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Umbrella sampling calculations of the bindning free energy in the UVR8 dimer.: key residues in uv-b regulated signalling pathway revealed using dft and md simulation methods
Göteborgs universitet.
Örebro University, School of Science and Technology, Örebro University, Sweden. (Biokemi)ORCID iD: 0000-0003-3315-8835
Göteborgs universitet.
2012 (English)In: Challenges in biomolecular modeling: from qm to coarse-graining. International Society of Quantum Biology and Pharmacology / [ed] Lennart Nilsson, Stockholm, 2012Conference paper, Abstract (Refereed)
Abstract [en]

The dimeric UVR8 protein is a ultraviolet-B radiation (280-315 nm) photoreceptor that is responsible for the first step in UV-B regulation of gene expression in plants1. Its action comprises the actual absorption of the UV quanta by a Trp array in the protein, followed by monomerisation, and subsequent aggregation with downstream signaling components2. Quantum theoretical DFT calculationsa of excitation spectra of both a large cluster model involving seven tryptophans at the interface of the UVR8 proteins where they are intermixed with positive residues (mainly arginines) and a couple of tyrosines, and smaller fragments thereof, reveal that absorption maxima appearing in the 280-300 nm range for the full cluster result from interactions between the central tryptophans and surrounding arginines2. This observation provides an explanation for the experimentally measured action spectrum of the UVR8-dependent UV-B stimulation of HY5 transcription in mature A. thaliana leaf tissue3. Umbrella sampling methodb was used to calculate the binding free energy for the wild type UVR8 dimer and three of its mutants (R286A, R338A and R286A/R338A), in order to verify the key mutants able to disrupt the dimeric structure.

See also attached document.

Place, publisher, year, edition, pages
Stockholm, 2012.
National Category
Theoretical Chemistry
Research subject
URN: urn:nbn:se:oru:diva-24338OAI: diva2:543824
Stockholm 17-20 June 2012
Available from: 2012-08-24 Created: 2012-08-10 Last updated: 2016-08-10Bibliographically approved

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Strid, Åke
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School of Science and Technology, Örebro University, Sweden
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