Stuchebrukhov research group           Department of Chemistry           University of California at Davis




Water in Catalytic Site:
MD Studies and
Free Energy Calculations




Zheng & Stuchebrukhov, BBA, 1557, 99, (2003)      Tashiro & Stuchebrukhov, JPC B, 109, 1015, (2005)

  • see MD movie (mpg, 11.8 mb)

    The main results from the MD and free energy calculations studies from our group show that it is energetically favorable and feasible for water molecules to be found in the catalytic region. The two chains of H-bonded water molecules are formed. One leads from Glu242 to PRDa3 and the second branch leads from Glu to the BNC. These water molecules are flexible and dynamic during the course of the simulation, however they yet still remain relatively stable and form relatively ordered structure.

    Conformational changes of Glu242 sidechain, during a course of MD simulation, has been also observed (Glu in downward and upward conformations), which we may refer as a proton input and proton output conformations of its side chain.




    The two water chains can be in principle utilized to provide the pathways for the PT from Glu242 to His291 (for the pump protons) and from Glu to OH– ligand in the BNC (for chemical protons, for reduction of O2 intermediates).