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@ARTICLE{Grudinin:44759,
      author       = {Grudinin, S. and Büldt, G. and Gordeliy, I. L. and
                      Baumgaertner, A.},
      title        = {{W}ater {M}olecules and {H}ydrogen-{B}onded {N}etworks in
                      {B}acteriorhodopsin-{M}olecular {D}ynamics {S}imulations of
                      the {G}round {S}tate and the {M}-{I}ntermediate},
      journal      = {Biophysical journal},
      volume       = {88},
      issn         = {0006-3495},
      address      = {New York, NY},
      publisher    = {Rockefeller Univ. Press},
      reportid     = {PreJuSER-44759},
      pages        = {3252 - 3261},
      year         = {2005},
      note         = {Record converted from VDB: 12.11.2012},
      abstract     = {Protein crystallography provides the structure of a
                      protein, averaged over all elementary cells during data
                      collection time. Thus, it has only a limited access to
                      diffusive processes. This article demonstrates how molecular
                      dynamics simulations can elucidate structure-function
                      relationships in bacteriorhodopsin (bR) involving water
                      molecules. The spatial distribution of water molecules and
                      their corresponding hydrogen-bonded networks inside bR in
                      its ground state (G) and late M intermediate conformations
                      were investigated by molecular dynamics simulations. The
                      simulations reveal a much higher average number of internal
                      water molecules per monomer (28 in the G and 36 in the M)
                      than observed in crystal structures (18 and 22,
                      respectively). We found nine water molecules trapped and 19
                      diffusive inside the G-monomer, and 13 trapped and 23
                      diffusive inside the M-monomer. The exchange of a set of
                      diffusive internal water molecules follows an exponential
                      decay with a 1/e time in the order of 340 ps for the G state
                      and 460 ps for the M state. The average residence time of a
                      diffusive water molecule inside the protein is approximately
                      95 ps for the G state and 110 ps for the M state. We have
                      used the Grotthuss model to describe the possible proton
                      transport through the hydrogen-bonded networks inside the
                      protein, which is built up in the picosecond-to-nanosecond
                      time domains. Comparing the water distribution and
                      hydrogen-bonded networks of the two different states, we
                      suggest possible pathways for proton hopping and water
                      movement inside bR.},
      keywords     = {Bacteriorhodopsins: chemistry / Biological Transport /
                      Biophysics: methods / Computer Simulation / Crystallography,
                      X-Ray / Diffusion / Dimerization / Halobacterium: metabolism
                      / Hydrogen Bonding / Models, Chemical / Models, Molecular /
                      Models, Statistical / Phosphatidylcholines: chemistry /
                      Protein Conformation / Protein Structure, Tertiary / Protons
                      / Software / Time Factors / Water: chemistry /
                      Phosphatidylcholines (NLM Chemicals) / Protons (NLM
                      Chemicals) / Bacteriorhodopsins (NLM Chemicals) /
                      1-palmitoyl-2-oleoylphosphatidylcholine (NLM Chemicals) /
                      Water (NLM Chemicals) / J (WoSType)},
      cin          = {IFF-TH-II / IBI-2},
      ddc          = {570},
      cid          = {I:(DE-Juel1)VDB31 / I:(DE-Juel1)VDB58},
      pnm          = {Kondensierte Materie / Neurowissenschaften},
      pid          = {G:(DE-Juel1)FUEK242 / G:(DE-Juel1)FUEK255},
      shelfmark    = {Biophysics},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:15731388},
      pmc          = {pmc:PMC1305474},
      UT           = {WOS:000228688800021},
      doi          = {10.1529/biophysj.104.047993},
      url          = {https://juser.fz-juelich.de/record/44759},
}