Specific Damage Induced by X-ray Radiation and Structural Changes in the Primary Photoreaction of Bacteriorhodopsin

Matsui, Yasuhiro; Sakai, Keisuke; Murakami, Midori; Shiro, Yoshitsugu; Adachi, Shin‐ichi; Okumura, Hideo; Kouyama, Tsutomu

doi:10.1016/s0022-2836(02)01110-5

Cited by 188 publications

(258 citation statements)

References 45 publications

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“…This stable structure will be perturbed upon photoisomerization of the retinal to 13-cis,15-anti. The three crystal structures reported 1,8,15 for the K state are in agreement with the conclusions from changes in the C=N stretch frequency that had suggested 46, 47 that the Schiff base loses its hydrogenbond. There is no such consensus for the L state.…”

supporting

confidence: 87%

“…The FTIR O-H stretch bands in L in the wild-type protein and several mutants are consistent only with model c), because they suggest 50-52 that the Schiff base becomes hydrogen-bonded to a water molecule specifically in the cytoplasmic region. The chemical shift of 15 N labeled Schiff base in L by solid-state NMR 30 is consistent only with models b) and c) because it indicates the existence of strong Schiff base counter-ion interaction. The NMR results suggest 30 twists around the C 13 =C 14 and C 15 =NZ double bonds in L, consistent with model b).…”

mentioning

confidence: 83%

“…In L, retinal atoms C 13 and C 15 , and especially C 14 , undergo considerable displacements (0.38 ± 0.06, 0.43 ± 0.06 and 0.64 ± 0.08 Å, respectively), but Lys216 NZ moves much less ( Figures 3, 4, and 5, Table 4). Full rotation of the C 13 =C 14 double-bond without other changes would turn the NZ-H vector to the cytoplasmic direction.…”

Section: Changes Of the Retinal In The L Statementioning

confidence: 99%

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Structural Changes in the L Photointermediate of Bacteriorhodopsin

Lanyi

Schobert

2007

Journal of Molecular Biology

126

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The L to M reaction of the bacteriorhodopsin photocycle includes the crucial proton transfer from the retinal Schiff base to Asp85. In spite of the importance of the L state in deciding central issues of the transport mechanism in this pump, the serious disagreements among the three published crystallographic structures of L have remained unresolved. Here we report on the x-ray diffraction structure of the L state, to 1.53 -1.73 Å resolutions, from replicate data sets collected from six independent crystals. Unlike in earlier studies, the partial occupancy refinement uses diffraction intensities from the same crystals before and after the illumination to produce the trapped L state. The high reproducibility of inter-atomic distances, and bond angles and torsions of the retinal, lends credibility to the structural model. The photoisomerized 13-cis retinal in L is twisted at the C 13 =C 14 and C 15 =NZ double-bonds so that the Schiff base does not lose its connection to wat402 and therefore to the proton acceptor Asp85. The protonation of Asp85 by the Schiff base in the L → M reaction is likely to occur, therefore, via wat402. It is evident from the L state structure that various conformational changes involving hydrogen-bonding residues and bound water begin to propagate from the retinal to the protein at this stage already, and in both extracellular and cytoplasmic directions. Their rationales in the transport can be deduced from the way their amplitudes increase in the intermediates that follow L in the reaction cycle, and from the proton transfer reactions with which they are associated. Keywordsbacteriorhodopsin; proton pumps; transport mechanism; membrane proteins; protein crystallography; photointermediates Much progress has been made in recent years in describing how protons are transported in the light driven pump, bacteriorhodopsin. The structure of the protein in the non-illuminated, but light-adapted, BR-state is available to 1.4-1.6 Å resolution 1, 2 , and the participation of the retinal Schiff base, acidic side-chains, and numerous bound water molecules, in the internal proton transfers and in proton release and uptake at the two membrane surfaces are now understood. High-resolution x-ray structural models of nearly all of the intermediate states of the transport cycle 1, 3-15 give a step by step atomic level "movie" containing details of the structural rearrangements in the protein up to the M and N states. Large-scale conformational changes in the second half of the photocycle have been described, in turn, by cryo-electron microscopy 16, 17 , low-resolution x-ray and neutron diffraction projection maps 18-22 , EPR spectroscopy with site-specific spin-labels 23-27 and cysteine reactivity changes 28 at the Correspondence to: Janos K. Lanyi. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and rev...

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supporting

confidence: 87%

mentioning

confidence: 83%

Section: Changes Of the Retinal In The L Statementioning

confidence: 99%

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Structural Changes in the L Photointermediate of Bacteriorhodopsin

Lanyi

Schobert

2007

Journal of Molecular Biology

126

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“…a, b comparison of L-state X-ray structural models with the bR resting state. The following color codes are used: green bR resting state [1,103]; iceblue 1VJM [6]; magenta 1UCQ [7]; blue 2NTW [9]; mauve 1O0A [8]. The Schiff base nitrogen atom is shown as a sphere.…”

Section: Role Of Internal Water Moleculesmentioning

confidence: 99%

“…For clarity, amino acids 32-79 containing the second transmembrane helical segment were not included in the figure. Figures 1 and 3a, b were prepared using the Visual Molecular Dynamics software [103] performed computations in which we considered different numbers and locations of water molecules in the active site. For example, we demonstrated that in the absence of w402 the barrier for proton transfer from the Schiff base to D85 is *6 kcal/mol lower than when w402 is present [30].…”

Section: Introductionmentioning

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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Low‐temperature Raman spectroscopy reveals small chromophore distortion in primary photointermediate of proteorhodopsin

et al. 2018

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Proteorhodopsin (PR) is a microbial rhodopsin functioning as a light-driven proton pump in aquatic bacteria. We performed low-temperature Raman measurements of PR to obtain the structure of the primary photoproduct, the K intermediate (PR ). PR showed the hydrogen-out-of-plane modes that are much less intense than those of bacteriorhodopsin as the prototypical light-driven proton pump from haloarchaea. The present results reveal the significantly relaxed chromophore structure in PR , which can be coupled to the slow kinetics of the K intermediate. This structure suggests that PR transports protons using the small energy storage within the chromophore at the start of its photocycle.

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Specific Damage Induced by X-ray Radiation and Structural Changes in the Primary Photoreaction of Bacteriorhodopsin

Cited by 188 publications

References 45 publications

Structural Changes in the L Photointermediate of Bacteriorhodopsin

Structural Changes in the L Photointermediate of Bacteriorhodopsin

Mechanism of a proton pump analyzed with computer simulations

Low‐temperature Raman spectroscopy reveals small chromophore distortion in primary photointermediate of proteorhodopsin

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