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Serine in BLUF domains displays spectral importance in computational models

Paper ID Volume ID Publish Year Pages File Format Full-Text
30393 44476 2009 9 PDF Available
Title
Serine in BLUF domains displays spectral importance in computational models
Abstract

The BLUF (blue-light sensing using flavine) domain of the AppA photoreceptor protein from Rhodobacter sphaeroides was modelled by using quantum chemical chromophore plus amino acid models at the (TD-)B3LYP/6-31G∗ level of theory. The models were based on NMR structures, and further refined by CHARMM force field molecular dynamics simulations. The goal is to explain the total redshift by about 10 nm in the UV/Vis spectra of BLUF domains after illumination, and to relate it to structural changes. For this purpose UV/Vis spectra of the available NMR structures were calculated and related to geometrical features. In particular, the hydrogen network embedding the central chromophore is discussed. Specifically, the position of a conserved glutamine, Q63, is found to be important in agreement with findings from previous works. Additionally, however, we find a systematic dependence also on the geometry of a conserved serine, S41. Based on a series of calculations with known structures and with artificial structural models, we argue that indeed the light-induced switching of both Q63 and S41 is necessary to explain the full ∼10 nm redshift in the light (signalling) state of serine containing BLUF domains. Following or accompanying the double switching, two structurally highly important residues W104 and M106 exchange places, but do not affect the overall UV/Vis properties of the chromophore.

Keywords
BLUF; Flavine protein; Time-dependent DFT Calculation; Molecular dynamics simulation; UV/Vis spectra calculation; Blue-light sensing
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Serine in BLUF domains displays spectral importance in computational models
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Publisher
Database: Elsevier - ScienceDirect
Journal: Journal of Photochemistry and Photobiology B: Biology - Volume 94, Issue 2, 9 February 2009, Pages 87–95
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us