Distance-Dependent Proton Transfer along Water Wires Connecting Acid−Base Pairs

Cox, M. Jocelyn; Timmer, R.L.A.; Bakker, Huib J.; Park, Soohyung; Agmon, Noam

doi:10.1021/jp9004778

Cited by 79 publications

(135 citation statements)

References 55 publications

(202 reference statements)

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“…The collective compression of the water wire and concerted motion of the three protons is one the central results of this work. These results are also consistent with recent experiments showing concerted proton transfer along water wires in acid-base pairs (7).…”

Section: Resultssupporting

confidence: 93%

“…Several processes involving proton transfer, such as proton conduction through proton wires in proteins, and acid-base neutralization have been receiving elevated attention (7)(8)(9). Water is a common solvent for many of these processes.…”

mentioning

confidence: 99%

“…1. Whether the dynamics of the proton from here occurs in a stepwise fashion, transferring over one intermediate water at a time analogous to the Grotthuss mechanism, or in a concerted way (7) has been a critical missing piece in the formulation of a complete recombination mechanism of hydronium and hydroxide ions in bulk water. In this work we advance the model put forward by Eigen and de Maeyer (11) by unravelling the recombination mechanism as the ions transition from the diffusive regime to contact distance.…”

mentioning

confidence: 99%

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On the recombination of hydronium and hydroxide ions in water

Hassanali

Prakash

Eshet

et al. 2011

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

173

191

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The recombination of hydronium and hydroxide ions following water ionization is one of the most fundamental processes determining the pH of water. The neutralization step once the solvated ions are in close proximity is phenomenologically understood to be fast, but the molecular mechanism has not been directly probed by experiments. We elucidate the mechanism of recombination in liquid water with ab initio molecular dynamics simulations, and it emerges as quite different from the conventional view of the Grotthuss mechanism. The neutralization event involves a collective compression of the water-wire bridging the ions, which occurs in approximately 0.5 ps, triggering a concerted triple jump of the protons. This process leaves the neutralized hydroxide in a hypercoordinated state, with the implications that enhanced collective compressions of several water molecules around similarly hypercoordinated states are likely to serve as nucleation events for the autoionization of liquid water.acid-base chemistry | concerted proton transfer | hydronium and hydroxide recombination T he mechanisms of proton transfer and transport through different media has been a subject of great interest in the fields of chemistry and biology (1-6). Several processes involving proton transfer, such as proton conduction through proton wires in proteins, and acid-base neutralization have been receiving elevated attention (7-9). Water is a common solvent for many of these processes. As an ionizable medium with hydrogen bonds that continuously break and reform, water presents a rich environment for sustaining several complex reactions. Perhaps one of the most fundamental studies in this regard is the dissociation of water and the consequent recombination of the ions. This process forms the cornerstone of textbook acid-base chemistry (10). The acid dissociation constant of water (K W ) at room temperature is 1 × 10 −14 , which means that H 2 O rarely autodissociates and the subsequent ionic products quickly recombine. Elucidating the molecular mechanisms of the autodissociation of water and recombination of the ions has far-reaching consequences in enriching our understanding of the anomalous conductivity of protons in different environments.Most of the acid-base neutralization studies are interpreted within the framework of the model proposed by Eigen and de Maeyer (11). This model attributes the rate-limiting step of recombination to the approach of the solvated ionic species by a Grotthuss-like structural diffusion, until a contact distance of about 6 Å (12). At contact distance, the hydronium and hydroxide ions are separated by two water molecules, which form a water wire between the ions as shown in Fig. 1 (11, 12). The Grotthuss mechanism (13) was proposed to explain how the excess proton occurring as H 3 O þ diffuses much faster than expected from its hydrodynamic radius (13). The general consensus on the modern view of the 200-yr-old Grotthuss mechanism (13) is that the excess proton diffuses with a proton transfer from H 3 O þ to the...

