On the use of advanced modelling techniques to investigate the conformational discrepancy between two X-ray structures of the AppA BLUF domain

Abstract

The conformation of the blue light utilising flavin domain of the signalling protein AppA in the dark state is a matter of intensive research, both experimental and theoretical, and has not yet unambiguously been determined. Two contradicting X-ray structures of the dark state have been published previously. We aim at resolving this seeming contradiction by exploring conformational pathways between the two X-ray structures using advanced modelling techniques, such as local-elevation searching and sampling, soft-core non-bonded interactions and protocols of successively biasing the sampling of sets of torsional angles which adopt different values in the two alternative X-ray structures. The results suggest a high energetic barrier for a change in the Trp104 side chain from a ‘Trp-in’ to a ‘Trp-out’ conformation or vice versa, and illustrate the complexity to model conformational transitions involving a large number of degrees of freedom.

Keywords:

• molecular dynamics simulation
• searching
• sampling
• BLUF

Acknowledgements

This work was financially supported by the National Center of Competence in Research (NCCR) in Structural Biology by grant number 200020-137827 of the Swiss National Science Foundation and by grant number 228076 of the European Research Council, which is gratefully acknowledged.