Structural transition of bacteriorhodopsin is preceded by deprotonation of Schiff base: microsecond time-resolved x-ray diffraction study of purple membrane

Structural studies of bacteriorhodopsin in BC era

It marked half a century since the discovery of bacteriorhodopsin two years ago. On this occasion, I have revisited historically important diffraction studies of this membrane protein, based on my recollections. X-ray diffraction and electron diffraction, and electron microscopy, described the low-resolution structure of bacteriorhodopsin within the purple membrane. Neutron diffraction was effective to assign the helical regions in the primary structure with 7 rods revealed by low-resolution structure as well as to describe the retinal position. Substantial conformational changes upon light illumination were clarified by the structures of various photointermediates. Early trials of time-resolved studies were also introduced. Models for the mechanism of light-driven proton pump based on the low-resolution structural studies are also described. Significantly, they are not far from the today's understanding. I believe that the spirit of the early research scientists in this field and the essence of their studies, which constitute the foundations of the field, still actively fertilizes current membrane protein research.

Picosecond pump-probe X-ray scattering at the Elettra SAXS beamline

A new setup for picosecond pump-probe X-ray scattering at the Austrian SAXS beamline at Elettra-Sincrotrone Trieste is presented. A high-power/high-repetion-rate laser has been installed on-site, delivering UV/VIS/IR femtosecond-pulses in-sync with the storage ring. Data acquisition is achieved by gating a multi-panel detector, capable of discriminating the single X-ray pulse in the dark-gap of the Elettra hybrid filling mode. Specific aspects of laser- and detection-synchronization, on-line beam steering as well protocols for spatial and temporal overlap of laser and X-ray beam are also described. The capabilities of the setup are demonstrated by studying transient heat-transfer in an In/Al/GaAs superlattice structure and results are confirmed by theoretical calculations.

Kinetics of low pH-induced lamellar to bicontinuous cubic phase transition in dioleoylphosphatidylserine∕monoolein

Recently, it has been well recognized that the modulation of electrostatic interactions due to surface charges can induce transitions between lamellar liquid-crystalline (L(α)) and inverse bicontinuous double-diamond cubic (Q(II)(D)) phases in biological lipids. To reveal their kinetic pathway and mechanism, we investigated the low pH-induced L(α) to Q(II)(D) phase transitions in 20%-dioleoylphosphatidylserine (DOPS)/80%-monoolein (MO) using time-resolved small-angle x-ray scattering and a rapid mixing method. At a final pH of 2.6-2.9, the L(α) phase was transformed completely into the hexagonal II (H(II)) phase within 2-10 s after mixing a low pH buffer with a suspension of multilamellar vesicles of 20%-DOPS∕80%-MO (the initial step). Subsequently, the H(II) phase slowly converted into the Q(II)(D) phase and completely disappeared within 15-30 min (the second step). The rate constants of the second step were obtained using the singular value decomposition analysis. On the basis of these data, we discuss the underlying mechanism of the kinetic pathway of the low pH-induced L(α) to Q(II)(D) phase transitions.

Probing specific molecular processes and intermediates by time-resolved Fourier transform infrared spectroscopy: application to the bacteriorhodopsin photocycle

We present a general approach for probing the kinetics of specific molecular processes in proteins by time-resolved Fourier transform infrared (IR) spectroscopy. Using bacteriorhodopsin (bR) as a model we demonstrate that by appropriately monitoring some selected IR bands it is possible obtaining the kinetics of the most important events occurring in the photocycle, namely changes in the chromophore and the protein backbone conformation, and changes in the protonation state of the key residues implicated in the proton transfers. Besides confirming widely accepted views of the bR photocycle, our analysis also sheds light into some disputed issues: the degree of retinal torsion in the L intermediate to respect the ground state; the possibility of a proton transfer from Asp85 to Asp212; the relationship between the protonation/deprotonation of Asp85 and the proton release complex; and the timing of the protein backbone dynamics. By providing a direct way to estimate the kinetics of photocycle intermediates the present approach opens new prospects for a robust quantitative kinetic analysis of the bR photocycle, which could also benefit the study of other proteins involved in photosynthesis, in phototaxis, or in respiratory chains.

pH dependence of light-driven proton pumping by an archaerhodopsin from Tibet: comparison with bacteriorhodopsin

The pH-dependence of photocycle of archaerhodopsin 4 (AR4) was examined, and the underlying proton pumping mechanism investigated. AR4 is a retinal-containing membrane protein isolated from a strain of halobacteria from a Tibetan salt lake. It acts as a light-driven proton pump like bacteriorhodopsin (BR). However, AR4 exhibits an "abnormal" feature--the time sequence of proton release and uptake is reversed at neutral pH. We show here that the temporal sequence of AR4 reversed to "normal"--proton release preceding proton uptake--when the pH is increased above 8.6. We estimated the pK(a) of the proton release complex (PRC) in the M-intermediate to be approximately 8.4, much higher than 5.7 of wide-type BR. The pH-dependence of the rate constant of M-formation shows that the pK(a) of PRC in the initial state of AR4 is approximately 10.4, whereas it is 9.7 in BR. Thus in AR4, the chromophore photoisomerization and subsequent proton transport from the Schiff base to Asp-85 is coupled to a decrease in the pK(a) of PRC from 10.4 to 8.4, which is 2 pK units less than in BR (4 units). This weakened coupling accounts for the lack of early proton release at neutral pH and the reversed time sequence of proton release and uptake in AR4. Nevertheless the PRC in AR4 effectively facilitates deprotonation of primary proton acceptor and recovery of initial state at neutral pH. We found also that all pK(a)s of the key amino acid residues in AR4 were elevated compared to those of BR.