A Study on the Mechanism of the Proton Transport in Bacteriorhodopsin: The Importance of the Water Molecule

Murata, Katsumi; Fujii, Yasuyuki; Enomoto, Nobuyuki; Hata, Masayuki; Hoshino, Tyuji; Tsuda, Minoru

doi:10.1016/s0006-3495(00)76352-1

Cited by 44 publications

(37 citation statements)

References 23 publications

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“…Challenges specific to bacteriorhodopsin and other retinal-containing proteins are the controversies regarding the details of the retinal geometry from X-ray crystal structures, and the need to use appropriate quantum chemical methods to describe retinal. The dramatic effect of water molecules on the retinal proton transfer reactions [30,76,98,99] highlight the importance of accurate information about the location and dynamics of water molecules in the interior of proton-pumping proteins. Such detailed information can only be derived by using MD simulations to assess the structures provided by X-ray crystallography.…”

Section: Discussionmentioning

confidence: 99%

Mechanism of a proton pump analyzed with computer simulations

2009

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Understanding the mechanism of proton pumping requires a detailed description of the energetics and sequence of events associated with the proton transfers, and of how proton transfer couples to conformational rearrangements of the protein. Here, we discuss our recent advances in using computer simulations to understand how bacteriorhodopsin pumps protons. We emphasize the importance of accurately describing the retinal geometry and the location of water molecules.

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Section: Discussionmentioning

confidence: 99%

Mechanism of a proton pump analyzed with computer simulations

2009

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“…In the ground state structure of bR (43, Deformation of Helix C in Bacteriorhodopsin L-intermediate 2154 6a), helping to stabilize their widely separated pK a values of 13.5 (71) and 2.2 (70), respectively, thus ensuring that the probability for proton transfer to occur in the resting state is negligible. Indeed theoretical studies have shown that the presence of Wat-402 stabilizes the protonated Schiff base, whereas a proton will spontaneously detach from the Schiff base only when Wat-402 is absent (91).…”

Section: Conformational Changes Near the Active Site In L Lt -Anmentioning

confidence: 99%

Deformation of Helix C in the Low Temperature L-intermediate of Bacteriorhodopsin

Edman

Royant

Larsson

et al. 2004

Journal of Biological Chemistry

112

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Light-driven vectorial proton translocation is basic to the mechanism of energy transduction by photosynthetic systems. Bacteriorhodopsin (bR)1 is the simplest known light-driven proton pump and has long served as a model system for understanding how protons may be transported "up hill" against a transmembrane proton motive potential. bR contains seven transmembrane ␣-helices that surround a proton translocation channel lined with strategically placed charged residues (3). Depending upon their protonation states, which change in a well orchestrated cascade as a proton is transported across the cell membrane, these charged residues can serve as either proton donors or proton acceptors. Light activation of the chromophore, an all-trans-retinal molecule covalently attached to Lys-216 in helix G via a protonated Schiff base (the primary proton donor) results in the 13-cis-retinal configuration with two-thirds quantum efficiency. Steric conflicts and mechanical stress resulting from photoisomerization initiate a sequence of conformational changes that can be characterized spectroscopically and that perturb the local environment of several key residues, strongly affecting their pK a values and creating transient pathways for proton transfer.The specific spectral intermediates of the bR photocycle have been well characterized, and a common reaction scheme is: bR 570 3 K 590 7 L 550 7 M 412 7 N 560 7 O 640 3 bR 570 (sub-

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“…This is an important notion, considering the fact that the structure and function of large (bio)molecules are often determined by water molecules that are confined in one or more dimensions . [7][8][9][10][11] Recently, the dynamics of water interacting with biomolecules were studied by comparing the spectral dynamics of a chromophore dissolved in bulk liquid water with those of the same chromophore embedded in a hydrated biomolecule. [12] These spectral dynamics reflect the collective rearrangement of the water near the chromophore, and were found to be much slower within the hydrated (bio)molecule than in bulk water.…”

Section: Introductionmentioning

confidence: 99%

Energy Transfer in Single Hydrogen‐Bonded Water Molecules

Bakker¹,

Gilijamse²,

Lock³

2005

ChemPhysChem

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We study the structure and dynamics of hydrogen-bonded complexes of H2O/HDO and acetone dissolved in carbon tetrachloride by probing the response of the O-H stretching vibrations with linear mid-infrared spectroscopy and femtosecond mid-infrared pump-probe spectroscopy. We find that the hydrogen bonds in these complexes break and reform with a characteristic time scale of approximately 1 ps. These hydrogen-bond dynamics are observed to play an important role in the equilibration of vibrational energy over the two O-H groups of the H2O molecule. For both H2O and HDO, the O-H stretching vibrational excitation relaxes with a time constant of 6.3+/-0.3 ps, and the molecular reorientation has a time constant of 6+/-1 ps.

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A Study on the Mechanism of the Proton Transport in Bacteriorhodopsin: The Importance of the Water Molecule

Cited by 44 publications

References 23 publications

Mechanism of a proton pump analyzed with computer simulations

Mechanism of a proton pump analyzed with computer simulations

Deformation of Helix C in the Low Temperature L-intermediate of Bacteriorhodopsin

Energy Transfer in Single Hydrogen‐Bonded Water Molecules

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