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Structural change of retinoic-acid receptor-related orphan receptor induced by binding of inverse-agonist: Molecular dynamics and ab initio molecular orbital simulations

To elucidate structural changes in the retinoic acid receptor-related orphan receptor gamma (RORγt) induced by the binding of an agonist or an inverse agonist, we conducted molecular dynamics (MD) simulations in explicit water. In addition, ab initio fragment molecular orbital calculations were carr...

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Autores principales: Suzuki, Shusuke, Nakamura, Toshiya, Saito, Ryosuke, Terauchi, Yuta, Kawai, Kentaro, Takimoto-Kamimura, Midori, Kurita, Noriyuki
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Research Network of Computational and Structural Biotechnology 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7338990/
https://www.ncbi.nlm.nih.gov/pubmed/32670507
http://dx.doi.org/10.1016/j.csbj.2020.06.034
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author Suzuki, Shusuke
Nakamura, Toshiya
Saito, Ryosuke
Terauchi, Yuta
Kawai, Kentaro
Takimoto-Kamimura, Midori
Kurita, Noriyuki
author_facet Suzuki, Shusuke
Nakamura, Toshiya
Saito, Ryosuke
Terauchi, Yuta
Kawai, Kentaro
Takimoto-Kamimura, Midori
Kurita, Noriyuki
author_sort Suzuki, Shusuke
collection PubMed
description To elucidate structural changes in the retinoic acid receptor-related orphan receptor gamma (RORγt) induced by the binding of an agonist or an inverse agonist, we conducted molecular dynamics (MD) simulations in explicit water. In addition, ab initio fragment molecular orbital calculations were carried out for certain characteristic structures obtained from the MD simulations to reveal important interactions between the amino acid residues of RORγt, and to distinguish the different effects in the binding of an agonist and an inverse agonist on the structure of RORγt. The results elucidate that the hydrogen bond between His479 of helix11 (H11) and Tyr502 of helix12 (H12) is important to keep the H12 conformation in the agonist-bound RORγt. In contrast, in the inverse-agonist-bound RORγt, the side chain of His479 rotates, significantly weakening the interaction between His479 and Tyr502, leading to a conformational change in H12. Therefore, the present molecular simulations clearly indicate that the conformational change in the side chain of His479 in the inverse-agonist-bound RORγt is the main reason for the H12 destabilization induced by the binding of the inverse agonist. Such a conformational change does not occur on the binding of the agonist in RORγt, owing to the strong hydrogen bond between His479 and Tyr502.
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spelling pubmed-73389902020-07-14 Structural change of retinoic-acid receptor-related orphan receptor induced by binding of inverse-agonist: Molecular dynamics and ab initio molecular orbital simulations Suzuki, Shusuke Nakamura, Toshiya Saito, Ryosuke Terauchi, Yuta Kawai, Kentaro Takimoto-Kamimura, Midori Kurita, Noriyuki Comput Struct Biotechnol J Research Article To elucidate structural changes in the retinoic acid receptor-related orphan receptor gamma (RORγt) induced by the binding of an agonist or an inverse agonist, we conducted molecular dynamics (MD) simulations in explicit water. In addition, ab initio fragment molecular orbital calculations were carried out for certain characteristic structures obtained from the MD simulations to reveal important interactions between the amino acid residues of RORγt, and to distinguish the different effects in the binding of an agonist and an inverse agonist on the structure of RORγt. The results elucidate that the hydrogen bond between His479 of helix11 (H11) and Tyr502 of helix12 (H12) is important to keep the H12 conformation in the agonist-bound RORγt. In contrast, in the inverse-agonist-bound RORγt, the side chain of His479 rotates, significantly weakening the interaction between His479 and Tyr502, leading to a conformational change in H12. Therefore, the present molecular simulations clearly indicate that the conformational change in the side chain of His479 in the inverse-agonist-bound RORγt is the main reason for the H12 destabilization induced by the binding of the inverse agonist. Such a conformational change does not occur on the binding of the agonist in RORγt, owing to the strong hydrogen bond between His479 and Tyr502. Research Network of Computational and Structural Biotechnology 2020-06-25 /pmc/articles/PMC7338990/ /pubmed/32670507 http://dx.doi.org/10.1016/j.csbj.2020.06.034 Text en © 2020 The Author(s) http://creativecommons.org/licenses/by/4.0/ This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Research Article
Suzuki, Shusuke
Nakamura, Toshiya
Saito, Ryosuke
Terauchi, Yuta
Kawai, Kentaro
Takimoto-Kamimura, Midori
Kurita, Noriyuki
Structural change of retinoic-acid receptor-related orphan receptor induced by binding of inverse-agonist: Molecular dynamics and ab initio molecular orbital simulations
title Structural change of retinoic-acid receptor-related orphan receptor induced by binding of inverse-agonist: Molecular dynamics and ab initio molecular orbital simulations
title_full Structural change of retinoic-acid receptor-related orphan receptor induced by binding of inverse-agonist: Molecular dynamics and ab initio molecular orbital simulations
title_fullStr Structural change of retinoic-acid receptor-related orphan receptor induced by binding of inverse-agonist: Molecular dynamics and ab initio molecular orbital simulations
title_full_unstemmed Structural change of retinoic-acid receptor-related orphan receptor induced by binding of inverse-agonist: Molecular dynamics and ab initio molecular orbital simulations
title_short Structural change of retinoic-acid receptor-related orphan receptor induced by binding of inverse-agonist: Molecular dynamics and ab initio molecular orbital simulations
title_sort structural change of retinoic-acid receptor-related orphan receptor induced by binding of inverse-agonist: molecular dynamics and ab initio molecular orbital simulations
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7338990/
https://www.ncbi.nlm.nih.gov/pubmed/32670507
http://dx.doi.org/10.1016/j.csbj.2020.06.034
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