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Section: Resultssupporting

confidence: 93%

mentioning

confidence: 99%

mentioning

confidence: 99%

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On the recombination of hydronium and hydroxide ions in water

Hassanali

Prakash

Eshet

et al. 2011

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

173

191

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“…S3) reveals that initial energy dissipation takes on multiple yet less directional pathways. The coherent low-frequency modes originate from vibronic coupling and are likely ubiquitous in photoexcited environments (22,(39)(40)(41), similar to the case of photoacid pyranine in various solvents (31,(42)(43)(44)(45). Pyranine undergoes ESPT in water following photoexcitation (45), but ESPT is blocked in methanol and multiple low-frequency modes are observed (31).…”

Section: Structural Dynamics In the Chromophore Local Environment Formentioning

confidence: 97%

Excited-state structural dynamics of a dual-emission calmodulin-green fluorescent protein sensor for calcium ion imaging

Oscar

Liu

Zhao

et al. 2014

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

191

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Fluorescent proteins (FPs) have played a pivotal role in bioimaging and advancing biomedicine. The versatile fluorescence from engineered, genetically encodable FP variants greatly enhances cellular imaging capabilities, which are dictated by excited-state structural dynamics of the embedded chromophore inside the protein pocket. Visualization of the molecular choreography of the photoexcited chromophore requires a spectroscopic technique capable of resolving atomic motions on the intrinsic timescale of femtosecond to picosecond. We use femtosecond stimulated Raman spectroscopy to study the excited-state conformational dynamics of a recently developed FP-calmodulin biosensor, GEM-GECO1, for calcium ion (Ca 2+ ) sensing. This study reveals that, in the absence of Ca 2+ , the dominant skeletal motion is a ∼170 cm −1 phenol-ring in-plane rocking that facilitates excited-state proton transfer (ESPT) with a time constant of ∼30 ps (6 times slower than wild-type GFP) to reach the green fluorescent state. The functional relevance of the motion is corroborated by molecular dynamics simulations. Upon Ca 2+ binding, this in-plane rocking motion diminishes, and blue emission from a trapped photoexcited neutral chromophore dominates because ESPT is inhibited. Fluorescence properties of site-specific protein mutants lend further support to functional roles of key residues including proline 377 in modulating the H-bonding network and fluorescence outcome. These crucial structural dynamics insights will aid rational design in bioengineering to generate versatile, robust, and more sensitive optical sensors to detect Ca 2+ in physiologically relevant environments.calcium-sensing fluorescent protein | femtosecond Raman spectroscopy | fluorescence modulation mechanism | molecular movie G reen fluorescent protein (GFP) first emerged as a revolutionary tool for bioimaging and molecular and cellular biology about 20 years ago (1-3), and the quest to discover and engineer biosensors with improved and expanded functionality has yielded exciting advances. Recently, the color palette of genetically encoded Ca 2+ sensors for optical imaging (the GECO series) has been expanded to include blue, improved green, red intensiometric, and emission ratiometric sensors (4-7). The GECO proteins belong to the GCaMP family of Ca 2+ sensors that are chimeras of a circularly permutated (cp)GFP, calmodulin (CaM), and a peptide derived from myosin light chain kinase (M13) (8). The CaM unit undergoes large-scale structural changes upon Ca 2+ binding as it wraps around M13. These changes, especially at the interfacial region where CaM interacts with cpGFP, allosterically alter the local environment of the tyrosine-derived chromophore and lead to dramatic fluorescence change in the presence of Ca 2+ (9, 10). Because GCaMP and GECO proteins are genetically encodable, show sensitivity to physiologically relevant Ca 2+ concentrations, and respond to Ca 2+ concentration changes rapidly, they have gained increasing popularity for in vivo imaging of Ca 2+ in neur...

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“…In addition, the excess proton is shared by OH4 0 and OH6 0 groups, forming a proton bound complex. This motif has appeared in other situations [55][56][57][58] and was identified spectroscopically. [6][7][8] It is analogous to proton wires observed in protein and peptides and we expect it to produce a spectroscopic manifestation similar to that observed in the case of protonated galactose.…”

Section: Trans H + Cb(2)mentioning

confidence: 78%