Regensburg 2013 – wissenschaftliches Programm
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BP: Fachverband Biologische Physik
BP 8: Posters: Proteins
BP 8.12: Poster
Montag, 11. März 2013, 17:30–19:30, Poster B2
The dynamics and flexibility of protein disulphide-isomerase (PDI): simulations predict experimentally-observed domain motions — J Emilio Jimenez-Roldan1, Moitrayee Bhattacharyya2, Stephen A Wells1, •Rudolf A Römer1,4, Saraswathi Vishweshwara2, and Robert B Freedman3 — 1Department of Physics, The University of Warwick, Coventry, UK — 2Department of Biochemistry, IISc, Bangalore, India — 3School of Life Sciences, The University of Warwick, Coventry, UK — 4Centre for Scientific Computing, The University of Warwick, Coventry, UK
We simulated the mobility of the folding catalyst, protein disulphide-isomerase (PDI), by molecular dynamics and by a rapid approach based on flexibility analysis. We analysed our simulations using measures of backbone movement, relative positions and orientations of domains, and distances between functional sites. Despite their different assumptions, the two methods are surprisingly consistent. Both methods show that motion of domains is dominated by hinge and rotation motion of the a and a’ domains relative to the central b-b’ domain core. Both methods identify the a’ domain as showing the greatest intra-domain mobility. However, only the flexibility method, which requires 104-fold less computer power, predicts some large-scale features of inter-domain motion that have been observed experimentally. We conclude that the methods provide complementary insight into the motion of this large protein and detailed structural models that characterise its functionally-significant conformational changes.