Zuordnung der Protonierungsmuster von Wassernetzwerken in Bakteriorhodopsin mittels berechneter Infrarotspektren

Rousseau, Roger; Kleinschmidt, Volker; Schmitt, Udo W.; Marx, Dominik

doi:10.1002/ange.200453857

Cited by 16 publications

(17 citation statements)

References 33 publications

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“…Following the approach described in previous MD studies, [18,20,21,24,26] the BR structures were embedded in a POPC (1-palmitoyl-2-oleyl-sn-glycero-3-phosphatidylcholine) membrane. The system was then entirely solvated with water molecules, thereby removing those water molecules that overlapped with the protein or the POPC membrane.…”

Section: Methodsmentioning

confidence: 99%

Potential Proton‐Release Channels in Bacteriorhodopsin

et al. 2008

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The protein bacteriorhodopsin pumps protons across a bacterial membrane; its pumping cycle is triggered by the photoisomerization of a retinal cofactor and involves multiple proton-transfer reactions between intermittent protonation sites. These transfers are either direct or mediated by hydrogen-bonded networks, which may include internal water molecules. The terminal step of the proton-transfer sequence is the proton release from a pocket near Glu194 and Glu204 to the extracellular bulk during the transition from the L to the M photointermediate states. The polar and charged side chains connecting these two regions in the crystal structures show no structural changes between the initial bR state and the L/M states, and no intermittent protonation changes have been detected so far in this region. Based on biomolecular simulations, we propose two potential proton-release channels, which connect the release pocket to the extracellular medium. In simulations of the L photointermediate we observe bulk water entering these channels and forming transient hydrogen-bonded networks, which could serve as fast deprotonation pathways from the release pocket to the bulk via a Grotthuss mechanism. For the first channel, we find that the triple Arg7, Glu9, and Tyr79 acts as a valve, thereby gating water uptake and release. The second channel has two release paths, which split at the position Asn76/Pro77 underneath the release group. Here, water molecules either exchange directly with the bulk or diffuse within the protein towards Arg 134/Lys129, where the exchange with the bulk occurs.

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Section: Methodsmentioning

confidence: 99%

Potential Proton‐Release Channels in Bacteriorhodopsin

et al. 2008

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“…[9][10][11][12] Modern discussions of acid-base reactions that involve proton transfer between Brønsted acids and Brønsted bases [13] have evolved from the seminal studies of Eigen [14,15] and Weller. [16] Eigens review of the field [14] outlined the general kinetic approach for acid-base reactions in aqueous solution (Figure 1 a).…”

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confidence: 99%

Base‐Induced Solvent Switches in Acid–Base Reactions

Mohammed,

Pines,

Nibbering

et al. 2007

Angew Chem Int Ed

203

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Fast switches: Eigen and Weller's classic diffusion reaction model for aqueous acid–base neutralization reactions is used to interpret the proton‐transfer dynamics between pyranine and trichloroacetate. Upon mutual diffusion of the acid and base to form an encounter reaction complex, solvent switches mediate the proton transfer between acid and base and provide a general framework for all observed dynamic features (see picture; ROH=acid, B=base).

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“…The AIMD approach to theoretical vibrational spectroscopy [20][21][22][23] has been demonstrated specifically for bare H 5 O 2 + itself [24][25][26][27] to compare favorably with traditional approaches based on qualitative assessments. Herein, using AIMD trajectories, approximate normal modes are determined which supply a full set of optimized vibrational coordinates that represent the fundamental modes; [23,28] details are given in the Supporting Information.…”

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confidence: 99%