Stretching frequency versus bond distance correlation of OD(H)⋯F hydrogen bonds in solid hydrates

Mikenda, W.; Steinböck, S.

doi:10.1016/0022-2860(94)08339-8

Cited by 37 publications

(54 citation statements)

References 21 publications

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“…before proton transfer) [104]. Because a standard (asymmetric double-well) H-bond possesses O -O distances of approximately 2.8 Å [36,106], the very short H-bond distances between W783 and His61 may be an indication of a proton being present on D2-His61, or possibly shared with W783, which would thus be functioning as part of the proton transfer pathway from TyrD.…”

Section: Second Proton Transfer and An Unusually Short H-bond Distancmentioning

confidence: 99%

Proton transfer reactions and hydrogen-bond networks in protein environments

Ishikita

Saito

2014

J. R. Soc. Interface.

178

169

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In protein environments, proton transfer reactions occur along polar or charged residues and isolated water molecules. These species consist of H-bond networks that serve as proton transfer pathways; therefore, thorough understanding of H-bond energetics is essential when investigating proton transfer reactions in protein environments. When the pK a values (or proton affinity) of the H-bond donor and acceptor moieties are equal, significantly short, symmetric H-bonds can be formed between the two, and proton transfer reactions can occur in an efficient manner. However, such short, symmetric H-bonds are not necessarily stable when they are situated near the protein bulk surface, because the condition of matching pK a values is opposite to that required for the formation of strong salt bridges, which play a key role in protein-protein interactions. To satisfy the pK a matching condition and allow for proton transfer reactions, proteins often adjust the pK a via electron transfer reactions or H-bond pattern changes. In particular, when a symmetric H-bond is formed near the protein bulk surface as a result of one of these phenomena, its instability often results in breakage, leading to large changes in protein conformation.

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Section: Second Proton Transfer and An Unusually Short H-bond Distancmentioning

confidence: 99%

Proton transfer reactions and hydrogen-bond networks in protein environments

Ishikita

Saito

2014

J. R. Soc. Interface.

178

169

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“…It is also reasonable to use the empirical u(D) of Mikenda (1986). Furthermore, it may also be useful to account for the complications due to the fact that the intra-molecular solute coordinate contributes to the apparent reorganization energy and is also coupled to the PT coordinate.…”

Section: K1mentioning

confidence: 99%

“…As already pointed out in §2b, the isotope effect increases upon increasing DR, reaching a value of 80 at DRZ0.6 Å for uZ 1500 cm K1 (which seems to be a reasonable representation of the lipoxygenase case). Another way to look at this problem is to assume a reasonable potential of mean force (PMF) (U(R)) in equation (2.15) and u(R) according to equation (2.14) or according to the empirical relationship of Mikenda (1986) and then to evaluate an average k ab . Such a treatment is summarized in figure 7, where we used the empirical dependence of Mikenda (1986).…”

Section: K1mentioning

confidence: 99%

“…Another way to look at this problem is to assume a reasonable potential of mean force (PMF) (U(R)) in equation (2.15) and u(R) according to equation (2.14) or according to the empirical relationship of Mikenda (1986) and then to evaluate an average k ab . Such a treatment is summarized in figure 7, where we used the empirical dependence of Mikenda (1986). Indeed, it is rather trivial to reproduce the temperature dependence of the KIE by adjusting U(R).…”

Section: K1mentioning

confidence: 99%

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Transition state theory can be used in studies of enzyme catalysis: lessons from simulations of tunnelling and dynamical effects in lipoxygenase and other systems

Olsson

Mavri

Warshel

2006

Phil. Trans. R. Soc. B

110

101

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The idea that enzyme catalysis involves special factors such as coherent fluctuations, quantum mechanical tunnelling and non-equilibrium solvation (NES) effects has gained popularity in recent years. It has also been suggested that transition state theory (TST) cannot be used in studies of enzyme catalysis. The present work uses reliable state of the art simulation approaches to examine the above ideas. We start by demonstrating that we are able to simulate any of the present catalytic proposals using the empirical valence bond (EVB) potential energy surfaces, the dispersed polaron model and the quantized classical path (QCP) approach, as well as the approximate vibronic method. These approaches do not treat the catalytic effects by phenomenological treatments and thus can be considered as first principles approaches (at least their ability to compare enzymatic reaction to the corresponding solution reactions). This work will consider the lipoxygenase reaction, and to lesser extent other enzymes, for specific demonstration. It will be pointed out that our study of the lipoxygenase reaction reproduces the very large observed isotope effect and the observed rate constant while obtaining no catalytic contribution from nuclear quantum mechanical (NQM) effects. Furthermore, it will be clarified that our studies established that the NQM effect decreases rather than increases when the donor-acceptor distance is compressed. The consequences of these findings in terms of the temperature dependence of the kinetic isotope effect and in terms of different catalytic proposals will be discussed. This paper will also consider briefly the dynamical effects and conclude that such effects do not contribute in a significant way to enzyme catalysis. Furthermore, it will be pointed out that, in contrast to recent suggestions, NES effects are not dynamical effects and should therefore be part of the activation free energy rather than the transmission factor. In view of findings of the present work and our earlier works, it seems that TST provides a quantitative tool for studies of enzyme catalysis and that the key open questions are related to the nature of the factors that lead to transition state stabilization.

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“…where A ϭ 2.11 ϫ 10 6 , and B ϭ 3.23 for the O water -D water …O acceptor bond (34). Note that these parameters were derived from spectroscopic and x-ray diffraction data for 61 different solid deuterates, e.g.…”

Section: Calculation Of the O-d Stretching Frequencies Of D 2 O From mentioning

confidence: 99%

Factors That Differentiate the H-bond Strengths of Water Near the Schiff Bases in Bacteriorhodopsin and Anabaena Sensory Rhodopsin

Saito

Kandori

Ishikita

2012

Journal of Biological Chemistry

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Background: Bacteriorhodopsin (BR) functions as a proton pump, whereas Anabaena sensory rhodopsin (ASR) functions as a photosensor. Results: pK a of the conserved Asp residues near the Schiff base significantly differ between BR and ASR. Conclusion:The O-D stretching frequencies for D 2 O are correlated with pK a (Asp). Significance: The presence of a strongly H-bonded water results from the proton-pumping activity in BR.

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Stretching frequency versus bond distance correlation of OD(H)⋯F hydrogen bonds in solid hydrates

Cited by 37 publications

References 21 publications

Proton transfer reactions and hydrogen-bond networks in protein environments

Proton transfer reactions and hydrogen-bond networks in protein environments

Transition state theory can be used in studies of enzyme catalysis: lessons from simulations of tunnelling and dynamical effects in lipoxygenase and other systems

Factors That Differentiate the H-bond Strengths of Water Near the Schiff Bases in Bacteriorhodopsin and Anabaena Sensory Rhodopsin

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