Cargando…

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

The planarity of the peptide bond is important for the stability and structure formation of proteins. However, substantial distortion of peptide bonds has been reported in several high-resolution structures and computational analyses. To investigate the peptide bond planarity, including hydrogen ato...

Descripción completa

Detalles Bibliográficos
Autores principales: Hanazono, Yuya, Hirano, Yu, Takeda, Kazuki, Kusaka, Katsuhiro, Tamada, Taro, Miki, Kunio
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Association for the Advancement of Science 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9122329/
https://www.ncbi.nlm.nih.gov/pubmed/35594350
http://dx.doi.org/10.1126/sciadv.abn2276
_version_ 1784711322805469184
author Hanazono, Yuya
Hirano, Yu
Takeda, Kazuki
Kusaka, Katsuhiro
Tamada, Taro
Miki, Kunio
author_facet Hanazono, Yuya
Hirano, Yu
Takeda, Kazuki
Kusaka, Katsuhiro
Tamada, Taro
Miki, Kunio
author_sort Hanazono, Yuya
collection PubMed
description The planarity of the peptide bond is important for the stability and structure formation of proteins. However, substantial distortion of peptide bonds has been reported in several high-resolution structures and computational analyses. To investigate the peptide bond planarity, including hydrogen atoms, we report a 1.2-Å resolution neutron structure of the oxidized form of high-potential iron-sulfur protein. This high-resolution neutron structure shows that the nucleus positions of the amide protons deviate from the peptide plane and shift toward the acceptors. The planarity of the H─N─C═O plane depends strongly on the pyramidalization of the nitrogen atom. Moreover, the orientation of the amide proton of Cys(75) is different in the reduced and oxidized states, possibly because of the electron storage capacity of the iron-sulfur cluster.
format Online
Article
Text
id pubmed-9122329
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher American Association for the Advancement of Science
record_format MEDLINE/PubMed
spelling pubmed-91223292022-06-01 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 Sci Adv Biomedicine and Life Sciences The planarity of the peptide bond is important for the stability and structure formation of proteins. However, substantial distortion of peptide bonds has been reported in several high-resolution structures and computational analyses. To investigate the peptide bond planarity, including hydrogen atoms, we report a 1.2-Å resolution neutron structure of the oxidized form of high-potential iron-sulfur protein. This high-resolution neutron structure shows that the nucleus positions of the amide protons deviate from the peptide plane and shift toward the acceptors. The planarity of the H─N─C═O plane depends strongly on the pyramidalization of the nitrogen atom. Moreover, the orientation of the amide proton of Cys(75) is different in the reduced and oxidized states, possibly because of the electron storage capacity of the iron-sulfur cluster. American Association for the Advancement of Science 2022-05-20 /pmc/articles/PMC9122329/ /pubmed/35594350 http://dx.doi.org/10.1126/sciadv.abn2276 Text en Copyright © 2022 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC). https://creativecommons.org/licenses/by-nc/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license (https://creativecommons.org/licenses/by-nc/4.0/) , which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.
spellingShingle Biomedicine and Life Sciences
Hanazono, Yuya
Hirano, Yu
Takeda, Kazuki
Kusaka, Katsuhiro
Tamada, Taro
Miki, Kunio
Revisiting the concept of peptide bond planarity in an iron-sulfur protein by neutron structure analysis
title Revisiting the concept of peptide bond planarity in an iron-sulfur protein by neutron structure analysis
title_full Revisiting the concept of peptide bond planarity in an iron-sulfur protein by neutron structure analysis
title_fullStr Revisiting the concept of peptide bond planarity in an iron-sulfur protein by neutron structure analysis
title_full_unstemmed Revisiting the concept of peptide bond planarity in an iron-sulfur protein by neutron structure analysis
title_short Revisiting the concept of peptide bond planarity in an iron-sulfur protein by neutron structure analysis
title_sort revisiting the concept of peptide bond planarity in an iron-sulfur protein by neutron structure analysis
topic Biomedicine and Life Sciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9122329/
https://www.ncbi.nlm.nih.gov/pubmed/35594350
http://dx.doi.org/10.1126/sciadv.abn2276
work_keys_str_mv AT hanazonoyuya revisitingtheconceptofpeptidebondplanarityinanironsulfurproteinbyneutronstructureanalysis
AT hiranoyu revisitingtheconceptofpeptidebondplanarityinanironsulfurproteinbyneutronstructureanalysis
AT takedakazuki revisitingtheconceptofpeptidebondplanarityinanironsulfurproteinbyneutronstructureanalysis
AT kusakakatsuhiro revisitingtheconceptofpeptidebondplanarityinanironsulfurproteinbyneutronstructureanalysis
AT tamadataro revisitingtheconceptofpeptidebondplanarityinanironsulfurproteinbyneutronstructureanalysis
AT mikikunio revisitingtheconceptofpeptidebondplanarityinanironsulfurproteinbyneutronstructureanalysis