structural analysis and mutational assessment of the photosystem ii chlorophyll-binding protein (cp47) in the cyanobacterium synechocystis sp. pcc 6803: modeling and simulation study

Cp47 is one of the essential components of photosystem ii (psii) in green plants, green algae, and cyanobacteria; which is involved in the light reactions of photosynthesis. various studies have shown that the binding of the extrinsic protein of 33 kda (psbo) to the large extrinsic loop of cp47 (e loop) is an essential photoautotrophic activity of the psii complex. moreover, the deletion of the amino acids between gly-351 and thr-365 within loop e failed to assemble stable psii centers. in this study, using computational methods, the effect of phenylalanine (phe) mutation at position 363 on synechocystis sp. pcc 6803 cp47 was investigated and then the mutant model was compared with the native one. because the experimental 3d structure of synechocystis sp. pcc 6803 cp47 and psbo proteins are not available in the protein data bank (pdb), the 3d structure of these proteins was modeled by homology modeling. after refining and energy minimization, the quality of protein geometry was assessed by different criteria such as procheck and prosa. then, structural analysis of mutant and native models was performed with molecular dynamic (md) simulation and docking method. the analysis of results obtained from md simulation shows that f363r mutation affects the flexibility of some regions and especially leads to an increase in mutation region and changes the conformation of cp47. in addition, the results of docking studies indicate that f363r mutation can decrease buried surface area (bsa) at the interface region and decrease the binding energy of cp47 and psbo. these data reinforce our hypothesis that an increase of flexibility at the position of f363 in the large extrinsic loop of cp47 may be an important factor in reducing interaction between cp47 and psbo extrinsic protein and then water oxidation. oxidation.