Infrared and Raman spectroscopy were applied to identify restraints for the structure determination of the 20 amino acid loop between two P-sheets of the N-terminal region of the PsbQ protein of the oxygen evolving complex of photosystem 11 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. (c) 2006 Elsevier Inc. All rights reserved.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, and No. MSM6007665808) and the Grant Agency of the Czech Republic (Grant No. 206/03/D082) are gratefully acknowledged. This work was also funded by the Spanish Ministry of Education and Science (Project Ref.: BFU2004-04914-C02-02/BMC).Peer reviewed