Water-Mediated Hydrogen-Bonded Network on the Cytoplasmic Side of the Schiff Base of the L Photointermediate of Bacteriorhodopsin

Maeda, Akio; Herzfeld, Judith; Belenky, Marina; Needleman, Richard; Gennis, Robert B.; Balashov, Sergei P.; Ebrey, Thomas G.

doi:10.1021/bi0301542

Cited by 15 publications

(15 citation statements)

References 47 publications

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“…Computer simulations also establish that a water molecule at this position can channel a proton to Asp85 through Thr89 (29). Another transient water molecule (Wat453) which forms H-bond interactions with the carbonyl oxygen of Lys216 and the backbone nitrogen of Gly220 was also predicted from FTIR spectroscopy studies (30) and is observed in the difference electron density.…”

Section: Conformational Changes Associated With Proton Transfermentioning

confidence: 75%

“…However, not all zero-energy ABSs are MBSs. For instance, in the nontopological or trivial phase, ABSs can move to zero energy at a particular Zeeman field, giving rise to a zerobias conductance peak, and then split again at higher fields, indicating a switch of fermion parity (30). On the other hand, zero-energy MBSs in short wires may also split as a function of chemical potential or Zeeman field (14).…”

Section: Mechanistic Overviewmentioning

confidence: 99%

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A three-dimensional movie of structural changes in bacteriorhodopsin

Nango

Royant

Kubo

et al. 2016

Science

399

392

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Bacteriorhodopsin (bR) is a light-driven proton pump and a model membrane transport protein. We used time-resolved serial femtosecond crystallography at an x-ray free electron laser to visualize conformational changes in bR from nanoseconds to milliseconds following photoactivation. An initially twisted retinal chromophore displaces a conserved tryptophan residue of transmembrane helix F on the cytoplasmic side of the protein while dislodging a key water molecule on the extracellular side. The resulting cascade of structural changes throughout the protein shows how motions are choreographed as bR transports protons uphill against a transmembrane concentration gradient.

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Section: Conformational Changes Associated With Proton Transfermentioning

confidence: 75%

Section: Mechanistic Overviewmentioning

confidence: 99%

A three-dimensional movie of structural changes in bacteriorhodopsin

Nango

Royant

Kubo

et al. 2016

Science

399

392

View full text Add to dashboard Cite

show abstract

“…The importance of the hydrogen‐bonding network in bacterial rhodopsins has become more and more evident recently (38), and the involvement of W182 in the hydrogen bonding in bR has been reported (24,25,29,39,40). We observed the difference in the stability of the M‐intermediate depending on the substituted amino acid residues (Fig.…”

Section: Discussionmentioning

confidence: 99%

Tryptophan 171 in Pharaonis Phoborhodopsin (Sensory Rhodopsin II) Interacts with the Chromophore Retinal and its Substitution with Alanine or Threonine Slowed Down the Decay of M- and O-intermediate†

Iwasa

Abe

Yakura

et al. 2007

Photochemistry and Photobiology

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Pharaonis phoborhodopsin (ppR), also called pharaonis sensory rhodopsin II, NpSRII, is a photoreceptor for the photophobic response of Natronomonas pharaonis. Tryptophan 182 (W182) of bacteriorhodopsin (bR) is near the chromophore retinal and has been suggested to interact with retinal during the photoreaction and also to be involved in the hydrogen-bonding network around the retinal. W182 of bR is conserved in ppR as tryptophan 171 (W171). To elucidate whether W171 of ppR interacts with retinal during the photoreaction and/or is involved in the hydrogen-bonding network as in bR, we formed W171-substituted mutants of ppR, W171A and W171T. Our low-temperature spectroscopic study has revealed that the substitution of W171 to Ala or Thr resulted in the stabilization of M- and O-intermediates. The stability of M and absorption spectral changes during the M-decay were different depending on the substituted residue. These findings suggest that W171 in ppR interacts with retinal and the degree of the interaction depends on the substituted residues, which might be rate determining in the M-decay. In addition, the involvement of W171 in the hydrogen-bonding network is suggested by the O-decay. We also found that glycerol slowed the decay of M and not of O.

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“…Mutational studies have suggested that the water molecules in question are present in L at 170 K as a cluster between the Schiff base and Asp96 (27,51). Similar vibrational bands of water were also shown to be present in N at 260 K (42).…”

Section: Changes In Water Molecules Are Coordinated With the L-to-m Tmentioning

confidence: 92%

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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Water-Mediated Hydrogen-Bonded Network on the Cytoplasmic Side of the Schiff Base of the L Photointermediate of Bacteriorhodopsin

Cited by 15 publications

References 47 publications

A three-dimensional movie of structural changes in bacteriorhodopsin

A three-dimensional movie of structural changes in bacteriorhodopsin

Tryptophan 171 in Pharaonis Phoborhodopsin (Sensory Rhodopsin II) Interacts with the Chromophore Retinal and its Substitution with Alanine or Threonine Slowed Down the Decay of M- and O-intermediate†

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

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