• 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

相似文献

1
Prediction of salt and mutational effects on the association rate of U1A protein and U1 small nuclear RNA stem/loop II.盐和突变对U1A蛋白与U1小核RNA茎环II结合速率影响的预测
J Phys Chem B. 2008 May 15;112(19):5955-60. doi: 10.1021/jp075919k. Epub 2007 Dec 22.
2
Investigating the binding specificity of U1A-RNA by computational mutagenesis.通过计算诱变研究U1A-RNA的结合特异性。
J Mol Biol. 2000 Jan 7;295(1):1-6. doi: 10.1006/jmbi.1999.3319.
3
Molecular dynamics simulations of the complex between human U1A protein and hairpin II of U1 small nuclear RNA and of free RNA in solution.人U1A蛋白与U1小核RNA发夹II复合物以及溶液中游离RNA的分子动力学模拟。
Biophys J. 1999 Sep;77(3):1284-305. doi: 10.1016/S0006-3495(99)76979-1.
4
Two functionally distinct steps mediate high affinity binding of U1A protein to U1 hairpin II RNA.两个功能不同的步骤介导U1A蛋白与U1发夹II RNA的高亲和力结合。
J Biol Chem. 2001 Jun 15;276(24):21476-81. doi: 10.1074/jbc.M101624200. Epub 2001 Apr 10.
5
Two structurally different RNA molecules are bound by the spliceosomal protein U1A using the same recognition strategy.两种结构不同的RNA分子通过剪接体蛋白U1A采用相同的识别策略进行结合。
Structure. 1996 May 15;4(5):621-31. doi: 10.1016/s0969-2126(96)00066-4.
6
Coevolution of Drosophila snf protein and its snRNA targets.果蝇 snf 蛋白与其 snRNA 靶标协同进化。
Biochemistry. 2010 Jun 8;49(22):4571-82. doi: 10.1021/bi100374d.
7
The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA.带正电荷的氨基酸和静电相互作用在U1A蛋白与U1发夹II RNA复合物中的作用。
Nucleic Acids Res. 2006 Jan 10;34(1):275-85. doi: 10.1093/nar/gkj436. Print 2006.
8
Investigation of a conserved stacking interaction in target site recognition by the U1A protein.对U1A蛋白在靶位点识别中保守堆积相互作用的研究。
Nucleic Acids Res. 2002 Jan 15;30(2):550-8. doi: 10.1093/nar/30.2.550.
9
Kinetic analysis of the role of the tyrosine 13, phenylalanine 56 and glutamine 54 network in the U1A/U1 hairpin II interaction.酪氨酸13、苯丙氨酸56和谷氨酰胺54网络在U1A/U1发夹II相互作用中的作用的动力学分析。
Nucleic Acids Res. 2005 May 24;33(9):2917-28. doi: 10.1093/nar/gki602. Print 2005.
10
Crystal structure at 1.92 A resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin.与RNA发夹结合的U1A剪接体蛋白RNA结合结构域在1.92埃分辨率下的晶体结构。
Nature. 1994 Dec 1;372(6505):432-8. doi: 10.1038/372432a0.

引用本文的文献

1
Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation.静电相互作用在蛋白质结构、折叠、结合和凝聚中的作用。
Chem Rev. 2018 Feb 28;118(4):1691-1741. doi: 10.1021/acs.chemrev.7b00305. Epub 2018 Jan 10.
2
Electrostatic effects on the folding stability of FKBP12.静电作用对FKBP12折叠稳定性的影响。
Protein Eng Des Sel. 2016 Aug;29(8):301-308. doi: 10.1093/protein/gzw014. Epub 2016 Jul 5.
3
Computational support for a scaffolding mechanism of centriole assembly.对中心粒组装支架机制的计算支持。
Sci Rep. 2016 Jun 8;6:27075. doi: 10.1038/srep27075.
4
Energetic evaluation of binding modes in the C3d and Factor H (CCP 19-20) complex.C3d与补体因子H（CCP 19-20）复合物结合模式的能量评估
Protein Sci. 2015 May;24(5):789-802. doi: 10.1002/pro.2650. Epub 2015 Mar 11.
5
PIPE: A Suite of Web Servers for Predictions Ranging From Protein Structure to Binding Kinetics.PIPE：一套用于从蛋白质结构到结合动力学预测的网络服务器。
Biophys Rev. 2013 Mar 1;5(1):41-46. doi: 10.1007/s12551-012-0086-7. Epub 2012 Jul 25.
6
Accurate Calculations of Binding, Folding, and Transfer Free Energies by a Scaled Generalized Born Method.通过缩放广义玻恩方法精确计算结合、折叠和转移自由能
J Chem Theory Comput. 2008 Oct 14;4(10):1733-1744. doi: 10.1021/ct8001656. Epub 2008 Sep 6.
7
On the Dielectric Boundary in Poisson-Boltzmann Calculations.泊松-玻尔兹曼计算中的介电边界
J Chem Theory Comput. 2008 Mar;4(3):507-514. doi: 10.1021/ct700319x. Epub 2008 Feb 21.
8
Poisson-Boltzmann Calculations: van der Waals or Molecular Surface?泊松-玻尔兹曼计算：范德华力还是分子表面？
Commun Comput Phys. 2013 Jan;13(1):1-12. doi: 10.4208/cicp.270711.140911s. Epub 2012 Jun 12.
9
Intrinsic disorder: signaling via highly specific but short-lived association.固有无序：通过高度特异性但短暂的关联进行信号传递。
Trends Biochem Sci. 2012 Feb;37(2):43-8. doi: 10.1016/j.tibs.2011.11.002. Epub 2011 Dec 7.
10
Automated prediction of protein association rate constants.蛋白质缔合速率常数的自动预测。
Structure. 2011 Dec 7;19(12):1744-51. doi: 10.1016/j.str.2011.10.015.

