Dataset Information

Nuclear Resonance Vibrational Spectroscopic Definition of the Facial Triad FeIV?O Intermediate in Taurine Dioxygenase: Evaluation of Structural Contributions to Hydrogen Atom Abstraction.

ABSTRACT: The ?-ketoglutarate (?KG)-dependent oxygenases catalyze a diverse range of chemical reactions using a common high-spin FeIV?O intermediate that, in most reactions, abstract a hydrogen atom from the substrate. Previously, the FeIV?O intermediate in the ?KG-dependent halogenase SyrB2 was characterized by nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT) calculations, which demonstrated that it has a trigonal-pyramidal geometry with the scissile C-H bond of the substrate calculated to be perpendicular to the Fe-O bond. Here, we have used NRVS and DFT calculations to show that the FeIV?O complex in taurine dioxygenase (TauD), the ?KG-dependent hydroxylase in which this intermediate was first characterized, also has a trigonal bipyramidal geometry but with an aspartate residue replacing the equatorial halide of the SyrB2 intermediate. Computational analysis of hydrogen atom abstraction by square pyramidal, trigonal bipyramidal, and six-coordinate FeIV?O complexes in two different substrate orientations (one more along [? channel] and another more perpendicular [? channel] to the Fe-O bond) reveals similar activation barriers. Thus, both substrate approaches to all three geometries are competent in hydrogen atom abstraction. The equivalence in reactivity between the two substrate orientations arises from compensation of the promotion energy (electronic excitation within the d manifold) required to access the ? channel by the significantly larger oxyl character present in the p? orbital oriented toward the substrate, which leads to an earlier transition state along the C-H coordinate.

SUBMITTER: Srnec M

PROVIDER: S-EPMC7642179 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Nuclear Resonance Vibrational Spectroscopic Definition of the Facial Triad FeIV═O Intermediate in Taurine Dioxygenase: Evaluation of Structural Contributions to Hydrogen Atom Abstraction.

Srnec Martin M Iyer Shyam R SR Dassama Laura M K LMK Park Kiyoung K Wong Shaun D SD Sutherlin Kyle D KD Yoda Yoshitaka Y Kobayashi Yasuhiro Y Kurokuzu Masayuki M Saito Makina M Seto Makoto M Krebs Carsten C Bollinger J Martin JM Solomon Edward I EI

Journal of the American Chemical Society 20201026 44

The α-ketoglutarate (αKG)-dependent oxygenases catalyze a diverse range of chemical reactions using a common high-spin FeIV═O intermediate that, in most reactions, abstract a hydrogen atom from the substrate. Previously, the FeIV═O intermediate in the αKG-dependent halogenase SyrB2 was characterized by nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT) calculations, which demonstrated that it has a trigonal-pyramidal geometry with the scis ...[more]

PMID: 33103886

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Project description:Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and interprotein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation. However, still, an all-encompassing theory that describes the vibrational solvatochromism, electrochromism, and dynamic fluctuation of vibrational frequencies has not been completely established mainly due to the intrinsic complexity of intermolecular interactions in condensed phases. In particular, the amount of data obtained from the linear and nonlinear vibrational spectroscopic experiments has been rapidly increasing, but the lack of a quantitative method to interpret these measurements has been one major obstacle in broadening the applications of these methods. Among various theoretical models, one of the most successful approaches is a semiempirical model generally referred to as the vibrational spectroscopic map that is based on a rigorous theory of intermolecular interactions. Recently, genetic algorithm, neural network, and machine learning approaches have been applied to the development of vibrational solvatochromism theory. In this review, we provide comprehensive descriptions of the theoretical foundation and various examples showing its extraordinary successes in the interpretations of experimental observations. In addition, a brief introduction to a newly created repository Web site (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-the-art multidimensional vibrational spectroscopy will be one of the most fruitful ways to study the structure and dynamics of chemical, biological, and functional molecular systems in the future.

Dataset Information

Nuclear Resonance Vibrational Spectroscopic Definition of the Facial Triad FeIV?O Intermediate in Taurine Dioxygenase: Evaluation of Structural Contributions to Hydrogen Atom Abstraction.

Publications

Nuclear Resonance Vibrational Spectroscopic Definition of the Facial Triad Fe<sup>IV</sup>═O Intermediate in Taurine Dioxygenase: Evaluation of Structural Contributions to Hydrogen Atom Abstraction.

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