The Solvent‐Dependent Shift of the Amide I Band of a Fully Solvated Peptide as a Local Probe for the Solvent Composition in the Peptide/Solvent Interface

Paschek, Dietmar; Pühse, Matthias; Perez-Goicochea, Arnold; Gnanakaran, S.; Garcı́a, Angel E.; Winter, Roland; Geiger, Alfons

doi:10.1002/cphc.200800540

Cited by 16 publications

(17 citation statements)

References 67 publications

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“…(35). It was deduced from experiments and simulations that the hydration of α-helices shifts the amide I vibration frequency down by 8-20 cm −1 due to H-bonding of water to the amide C=O (36,37). Correspondingly, a frequency upshift is expected for the amide II frequency, given that the H-bonding of water to the amide C=O will weaken the H-bond between amide C=O and N-H pairs, leading to a stronger N-H bond.…”

Section: Structural Changes Of the Protein Backbonementioning

confidence: 99%

Transient protonation changes in channelrhodopsin-2 and their relevance to channel gating

Lórenz-Fonfrı́a

Resler

Krause

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

160

414

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The discovery of the light-gated ion channel channelrhodopsin (ChR) set the stage for the novel field of optogenetics, where cellular processes are controlled by light. However, the underlying molecular mechanism of light-induced cation permeation in ChR2 remains unknown. Here, we have traced the structural changes of ChR2 by time-resolved FTIR spectroscopy, complemented by functional electrophysiological measurements. We have resolved the vibrational changes associated with the open states of the channel (P 2 390 and P 3 520 ) and characterized several proton transfer events. Analysis of the amide I vibrations suggests a transient increase in hydration of transmembrane α-helices with a t 1/2 = 60 μs, which tallies with the onset of cation permeation. Aspartate 253 accepts the proton released by the Schiff base (t 1/2 = 10 μs), with the latter being reprotonated by aspartic acid 156 (t 1/2 = 2 ms). The internal proton acceptor and donor groups, corresponding to D212 and D115 in bacteriorhodopsin, are clearly different from other microbial rhodopsins, indicating that their spatial position in the protein was relocated during evolution. Previous conclusions on the involvement of glutamic acid 90 in channel opening are ruled out by demonstrating that E90 deprotonates exclusively in the nonconductive P 4 480 state. Our results merge into a mechanistic proposal that relates the observed proton transfer reactions and the protein conformational changes to the gating of the cation channel.O ptogenetics provides new tools to neurophysiologists to steer cellular responses with unprecedented temporal and spatial resolution. The former takes advantage of light as an ultrashort trigger, whereas the latter is achieved by genetically encoding and directing photosensitive proteins to specific cell types. The most prominent among the optogenetics tools is channelrhodopsin (ChR), which was found to be the first light-gated ion channel of its kind (1, 2). This discovery paved the way for an exponentially growing number of neurophysiological applications, ranging from single cells to living animals (3). Light-gated ion permeation by ChR expands the various modes of action of the large family of microbial rhodopsins already comprising light-driven ion pumps and sensors (4). Among the various ChRs, which differ mostly in cation selectivity (3), ChR2 is used in the majority of optogenetic applications because of the higher expression yield in mammalian cells.A projection structure of the heptahelical ChR2 showed a dimer with the contact interface between helices C and D suggested to form the cation channel (5). More recently, a chimeric ChR (C1C2) was constructed by linking the last two helices (F and G) of ChR2 to the first five (A to E) of ChR1 and resolved by X-ray crystallography to 2.3 Å (6). The high-resolution structure confirmed the dimeric arrangement and identified an electronegative extracellular pore in each monomer framed by helices A, B, C, and G. Accompanying electrophysiological experiments on point mutants indicated r...

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Section: Structural Changes Of the Protein Backbonementioning

confidence: 99%

Transient protonation changes in channelrhodopsin-2 and their relevance to channel gating

Lórenz-Fonfrı́a

Resler

Krause

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

160

414

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“…[10] In another article, adetailed MD analysis is given for the non-ideal mixingb ehavior explained by simple lattice models. [17] Thus, despite this often observed ideal macroscopic mixing behavior,s everal exciting applications are possible for which preferential solvation by,f or example, hydrogen bonding gives rise to non-additivee ffects, which may lead to improvements in the performance of the given ILs relative to that of the pure components. [7] Beside mixing, the interesting features of ILs can also be altered by their functionalization.…”

Section: Introductionmentioning

confidence: 99%

Triphilic Ionic‐Liquid Mixtures: Fluorinated and Non‐fluorinated Aprotic Ionic‐Liquid Mixtures

et al. 2015

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We present here the possibility of forming triphilic mixtures from alkyl- and fluoroalkylimidazolium ionic liquids, thus, macroscopically homogeneous mixtures for which instead of the often observed two domains—polar and nonpolar—three stable microphases are present: polar, lipophilic, and fluorous ones. The fluorinated side chains of the cations indeed self-associate and form domains that are segregated from those of the polar and alkyl domains. To enable miscibility, despite the generally preferred macroscopic separation between fluorous and alkyl moieties, the importance of strong hydrogen bonding is shown. As the long-range structure in the alkyl and fluoroalkyl domains is dependent on the composition of the liquid, we propose that the heterogeneous, triphilic structure can be easily tuned by the molar ratio of the components. We believe that further development may allow the design of switchable, smart liquids that change their properties in a predictable way according to their composition or even their environment.

