Peter L. Freddolino, Markus Dittrich, and Klaus Schulten.
Dynamic switching mechanisms in LOV1 and LOV2 domains of plant
phototropins.
Biophysical Journal, 91:3630-3639, 2006.
(PMC: 1630464)
FRED2006A
IMPORTANT TECHNICAL NOTE: Users wishing to apply the FMN parameters for this paper
should first view the discussion on different FMN parameter sets at the LOV domain
research page (http://www.ks.uiuc.edu/Research/biological_photoreceptors/#fmnnote).
LOV domains are the light sensitive portion of plant phototropins. They absorb light
through a flavin cofactor, photochemically form a covalent bond between the
chromophore and a cysteine residue in the protein, and proceed to mediate activation of
an attached kinase domain. Although the photoreaction itself is now well characterized
experimentally and computationally, it is still unclear how the formation of the adduct
leads to kinase activation. We have performed molecular dynamics simulations on the
LOV1 domain of C. reinhardtii and the LOV2 domain of A. sativa, both before and after the
photoreaction, to answer this question. The extensive simulations, over 240 ns in
duration, reveal significant differences in how the LOV1 and LOV2 domains respond to
photoactivation. The simulations indicate that LOV1 activation is likely caused by a change
in hydrogen bonding between protein and ligand which destabilizes a highly conserved
salt bridge, whereas LOV2 activation seems to result from a change in the flexibility of a
set of protein loops. Results of electrostatics calculations, principal component analysis,
sequence alignments, and RMSD analysis corroborate the above findings.
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