| アイテムタイプ |
itemtype_ver1(1) |
| 公開日 |
2025-01-27 |
| タイトル |
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タイトル |
Thermal Energy Transport through Nonbonded Native Contacts in Protein |
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言語 |
en |
| 著者 |
Wang, Tingting
Yamato, Takahisa
Sugiura, Wataru
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| アクセス権 |
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アクセス権 |
open access |
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アクセス権URI |
http://purl.org/coar/access_right/c_abf2 |
| 権利 |
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権利情報 |
This document is the Accepted Manuscript version of a Published Work that appeared in final form in [The Journal of Physical Chemistry B], copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see [https://pubs.acs.org/articlesonrequest/AOR-9TYKEESGN6YZK6AECWBR].” |
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言語 |
en |
| 内容記述 |
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内容記述タイプ |
Abstract |
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内容記述 |
Within the protein interior, where we observe various types of interactions, nonuniform flow of thermal energy occurs along the polypeptide chain and through nonbonded native contacts, leading to inhomogeneous transport efficiencies from one site to another. The folded native protein serves not merely as thermal transfer medium but, more importantly, as sophisticated molecular nanomachines in cells. Therefore, we are particularly interested in what sort of “communication” is mediated through native contacts in the folded proteins and how such features are quantitatively depicted in terms of local transport coefficients of heat currents. To address the issue, we introduced a concept of inter-residue thermal conductivity and characterized the nonuniform thermal transport properties of a small globular protein, HP36, using equilibrium molecular dynamics simulation and the Green–Kubo formula. We observed that the thermal transport of the protein was dominated by that along the polypeptide chain, while the local thermal conductivity of nonbonded native contacts decreased in the order of H-bonding > π-stacking > electrostatic > hydrophobic contacts. Furthermore, we applied machine learning techniques to analyze the molecular mechanism of protein thermal transport. As a result, the contact distance, variance in contact distance, and H-bonding occurrence probability during MD simulations are found to be the top three important determinants for predicting local thermal transport coefficients. |
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言語 |
en |
| 出版者 |
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出版者 |
ACS Publications |
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言語 |
en |
| 言語 |
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言語 |
eng |
| 資源タイプ |
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資源タイプresource |
http://purl.org/coar/resource_type/c_6501 |
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タイプ |
journal article |
| 出版タイプ |
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出版タイプ |
AM |
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出版タイプResource |
http://purl.org/coar/version/c_ab4af688f83e57aa |
| 関連情報 |
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関連タイプ |
isVersionOf |
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識別子タイプ |
DOI |
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関連識別子 |
https://doi.org/10.1021/acs.jpcb.4c03475 |
| 収録物識別子 |
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収録物識別子タイプ |
PISSN |
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収録物識別子 |
1520-6106 |
| 書誌情報 |
en : The Journal of Physical Chemistry B
巻 128,
号 36,
p. 8641-8650,
発行日 2024-09-12
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| ファイル公開日 |
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日付 |
2025-09-12 |
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日付タイプ |
Available |
2_Manuscript-0807.pdf (4.3 MB)
