Hydrogen Bonds with Large Proton Polarizability and Proton Transfer Processes in Electrochemistry and Biology

Zuńdel, Georg

doi:10.1002/9780470141700.ch1

Cited by 196 publications

(138 citation statements)

References 251 publications

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“…Internal proton transfer is an expected property of hydrogen bonds formed between groups with similar proton affinities. Our observation of incremental proton transfer from Y16 to the bound phenolate as the proton affinity of the phenol approaches that of Y16 is consistent with extensive studies of hydrogen bond-mediated proton transfer based on small-molecule complexes in solution (19,34,42,59) and is not a unique property of hydrogen bonds formed within the heterogeneous protein environment. The systematic variation in relative ionized fractions of Y16 and Y57 is readily accounted for by a model in which the energetic stabilization of the Y16 anion provided by the phenol-Y16 hydrogen bond decreases with increasing phenol pK a .…”

Section: Electrostatic Effects Of Charge Rearrangement Within the Actsupporting

confidence: 68%

Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site

Sigala¹,

Fafarman²,

Schwans³

et al. 2013

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

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Hydrogen bond networks are key elements of protein structure and function but have been challenging to study within the complex protein environment. We have carried out in-depth interrogations of the proton transfer equilibrium within a hydrogen bond network formed to bound phenols in the active site of ketosteroid isomerase. We systematically varied the proton affinity of the phenol using differing electron-withdrawing substituents and incorporated sitespecific NMR and IR probes to quantitatively map the proton and charge rearrangements within the network that accompany incremental increases in phenol proton affinity. The observed ionization changes were accurately described by a simple equilibrium proton transfer model that strongly suggests the intrinsic proton affinity of one of the Tyr residues in the network, Tyr16, does not remain constant but rather systematically increases due to weakening of the phenol-Tyr16 anion hydrogen bond with increasing phenol proton affinity. Using vibrational Stark spectroscopy, we quantified the electrostatic field changes within the surrounding active site that accompany these rearrangements within the network. We were able to model these changes accurately using continuum electrostatic calculations, suggesting a high degree of conformational restriction within the protein matrix. Our study affords direct insight into the physical and energetic properties of a hydrogen bond network within a protein interior and provides an example of a highly controlled system with minimal conformational rearrangements in which the observed physical changes can be accurately modeled by theoretical calculations.computational modeling | enzyme catalysis | protein electrostatics | protein semisynthesis | active site environment H ydrogen bond networks are ubiquitous structural features within proteins, and they play key roles linking secondary and tertiary structural elements and spanning protein-protein interfaces. Such networks are especially common within enzyme active sites, where they position protein and substrate groups for catalysis, stabilize charge rearrangements during chemical transformations, and mediate proton transfers (1). Despite the prevalence and critical structural and functional roles of hydrogen bond networks, incisive dissection of their physical properties within the idiosyncratic interior of folded proteins remains difficult.Hydrogen-bonded protons are not observed in the vast majority of protein X-ray structures due to the low X-ray scattering power of hydrogen atoms (2). Thus, the presence of hydrogen bond networks is typically inferred from the proximity and orientation of hydrogen bond donor and acceptor groups within refined protein structural models. The inherent inability of most X-ray diffraction studies to monitor proton positions imposes additional challenges for dissecting the physical features that influence the equilibrium protonation states of specific residues along a hydrogen-bonded proton transfer network. Furthermore, it remains extremely challenging t...

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Section: Electrostatic Effects Of Charge Rearrangement Within the Actsupporting

confidence: 68%

Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site

Sigala¹,

Fafarman²,

Schwans³

et al. 2013

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

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“…A similar concept of "proton trap" has also been put forward from molecular dynamics studies of cytochrome c oxidase (80)(81)(82). The presence of a Zundel (83) , respectively) was revealed from the broad IR continuum change during the bacteriorhodopsin photocycle (78,79). It was shown to interact with 9 residues and result in a broad sharing of the excess proton.…”

Section: Qbmentioning

confidence: 96%

Evidence for Delocalized Anticooperative Flash Induced Proton Binding as Revealed by Mutants at the M266His Iron Ligand in Bacterial Reaction Centers

et al. 2007

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Bacterial reaction centers (RCs) convert light energy into chemical free energy Via the double reduction and protonation of the secondary quinone electron acceptor, Q B , to the dihydroquinone Q B H 2 . Two RC mutants (M266His f Leu and M266His f Ala) with a modified ligand of the non-heme iron have been studied by flash-induced absorbance change spectroscopy. No important changes were observed for the rate constants of the first and second electron transfers between the first quinone electron acceptor, Q A , and Q B . However, in the M266HL mutant a destabilization of ∼40 meV of the free energy level of Q A -was observed, at variance with the M266HA mutant. The superposition of the three-dimensional X-ray structures of the three proteins in the Q A region provides no obvious explanation for the energy modification in the M266HL mutant. The shift of the midpoint redox potential of Q A /Q A -in M266HL caused accelerated recombination of the charges in the P + Q A -state of the RCs where the native Q A was replaced by a low potential anthraquinone (AQ A ). As previously reported for the native RCs, in the M266HL we observed a biphasicity of the P + AQ A -f PAQ A charge recombination. Interestingly, both phases present a similar acceleration in the M266HL mutant with respect to the wild type. The pH dependencies of the proton uptake upon Q A -and Q B -formations are superimposable in both mutants but very different from those of native RCs. The data measured in mutants are similar to those that we previously obtained on strains modified at various sites of the cytoplasmic region. The similarity of the response to these different mutations is puzzling, and we propose that it arises from a collective behavior of multiple acidic residues resulting in strongly anticooperative proton binding. The unspecific disappearance of the high pH band of proton uptake observed in all these mutants appears as the natural consequence of removing any member of an interactive proton cluster. This long range interaction also accounts for the similar responses to mutations of the proton uptake pattern induced by either Q A -or Q B -. We surmise that the presence of an extended protonated water H-bond network providing protons to Q B is responsible for these effects.Bacterial reaction centers (RCs 1 ) convert light excitation energy into chemical free energy in a similar way as the photosystem II of oxygen evolving complexes (1). RCs are membrane proteins composed of three subunits, L, M, and H, with a total molecular weight of about 100 kDa. The initial electronic excitation of a dimer of bacteriochlorophylls, P, situated on the periplasmic side of the RCs produces its electronic excited singlet state of lowest energy P*. Within about 200 ps an electron is sent from P* Via intermediate carriers (a monomer of bacteriochlorophyll and a bacteriopheophytin, H) to a ubiquinone acceptor named Q A , located on the cytoplasmic side of the complex. The electron is then transferred, in the hundred microseconds time scale, to the seconda...

