Charge transport along proton wires

Karahka, Markus; Kreuzer, H. J.

doi:10.1186/1559-4106-8-13

Cited by 8 publications

(5 citation statements)

References 46 publications

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“…These results on water whiskers have been used to look at the quantum mechanics of charge transport along water wires in cell membranes both with free ends and donor/acceptor terminated [25], see Fig. 9.…”

Section: Water Whiskers In a High Field And Proton Wiresmentioning

confidence: 99%

New physics and chemistry in high electrostatic fields

Karahka

Kreuzer

2016

Surface Science

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Fields of the order of volts per meter exist along micron-sized tips. They are of the magnitude of fields inside atoms and molecules and can affect their electronic structure. This leads to a continuous Periodic Table resulting in new field-induced chemistry. We will present a tutorial treatment of this new physics and chemistry explaining such surprising phenomena like covalent bonding of Helium to metal surfaces, metallization of semiconductors and insulators, and more.

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Section: Water Whiskers In a High Field And Proton Wiresmentioning

confidence: 99%

New physics and chemistry in high electrostatic fields

Karahka

Kreuzer

2016

Surface Science

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“…Several computational works, using quantum-mechanical (QM) or hybrid QM/MM methods, demonstrated the utilization of proton − and water ,− wires as an effective mode for PT inside proteins. However, due to obvious computational limitations, these studies focused on a small number of PT events, usually near the active site.…”

Section: Introductionmentioning

confidence: 99%

Proton Wire Dynamics in the Green Fluorescent Protein

Shinobu

Agmon

2016

J. Chem. Theory Comput.

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Inside proteins, protons move on proton wires (PWs). Starting from the highest resolution X-ray structure available, we conduct a 306 ns molecular dynamics simulation of the (A-state) wild-type (wt) green fluorescent protein (GFP) to study how its PWs change with time. We find that the PW from the chromophore via Ser205 to Glu222, observed in all X-ray structures, undergoes rapid water molecule insertion between Ser205 and Glu222. Sometimes, an alternate Ser205-bypassing PW exists. Side chain rotations of Thr203 and Ser205 play an important role in shaping the PW network in the chromophore region. Thr203, with its bulkier side chain, exhibits slower transitions between its three rotameric states. Ser205 experiences more frequent rotations, slowing down when the Thr203 methyl group is close by. The combined states of both residues affect the PW probabilities. A random walk search for PWs from the chromophore reveals several exit points to the bulk, one being a direct water wire (WW) from the chromophore to the bulk. A longer WW connects the "bottom" of the GFP barrel with a "water pool" (WP1) situated below Glu222. These two WWs were not observed in X-ray structures of wt-GFP, but their analogues have been reported in related fluorescent proteins. Surprisingly, the high-resolution X-ray structure utilized herein shows that Glu222 is protonated at low temperatures. At higher temperatures, we suggest ion pairing between anionic Glu222 and a proton hosted in WP1. Upon photoexcitation, these two recombine, while a second proton dissociates from the chromophore and either exits the protein using the short WW or migrates along the GFP-barrel axis on the long WW. This mechanism reconciles the conflicting experimental and theoretical data on proton motion within GFP.

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“…Computational studies aimed at characterizing proton wires have in general employed methods such as conventional Molecular Dynamics (MD) 13,14,22,25 , Q-Hop MD 23 , discretized Feynman Path Integral MD 24 , Empirical Valence Bond (EVB) 15,20,21,27 , QM [33][34][35][36] , and QM/MM 10,11,37,38 , among others 16,17 . These studies have greatly contributed to the biophysical description of proton transfer networks and provided further evidence concerning their involvement in protein function.…”

Section: Introductionmentioning

confidence: 99%

“…Computational studies aimed at characterizing proton wires have in general employed methods such as conventional molecular dynamics (MD), ,,, Q-Hop MD, discretized Feynman path integral MD, empirical valence bond (EVB), ,,, QM, − and QM/MM, ,,, among others. , These studies have greatly contributed to the biophysical description of proton transfer networks and provided further evidence concerning their involvement in protein function. Furthermore, these studies have reinforced the importance of accounting for structural dynamics when addressing challenging problems of this nature.…”

Section: Introductionmentioning

confidence: 99%

Time-Averaged Distributions of Solute and Solvent Motions: Exploring Proton Wires of GFP and PfM2DH

Velez-Vega¹,

McKay²,

Aravamuthan³

et al. 2014

J. Chem. Inf. Model.

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Proton translocation pathways of selected variants of the green fluorescent protein (GFP) and Pseudomonas fluorescens mannitol 2-dehydrogenase (PfM2DH) were investigated via an explicit solvent molecular dynamics-based analysis protocol that allows for direct quantitative relationship between a crystal structure and its time-averaged solute-solvent structure obtained from simulation. Our study of GFP is in good agreement with previous research suggesting that the proton released from the chromophore upon photoexcitation can diffuse through an extended internal hydrogen bonding network that allows for the proton to exit to bulk or be recaptured by the anionic chromophore. Conversely for PfM2DH, we identified the most probable ionization states of key residues along the proton escape channel from the catalytic site to bulk solvent, wherein the solute and high-density solvent crystal structures of binary and ternary complexes were properly reproduced. Furthermore, we proposed a plausible mechanism for this proton translocation process that is consistent with the state-dependent structural shifts observed in our analysis. The time-averaged structures generated from our analyses facilitate validation of MD simulation results and provide a comprehensive profile of the dynamic all-occupancy solvation network within and around a flexible solute, from which detailed hydrogen-bonding networks can be inferred. In this way, potential drawbacks arising from the elucidation of these networks by examination of static crystal structures or via alternate rigid-protein solvation analysis procedures can be overcome. Complementary studies aimed at the effective use of our methodology for alternate implementations (e.g., ligand design) are currently underway.

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Charge transport along proton wires

Cited by 8 publications

References 46 publications

New physics and chemistry in high electrostatic fields

New physics and chemistry in high electrostatic fields

Proton Wire Dynamics in the Green Fluorescent Protein

Time-Averaged Distributions of Solute and Solvent Motions: Exploring Proton Wires of GFP and PfM2DH

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