66
Views
13
CrossRef citations to date
0
Altmetric
Original Articles

Can coordinate driving describe proton transfer coupled to complex protein motions?

, , , &
Pages 47-52 | Published online: 01 Feb 2007

References

References

  • Braiman MS Mogi T Marti T Stern LJ, et al. 1983 Vibrational spectroscopy of bacteriorhodopsin mutants: light-driven proton transport involves protonation changes of aspartic residues 85, 96, and 212 Biochem. 27 8516
  • Brooks BR Bruccoleri RE Olafson BD States DJ et al. 1983 CHARMM: a program for macromolecular energy minimization and dynamics calculations J. Comput. Chem. 4 187
  • Brown , LS . 2000 . Reconciling crystallography and mutagenesis: a synthetic approach to the creation of a comprehensive model for proton pumping by bacteriorhodopsin . Biochim. Biophys. Acta. , 1460 : 49
  • Brown LS Sasaki J Kandori H Maeda A et al. 1995 Glutamic acid 204 is the terminal proton release group at the extracellular surface of bacteriorhodopsin J. Biol. Chem. 270 27122
  • Cui Q Elstner M Kaxiras E Frauenheim T et al. 2001 A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method J. Phys. Chem. B 105 569
  • Edman K Nollert P Royant A Belrhali H et al. 1999 High-resolution X-ray structure of an early intermediate in the bacteriorhodopsin photocycle Nature 401 822
  • Elstner M Porezag D Jungnickel G Elsner J et al. 1998 Self-consistent-charge density-functional tight-binding method for simulating complex material properties Phys. Rev. B 58 7260
  • Fischer , S , Dunbrack , R and Karplus , M . 1994 . Cis-trans imide isomerization in the proline dipeptide . J. Am. Chem. Soc. , 194 : 252
  • Fischer , S and Karplus , M . 1992 . Conjugate peak refinement: an algorithm for finding reaction paths and accurate transition states in systems with many degrees of freedom . Chem. Phys. Lett. , 194 : 252
  • Gerwert , K , Hess , B , Soppa , J and Oesterhelt , D . 1989 . Role of aspartate 96 in proton translocation by bacteriorhodopsin . Proc. Natl. Acad. Sci. USA , 86 : 4943
  • Gerwert , K , Souvignier , G and Hess , B . 1990 . Simultaneous monitoring of light-induced changes in protein side-group protonation, chromophore isomerization, and backbone motion of bacteriorhodopsin by time-resolved Fourier-transform infrared spectroscopy . Proc. Natl. Acad. Sci. USA , 87 : 9774
  • Haupts , U , Tittor , J and Oesterhelt , D . 1999 . Closing in on bacteriorhodopsin: progress in understanding the molecule . Ann. Rev. Biophys. Biomol. Struct. , 28 : 367
  • Heberle , J . 2000 . Proton transfer reaction across bacteriorhodopsin and along the membrane . Biochim. Biophys. Acta. , 1458 : 135
  • Jorgensen WL Chandrasekhar J Madura JD Impey RW et al. 1983 Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 926
  • Lanyi , JK . 2000 . Molecular mechanism of ion transport in bacteriorhodopsin: insights from crystallographic, spectroscopic, kinetic, and mutational studies . J. Phys. Chem. B , 104 : 11441
  • Ludmann , K , Gergely , C and Váró , G . 1998 . Kinetic and thermodynamic study of the bacteriorhodopsin photocycle over a wide pH range . Biophys. J. , 75 : 3110
  • Luecke , H . 2000 . Atomic resolution structures of bacteriorhodopsin photocycle intermediates: the role of discrete water molecules in the function of this light-driven ion pump . Biochim. Biophys. Acta. , 1460 : 133
  • Straub JE 2001 Reaction rates and transition pathways In: Becker, O.M., MacKerell, A.D., Jr, B.R., Watanabe, M. (Eds.) Computational Biochemistry and Biophysics p. 199 Marcel Dekker, Inc. New York Basel

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.