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“…The MD simulation was performed on a single Na ϩ OH Ϫ ion pair solvated by 214 H2O molecules in a cubic box with periodic boundary conditions (density ϭ 1.01 g/cm 3 ) by using the MS-EVB model developed from a classical simulation model of aqueous NaOH (31). The system was equilibrated for 100 ps by using velocity rescaling (T ϭ 303 Ϯ 8 K) before making a production run 900 ps in length in the NVE ensemble with the velocity Verlet integrator and a 0.5-fs time step.…”

Section: Methodsmentioning

confidence: 99%

“…In a 2D IR measurement, a series of femtosecond pulses infrared pulses drive the O-H vibrations of the sample and stimulate the emission of a signal field that is interferometrically characterized. The Fourier transform 2D IR spectrum is related to the joint probability of exciting a molecule with initial frequency, 1 , and detecting that molecule at a different frequency, 3 , after a waiting period 2 (25,26). In a typical experiment, at small values of 2 , a diagonally elongated line shape is expected because molecules have not had time to sample their environments and lose memory of their initial excitation frequencies.…”

Section: Infrared Spectroscopy Of Isotopically Dilute Hydroxidementioning

confidence: 99%

Observation of a Zundel-like transition state during proton transfer in aqueous hydroxide solutions

Roberts

Petersen

Ramasesha

et al. 2009

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

114

150

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It is generally accepted that the anomalous diffusion of the aqueous hydroxide ion results from its ability to accept a proton from a neighboring water molecule; yet, many questions exist concerning the mechanism for this process. What is the solvation structure of the hydroxide ion? In what way do water hydrogen bond dynamics influence the transfer of a proton to the ion? We present the results of femtosecond pump-probe and 2D infrared experiments that probe the O-H stretching vibration of a solution of dilute HOD dissolved in NaOD/D2O. Upon the addition of NaOD, measured pump-probe transients and 2D IR spectra show a new feature that decays with a 110-fs time scale. The calculation of 2D IR spectra from an empirical valence bond molecular dynamics simulation of a single NaOH molecule in a bath of H2O indicates that this fast feature is due to an overtone transition of Zundel-like H3O 2 ؊ states, wherein a proton is significantly shared between a water molecule and the hydroxide ion. Given the frequency of vibration of shared protons, the observations indicate the shared proton state persists for 2-3 vibrational periods before the proton localizes on a hydroxide. Calculations based on the EVB-MD model argue that the collective electric field in the proton transfer direction is the appropriate coordinate to describe the creation and relaxation of these Zundel-like transition states.Grotthuss mechanism ͉ 2D infrared spectroscopy P roton transfer in water is the process at the heart of biological redox chemistry and energy conversion processes such as photosynthesis and cellular respiration (1). Although its extraordinary speed and efficiency has generally been attributed to the rearrangement of O-H bonds that effectively move the charge rather than a specific proton, the water structure around the charge defect and the mechanism of translocation remain challenging to study experimentally. Researchers commonly discuss the solvated excess proton in terms of 2 limiting structures, the Eigen cation (2), a triply solvated hydronium ion (H 3 O ϩ ⅐3H 2 O), and the Zundel ion (3), a proton equally shared between 2 water molecules (H 5 O 2 ϩ or H 2 O⅐H⅐OH 2 ϩ ). However, the difference in energy between these 2 configurations is small, on the order of the energy of a hydrogen bond (2-3 kcal/mol) (4), which allows these structures to interconvert on femtosecond to picosecond time scales (5, 6). Thus, to meaningfully address the structure of the excess proton, one must also consider its dynamics. Similar questions related to this view of aqueous proton transfer (PT) exist for the hydroxide ion, whereby proton transfer occurs from water to OH Ϫ . What are the ion's limiting structures, and in what manner do changes in the water structure influence the ion's structural diffusion?Initial proposals for transport of the hydroxide ion described the process as the mirror image of that observed in acids (7) and postulated the existence of a stable H 3 O 2 Ϫ state (8). Ab initio simulations (9-11) suggest a different scenario in whi...

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Hydrogen Bonds with Large Proton Polarizability and Proton Transfer Processes in Electrochemistry and Biology

Cited by 196 publications

References 251 publications

Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site

Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site

Evidence for Delocalized Anticooperative Flash Induced Proton Binding as Revealed by Mutants at the M266His Iron Ligand in Bacterial Reaction Centers

Observation of a Zundel-like transition state during proton transfer in aqueous hydroxide solutions

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