing long-range links significantly reduces averagepath lengths and retains much of the clustering and positive degree-degreecorrelation inherent in protein contact networks. Hence there can beexplanations, other than the excluded volume argument, beneath the topologicallimits of protein contact networks.

Why aren't the small worlds of protein contact networks smaller