本文引用的文献

1
Affinity and specificity of protein U1A-RNA complex formation based on an additive component free energy model.基于无添加剂成分自由能模型的蛋白质U1A-RNA复合物形成的亲和力和特异性。
J Mol Biol. 2007 Aug 31;371(5):1405-19. doi: 10.1016/j.jmb.2007.06.003. Epub 2007 Jun 9.
2
Do electrostatic interactions destabilize protein-nucleic acid binding?静电相互作用会使蛋白质-核酸结合不稳定吗？
Biopolymers. 2007 Jun 5;86(2):112-8. doi: 10.1002/bip.20708.
3
Prediction of protein-protein association rates from a transition-state theory.基于过渡态理论预测蛋白质-蛋白质结合速率
Structure. 2007 Feb;15(2):215-24. doi: 10.1016/j.str.2007.01.005.
4
Energy landscape and transition state of protein-protein association.蛋白质-蛋白质相互作用的能量景观与过渡态
Biophys J. 2007 Mar 1;92(5):1486-502. doi: 10.1529/biophysj.106.096024. Epub 2006 Dec 1.
5
Electrostatic contribution to the binding stability of protein-protein complexes.静电作用对蛋白质-蛋白质复合物结合稳定性的贡献。
Proteins. 2006 Oct 1;65(1):87-102. doi: 10.1002/prot.21070.
6
Simulation of electron transfer between cytochrome C2 and the bacterial photosynthetic reaction center: Brownian dynamics analysis of the native proteins and double mutants.细胞色素C2与细菌光合反应中心之间电子转移的模拟：天然蛋白质和双突变体的布朗动力学分析
J Phys Chem B. 2005 Apr 21;109(15):7529-34. doi: 10.1021/jp045417w.
7
A Brownian dynamics study of the interactions of the luminal domains of the cytochrome b6f complex with plastocyanin and cytochrome c6: the effects of the Rieske FeS protein on the interactions.细胞色素b6f复合体腔结构域与质体蓝素和细胞色素c6相互作用的布朗动力学研究： Rieske铁硫蛋白对相互作用的影响
Biophys J. 2006 Oct 1;91(7):2589-600. doi: 10.1529/biophysj.106.085936. Epub 2006 Jul 14.
8
The role of RNA structure in the interaction of U1A protein with U1 hairpin II RNA.RNA结构在U1A蛋白与U1发夹II RNA相互作用中的作用。
RNA. 2006 Jul;12(7):1168-78. doi: 10.1261/rna.75206. Epub 2006 May 31.
9
High-resolution structural validation of the computational redesign of human U1A protein.人类U1A蛋白计算重新设计的高分辨率结构验证
Structure. 2006 May;14(5):847-56. doi: 10.1016/j.str.2006.02.011.
10
The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA.带正电荷的氨基酸和静电相互作用在U1A蛋白与U1发夹II RNA复合物中的作用。
Nucleic Acids Res. 2006 Jan 10;34(1):275-85. doi: 10.1093/nar/gkj436. Print 2006.

盐和突变对U1A蛋白与U1小核RNA茎环II结合速率影响的预测

Prediction of salt and mutational effects on the association rate of U1A protein and U1 small nuclear RNA stem/loop II.

作者信息

Qin Sanbo, Zhou Huan-Xiang

机构信息

Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, Florida 32306, USA.

出版信息

J Phys Chem B. 2008 May 15;112(19):5955-60. doi: 10.1021/jp075919k. Epub 2007 Dec 22.

DOI:10.1021/jp075919k
PMID:18154282
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3526768/
Abstract

We have developed a computational approach for predicting protein-protein association rates (Alsallaq and Zhou, Structure 2007, 15, 215). Here we expand the range of applicability of this approach to protein-RNA binding and report the first results for protein-RNA binding rates predicted from atomistic modeling. The system studied is the U1A protein and stem/loop II of the U1 small nuclear RNA. Experimentally it was observed that the binding rate is significantly reduced by increasing salt concentration while the dissociation changes little with salt concentration, and charges distant from the binding site make marginal contribution to the binding rate. These observations are rationalized. Moreover, predicted effects of salt and charge mutations are found to be in quantitative agreement with experimental results.

摘要

我们开发了一种用于预测蛋白质-蛋白质结合速率的计算方法（Alsallaq和Zhou，《结构》，2007年，第15卷，第215页）。在此，我们将该方法的适用范围扩展到蛋白质-RNA结合，并报告了通过原子模型预测的蛋白质-RNA结合速率的首批结果。所研究的系统是U1A蛋白和U1小核RNA的茎环II。实验观察到，随着盐浓度的增加，结合速率显著降低，而解离速率随盐浓度变化不大，且远离结合位点的电荷对结合速率的贡献很小。这些观察结果得到了合理的解释。此外，发现盐和电荷突变的预测效应与实验结果在数量上一致。