Revisiting the concept of peptide bond planarity in an iron-sulfur protein by neutron structure analysis

Hanazono, Yuya; Hirano, Yu; Takeda, Kazuki; Kusaka, Katsuhiro; Tamada, Taro; Miki, Kunio

doi:10.1126/sciadv.abn2276

Cited by 12 publications

(5 citation statements)

References 54 publications

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“…Neutron crystallography that can visualize H atoms is an extremely useful technique for that purpose. Structural details of NH–S bonds with ligand atoms of metalloproteins have only recently started to be uncovered by neutron and sub-ångström resolution X-ray crystallography, − whereas it is well-known that they control redox potentials. The presence of the NH–S bond at metal centers of various metalloproteins suggests that it is one of nature’s favorite strategies to tune the metalloprotein activity.…”

Section: Discussionmentioning

confidence: 99%

Overlooked Hydrogen Bond in a Blue Copper Protein Uncovered by Neutron and Sub-Ångström Resolution X-ray Crystallography

Fukuda,

Lintuluoto,

Kurihara

et al. 2024

Biochemistry

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Metalloproteins play fundamental roles in organisms and are utilized as starting points for the directed evolution of artificial enzymes. Knowing the strategies of metalloproteins, by which they exquisitely tune their activities, will not only lead to an understanding of biochemical phenomena but also contribute to various applications. The blue copper protein (BCP) has been a renowned model system to understand the biology, chemistry, and physics of metalloproteins. Pseudoazurin (Paz), a blue copper protein, mediates electron transfer in the bacterial anaerobic respiratory chain. Its redox potential is finely tuned by hydrogen (H) bond networks; however, difficulty in visualizing H atom positions in the protein hinders the detailed understanding of the protein's structure−function relationship. We here used neutron and sub-ångstrom resolution X-ray crystallography to directly observe H atoms in Paz. The 0.86-Åresolution X-ray structure shows that the peptide bond between Pro80 and the His81 Cu ligand deviates from the ideal planar structure. The 1.9-Å-resolution neutron structure confirms a long-overlooked H bond formed by the amide of His81 and the S atom of another Cu ligand Cys78. Quantum mechanics/molecular mechanics calculations show that this H bond increases the redox potential of the Cu site and explains the experimental results well. Our study demonstrates the potential of neutron and sub-ångstrom resolution X-ray crystallography to understand the chemistry of metalloproteins at atomic and quantum levels.

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Section: Discussionmentioning

confidence: 99%

Overlooked Hydrogen Bond in a Blue Copper Protein Uncovered by Neutron and Sub-Ångström Resolution X-ray Crystallography

Fukuda,

Lintuluoto,

Kurihara

et al. 2024

Biochemistry

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“…Recently, Hanazono et al (2022) reported the results of high‐resolution neutron crystallography. They obtained non‐hydrogen atom coordinates from 0.66 Å resolution x‐ray data of a high‐potential iron–sulfur protein and introduced them to the 1.2 Å resolution neutron crystallography to optimize the hydrogen positions (HiPIP; PDB http://firstglance.jmol.org/fg.htm?mol=7VOS).…”

Section: Discussionmentioning

confidence: 99%

Site‐specific relaxation of peptide bond planarity induced by electrically attracted proton/deuteron observed by neutron crystallography

Chiba,

Matsui,

Chatake

et al. 2023

Protein Science

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In structural biology, peptide bonds, fundamental linkages between hundreds of amino acids, of which a protein molecule is composed, have been commonly treated as a plane structure just as Linus Pauling et al. proposed. In this paper, a site‐specific peptide bond relaxation mechanism by deuterons whose localization has been suggested by neutron crystallography is proposed. Such deuteron was observed as an arm of neutron scattering length density protruding from the carbonyl oxygen atoms in the main chain in the omit map drawn by neutron crystallography of human lysozyme. Our comprehensive study using X‐ray and neutron diffraction and 15N chemical shifts of individual amide nitrogen atoms within the same peptide bond strongly suggests the relaxation of the electronic resonance structure because of site‐specific modulation by protons/deuterons localized on the electron orbital of the carbonyl oxygen. All experimental data used in this examination were obtained at room temperature, which is preferable for enzymatic activity. Such a close interaction between the electron resonance structure of a peptide bond and the exchangeable protons/deuterons well agreed with that observed in an intermediate state in an amide hydrolytic reaction simulated by the ab‐initio calculation including water molecules.This article is protected by copyright. All rights reserved.

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“… Electron and nuclear density of HiPIP [ 13 ]. (A) Electron and nuclear density maps around the peptide bond between Pro12 and Thr13, and between Asn70 and Val71.…”

Section: Figurementioning

confidence: 99%

“…We have previously published our works on the X-ray crystal structures of both the reduced (~0.48 Å resolution) and oxidized (~0.80 Å resolution) states of HiPIP derived from a thermophilic purple bacterium, Thermochromatium tepidum [7][8][9][10][11][12]. Recently, we have collected neutron diffraction data at 1.2 Å resolution and X-ray diffraction data at 0.66 Å resolution for the oxidized state of HiPIP from T. tepidum, substantially high resolutions for protein structural research [13][14][15]. Generally, the coordinates of hydrogen atoms are constrained to ensure that the bond distances and angles with the atoms to which they are bonded maintain ideal geometries.…”

Section: Introductionmentioning

confidence: 99%

Description of peptide bond planarity from high-resolution neutron crystallography

Hanazono,

Hirano,

Tamada

et al. 2023

BIOPHYSICS

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Neutron crystallography is a highly effective method for visualizing hydrogen atoms in proteins. In our recent study, we successfully determined the high-resolution (1.2 Å) neutron structure of high-potential iron-sulfur protein, refining the coordinates of some amide protons without any geometric restraints. Interestingly, we observed that amide protons are deviated from the peptide plane due to electrostatic interactions. Moreover, the difference in the position of the amide proton of Cys75 between reduced and oxidized states is possibly attributed to the electron storage capacity of the iron-sulfur cluster. Additionally, we have discussed about the rigidity of the iron-sulfur cluster based on the results of the hydrogen-deuterium exchange. Our research underscores the significance of neutron crystallography in protein structure elucidation, enriching our understanding of protein functions at an atomic resolution.

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Revisiting the concept of peptide bond planarity in an iron-sulfur protein by neutron structure analysis

Cited by 12 publications

References 54 publications

Overlooked Hydrogen Bond in a Blue Copper Protein Uncovered by Neutron and Sub-Ångström Resolution X-ray Crystallography

Overlooked Hydrogen Bond in a Blue Copper Protein Uncovered by Neutron and Sub-Ångström Resolution X-ray Crystallography

Site‐specific relaxation of peptide bond planarity induced by electrically attracted proton/deuteron observed by neutron crystallography

Description of peptide bond planarity from high-resolution neutron crystallography

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