Structural Changes In Bacteriorhodopsin Research Articles

Protein Dynamics Preceding Photoisomerization of the Retinal Chromophore in Bacteriorhodopsin Revealed by Deep-UV Femtosecond Stimulated Raman Spectroscopy.

Bacteriorhodopsin is a prototypical photoreceptor protein that functions as a light-driven proton pump. The retinal chromophore of bacteriorhodopsin undergoes C13═C14 trans-to-cis isomerization upon photoexcitation, and it has been believed to be the first event that triggers the cascaded structural changes in bacteriorhodopsin. We investigated the protein dynamics of bacteriorhodopsin using deep-ultraviolet resonance femtosecond stimulated Raman spectroscopy. It was found that the stimulated Raman signals of tryptophan and tyrosine residues exhibit significant changes within 0.2 ps after photoexcitation while they do not noticeably change during the isomerization process. This result implies that the protein environment changes first, and its change is small during isomerization. The obtained femtosecond stimulated Raman data indicate that ultrafast change is induced in the protein part by the sudden creation of the large dipole of the excited-state chromophore, providing an environment that realizes efficient and selective isomerization.

Microwave-Induced Structural Changes in Bacteriorhodopsin: Studies by Optical and Fourier Transform Infrared Difference Spectroscopy

Abstract—Using optical and Fourier transform infrared (FTIR) difference spectroscopy, microwave radiation was found to affect the bacteriorhodopsin (BR) structure in films at a 30% relative humidity. This study is the first to demonstrate that a transition from the dark-adapted basal state BR560 to a state similar to the light-adapted state BR568, which is a mixture of BR568 and other isomeric forms, occurs in the absence of external photoexcitation on exposure to microwave radiation with a frequency range of 8 ≤ f ≤ 18 GHz and an intensity lower than 10 mW/cm2. The initial response of dark-adapted BR to microwave radiation included collective motion of a large portion of protein atoms, producing relatively strong signals in the regions 3700–3300, 2400–2300, and 800–600 cm–1 of the FTIR difference spectrum. Relatively weak amplitude responses were detected in the frequency range characteristics of the retinal chromophore and amide bands (Amide I and Amide II). The effects reflected changes in the retinal chromophore structure and local changes in the chromophore microenvironment.

Time-resolved serial femtosecond crystallography studies at an X-ray free electron laser reveals structural changes in bacteriorhodopsin

Time-resolved serial femtosecond crystallography studies at an X-ray free electron laser reveals structural changes in bacteriorhodopsin

A molecular movie of structural changes in bacteriorhodopsin

A molecular movie of structural changes in bacteriorhodopsin

A three-dimensional movie of structural changes in bacteriorhodopsin.

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.

Structural Changes in Bacteriorhodopsin Caused by Two-Photon-Induced Photobleaching

Bacteriorhodopsin (BR) is the key protein of the halobacterial photosynthetic system. BR assembles into two-dimensional crystalline patches, the so-called purple membranes (PM), and acts as a light-driven proton pump converting light energy into the chemical energy of a proton gradient over the cell membrane. The two-photon absorption (TPA) of BR is so far not fully understood. Astonishingly high TPA cross sections have been reported, but the molecular mechanisms have not been elucidated. In this work, we address structural changes in BR and PM upon TPA, investigating its TPA photochemistry by spectroscopy, small-angle X-ray scattering, as well as electron and atomic force microscopy. We observe that TPA of BR leads to formation of an UV-absorbing N-retinyl-bacterioopsin state, which is accompanied by the loss of crystalline order in PM. FTIR and CD spectroscopy confirm that BR trimers as well as the secondary structure of the BR molecules are preserved. We demonstrate that excitation by TPA results in the photochemical reduction of the retinal Schiff base, which in turn causes a permanent asymmetric shape change of BR, similar to the one transiently observed during the photocycle-related opening and closing of the cytoplasmic proton half channel. This shape change causes PM sheets to merely roll up toward the extracellular side and causes the loss of crystallinity of PM. We present a model for the TPA photoresponse of BR, which also explains the irreversibility of the process in terms of a photochemical reduction of the Schiff base.

