Modeling and simulation of ion channels.
作者信息
Maffeo Christopher, Bhattacharya Swati, Yoo Jejoong, Wells David, Aksimentiev Aleksei
机构信息
Department of Physics, University of Illinois, 1110 W. Green Street, Urbana, Illinois 61801, United States.
出版信息
Chem Rev. 2012 Dec 12;112(12):6250-84. doi: 10.1021/cr3002609. Epub 2012 Oct 4.
Abstract
摘要
相似文献
1
Modeling and simulation of ion channels.离子通道的建模与模拟
Chem Rev. 2012 Dec 12;112(12):6250-84. doi: 10.1021/cr3002609. Epub 2012 Oct 4.
2
3D-model of the ion channel of NMDA receptor: qualitative and quantitative modeling of the blocker binding.N-甲基-D-天冬氨酸受体离子通道的三维模型：阻滞剂结合的定性和定量建模
Dokl Biochem Biophys. 2004 May-Jun;396:181-6. doi: 10.1023/b:dobi.0000033524.51696.37.
3
Growing momentum in the molecular study of ion channels.离子通道分子研究的势头日益强劲。
Nat Struct Biol. 1999 Sep;6(9):811-4. doi: 10.1038/12266.
4
Molecular modeling and simulation studies of ion channel structures, dynamics and mechanisms.离子通道结构、动力学和机制的分子建模与模拟研究
Methods Cell Biol. 2008;90:233-65. doi: 10.1016/S0091-679X(08)00812-1.
5
ModFossa: A library for modeling ion channels using Python.ModFossa：一个使用Python对离子通道进行建模的库。
J Bioinform Comput Biol. 2016 Jun;14(3):1642003. doi: 10.1142/S0219720016420038. Epub 2016 Mar 2.
6
A review of molecular modeling approaches to pharmacophore models and structure-activity relationships of ion channel modulators in CNS.中枢神经系统中离子通道调节剂的药效团模型和构效关系的分子建模方法综述。
Curr Pharm Des. 2002;8(2):99-110. doi: 10.2174/1381612023396546.
7
Molecular simulations of ion channels: a quantum chemist's perspective.离子通道的分子模拟：一位量子化学家的视角
J Gen Physiol. 2010 Jun;135(6):549-54. doi: 10.1085/jgp.201010404.
8
[Structure and function of ion channels].[离子通道的结构与功能]
Duodecim. 1990;106(22):1516-25.
9
The glutamate receptor ion channels.谷氨酸受体离子通道
Pharmacol Rev. 1999 Mar;51(1):7-61.
10
Perspectives on: conformational coupling in ion channels: thermodynamics of electromechanical coupling in voltage-gated ion channels.关于离子通道构象偶联的观点：电压门控离子通道中机电偶联的热力学
J Gen Physiol. 2012 Dec;140(6):613-23. doi: 10.1085/jgp.201210840.
引用本文的文献
1
A covalent organic framework membrane with highly selective and permeable artificial sodium channels via ion recognition.一种通过离子识别具有高选择性和渗透性人工钠通道的共价有机框架膜。
Nat Commun. 2025 Aug 9;16(1):7346. doi: 10.1038/s41467-025-62329-1.
2
Transcriptomic profiles link corticostriatal microarchitecture to genetics of neurodevelopment and neuropsychiatric risks.转录组学图谱将皮质纹状体微结构与神经发育遗传学和神经精神疾病风险联系起来。
Transl Psychiatry. 2025 Feb 11;15(1):48. doi: 10.1038/s41398-025-03260-3.
3
Balancing Group 1 Monoatomic Ion-Polar Compound Interactions in the Polarizable Drude Force Field: Application in Protein and Nucleic Acid Systems.在可极化德鲁德力场中平衡第1族单原子离子-极性化合物相互作用：在蛋白质和核酸系统中的应用
J Phys Chem B. 2024 Dec 12;128(49):12078-12091. doi: 10.1021/acs.jpcb.4c06354. Epub 2024 Dec 3.
4
Nernst equilibrium, rectification, and saturation: Insights into ion channel behavior.能斯特平衡、整流与饱和：对离子通道行为的见解
Biophys J. 2024 Dec 17;123(24):4304-4315. doi: 10.1016/j.bpj.2024.10.016. Epub 2024 Oct 30.
5
Structural lesions and transcriptomic specializations shape gradient perturbations in Wilson disease.结构损伤和转录组特化塑造了威尔逊病中的梯度扰动。
Brain Commun. 2024 Sep 24;6(5):fcae329. doi: 10.1093/braincomms/fcae329. eCollection 2024.
