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Detecting O2 binding sites in protein cavities

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Detecting O2 binding sites in protein cavities. / Kitahara, Ryo; Yoshimura, Yuichi; Xue, Mengjun et al.

In: Scientific Reports, Vol. 6, 20534, 2016.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

Harvard

Kitahara, R, Yoshimura, Y, Xue, M, Kameda, T & Mulder, FAA 2016, 'Detecting O2 binding sites in protein cavities', Scientific Reports, vol. 6, 20534. https://doi.org/10.1038/srep20534

APA

Kitahara, R., Yoshimura, Y., Xue, M., Kameda, T., & Mulder, F. A. A. (2016). Detecting O2 binding sites in protein cavities. Scientific Reports, 6, [20534]. https://doi.org/10.1038/srep20534

CBE

Kitahara R, Yoshimura Y, Xue M, Kameda T, Mulder FAA. 2016. Detecting O2 binding sites in protein cavities. Scientific Reports. 6:Article 20534. https://doi.org/10.1038/srep20534

MLA

Vancouver

Kitahara R, Yoshimura Y, Xue M, Kameda T, Mulder FAA. Detecting O2 binding sites in protein cavities. Scientific Reports. 2016;6. 20534. https://doi.org/10.1038/srep20534

Author

Kitahara, Ryo ; Yoshimura, Yuichi ; Xue, Mengjun et al. / Detecting O2 binding sites in protein cavities. In: Scientific Reports. 2016 ; Vol. 6.

Bibtex

@article{3779fc01d84f4028a0fb703aac85ed81,
title = "Detecting O2 binding sites in protein cavities",
abstract = "Internal cavities are important elements in protein structure, dynamics, stability and function. Here we use NMR spectroscopy to investigate the binding of molecular oxygen (O2) to cavities in a well-studied model for ligand binding, the L99A mutant of T4 lysozyme. On increasing the O2 concentration to 8.9 mM, changes in (1)H, (15)N, and (13)C chemical shifts and signal broadening were observed specifically for backbone amide and side chain methyl groups located around the two hydrophobic cavities of the protein. O2-induced longitudinal relaxation enhancements for amide and methyl protons could be adequately accounted for by paramagnetic dipolar relaxation. These data provide the first experimental demonstration that O2 binds specifically to the hydrophobic, and not the hydrophilic cavities, in a protein. Molecular dynamics simulations visualized the rotational and translational motions of O2 in the cavities, as well as the binding and egress of O2, suggesting that the channel consisting of helices D, E, G, H, and J could be the potential gateway for ligand binding to the protein. Due to strong paramagnetic relaxation effects, O2 gas-pressure NMR measurements can detect hydrophobic cavities when populated to as little as 1%, and thereby provide a general and highly sensitive method for detecting oxygen binding in proteins.",
author = "Ryo Kitahara and Yuichi Yoshimura and Mengjun Xue and Tomoshi Kameda and Mulder, {Frans A A}",
year = "2016",
doi = "10.1038/srep20534",
language = "English",
volume = "6",
journal = "Scientific Reports",
issn = "2045-2322",
publisher = "Nature Publishing Group",

}

RIS

TY - JOUR

T1 - Detecting O2 binding sites in protein cavities

AU - Kitahara, Ryo

AU - Yoshimura, Yuichi

AU - Xue, Mengjun

AU - Kameda, Tomoshi

AU - Mulder, Frans A A

PY - 2016

Y1 - 2016

N2 - Internal cavities are important elements in protein structure, dynamics, stability and function. Here we use NMR spectroscopy to investigate the binding of molecular oxygen (O2) to cavities in a well-studied model for ligand binding, the L99A mutant of T4 lysozyme. On increasing the O2 concentration to 8.9 mM, changes in (1)H, (15)N, and (13)C chemical shifts and signal broadening were observed specifically for backbone amide and side chain methyl groups located around the two hydrophobic cavities of the protein. O2-induced longitudinal relaxation enhancements for amide and methyl protons could be adequately accounted for by paramagnetic dipolar relaxation. These data provide the first experimental demonstration that O2 binds specifically to the hydrophobic, and not the hydrophilic cavities, in a protein. Molecular dynamics simulations visualized the rotational and translational motions of O2 in the cavities, as well as the binding and egress of O2, suggesting that the channel consisting of helices D, E, G, H, and J could be the potential gateway for ligand binding to the protein. Due to strong paramagnetic relaxation effects, O2 gas-pressure NMR measurements can detect hydrophobic cavities when populated to as little as 1%, and thereby provide a general and highly sensitive method for detecting oxygen binding in proteins.

AB - Internal cavities are important elements in protein structure, dynamics, stability and function. Here we use NMR spectroscopy to investigate the binding of molecular oxygen (O2) to cavities in a well-studied model for ligand binding, the L99A mutant of T4 lysozyme. On increasing the O2 concentration to 8.9 mM, changes in (1)H, (15)N, and (13)C chemical shifts and signal broadening were observed specifically for backbone amide and side chain methyl groups located around the two hydrophobic cavities of the protein. O2-induced longitudinal relaxation enhancements for amide and methyl protons could be adequately accounted for by paramagnetic dipolar relaxation. These data provide the first experimental demonstration that O2 binds specifically to the hydrophobic, and not the hydrophilic cavities, in a protein. Molecular dynamics simulations visualized the rotational and translational motions of O2 in the cavities, as well as the binding and egress of O2, suggesting that the channel consisting of helices D, E, G, H, and J could be the potential gateway for ligand binding to the protein. Due to strong paramagnetic relaxation effects, O2 gas-pressure NMR measurements can detect hydrophobic cavities when populated to as little as 1%, and thereby provide a general and highly sensitive method for detecting oxygen binding in proteins.

U2 - 10.1038/srep20534

DO - 10.1038/srep20534

M3 - Journal article

C2 - 26830762

VL - 6

JO - Scientific Reports

JF - Scientific Reports

SN - 2045-2322

M1 - 20534

ER -