Structural Changes in Bacteriorhodopsin in Response to Alternate Illumination Observed by High‐Speed Atomic Force Microscopy

Structural Changes in Bacteriorhodopsin in Response to Alternate Illumination Observed by High‐Speed Atomic Force Microscopy

Structural Changes in Bacteriorhodopsin in Response to Alternate Illumination Observed by High‐Speed Atomic Force Microscopy

Structural Changes in Bacteriorhodopsin in Response to Alternate Illumination Observed by High‐Speed Atomic Force Microscopy

Structural Changes in Bacteriorhodopsin during In Vitro Refolding from a Partially Denatured State

We report on the formation of the secondary and tertiary structure of bacteriorhodopsin during its in vitro refolding from an SDS-denatured state. We used the mobility of single spin labels in seven samples, attached at various locations to six of the seven helical segments to engineered cysteine residues, to follow coil-to-helix formation. Distance measurements obtained by spin dipolar quenching in six samples labeled at either the cytoplasmic or extracellular ends of pairs of helices revealed the time dependence of the recovery of the transmembrane helical bundle. The secondary structure in the majority of the helical segments refolds with a time constant of <100–140 ms. Recovery of the tertiary structure is achieved by sequential association of the helices and occurs in at least three distinct steps with time constants of 1), well below 1 s; 2), 3–4 s; and 3), 60–130 s (the latter depending on the helical pair). The slowest of these processes occurs in concert with recovery of the retinal chromophore.

Conformational Structural Changes of Bacteriorhodopsin Adsorbed onto Single-Walled Carbon Nanotubes

The interaction between purple membranes, composed of proteins of bacteriorhodopsin (bR) and their native surrounding lipids, and single-walled carbon nanotubes (SWNT) has been investigated. In this work, sonication has been used to debundle SWNT in buffer solution without surfactant before the addition of native purple membranes. The sample was then sonicated in a bath for a short time, followed by a centrifugation. The supernatants contain proteins in excess and SWNT as individual and small bundles covered by a bR layer with an average thickness of 1.5 nm. TEM and AFM observations support the idea that only a protein monolayer surrounds the tubes. Optical absorption and infrared spectroscopy measurements provide evidence that the proteins adsorbed onto the SWNT undergo orientational changes of the helical segments in bR and helix conformational changes. We ascribe the main driving force to the hydrophobic interactions between the sidewall of the SWNT and the hydrophobic residues of the alpha-helices of bR.

Structural Changes in Bacteriorhodopsin in Purple Membranes Induced by Irreversible Photobleaching with Heterogeneous and Homogeneous Stability

Kinetic studies of irreversible photobleaching of bacteriorhodopsin (bR) in purple membrane (PM) at neutral pH have previously indicated the existence of two kinds of species which differ in their structural stability. bR was shown to have kinetically slow- and fast-decayed components with the faster one increasing with changes in intra- and intermolecular structures in darkness. However, our recent work reported that photobleaching kinetics above pH 10 were characterized by a single-decay component. In order to elucidate the factors responsible for the heterogeneous or homogeneous stability of photobleaching, we conducted investigations into the structural changes in bR in PM induced by photobleaching at pH 7 and 11 by attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy. ATR-FTIR spectra of bR photobleached at pH 7 and 11 showed that an increase in IR peak intensity at 1656 cm(-1) occurred simultaneously with decreases at 1666 cm(-1), indicating an alpha(II)-to-alpha(I) transition in transmembrane helices during photobleaching. The most significant change in IR spectra occurred at 1626 cm(-1) for samples photobleached at pH 7, and was attributed to structures formed between adjacent molecules. The origin of the heterogeneity of photobleaching is discussed on the basis of structural characteristics found in the bleached membranes.

Participation of the BC Loop in the Correct Folding of Bacteriorhodopsin as Revealed by Solid‐state NMR†

Structural changes in bacteriorhodopsin (bR) in two different processes of retinal reconstitutions were investigated by observing the (13)C and (15)N solid-state NMR spectra of [1-(13)C]Val- and [(15)N]Pro-labeled bR. We found that NMR signals of the BC loop were sensitive to changes in protein structure and dynamics, from wild-type (WT) bR to bacterio-opsin (bO), regenerated bR and E1001 bR. Regenerated bR was prepared following the addition of retinal into bO obtained from photobleached WT-bR. E1001 bR was cultured from a retinal-deficient strain termed E1001 following the addition of retinal to growing cells. (15)N NMR signal at Pro70 in the BC loop in WT-bR was observed at 122.4 p.p.m., whereas signals were not apparent or partly suppressed in bO and regenerated bR, respectively. Similarly, the (13)C NMR signal at Val69 in the BC loop at 172.0 p.p.m. that was observed in WT-bR was significantly decreased in both regenerated bR and bO. These results suggest that the dynamic structure of the BC loop in bO was substantially altered following the removal of retinal. As a consequence, the correct protein structure failed to be recovered via the regenerating process of retinal to bO. On the other hand, (13)C and (15)N NMR signals at the BC loop in E1001 bR appeared at positions identical to those of WT-bR. The results of the current study indicate that the BC loop may not always fold correctly in the regenerated bR, which leads to different properties in the regenerated bR compared to that of WT-bR.

