• 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

无规卷曲蛋白质的伪二面角模型。

Pseudo-Improper-Dihedral Model for Intrinsically Disordered Proteins.

机构信息

Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland.

出版信息

J Chem Theory Comput. 2020 Jul 14;16(7):4726-4733. doi: 10.1021/acs.jctc.0c00338. Epub 2020 Jun 12.

DOI:10.1021/acs.jctc.0c00338
PMID:32436706
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7588027/
Abstract

We present a new coarse-grained C-based protein model with a nonradial multibody pseudo-improper-dihedral potential that is transferable, time-independent, and suitable for molecular dynamics. It captures the nature of backbone and side-chain interactions between amino acid residues by adapting a simple improper dihedral term for a one-bead-per-residue model. It is parameterized for intrinsically disordered proteins and applicable to simulations of such proteins and their assemblies on millisecond time scales.

摘要

我们提出了一种新的基于 C 的粗粒蛋白模型，该模型具有非径向多体伪非键二面角势能，具有可转移性、与时间无关性和适合分子动力学的特点。它通过为单珠每残基模型适应简单的非键二面角项来捕捉氨基酸残基之间的主链和侧链相互作用的性质。它针对无规卷曲蛋白质进行了参数化，适用于此类蛋白质及其组装体在毫秒时间尺度上的模拟。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b46b/7588027/01415ed3db33/ct0c00338_0007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b46b/7588027/79ac9df2cf71/ct0c00338_0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b46b/7588027/a438e8c126db/ct0c00338_0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b46b/7588027/4877805aceb7/ct0c00338_0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b46b/7588027/b2aa8b56dbb5/ct0c00338_0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b46b/7588027/caa908b3f64d/ct0c00338_0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b46b/7588027/6fbf217c37cd/ct0c00338_0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b46b/7588027/01415ed3db33/ct0c00338_0007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b46b/7588027/79ac9df2cf71/ct0c00338_0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b46b/7588027/a438e8c126db/ct0c00338_0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b46b/7588027/4877805aceb7/ct0c00338_0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b46b/7588027/b2aa8b56dbb5/ct0c00338_0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b46b/7588027/caa908b3f64d/ct0c00338_0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b46b/7588027/6fbf217c37cd/ct0c00338_0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b46b/7588027/01415ed3db33/ct0c00338_0007.jpg