6
Nernst Equilibrium, Rectification, and Saturation: Insights into Ion Channel Behavior.能斯特平衡、整流与饱和：对离子通道行为的见解
bioRxiv. 2024 Aug 17:2024.08.16.608320. doi: 10.1101/2024.08.16.608320.
7
ezAlign: A Tool for Converting Coarse-Grained Molecular Dynamics Structures to Atomistic Resolution for Multiscale Modeling.ezAlign：一种用于将粗粒度分子动力学结构转换为原子分辨率以进行多尺度建模的工具。
Molecules. 2024 Jul 28;29(15):3557. doi: 10.3390/molecules29153557.
8
Molecular mechanism of anion permeation through aquaporin 6.水通道蛋白 6 介导阴离子渗透的分子机制。
Biophys J. 2024 Aug 20;123(16):2496-2505. doi: 10.1016/j.bpj.2024.06.013. Epub 2024 Jun 17.
9
Electro-osmotic Flow Generation via a Sticky Ion Action.黏附离子作用驱动的电渗透流产生。
ACS Nano. 2024 Jul 9;18(27):17521-17533. doi: 10.1021/acsnano.4c00829. Epub 2024 Jun 4.
10
Random fluctuations and synaptic plasticity enhance working memory activities in the neuron-astrocyte network.随机波动和突触可塑性增强了神经元-星形胶质细胞网络中的工作记忆活动。
Cogn Neurodyn. 2024 Apr;18(2):503-518. doi: 10.1007/s11571-023-10002-y. Epub 2023 Sep 1.
本文引用的文献
1
The MARTINI Coarse-Grained Force Field: Extension to Proteins.MARTINI 粗粒化力场：在蛋白质中的扩展。
J Chem Theory Comput. 2008 May;4(5):819-34. doi: 10.1021/ct700324x.
2
Developing Improved Charge Sets for the Modeling of the KcsA K(+) Channel Using QM/MM Electrostatic Potentials.利用量子力学/分子力学静电势开发用于KcsA钾离子通道建模的改进电荷集。
J Chem Theory Comput. 2009 Aug 11;5(8):2173-9. doi: 10.1021/ct9001619.
3
A High-Throughput Steered Molecular Dynamics Study on the Free Energy Profile of Ion Permeation through Gramicidin A.通过 Gramicidin A 离子渗透的自由能分布的高通量导向分子动力学研究。
J Chem Theory Comput. 2011 Jun 14;7(6):1943-50. doi: 10.1021/ct100707s. Epub 2011 May 6.
4
PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions.PROPKA3：经验 pKa 预测中内部残基和表面残基的一致处理。
J Chem Theory Comput. 2011 Feb 8;7(2):525-37. doi: 10.1021/ct100578z. Epub 2011 Jan 6.
5
Membrane Protein Simulations Using AMBER Force Field and Berger Lipid Parameters.使用AMBER力场和伯杰脂质参数进行膜蛋白模拟。
J Chem Theory Comput. 2012 Mar 13;8(3):948-58. doi: 10.1021/ct200491c. Epub 2012 Feb 21.
6
A Combined Metadynamics and Umbrella Sampling Method for the Calculation of Ion Permeation Free Energy Profiles.一种用于计算离子渗透自由能分布的元动力学和伞形采样组合方法。
J Chem Theory Comput. 2011 Jul 12;7(7):2277-2283. doi: 10.1021/ct200100e.
7
All-atom empirical potential for molecular modeling and dynamics studies of proteins.蛋白质分子建模和动力学研究的全原子经验势。
J Phys Chem B. 1998 Apr 30;102(18):3586-616. doi: 10.1021/jp973084f.
8
Computational modeling of ion transport through nanopores.离子通过纳米孔的输运的计算建模。
Nanoscale. 2012 Oct 21;4(20):6166-80. doi: 10.1039/c2nr31024d.
9
BROMOC-D: Brownian Dynamics/Monte-Carlo Program Suite to Study Ion and DNA Permeation in Nanopores.BROMOC-D：用于研究纳米孔中离子与DNA渗透的布朗动力学/蒙特卡罗程序套件。
J Chem Theory Comput. 2012 Jul 10;8(7):2540-2551. doi: 10.1021/ct3004244. Epub 2012 May 24.
10
Assessing graphene nanopores for sequencing DNA.评估用于测序 DNA 的石墨烯纳米孔。
Nano Lett. 2012 Aug 8;12(8):4117-23. doi: 10.1021/nl301655d. Epub 2012 Jul 17.
Zotero 插件