Molecular mechanism of a large conformational change of the quinone cofactor in the semiquinone intermediate of bacterial copper amine oxidase

Murakawa, T.; Nakanishi, Shota; Boero, Mauro; Shigeta, Yasuteru; Hayashi, Hideyuki; Okajima, Toshihide

doi:10.1039/d2sc01356h

Cited by 18 publications

(12 citation statements)

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“…[21][22][23][24] Additionally, this DFT approach provides accurate atomic charge distribution and structures of protein-active sites. [25][26][27] We used Chemcraft software 28 to visualize the molecular structures. The Cartesian coordinates of all obtained structures in this study are listed in Tables S1-S17.…”

Section: Methodsmentioning

confidence: 99%

“…We have assessed the reliability of the DFT method by reproducing the relative energies with an accuracy close to that of CCSD(T)/cc‐pVTZ and absorption spectra 21–24 . Additionally, this DFT approach provides accurate atomic charge distribution and structures of protein‐active sites 25–27 . We used Chemcraft software 28 to visualize the molecular structures.…”

Section: Methodsmentioning

confidence: 99%

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Organocatalytic‐racemization reaction elucidation of aspartic acid by density functional theory

et al. 2023

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Aldehydes and carboxylic acids are widely used as catalysts for efficient racemization process of amino acids. However, the detailed reaction mechanism remains unclear. This work aims to clarify the racemization mechanism of aspartic acid (Asp) catalyzed by salicylaldehyde and acetic acid by using computational approaches. Density functional theory was used to obtain the structures and relative energies of 10 intermediates and five transition states, thus characterizing the main stages of the reaction. The calculated energy diagram shows that the dehydration step has the highest energy barrier, followed by the reaction step to change the chirality of Asp, which is a crucial process for racemization. In the dehydration reaction, water molecules can induce a remarkable decrease in the required energy.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Organocatalytic‐racemization reaction elucidation of aspartic acid by density functional theory

et al. 2023

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“…23 Moreover, such a DFT approach provided reliable structures for larger-size molecules containing intermolecular interactions in active sites of the proteins. [26][27][28] In the present study, DNPNO-CCSD(T)/cc-pVTZ calculations implemented in the ORCA 5.0 package 29 were further carried out to validate the DFT results. The solvation effect of water was incorporated by the polarizable continuum model (PCM).…”

Section: Computational Detailsmentioning

confidence: 99%

Enantioselective amino acid interactions in solution

Watanabe

Miyagawa

Hori

et al. 2023

Phys. Chem. Chem. Phys.

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“…Proteins with metal cofactors and ions are called metal proteins, where a metal ion and its environment work as a catalytic active center. Because metal proteins enable biochemical reactions not possible with ordinary proteins, many researchers pay attention to them [1][2][3][4][5]. Heme proteins are the largest class of metal proteins and serve pivotal biological functions.…”

Section: Introductionmentioning

confidence: 99%

Prediction of Protein Function from Tertiary Structure of the Active Site in Heme Proteins by Convolutional Neural Network

Kondo¹,

Iizuka²,

Masumoto³

et al. 2022

Preprint

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Structure–function relationships in proteins have been one of the crucial scientific topics. Heme proteins have diverse and pivotal biological functions. Therefore, clarifying their structure–function correlation is significant to understand their functional mechanism and is informative for various fields of science. In this study, we constructed convolutional neural network models for predicting protein functions from the tertiary structures of heme-binding sites (active sites) of heme proteins to examine the structure–function correlation. As a result, we succeeded in the classification of oxygen-binding protein (OB), oxidoreductase (OR), proteins with both functions (OB–OR), and electron transport protein (ET) with high accuracy. Although the misclassification rate for OR and ET was high, the rates between OB and ET and between OB and OR were almost zero, indicating that the prediction model works well between protein groups with very different functions. However, predicting the function of proteins modified with amino acid mutation(s) remains a challenge. Our findings indicate a structure–function correlation in the active site of heme proteins. This study is expected to be applied to the prediction of more detailed protein functions such as catalytic reactions.

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Molecular mechanism of a large conformational change of the quinone cofactor in the semiquinone intermediate of bacterial copper amine oxidase

Abstract: The copper amine oxidase from Arthrobacter globiformis (AGAO) catalyses the oxidative deamination of primary amines via a large conformational change of a topaquinone (TPQ) cofactor during the semiquinone formation step....

Cited by 18 publications

References 61 publications

Organocatalytic‐racemization reaction elucidation of aspartic acid by density functional theory

Organocatalytic‐racemization reaction elucidation of aspartic acid by density functional theory

Enantioselective amino acid interactions in solution

Prediction of Protein Function from Tertiary Structure of the Active Site in Heme Proteins by Convolutional Neural Network

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