Operation of the Proton Wire in Green Fluorescent Protein. A Quantum Dynamics Simulation

Vendrell, Oriol; Gelabert, Ricard; Moreno, Miquel; Lluch, José M.

doi:10.1021/jp801169z

Cited by 58 publications

(98 citation statements)

References 46 publications

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“…Concerted transport phenomena of protons have recently been observed in systems involving acid-base neutralization (7) as well as photoactive proteins like bacteriorhodopsin (34) and the green fluorescent protein (GFP) (35,36). GFP consists of a high density of negatively charged residues on the surface that attracts protons and funnels them through a water wire to the active site (37).…”

Section: Resultsmentioning

confidence: 99%

On the recombination of hydronium and hydroxide ions in water

Hassanali

Prakash

Eshet

et al. 2011

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

172

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: Resultsmentioning

confidence: 99%

On the recombination of hydronium and hydroxide ions in water

Hassanali

Prakash

Eshet

et al. 2011

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

172

191

View full text Add to dashboard Cite

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“…In contrast to the single ESIPT process present in HBX, SA, and other related systems, GFP-like systems may undergo two or more ESIPT processes. [17,18] This opens the door to several reaction paths so that the possibility of obtaining a stable structure upon photoexcitation at a given wavelength largely increases. In fact, a GFP-like fluorescent protein called Dronpa has recently been proposed as a very promising candidate for a molecular photomemory.…”

Section: Introductionmentioning

confidence: 99%

Study of the Photochemical Properties and Conical Intersections of [2,2′‐Bipyridyl]‐3‐amine‐3′‐ol

et al. 2008

Self Cite

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The two isoelectronic bipyridyl derivatives [2,2'-bipyridyl]-3,3'-diamine and [2,2'-bipyridyl]-3,3'-diol are experimentally known to undergo very different excited-state double-proton-transfer processes, which result in fluorescence quantum yields that differ by four orders of magnitude. In a previous study, these differences were explained from a theoretical point of view, because of topographical features in the potential energy surface and the presence of conical intersections (CIs). Here, we analyze the photochemical properties of a new molecule, [2,2'-bipyridyl]-3-amine-3'-ol [BP(OH)(NH(2))], which is, in fact, a hybrid of the former two. Our density functional theory (DFT), time-dependent DFT (TDDFT), and complete active space self-consistent field (CASSCF) calculations indicate that the double-proton-transfer process in the ground and first singlet pi-->pi* excited state in BP(OH)(NH(2)) presents features that are between those of their "parents". The presence of two CIs and the role they may play in the actual photochemistry of BP(OH)(NH(2)) and other bipyridyl derivatives are also discussed.

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“…see ref. 13,[20][21][22][23][24][25][26][27][28][29][30][31]. Although quantum mechanical/molecular mechanical (QM/MM) methods have been developed considerably over the past decade (for recent reviews see ref.…”

Section: Introductionmentioning

confidence: 99%

Isomerization mechanism of the HcRed fluorescent protein chromophore

Sun¹,

Lan

et al. 2012

Phys. Chem. Chem. Phys.

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To understand how the protein achieves fluorescence, the isomerization mechanism of the HcRed chromophore is studied both under vacuum and in the solvated red fluorescent protein. Quantum mechanical (QM) and quantum mechanical/molecular mechanical (QM/MM) methods are applied both for the ground and the first excited state. The photoinduced processes in the chromophore mainly involve torsions around the imidazolinone-bridge bond (t) and the phenoxy-bridge bond (j). Under vacuum, the isomerization of the cis-trans chromophore essentially proceeds by t twisting, while the radiationless decay requires j torsion. By contrast, the isomerization of the cis-trans chromophore in HcRed occurs via simultaneous t and j twisting. The protein environment significantly reduces the barrier of this hula twist motion compared with vacuum. The excited-state isomerization barrier via the j rotation of the cis-coplanar conformer in HcRed is computed to be significantly higher than that of the trans-non-coplanar conformer. This is consistent with the experimental observation that the cis-coplanar-conformation of the chromophore is related to the fluorescent properties of HcRed, while the trans-non-planar conformation is weakly fluorescent or non-fluorescent. Our study shows how the protein modifies the isomerization mechanism, notably by interactions involving the nearby residue Ile197, which keeps the chromophore coplanar and blocks the twisting motion that leads to photoinduced radiationless decay.

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Operation of the Proton Wire in Green Fluorescent Protein. A Quantum Dynamics Simulation

Cited by 58 publications

References 46 publications

On the recombination of hydronium and hydroxide ions in water

On the recombination of hydronium and hydroxide ions in water

Study of the Photochemical Properties and Conical Intersections of [2,2′‐Bipyridyl]‐3‐amine‐3′‐ol

Isomerization mechanism of the HcRed fluorescent protein chromophore

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