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In recent past, experiments and simulations have suggested that
apart from the solvent friction, friction arising from the protein
itself plays an important role in protein folding by affecting the
intra-chain loop formation dynamics [1]. This friction is termed as
internal friction in the literature. Using a flexible Gaussian chain
with internal friction we analyze the intra-chain reconfiguration
and loop formation times for all three topology classes namely
end-to-end [2], end-to-interior and interior-to-interior. We also
analyze the effect of tail length on the looping dynamics. When
compared with available simulation data [3], our study shows that
similar to excluded volume interactions, internal friction also slows
down the looping dynamics [4].
[1]. B. G. W. Alessandro Borgia, A. Soranno, D. Nettels, M. B.
Borgia, A. Hoffmann, S. H. Pfeil, |