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“…We scrutinized a small molecule of high relevance to biophysics at extreme pressures: TMAO, the most potent piezolyte known to stabilize proteins against pressure‐induced denaturation in deep‐sea organisms. The observed peak shifts are of the same order of magnitude as those that allow one to distinguish α‐helix from β‐sheet conformations of proteins or to probe cosolvent perturbations of proteins . For TMAO, our analyses directly connect pressure‐induced changes in its IR spectrum to a locally enhanced H‐bonding network at high compression.…”

Section: Figurementioning

confidence: 75%

Toward Extreme Biophysics: Deciphering the Infrared Response of Biomolecular Solutions at High Pressures

et al. 2016

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Biophysics under extreme conditions is the fundamental platform for scrutinizing life in unusual habitats,s uch as those in the deep sea or continental subsurfaces,but also for putative extraterrestrial organisms.T herefore,a ni mportant thermodynamic variable to explore is pressure.Itisshown that the combination of infrared spectroscopywith simulation is an exquisite approach for unraveling the intricate pressure response of the solvation pattern of TMAOi nw ater,w hichi s expected to be transferable to biomolecules in their native solvent. Pressure-enhanced hydrogen bonding was found for TMAOi nw ater.T MAOi samolecule knownt os tabilize proteins against pressure-induced denaturation in deep-sea organisms.Anever-increasing number of microorganisms are known that flourish only when subjected to extreme environmental conditions,including high pressures in the kilobar regime. [1][2][3][4] In fact, the deep sea, the sub-seafloor,a nd the continental subsurface together provide the largest microbial habitats on Earth. [5] Laboratory experiments in the multi-gigapascal (10 kbar) range even point to survival at higher pressures than achieved on Earth. [6,7] Although it is well-known that organisms living in such extreme conditions must have strategies to adapt to those conditions,t he underlying molecular adaptation mechanisms still remain largely unknown. [1][2][3][4] One such strategy involves the intracellular accumulation of small molecules,t ermed piezolytes,t hat stabilize protein structures at extreme pressures. [6,7] Tr imethylamine N-oxide (TMAO), in particular,i sk nown to efficiently offset the perturbing effects of high hydrostatic pressure in deep-sea animals. [8,9] Although the consensus view on the stabilizing effect of TMAOu nder ambient conditions implies that it functions as aso-called molecular crowder that depletes from protein surfaces, [10][11][12] there exists no coherent molecular picture of the stabilizing effect of TMAOu nder extreme-pressure conditions,d espite the fact that experi-ments have revealed its strong potencya lso at high pressures. [13] Moreover,even the molecular-level effect of TMAO on the pressure-dependent structure and dynamics of water remains unknown. [14] It is the realm of an emerging field, "extreme biophysics", to elucidate the (bio)molecular foundations that allow for life far away from the usual physiological conditions which govern ambient life. [15][16][17][18][19][20][21][22][23] Although temperature effects have been studied extensively over the last 30 years,e xtreme pressures are much more difficult to access in the laboratory. This difficulty constitutes ac ritical bottleneck because pressure,b eing ac rucial thermodynamic variable next to temperature and concentration, could otherwise be used as ag ateway to gain fundamental insight into the structure, dynamics,a nd hence function of these systems. [15][16][17][18][19][20][21][22][23] In at hrust to push forward extreme biophysics,w ef ocus herein on Fourier transform infrared (FTIR) spectroscopy as ap robe t...

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The Solvent‐Dependent Shift of the Amide I Band of a Fully Solvated Peptide as a Local Probe for the Solvent Composition in the Peptide/Solvent Interface

Cited by 16 publications

References 67 publications

Transient protonation changes in channelrhodopsin-2 and their relevance to channel gating

Transient protonation changes in channelrhodopsin-2 and their relevance to channel gating

Triphilic Ionic‐Liquid Mixtures: Fluorinated and Non‐fluorinated Aprotic Ionic‐Liquid Mixtures

Toward Extreme Biophysics: Deciphering the Infrared Response of Biomolecular Solutions at High Pressures

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