2P-240 バクテリオロドプシンのアルカリpHでの光誘起構造変化(生体膜/人工膜・ダイナミクス,第46回日本生物物理学会年会)

2P-240 バクテリオロドプシンのアルカリpHでの光誘起構造変化(生体膜/人工膜・ダイナミクス,第46回日本生物物理学会年会)

1P099 中性およびアルカリpH条件下における光退色が引き起こす紫膜中のバクテリオロドプシンの構造変化(膜蛋白質,ポスター発表,第45回日本生物物理学会年会)

1P099 中性およびアルカリpH条件下における光退色が引き起こす紫膜中のバクテリオロドプシンの構造変化(膜蛋白質,ポスター発表,第45回日本生物物理学会年会)

Electron Paramagnetic Resonance Study of Structural Changes in the O Photointermediate of Bacteriorhodopsin

The structural changes of bacteriorhodopsin during its photochemical cycle, as revealed by crystal structures of trapped intermediates, have provided insights to the proton translocation mechanism. Because accumulation of the last photointermediate, O, appears to be hindered by lattice forces in the crystals, the only information about the structure of this state is from suggested analogies with the determined structures of the non-illuminated D85S mutant and wild-type bacteriorhodopsin at low pH. We used electron paramagnetic resonance spectroscopy of site-directed spin labels at the extracellular protein surface in membranes to test these models. Spin–spin dipolar interactions in the authentic O state compared to the non-illuminated state revealed that the distance between helices C and F increases by ca 4 Å, there is no distance change between helices D and F, and the distance between helix D and helix B of the adjacent monomer increases. Further, the mobility changes of single labels indicate that helices E and F move outward from the proton channel at the center of the protein, and helix D tilts inward. The overall pattern of movements suggests that the model at acid pH is a better representation of the O state than D85S. However, the mobility analysis of spin-labels on the B–C interhelical loop indicates that the antiparallel β-sheet maintains its ordered secondary structure in O, instead of the predicted disorder in the two structural models. During decay of the O state, the last step of the photocycle, a proton is transferred from Asp85 to proton release complex in the extracellular proton channel. The structural changes in O suggest the need of large conformational changes to drive the Arg82 side-chain back to its initial orientation towards Asp85, and to rearrange the numerous water molecules in this region in order to conduct the proton away from Asp85.

Structural Changes in Bacteriorhodopsin following Retinal Photoisomerization from the 13-Cis Form

Bacteriorhodopsin (BR), a light-driven proton pump in Halobacterium salinarum, accommodates two resting forms of the retinylidene chromophore, the all-trans form (AT-BR) and the 13-cis,15-syn form (13C-BR). Both isomers are present in thermal equilibrium in the dark, but only the all-trans form has proton-pump activity. In this study, we applied low-temperature Fourier-transform infrared (FTIR) spectroscopy to 13C-BR at 77 K and compared the local structure around the chromophore before and after photoisomerization with that in AT-BR. Strong hydrogen-out-of-plane (HOOP) vibrations were observed at 964 and 958 cm(-)(1) for the K state of 13C-BR (13C-BR(K)) versus a vibration at 957 cm(-)(1) for the K state of AT-BR (AT-BR(K)). In AT-BR(K), but not in 13C-BR(K), the HOOP modes exhibit isotope shifts upon deuteration of the retinylidene at C15 and at the Schiff base nitrogen. Whereas the HOOP modes of AT-BR(K) were significantly affected by the mutation of Thr89, this was not the case for the HOOP modes of 13C-BR(K). These observations imply that, while the chromophore distortion is localized near the Schiff base in AT-BR(K), it is located elsewhere in 13C-BR(K). By use of [zeta-(15)N]lysine-labeled BR, we identified the N-D stretching vibrations of the 13C-BR Schiff base (in D(2)O) at 2173 and 2056 cm(-)(1), close in frequency to those of AT-BR. These frequencies indicate strong hydrogen bonding of the Schiff base in 13C-BR, presumably with a water molecule as in AT-BR. In contrast, the N-D stretching vibration appears at 2332 and 2276 cm(-)(1) in 13C-BR(K) versus values of 2495 and 2468 cm(-)(1) for AT-BR(K), suggesting that the rupture of the Schiff base hydrogen bond that occurs in AT-BR(K) does not occur in 13C-BR(K). Rotational motion of the Schiff base upon retinal isomerization is probably smaller in magnitude for 13C-BR than for AT-BR. These differences in the primary step are possibly related to the absence of light-driven proton pumping by 13C-BR.

