Parkinson's disease, the most common age-related movement disorder, is a progressive neurodegenerative disease with unclear etiology. Key neuropathological hallmarks are Lewy bodies and Lewy neurites: neuronal inclusions immunopositive for the protein α-synuclein. In-depth ultrastructural analysis of Lewy pathology is crucial to understanding pathogenesis of this disease. Using correlative light and electron microscopy/tomography on post-mortem human brain tissue from Parkinson's disease brain donors, we identified α-synuclein immunopositive Lewy pathology and show a crowded environment of membranes therein, including vesicular structures and dysmorphic organelles. Filaments interspersed between the membranes and organelles were identifiable in many, but not all aSyn inclusions. Crowding of organellar components was confirmed by STED-based superresolution microscopy, and high lipid content within α-synuclein immunopositive inclusions was corroborated by confocal imaging, CARS/FTIRimaging and lipidomics. Applying such correlative high-resolution imaging and biophysical approaches, we discovered an aggregated protein-lipid compartmentalization not previously described in the PD brain.

Much progress has been made in our understanding of water molecule reactions on surfaces, proton solvation in gas-phase water clusters and proton transfer through liquids. Compared with our advanced understanding of these physico-chemical systems, much less is known about individual water molecules and their cooperative behaviour in heterogeneous proteins during enzymatic reactions. Here we use time-resolved Fourier transform infrared spectroscopy (trFTIR) and in situ H2(18)O/H2(16)O exchange FTIR to determine how the membrane protein bacteriorhodopsin uses the interplay among strongly hydrogen-bonded water molecules, a water molecule with a dangling hydroxyl group and a protonated water cluster to transfer protons. The precise arrangement of water molecules in the protein matrix results in a controlled Grotthuss proton transfer, in contrast to the random proton migration that occurs in liquid water. Our findings support the emerging paradigm that intraprotein water molecules are as essential for biological functions as amino acids.

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Proton transfer reactions in bacteriorhodopsin were investigated by Fourier transform infrared spectroscopy, using a mutant protein in which Asp-96 was replaced by . By comparison of the BR -K, BR -L, and BR -M difference spectra (BR indicating bacteriorhodopsin ground state and K, L, and M indicating photo-intermediates) of the wild-type protein with the corresponding difference spectra of the mutant protein, detailed insight into the functional role of this residue in the proton pump mechanism is obtained. is protonated in BR, as well as another aspartic residue, which is tentatively assigned to be Asp-115. Asp-96 is not affected in the primary photoreaction. During formation of the L intermediate it is subjected to a change in the H-bonding character of its carboxylic group, but no deprotonation occurs at this reaction step. Also, in the mutant protein a light-induced structural change of the protein interior near the Asn-96 residue is probed. The BR -M difference spectrum of the mutant protein lacks the negative carbonyl band at 1742 cm1 of Asp-96 and in addition a positive band at about 1378 cm-, which is most likely to be caused by the carboxylate vibration of Asp-96. This argues for a deprotonation ofAsp-96 in the time range of the M intermediate during its photostationary accumulation. On the basis of these results, it is suggested that the point mutation does not induce a gross change of the protein structure, but a proton-binding site in the proton pathway from the cytoplasmic side to the Schiff base is lost.The mechanism of vectorial proton transfer in proteins is one of the central questions in bioenergetics. To obtain insight into this mechanism at an atomic level, the proton pump of bacteriorhodopsin is a suitable model and Fourier-transform infrared (FTIR), a powerful method.The (4,14). Uniform labeling, however, prevented assignment to specific aspartic residues of the sequence. Structural models, on the other hand, suggest that of the nine aspartic residues present in the protein, only Asp-85, Asp-96, Asp-115, and Asp-212 are located in the helical intramembrane region of the protein (5). Point mutations of Asp-85, Asp-96, Asp-115, and Asp-212 to asparagine affected the pump activity of bacteriorhodopsin (6). However, these results could not distinguish between an indirect effect, in which neutralization of a charge could influence the protein structure, and a direct effect on the pump mechanism, in which part of the proton pathway is blocked.Therefore, one of them, the Asn-96 mutant protein, was investigated by FTIR difference spectroscopy. This allows one to compare the light-induced intramolecular reactions of the mutant with those of the wild type on an atomic level. In contrast to ref. 6, the Asn-96 mutant was obtained not by site-specific mutagenesis of bacteriorhodopsin expressed in Escherichia coli but by selection of phototrophically negative mutants of Halobacterium, allowing isolation of functionally defective bacteriorhodopsin and its analysis in a natural membrane environm...

