• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利：CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法，用中文像聊天一样搜索，搜遍4000万医学文献。AI智能推荐，让科研检索更轻松。

立即免费搜索

文件翻译

保留排版，准确专业，支持PDF/Word/PPT等文件格式，支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述，25分钟生成高质量综述，智能提取关键信息，辅助科研写作。

立即免费体验

关于 ATSP、PDIQ 和 P53 肽结合驱动力的计算研究：协同作用的 C═O···C═O 四电子键相互作用。

Computational Study of Driving Forces in ATSP, PDIQ, and P53 Peptide Binding: C═O···C═O Tetrel Bonding Interactions at Work.

机构信息

Chemistry Department, University of Florida, Gainesville, Florida 32611, United States.

Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain.

出版信息

J Chem Inf Model. 2023 May 22;63(10):3018-3029. doi: 10.1021/acs.jcim.3c00024. Epub 2023 Apr 4.

DOI:10.1021/acs.jcim.3c00024
PMID:37014944
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10207270/
Abstract

Understanding the molecular interactions that drive peptide folding is crucial to chemistry and biology. In this study, we analyzed the role of CO···CO tetrel bonding (TtB) interactions in the folding mechanism of three different peptides (ATSP, pDIQ, and p53), which exhibit a different propensity to fold in an α helix motif. To achieve this goal, we used both a recently developed Bayesian inference approach (MELDxMD) and Quantum Mechanics (QM) calculations at the RI-MP2/def2-TZVP level of theory. These techniques allowed us to study the folding process and to evaluate the strength of the CO···CO TtBs as well as the synergies between TtBs and hydrogen-bonding (HB) interactions. We believe that the results derived from our study will be helpful for those scientists working in computational biology, peptide chemistry, and structural biology.

摘要

理解驱动肽折叠的分子相互作用对化学和生物学至关重要。在这项研究中，我们分析了 CO···CO 四中心键（TtB）相互作用在三种不同肽（ATSP、pDIQ 和 p53）折叠机制中的作用，这三种肽表现出不同的倾向以形成 α 螺旋结构。为了实现这一目标，我们同时使用了最近开发的贝叶斯推断方法（MELDxMD）和量子力学（QM）计算，理论水平为 RI-MP2/def2-TZVP。这些技术使我们能够研究折叠过程，并评估 CO···CO TtB 的强度以及 TtB 与氢键（HB）相互作用之间的协同作用。我们相信，我们的研究结果将有助于那些从事计算生物学、肽化学和结构生物学的科学家。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aae0/10207270/7bd198c2f5e7/ci3c00024_0012.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aae0/10207270/60ae8d063acc/ci3c00024_0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aae0/10207270/f9223ddc0dc6/ci3c00024_0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aae0/10207270/22f6dcd941b7/ci3c00024_0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aae0/10207270/b6b8fb63b935/ci3c00024_0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aae0/10207270/46f033ff421e/ci3c00024_0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aae0/10207270/3f3d83207835/ci3c00024_0007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aae0/10207270/8d89c92fdd8c/ci3c00024_0008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aae0/10207270/7cd90e0cfb2e/ci3c00024_0009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aae0/10207270/b7027719e40f/ci3c00024_0010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aae0/10207270/3e07aa022690/ci3c00024_0011.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aae0/10207270/7bd198c2f5e7/ci3c00024_0012.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aae0/10207270/60ae8d063acc/ci3c00024_0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aae0/10207270/f9223ddc0dc6/ci3c00024_0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aae0/10207270/22f6dcd941b7/ci3c00024_0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aae0/10207270/b6b8fb63b935/ci3c00024_0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aae0/10207270/46f033ff421e/ci3c00024_0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aae0/10207270/3f3d83207835/ci3c00024_0007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aae0/10207270/8d89c92fdd8c/ci3c00024_0008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aae0/10207270/7cd90e0cfb2e/ci3c00024_0009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aae0/10207270/b7027719e40f/ci3c00024_0010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aae0/10207270/3e07aa022690/ci3c00024_0011.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aae0/10207270/7bd198c2f5e7/ci3c00024_0012.jpg

