Tryptophan perturbation in the L intermediate of bacteriorhodopsin: Fourier transform infrared analysis with indole-nitrogen-15 shift

Maeda, Akio; Sasaki, Jun; Ohkita, Yoshihiro J.; Simpson, Michelle; Herzfeld, Judith

doi:10.1021/bi00165a001

Cited by 31 publications

(35 citation statements)

References 22 publications

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“…38,39 The observation (4) is in line with recent FTIR studies demonstrating that the indole nitrogen of Trp182 is not hydrogen bonded in the L intermediate. 40,41 The observation (6) is consistent with a recent FTIR study showing that a strong interaction between Asp85 and the OH group of Thr89 remains unchanged in the L intermediate. 42 These coincidences suggest that the structural change observed in the present study takes place under the physiological condition.…”

Section: Discussionsupporting

confidence: 89%

Crystal Structure of the L Intermediate of Bacteriorhodopsin: Evidence for Vertical Translocation of a Water Molecule during the Proton Pumping Cycle

Kouyama

Nishikawa

Tokuhisa

et al. 2004

Journal of Molecular Biology

113

173

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Section: Discussionsupporting

confidence: 89%

Crystal Structure of the L Intermediate of Bacteriorhodopsin: Evidence for Vertical Translocation of a Water Molecule during the Proton Pumping Cycle

Kouyama

Nishikawa

Tokuhisa

et al. 2004

Journal of Molecular Biology

113

173

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“…The photoproducts of V49A at 80 K contained about 15% L, as judged from the L-specific band of Trp182 at 3486 cm -1 (43). Subtraction of 15% of L leaves a K-like spectrum with an intense 1194 cm -1 band, though the K-specific intense HOOP band at 951 cm -1 is missing.…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2003

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The L intermediate in the proton-motive photocycle of bacteriorhodopsin is the starting state for the first proton transfer, from the Schiff base to Asp85, in the formation of the M intermediate. Previous FTIR studies of L have identified unique vibration bands caused by the perturbation of several polar amino acid side chains and several internal water molecules located on the cytoplasmic side of the retinylidene chromophore. In the present FTIR study we describe spectral features of the L intermediate in D(2)O in the frequency region which includes the N-D stretching vibrations of the backbone amides. We show that a broad band in the 2220-2080 cm(-1) region appears in L. By use of appropriate (15)N labeling and mutants, the lower frequency side of this band in L is assigned to the amides of Lys216 and Gly220. These amides are coupled to each other, and interact with Thr46 and Val49 in helix B and Asp96 in helix C via weakly H-bonding water molecules that exhibit O-D stretching vibrations at 2621 and 2605 cm(-1). These water molecules are part of a hydrogen-bonded network characteristic of L which includes other water molecules located closer to the chromophore that exhibit an O-D stretching vibration at 2589 cm(-1). This structure, extending from the Schiff base to the internal proton donor Asp96, stabilizes L and affects the L-to-M transition.

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“…For example, the L intermediate in BR gives rise to an NH stretch mode in the tryptophan indole group at 3,477 cm −1 [50]. A positive band near 3,511 cm −1 and smaller features at 3,496 cm −1 (−) were assigned in the BR→M difference spectrum to a threonine residue (OH stretch) on the basis of [3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18] O]Thr labeling, while a much smaller band appearing at 3,486 cm −1 was tentatively assigned to a tryptophan [51] (NH stretch).…”

Section: Structural Changes Of Weakly Hydrogen Bonded Internal Water mentioning

confidence: 99%

Conformational changes in the archaerhodopsin-3 proton pump: detection of conserved strongly hydrogen bonded water networks

et al. 2011

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Archaerhodopsin-3 (AR3) is a light-driven proton pump from Halorubrum sodomense, but little is known about its photocycle. Recent interest has focused on AR3 because of its ability to serve both as a high-performance, genetically-targetable optical silencer of neuronal activity and as a membrane voltage sensor. We examined light-activated structural changes of the protein, retinal chromophore, and internal water molecules during the photocycle of AR3. Low-temperature and rapid-scan time-resolved FTIR-difference spectroscopy revealed that conformational changes during formation of the K, M, and N photocycle intermediates are similar, although not identical, to bacteriorhodopsin (BR). Positive/negative bands in the region above 3,600 cm −1 , which have previously been assigned to structural changes of weakly hydrogen bonded internal water molecules, were substantially different between AR3 and BR. This included the absence of positive bands recently associated with a chain of proton transporting water molecules in the cytoplasmic channel and a weakly hydrogen bonded water (W401), which is part of a hydrogenbonded pentagonal cluster located near the retinal Schiff base. However, many of the broad IR continuum absorption changes below 3,000 cm −1 assigned to networks of water molecules involved in proton transport through cytoplasmic and extracellular portions in BR were very similar in AR3. This work and subsequent studies comparing BR and AR3 structural changes will help identify conserved elements in BR-like proton pumps as well as bioengineer AR3 to optimize neural silencing and voltage sensing.

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Tryptophan perturbation in the L intermediate of bacteriorhodopsin: Fourier transform infrared analysis with indole-nitrogen-15 shift

Cited by 31 publications

References 22 publications

Crystal Structure of the L Intermediate of Bacteriorhodopsin: Evidence for Vertical Translocation of a Water Molecule during the Proton Pumping Cycle

Crystal Structure of the L Intermediate of Bacteriorhodopsin: Evidence for Vertical Translocation of a Water Molecule during the Proton Pumping Cycle

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

Conformational changes in the archaerhodopsin-3 proton pump: detection of conserved strongly hydrogen bonded water networks

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