Plant type ferredoxin NADP+ oxidoreductase (FNR), as a key enzyme in the electrons flow in photosynthesis, performs the role of electron transfer from the reduced cofactor FAD to ferredoxin, through the NADP+. The enzyme FNR accomplishes association with the thylakoid membrane, through binding with the transmembrane proteins Tic62 and TROL. FNR binds the ITEP domain of these proteins in a form of a dimer. Experimental data show that this protein complex stability depends on the pH of the chloroplast stroma. The aim of this thesis was to confirm the pH dependence of the protein complex stability, and to clarify the molecular basis behind such pH dependence, using computational simulations. The goal of simulations was to study how will the change in the pH of the environment lead to the changes in the appearance and dynamics of the protein complex. Functionally important networks of hydrogen bonds and van der Waals interactions between ITEP domain and FNR dimer were identified and described into details. In silico mutations of selected amino acids in the ITEP domain of protein TROL were used to destabilise the identified group of non-covalent interactions in order to investigate their importance for structural and dynamical properties of studied systems. All results were based on 30 to 40 ns long molecular dynamics simulations of 46 systems. Simulations include systems of the protein complex, and systems of the isolated ITEP domain of protein TROL. The systems were simulated at a number of different pH.