相似文献

1
Computational Study of Driving Forces in ATSP, PDIQ, and P53 Peptide Binding: C═O···C═O Tetrel Bonding Interactions at Work.关于 ATSP、PDIQ 和 P53 肽结合驱动力的计算研究：协同作用的 C═O···C═O 四电子键相互作用。
J Chem Inf Model. 2023 May 22;63(10):3018-3029. doi: 10.1021/acs.jcim.3c00024. Epub 2023 Apr 4.
2
Binding Ensembles of -MDM2 Peptide Inhibitors by Combining Bayesian Inference and Atomistic Simulations.通过贝叶斯推断和原子模拟相结合来结合 -MDM2 肽抑制剂的结合物。
Molecules. 2021 Jan 2;26(1):198. doi: 10.3390/molecules26010198.
3
Thermodynamic and computational studies on the binding of p53-derived peptides and peptidomimetic inhibitors to HDM2.p53衍生肽及拟肽抑制剂与HDM2结合的热力学和计算研究
Chembiochem. 2009 May 25;10(8):1360-8. doi: 10.1002/cbic.200900008.
4
Substituent Effects in Tetrel Bonds Involving Aromatic Silane Derivatives: An ab initio Study.涉及芳香硅烷衍生物的四中心键中的取代基效应：从头算研究。
Molecules. 2023 Mar 5;28(5):2385. doi: 10.3390/molecules28052385.
5
Tetrel bonds involving a CF group participate in protein-drug recognition: a combined crystallographic and computational study.涉及 CF 基团的四面体键参与蛋白-药物识别：晶体学和计算研究的综合分析。
Phys Chem Chem Phys. 2023 May 3;25(17):12409-12419. doi: 10.1039/d3cp00839h.
6
O‧‧‧C═O interaction, its occurrence and implications for protein structure and folding.O‧‧‧C═O 相互作用及其对蛋白质结构和折叠的发生和意义。
Proteins. 2022 May;90(5):1159-1169. doi: 10.1002/prot.26298. Epub 2022 Jan 18.
7
Molecular design and validation of halogen bonding orthogonal to hydrogen bonding in breast cancer MDM2-peptide complex.乳腺癌MDM2-肽复合物中与氢键正交的卤键的分子设计与验证
J Mol Graph Model. 2016 Nov;70:40-44. doi: 10.1016/j.jmgm.2016.09.007. Epub 2016 Sep 13.
8
Modeling of folding and unfolding mechanisms in alanine-based alpha-helical polypeptides.基于丙氨酸的α-螺旋多肽折叠与解折叠机制的建模
J Phys Chem B. 2006 Oct 19;110(41):20555-61. doi: 10.1021/jp061781e.
9
"Like-like" tetrel bonding interactions between Sn centres: a combined ab initio and CSD study.锡中心之间的“类-类”四元键相互作用：从头算和剑桥晶体结构数据库联合研究
Dalton Trans. 2019 Aug 14;48(30):11208-11216. doi: 10.1039/c9dt01953g. Epub 2019 Jun 26.
10
The balance between side-chain and backbone-driven association in folding of the α-helical influenza A transmembrane peptide.α-螺旋流感 A 跨膜肽折叠中环和骨架驱动的缔合平衡。
J Comput Chem. 2020 Sep 30;41(25):2177-2188. doi: 10.1002/jcc.26381. Epub 2020 Jul 31.

本文引用的文献

1
Matching protein surface structural patches for high-resolution blind peptide docking.用于高分辨率盲肽对接的蛋白质表面结构补丁匹配。
Proc Natl Acad Sci U S A. 2022 May 3;119(18):e2121153119. doi: 10.1073/pnas.2121153119. Epub 2022 Apr 28.
2
Peptide-based nanomaterials: Self-assembly, properties and applications.基于肽的纳米材料：自组装、性质及应用
Bioact Mater. 2021 Sep 28;11:268-282. doi: 10.1016/j.bioactmat.2021.09.029. eCollection 2022 May.
3
Observations of tetrel bonding between sp-carbon and THF.关于sp-碳与四氢呋喃之间的四元rel键合的观察结果。
Chem Sci. 2020 May 7;11(20):5289-5293. doi: 10.1039/d0sc01559h.
4
Computational Modeling as a Tool to Investigate PPI: From Drug Design to Tissue Engineering.作为研究蛋白质-蛋白质相互作用工具的计算建模：从药物设计到组织工程
Front Mol Biosci. 2021 May 20;8:681617. doi: 10.3389/fmolb.2021.681617. eCollection 2021.
5
Increasing protein stability by engineering the n → π* interaction at the β-turn.通过设计β-转角处的n→π*相互作用来提高蛋白质稳定性。
Chem Sci. 2020 Jul 30;11(35):9480-9487. doi: 10.1039/d0sc03060k.
6
Origins and properties of the tetrel bond.碳族元素键的起源与性质。
Phys Chem Chem Phys. 2021 Mar 18;23(10):5702-5717. doi: 10.1039/d1cp00242b.
7
Trends in peptide drug discovery.肽类药物研发趋势。
Nat Rev Drug Discov. 2021 Apr;20(4):309-325. doi: 10.1038/s41573-020-00135-8. Epub 2021 Feb 3.
8
Binding Ensembles of -MDM2 Peptide Inhibitors by Combining Bayesian Inference and Atomistic Simulations.通过贝叶斯推断和原子模拟相结合来结合 -MDM2 肽抑制剂的结合物。
Molecules. 2021 Jan 2;26(1):198. doi: 10.3390/molecules26010198.
9
Computational structure modeling for diverse categories of macromolecular interactions.计算结构建模用于多种类型的大分子相互作用。
Curr Opin Struct Biol. 2020 Oct;64:1-8. doi: 10.1016/j.sbi.2020.05.017. Epub 2020 Jun 27.
10
Engineering Crystals Using sp -C Centred Tetrel Bonding Interactions.利用 sp^C 中心的四中心键合相互作用来工程晶体。
Chemistry. 2020 Aug 6;26(44):10126-10132. doi: 10.1002/chem.202002613. Epub 2020 Jul 20.