Computational studies of signalling proteins
Title: Computational studies of signalling proteins
DNr: SNIC 2016/1-30
Project Type: SNIC Medium Compute
Principal Investigator: Sebastian Westenhoff <sebastian.westenhoff@kemi.uu.se>
Affiliation: Göteborgs universitet
Duration: 2016-02-01 – 2017-02-01
Classification: 10602
Homepage: http://www.csb.gu.se/sebastian-westenhoff
Keywords:

Abstract

Identifying structural changes in proteins is important, because it reveals how the enzymes function. We use time-resolved X-ray scattering to characterize structural change in light-driven proteins. To structurally interpret these data it is essential to use computational methods. The systems under study are light-sensing proteins such as phytochromes [Takala, … Westenhoff, Nature 2014, 509, 245-248.] and YF1 [Möglich, Ayers and Moffat, J. Mol. Biol. 2009, 385, 1433-1444.]. Analyzing the experimental diffusive X-ray scattering requires extensive molecular dynamics studies with long simulation times to be able to sample the light-driven conformational changes [Takala et al., Nature 2014, 509, 245-248.]. Recently we have also implemented a method to use experimental scattering data to directly guide molecular dynamics simulations in Gromacs [Björling, … Westenhoff, J. Chem. Theo. Comput. 2015, 11, 780-787.]. We now plan to extend the calculations to fit experimental scattering data on different phytochromes and YF1 mutants. Our results will help to identify the structural photocycle of photosensor proteins, which control the light response of plants and bacteria. The simulations add a atomic scale resolution to the low-resolution experimental results and with this enhance the chemicalrelevance considerably.