相似文献

1
Pseudo-Improper-Dihedral Model for Intrinsically Disordered Proteins.无规卷曲蛋白质的伪二面角模型。
J Chem Theory Comput. 2020 Jul 14;16(7):4726-4733. doi: 10.1021/acs.jctc.0c00338. Epub 2020 Jun 12.
2
Testing the transferability of a coarse-grained model to intrinsically disordered proteins.测试粗粒度模型对内在无序蛋白质的可转移性。
Phys Chem Chem Phys. 2015 Dec 21;17(47):31741-9. doi: 10.1039/c5cp05652g.
3
HyRes: a coarse-grained model for multi-scale enhanced sampling of disordered protein conformations.HyRes：一种用于无序蛋白质构象多尺度增强采样的粗粒度模型。
Phys Chem Chem Phys. 2017 Dec 13;19(48):32421-32432. doi: 10.1039/c7cp06736d.
4
Assessing the Intricate Balance of Intermolecular Interactions upon Self-Association of Intrinsically Disordered Proteins.评估无序蛋白质自组装时分子间相互作用的复杂平衡。
J Mol Biol. 2019 Feb 1;431(3):511-523. doi: 10.1016/j.jmb.2018.11.027. Epub 2018 Dec 7.
5
Temperature Dependence of Intrinsically Disordered Proteins in Simulations: What are We Missing?模拟中无规卷曲蛋白质的温度依赖性：我们遗漏了什么？
J Chem Theory Comput. 2019 Apr 9;15(4):2672-2683. doi: 10.1021/acs.jctc.8b01281. Epub 2019 Mar 27.
6
Direct Observation of the Intrinsic Backbone Torsional Mobility of Disordered Proteins.无序蛋白质内在主链扭转流动性的直接观察。
Biophys J. 2016 Aug 23;111(4):768-774. doi: 10.1016/j.bpj.2016.07.023.
7
New force field on modeling intrinsically disordered proteins.用于对内在无序蛋白质进行建模的新力场。
Chem Biol Drug Des. 2014 Sep;84(3):253-69. doi: 10.1111/cbdd.12314. Epub 2014 Jul 1.
8
Progress in studying intrinsically disordered proteins with atomistic simulations.利用原子模拟研究内在无序蛋白质的进展。
Prog Biophys Mol Biol. 2015 Oct;119(1):47-52. doi: 10.1016/j.pbiomolbio.2015.03.003. Epub 2015 Mar 23.
9
DiAMoNDBack: Diffusion-Denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces.DiAMoNDBack：用于 Cα 蛋白质轨迹非确定性反向映射的扩散去噪自回归模型。
J Chem Theory Comput. 2023 Nov 14;19(21):7908-7923. doi: 10.1021/acs.jctc.3c00840. Epub 2023 Oct 31.
10
Utilizing Coarse-Grained Modeling and Monte Carlo Simulations to Evaluate the Conformational Ensemble of Intrinsically Disordered Proteins and Regions.利用粗粒度建模和蒙特卡罗模拟评估固有无序蛋白质和区域的构象集合。
J Mol Biol. 2018 Aug 3;430(16):2478-2492. doi: 10.1016/j.jmb.2018.03.006. Epub 2018 Mar 21.

引用本文的文献

1
Theoretical Methods for Assessing the Density of Protein Nanodroplets.评估蛋白质纳米液滴密度的理论方法
Int J Mol Sci. 2025 Sep 4;26(17):8631. doi: 10.3390/ijms26178631.
2
Toward Consistent Physics-Based Modeling of Local Backbone Structures and Chirality Change of Proteins in Coarse-Grained Approaches.朝着在粗粒化方法中对局部骨架结构和蛋白质手性变化进行一致的基于物理的建模。
J Phys Chem Lett. 2023 Nov 9;14(44):9824-9833. doi: 10.1021/acs.jpclett.3c01988. Epub 2023 Oct 27.
3
Choosing the right density for a concentrated protein system like gluten in a coarse-grained model.

