Suppression of the back proton-transfer from Asp85 to the retinal Schiff base in bacteriorhodopsin: a theoretical analysis of structural elements.
The transfer of a proton from the retinal Schiff base to the nearby Asp85 protein group is an essential step in the directional proton-pumping by bacteriorhodopsin. To avoid the wasteful back reprotonation of the Schiff base from Asp85, the protein must ensure that, following Schiff base deprotonation, the energy barrier for back proton-transfer from Asp85 to the Schiff base is larger than that for proton-transfer from the Schiff base to Asp85. Here, three structural elements that may contribute to suppressing the back proton-transfer from Asp85 to the Schiff base are investigated: (i) retinal twisting; (ii) hydrogen-bonding distances in the active site; and (iii) the number and location of internal water molecules. The impact of the pattern of bond twisting on the retinal deprotonation energy is dissected by performing an extensive set of quantum-mechanical calculations. Structural rearrangements in the active site, such as changes of the Thr89:Asp85 distance and relocation of water molecules hydrogen-bonding to the Asp85 acceptor group, may participate in the mechanism which ensures that following the transfer of the Schiff base proton to Asp85 the protein proceeds with the subsequent photocycle steps, and not with back proton transfer from Asp85 to the Schiff base.
Bondar
Ana-Nicoleta
AN
Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany.
Suhai
Sándor
S
Fischer
Stefan
S
Smith
Jeremy C
JC
Elstner
Marcus
M
D000818:Animals; D001224:Aspartic Acid / Q000737:chemistry*; D001436:Bacteriorhodopsins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D006801:Humans; D006860:Hydrogen Bonding; D011487:Protein Conformation; D017494:Proton Pumps / Q000737:chemistry* / Q000378:metabolism; D011522:Protons; D012160:Retina / Q000502:physiology; D012545:Schiff Bases / Q000737:chemistry; D013912:Threonine / Q000737:chemistry; D014867:Water / Q000737:chemistry
D017494:Proton Pumps; D011522:Protons; D012545:Schiff Bases; D014867:Water; D013912:Threonine; D001224:Aspartic Acid; D001436:Bacteriorhodopsins