Proton transfer is crucial for many enzyme reactions. Here, we show that in addition to protonatable amino acid side chains, water networks could constitute proton-binding sites in proteins. A broad IR continuum absorbance change during the proton pumping photocycle of bacteriorhodopsin (bR) indicates most likely deprotonation of a protonated water cluster at the proton release site close to the surface. We investigate the influence of several mutations on the proton release network and the continuum change, to gain information about the location and extent of the protonated water network and to reveal the participating residues necessary for its stabilization. We identify a protonated water cluster consisting in total of one proton and about five water molecules surrounded by six side chains and three backbone groups (Tyr-57, Arg-82, Tyr-83, Glu-204, Glu-194, Ser-193, Pro-77, Tyr-79, and Thr-205). The observed perturbation of proton release by many single-residue mutations is now explained by the influence of numerous side chains on the protonated H bonded network. In situ hydrogen͞deuterium exchange Fourier transform IR measurements of the bR ground state, show that the proton of the release group becomes localized on Glu-204 and Asp-204 in the ground state of the mutants E194D and E204D, respectively, even though it is delocalized in the ground state of wild-type bR. Thus, the release mechanism switches between the wild-type and mutated proteins from a delocalized to a localized proton-binding site.bacteriorhodopsin ͉ hydrogen bonded network ͉ proton release

In its proton-pumping photocycle, bacteriorhodopsin releases a proton to the extracellular surface at pH 7 in the transition from intermediate L to intermediate M. The proton-release group, named XH, was assigned in low-temperature FT-IR studies to a single residue, E204 [Brown, L. S., Sasaki, J., Kandori, H., Maeda, A., Needleman, R. , and Lanyi, J. K. (1995) J. Biol. Chem. 270, 27122-27126]. The time-resolved room-temperature step-scan FT-IR photocycle studies on wild-type and E204Q-, and E204D-mutated bacteriorhodopsin, which we present here, show in contrast that the FT-IR data give no evidence for deprotonation of E204 in the L-to-M transition. Therefore, it is unlikely that E204 represents XH. On the other hand, IR continuum absorbance changes indicate intramolecular proton transfer via an H-bonded network to the surface of the protein. It appears that this H-bonded network is spanned between the Schiff base and the protein surface. The network consists at least partly of internally bound water molecules and is stabilized by E204 and R82. Other not yet identified groups may also contribute. At pH 5, the intramolecular proton transfer to the surface of the protein seems not to be disturbed. The proton seems to be buffered at the surface and later in the photocycle released into the bulk during BR recovery. Intramolecular proton transfer via a complex H-bonded network is proposed to be a general feature of proton transfer in proteins.

By using factor analysis and decomposition, bacteriorhodopsin's intramolecular reactions have been assigned to photocycle intermediates. Independent of specific kinetic models, the pure BR-L, BR-M, BR-N, and BR-O difference spectra were calculated by analyzing simultaneously two different measurements in the visible and infrared spectral region performed at pH 6.5, 298 K, 1 M KCl, and pH 7.5, 288 K, 1 M KCl. Even though after M formation L, M, N, and O intermediates kinetically overlap under physiological conditions, their pure spectra have been separated by this analysis in contrast to other approaches at which unphysiological conditions or mutants have been used or specific photocycle models have been assumed. The results now provide a set reference spectra for further studies. The following conclusions for physiologically relevant reactions are drawn: (a) the catalytic proton release binding site, asp 85, is protonated in the L to M transition and remains protonated in the intermediates N and O; (b) the catalytic proton uptake binding site asp 96 is deprotonated in the M to N transition and already reprotonated in the N to O transition; (c) proton transfer between asp 96 and the Schiff base is facilitated by backbone movements of a few peptide carbonyl groups in the M to N transition.

The molecular events during the photocycle of bacteriorhodopsin have been studied by the method of time-resolved and static infrared difference spectroscopy. Characteristic spectral changes involving the C=O stretching vibration of protonated carboxylic groups were detected. To identify the corresponding groups with either glutamic or aspartic acid, BR was selectively labeled with [4-13C]aspartic acid. An incorporation of ca. 70% was obtained. The comparison of the difference spectra in the region of the CO2- stretching vibrations of labeled and unlabeled BR indicates that ionized aspartic acids are influenced during the photocycle, the earliest effect being observed already at the K610 intermediate. Taken together, the results provide evidence that four internal aspartic acids undergo protonation changes and that one glutamic acid, remaining protonated, is disturbed. The results are discussed in relation to the various aspects of the proton pumping mechanism, such as retinal isomerization, charge separation, pK changes, and proton pathway.