本文引用的文献

1
Protein droplets in systems of disordered homopeptides and the amyloid glass phase.无序同聚肽体系中的蛋白液滴和淀粉样玻璃相。
Phys Chem Chem Phys. 2020 Jul 21;22(27):15592-15599. doi: 10.1039/d0cp01635g. Epub 2020 Jul 2.
2
Hierarchical Ensembles of Intrinsically Disordered Proteins at Atomic Resolution in Molecular Dynamics Simulations.原子分辨分子动力学模拟中无规卷曲蛋白的层次组合。
J Chem Theory Comput. 2020 Jan 14;16(1):725-737. doi: 10.1021/acs.jctc.9b00809. Epub 2019 Dec 26.
3
AWSEM-IDP: A Coarse-Grained Force Field for Intrinsically Disordered Proteins.
为粗粒化模型中的浓缩蛋白体系（如面筋）选择合适的密度。
Eur Biophys J. 2023 Oct;52(6-7):583-591. doi: 10.1007/s00249-023-01667-8. Epub 2023 Jun 28.
4
Myofilament-associated proteins with intrinsic disorder (MAPIDs) and their resolution by computational modeling.肌球蛋白相关具有内在无序性的蛋白（MAPIDs）及其通过计算建模的解析。
Q Rev Biophys. 2023 Jan 11;56:e2. doi: 10.1017/S003358352300001X.
5
Developing Bonded Potentials for a Coarse-Grained Model of Intrinsically Disordered Proteins.发展本征无序蛋白粗粒模型的键合势能。
J Chem Inf Model. 2022 Sep 26;62(18):4474-4485. doi: 10.1021/acs.jcim.2c00450. Epub 2022 Sep 6.
6
Global Structure of the Intrinsically Disordered Protein Tau Emerges from Its Local Structure.内在无序蛋白Tau的全局结构源自其局部结构。
JACS Au. 2022 Mar 1;2(3):673-686. doi: 10.1021/jacsau.1c00536. eCollection 2022 Mar 28.
7
Computational Models for the Study of Protein Aggregation.计算模型在蛋白质聚集研究中的应用。
Methods Mol Biol. 2022;2340:51-78. doi: 10.1007/978-1-0716-1546-1_4.
8
Unifying coarse-grained force fields for folded and disordered proteins.统一折叠和无规蛋白质的粗粒力场。
Curr Opin Struct Biol. 2022 Feb;72:63-70. doi: 10.1016/j.sbi.2021.08.006. Epub 2021 Sep 15.
9
Consistent Force Field Captures Homologue-Resolved HP1 Phase Separation.一致力场捕获同源物分辨的 HP1 液-液相分离。
J Chem Theory Comput. 2021 May 11;17(5):3134-3144. doi: 10.1021/acs.jctc.0c01220. Epub 2021 Apr 7.
10
Viscoelastic properties of wheat gluten in a molecular dynamics study.分子动力学研究中小麦面筋的粘弹性特性
PLoS Comput Biol. 2021 Mar 24;17(3):e1008840. doi: 10.1371/journal.pcbi.1008840. eCollection 2021 Mar.
AWSEM-IDP：一种用于固有无序蛋白质的粗粒度力场。
J Phys Chem B. 2018 Dec 13;122(49):11115-11125. doi: 10.1021/acs.jpcb.8b05791. Epub 2018 Aug 9.
4
Disordered peptide chains in an α-C-based coarse-grained model.无序的α-C 基粗粒模型中的肽链。
Phys Chem Chem Phys. 2018 Jul 18;20(28):19057-19070. doi: 10.1039/c8cp03309a.
5
Utilizing Coarse-Grained Modeling and Monte Carlo Simulations to Evaluate the Conformational Ensemble of Intrinsically Disordered Proteins and Regions.利用粗粒度建模和蒙特卡罗模拟评估固有无序蛋白质和区域的构象集合。
J Mol Biol. 2018 Aug 3;430(16):2478-2492. doi: 10.1016/j.jmb.2018.03.006. Epub 2018 Mar 21.
6
Sequence determinants of protein phase behavior from a coarse-grained model.从粗粒度模型中得出蛋白质相行为的序列决定因素。
PLoS Comput Biol. 2018 Jan 24;14(1):e1005941. doi: 10.1371/journal.pcbi.1005941. eCollection 2018 Jan.
7
Structural Characterization of Highly Flexible Proteins by Small-Angle Scattering.小角散射研究高弹性蛋白的结构特征。
Adv Exp Med Biol. 2017;1009:107-129. doi: 10.1007/978-981-10-6038-0_7.
8
HyRes: a coarse-grained model for multi-scale enhanced sampling of disordered protein conformations.HyRes：一种用于无序蛋白质构象多尺度增强采样的粗粒度模型。
Phys Chem Chem Phys. 2017 Dec 13;19(48):32421-32432. doi: 10.1039/c7cp06736d.
9
Self-assembly of model proteins into virus capsids.模型蛋白自组装成病毒衣壳。
J Phys Condens Matter. 2017 Nov 29;29(47):474003. doi: 10.1088/1361-648X/aa9351.
10
Sequence dependent aggregation of peptides and fibril formation.序列依赖性肽聚集和纤维形成。
J Chem Phys. 2017 Sep 14;147(10):105102. doi: 10.1063/1.5001517.