The structures of the active center in dark-adapted bacteriorhodopsin by solution-state NMR spectroscopy

Abstract

The two forms of bacteriorhodopsin present in the dark-adapted state, containing either all-trans or 13-cis,15-syn retinal, were examined by using solution state NMR, and their structures were determined. Comparison of the all-trans and the 13-cis,15-syn forms shows a shift in position of about 0.25 Å within the pocket of the protein.Comparing this to the 13-cis,15-anti chromophore of the catalytic cycle M-intermediate structure, the 13-cis,15-syn form demonstrates a less pronounced up-tilt of the retinal C12OC14 region, while leaving W182 and T178 essentially unchanged. The NOH dipole of the Schiff base orients toward the extracellular side in both forms, however, it reorients toward the intracellular side in the 13-cis,15-anti configuration to form the catalytic M-intermediate. Thus, the change of the NOH dipole is considered primarily responsible for energy storage, conformation changes of the protein, and the deprotonation of the Schiff base. The structural similarity of the all-trans and 13-cis,15-syn forms is taken as strong evidence for the ion dipole dragging model by which proton (hydroxide ion) translocation follows the change of the dipole.A number of important biological processes, including the reception of hormon-or light-encoded signals, depend on the function of hepta-helical transmembrane proteins (1, 2). Certain members of this family, like the visual pigment rhodopsin and the archaeal proton pump bacteriorhodopsin (BR), contain a light reactive prosthetic retinal group that is attached via a protonated Schiff base linkage (ϪC ϭ NHϩ) to the -amino group of a lysine residue in the seventh helix. Their light sensitivity is based on photoisomerization of this retinal moiety. The specific amino acid composition in the active center determines the wavelength of chromophore absorption, the energy barriers for bond rotation in the retinylidene moiety, and the regioselectivity of isomerization. Pioneering structural investigations were done with electron microscopy (3). Recently, high-resolution three-dimensional structures of BR (4-13) (initial state and M-, K-intermediates), the related halorhodopsin (14), and rhodopsin (15) have been made available.Bacteriorhodopsin converts light energy into that of a proton gradient that is subsequently used by the transmembrane protein ATP-synthase to produce chemical energy in the form of ATP. At the beginning of the photocycle, the catalytically active form of BR absorbs a photon by the all-trans,15-anti retinal cofactor that is linked to K216 forming a Schiff base. During the photoexcitation, the retinal undergoes a rearrangement of the electronic structure of its extended conjugated system, resulting in the trans 3 cis isomerization to a 13-cis,15-anti form, and causing reduced proton affinity on the charged Schiff base. The M intermediate is formed by the transfer of a proton from the Schiff base to D85 in the extracellular half-channel. Reprotonation of the Schiff base is mediated by D96 in the cytoplasmic half-channel of the protein in response to the larg...

Kinetic Folding Mechanism of an Integral Membrane Protein Examined by Pulsed Oxidative Labeling and Mass Spectrometry

“…Also, slow (tens of minutes) changes may occur after BR formation as the chromophore equilibrates into the dark-adapted state. 72,86,87 One point that remains somewhat unclear is whether the earliest intermediate detected in our experiments is entirely equivalent to the "I 1 " species proposed by Booth et al 61,72 Overall, this study demonstrates how pulsed covalent labeling can provide mechanistic insights into kinetic folding transitions of membrane proteins. The information obtained in this way is complementary to data obtained by classical stopped-flow spectroscopy.…”

Transition of Rhodopsin into the Active Metarhodopsin II State Opens a New Light-induced Pathway Linked to Schiff Base Isomerization

“…Vogel et al have recently shown (22) that the all-trans-retinal is bound to Lys 296 via a Schiff base linkage in the 15-syn configuration, whereas in dark-adapted Rh and in Meta II, the configuration of the retinal is 15-anti. Such a syn/anti conversion is not uncommon for retinal proteins and also occurs in the proton pump bacteriorhodopsin during extended periods of darkness (34). Thus, when Meta III forms, the retinylidene bond and not the central C 11 ϭC 12 double bond is isomerized.…”

Advanced and In Situ Analytical Methods for Solar Fuel Materials

“…9 Schematic for the photocycle of the membrane protein bacteriorhodopsin with characteristic spectroscopy states and proton motion activity. Adapted from Pieper et al [71] and Patzelt et al [72] states, i.e., BR-568 (solid line) and at an intermediate position in the photocycle, referred to as state M. The Bragg reflections are indexed vs a hexagonal lattice. We notice minute but clearly distinguishable changes in the peak heights for the (2,0), (2,1), (2,2), (3,1), (4,0), (4,1), and (4,2) indexed Bragg peaks, which are interpreted as structural signatures for conformational changes [73].…”