Crystal Structure of the M Intermediate of Bacteriorhodopsin: Allosteric Structural Changes Mediated by Sliding Movement of a Transmembrane Helix

Takeda, Kazuki; Matsui, Yasuhiro; Kamiya, Nobuo; Adachi, Shin‐ichi; Okumura, Hideo; Kouyama, Tsutomu

doi:10.1016/j.jmb.2004.06.080

Cited by 89 publications

(138 citation statements)

References 69 publications

(90 reference statements)

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“…The present study shows that one O-H bond that does not form an Hbond in BR subsequently forms an H-bond in L, M and N under physiological conditions. Evidence for the interaction of this water O-H group with Asp85 in M has previously been presented by FTIR and crystallographic studies (23,26).…”

Section: Water Forms H-bonds With Asp85 In L M and N At 298 Kmentioning

confidence: 77%

“…To explain these results, it was proposed that water molecules are present in M in the region around Thr46-Phe219 and that in N some of them have moved to the region around Val49 and the Schiff base. A crystallographic structure of M from a sample in which the intermediate was produced at room temperature and then cooled to 100 K for diffraction studies (23), shows two water molecules in a cavity surrounded by Phe219, Trp182, Leu93, Thr46 and Thr178 (Figure 6). This non-polar cavity is on the cytoplasmic side of bacteriorhodopsin near Asp96, but no water molecules were detected on the cytoplasmic side in the neighborhood of the Schiff base.…”

Section: Water Molecules In the Phe219-thr46-asp96 Region In Mmentioning

confidence: 99%

“…Parts of a structural model of the M intermediate of wild-type bacteriorhodopsin showing water molecules surrounded by protein in the region surrounded by Phe219, Asp96, Thr46, Leu93, Trp182, and Thr178, and those interacting with Asp85 and positioned along the sidechain of Arg82. The picture is based on the crystallographic model of Takeda et al (23); protein data bank entry 1iw9 and was drawn using RasMol.…”

Section: Water Network Between the Schiff Base And Asp96 In L And Mmentioning

confidence: 99%

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Water Structural Changes in the L and M Photocycle Intermediates of Bacteriorhodopsin as Revealed by Time-Resolved Step-Scan Fourier Transform Infrared (FTIR) Spectroscopy

et al. 2007

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In previous FTIR studies of the photocycle intermediates of bacteriorhodopsin at cryogenic temperatures, water molecules were observed in the L intermediate, in the region surrounded by protein residues between the Schiff base and Asp96. In the M intermediate, the water molecules had moved away towards the Phe219-Thr46 region, but in the N intermediate they were again observed near the Schiff base. In order to evaluate the relevance of this scheme at room temperature, time resolved FTIR difference spectra of bacteriorhodopsin, including the water O-H stretching vibration frequency regions, were recorded in the μsec and msec time ranges. Vibrational changes of weakly-H-bonded water molecules were observed in L, M, and N. In each of these intermediates, the depletion of a water O-H stretching vibration at 3645 cm −1 originating from the initial unphotolzyed bacteriorhodopsin was observed as a trough in the difference spectrum. This vibration is due to the dangling O-H group of a water molecule which interacts with Asp85, and its absence in each of these intermediates indicates that there is perturbation of this O-H group. The formation of M is accompanied by the appearance of water O-H stretching vibrations at 3670 and 3657 cm −1 . These bands are due to water molecules present in the region surrounded by Thr46, Asp96 and Phe219. Formation of L at 298 K is accompanied by the perturbations of Asp96 and the Schiff base, though in different ways from what is observed at 170 K. Changes in a broad water vibrational feature, centered around 3610 cm −1 , are kinetically correlated with the L-to-M transition. These results imply that even at room temperature, water molecules interact with Asp96 and the Schiff base in L, though with a less rigid structure than at cryogenic temperatures.Bacteriorhodopsin is a light-driven proton pump. It undergoes a photocycle initiated by the absorption of light by a retinal chromophore which is covalently linked to Lys216 forming a protonated Schiff base. The initial consequence of light absorption is the trans-to-cis isomerization of the C 13 =C 14 bond of the retinal. Proton pumping takes place as the protein undergoes conformational changes from the initial unphotolyzed state with an all-trans retinal chromophore (BR 1 ) through a sequence of intermediates, and back to the BR state. Spectroscopic and kinetic studies, including FTIR studies have distinguished a sequence of + This work was supported by an NIH grant HL 16101 (to RBG).

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Section: Water Forms H-bonds With Asp85 In L M and N At 298 Kmentioning

confidence: 77%

Section: Water Molecules In the Phe219-thr46-asp96 Region In Mmentioning

confidence: 99%

Section: Water Network Between the Schiff Base And Asp96 In L And Mmentioning

confidence: 99%

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Water Structural Changes in the L and M Photocycle Intermediates of Bacteriorhodopsin as Revealed by Time-Resolved Step-Scan Fourier Transform Infrared (FTIR) Spectroscopy

et al. 2007

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“…The crystal structures of M indicating only one [23] or two water molecules [11,24] in the D85/D212 region, as compared to three water molecules in the bR resting state [1,2], suggest that in M the active-site water molecules may have an enhanced mobility, or may relocate to other sites. To assess the role of water molecules on the energetics of proton transfer from D85 back to the retinal Schiff base we performed QM/MM calculations of proton transfer paths with various numbers of active-site water molecules, and QM computations on gas-phase models of the D85/water interactions.…”

Section: Role Of Internal Water Moleculesmentioning

confidence: 97%

“…1). Indeed, except for the crystal structure of a putative early-M [10], the crystal structures of the M state indicate coordinates for only one [23] or two [7,11,24] water molecules in the active site, suggesting that in M water molecules from the active site are either more mobile than before, or have relocated to other sites. Stabilization of the proton on D85 upon relocation of active-site water molecules would allow the protein to sample conformations other than when the Schiff base is protonated.…”

Section: Introductionmentioning

confidence: 97%

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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Neutrons to Study the Structure and Dynamics of Membrane Proteins

Wood

Zaccaı̈

2007

Biophysical Analysis of Membrane Proteins

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Crystal Structure of the M Intermediate of Bacteriorhodopsin: Allosteric Structural Changes Mediated by Sliding Movement of a Transmembrane Helix

Cited by 89 publications

References 69 publications

Water Structural Changes in the L and M Photocycle Intermediates of Bacteriorhodopsin as Revealed by Time-Resolved Step-Scan Fourier Transform Infrared (FTIR) Spectroscopy

Water Structural Changes in the L and M Photocycle Intermediates of Bacteriorhodopsin as Revealed by Time-Resolved Step-Scan Fourier Transform Infrared (FTIR) Spectroscopy

Mechanism of a proton pump analyzed with computer simulations

Neutrons to Study the Structure and Dynamics of Membrane Proteins

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