Structure and dynamics of the oxygen evolving complex of photosystem II: Role of the N-terminal loop of PsbQ

Rüdiger Ettrich¹, Jaroslava Ristvejova¹, Vladimír Kopecky jr.², Žofie Sovova¹, Kateřina Hofbauerová³, Juan B. Arellano⁴

¹Laboratory of High Performance Computing, Institute of Systems Biology and Ecology ASCR and Institute of Physical Biology USB, Zamek 136, 37333 Nové Hrady, Czech Republic.email:ettrich@greentech.cz

²Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 12116 Prague 2, Czech Republic

³Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic

⁴Instituto de Recursos Naturales y Agrobiología (CSIC), Cordel de Marinas 52, 37008 Salamanca, Spain

Infrared and Raman spectroscopy were applied to identify restraints for the structure determination of the 20 amino acid loop between two beta-sheets of the N-terminal region of the PsbQ protein of the oxygen evolving complex of photosystem II from Spinacia oleracea by restraint-based homology modeling. One of the initial models has shown a stable fold of the loop in a 20 ns molecular dynamics simulation that is in accordance with spectroscopic data. Cleavage of the first 12 amino acids leads to a permanent drift in the root means square deviation of the protein backbone and induces major structural changes.

Figure 1: Lys96, one of the four lysyl residues which are probably orientated to the lumenal facing intrinsic proteins of PSII, lies on the opposite side as are the other three lysyl residues and the conserved loop residue Asp24, in a distance from 6–12 Å and 7–13 Å to the loop residues Thr20 and Glu21, respectively. in the MD simulation

The probable binding site of PsbQ to the complex could be formed by the lysyl rich region of the helix bundle and the N-terminal loop region around Asp24 and thus would contain a large positively charged region and a small negatively one. We hypothesize that after binding to PSII the loop loses its high flexibility and bends in the direction of Lys96 with Thr20 and Glu21 interacting with this residue and so burying it under the accessible surface (Fig. 1). Thus Lys96 could probably behave as a molecular hook holding Glu21 by a salt bridge.¹

Acknowledgements.

Supports from the Institutional Research Concept of the Academy of Science of the Czech Republic (No. AVOZ60870520) and from the Ministry of Education of the Czech Republic (No. LC 06010, No. MSM0021620835, No. MSM6007665808) are gratefully acknowledged. This work was also funded by the Spanish Ministry of Education and Science (Project Ref.: BFU2004-04914-C02-02/BMC).

1. Ristvejova, J., Kopecky, V., Sovova, Z., Balsera, M., Arellano, J.B., Green, M., Ettrich, R., Biochem. Biophys. Res. Comm., 2006, 345 (1), 287-291.