1P063 バクテリオロドプシンのアルカリ化に伴う構造変化と光退色現象(蛋白質 C) 物生(安定性、折れたたみなど)))

1P063 バクテリオロドプシンのアルカリ化に伴う構造変化と光退色現象(蛋白質 C) 物生(安定性、折れたたみなど)))

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

X-ray and electron diffraction studies of specific reaction intermediates, or reaction intermediate analogues, have produced a consistent picture of the structural mechanism of light-driven proton pumping by bacteriorhodopsin. Of central importance within this picture is the structure of the L-intermediate, which follows the retinal all-trans to 13-cis photoisomerization step of the K-intermediate and sets the stage for the primary proton transfer event from the positively charged Schiff base to the negatively charged Asp-85. Here we report the structural changes in bacteriorhodopsin following red light illumination at 150 K. Single crystal microspectrophotometry showed that only the L-intermediate is populated in three-dimensional crystals under these conditions. The experimental difference Fourier electron density map and refined crystallographic structure were consistent with those previously presented (Royant, A., Edman, K., Ursby, T., Pebay-Peyroula, E., Landau, E. M., and Neutze, R. (2000) Nature 406, 645-648; Royant, A., Edman, K., Ursby, T., Pebay-Peyroula, E., Landau, E. M., and Neutze, R. (2001) Photochem. Photobiol. 74, 794-804). Based on the refined crystallographic structures, molecular dynamic simulations were used to examine the influence of the conformational change of the protein that is associated with the K-to-L transition on retinal dynamics. Implications regarding the structural mechanism for proton pumping by bacteriorhodopsin are discussed.

Structural Changes in Bacteriorhodopsin during the Photocycle Measured by Time-Resolved Polarized Fourier Transform Infrared Spectroscopy

The structural changes in bacteriorhodopsin during the photocycle are investigated. Time resolved polarized infrared spectroscopy in combination with photoselection is used to determine the orientation and motion of certain structural units of the molecule: Asp-85, Asp-96, Asp-115, the Schiff base, and several amide I vibrations. The results are compared with recently published x-ray diffraction data with atomic resolution about conformational motions during the photocycle. The orientation of the measured vibrations are also calculated from the structure data, and based on the comparison of the values from the two techniques new information is obtained: several amide I bands in the infrared spectrum are assigned, and we can also identify the position of the proton in the protonated Asp residues.

Helix deformation is coupled to vectorial proton transport in the photocycle of bacteriorhodopsin.

A wide variety of mechanisms are used to generate a proton-motive potential across cell membranes, a function lying at the heart of bioenergetics. Bacteriorhodopsin, the simplest known proton pump, provides a paradigm for understanding this process. Here we report, at 2.1 A resolution, the structural changes in bacteriorhodopsin immediately preceding the primary proton transfer event in its photocycle. The early structural rearrangements propagate from the protein's core towards the extracellular surface, disrupting the network of hydrogen-bonded water molecules that stabilizes helix C in the ground state. Concomitantly, a bend of this helix enables the negatively charged primary proton acceptor, Asp 85, to approach closer to the positively charged primary proton donor, the Schiff base. The primary proton transfer event would then neutralize these two groups, cancelling their electrostatic attraction and facilitating a relaxation of helix C to a less strained geometry. Reprotonation of the Schiff base by Asp 85 would thereby be impeded, ensuring vectorial proton transport. Structural rearrangements also occur near the protein's surface, aiding proton release to the extracellular medium.