OPEP蛋白模型：从单分子、淀粉样蛋白形成、拥挤效应和流体动力学到DNA/RNA系统
The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems.
作者信息
Sterpone Fabio, Melchionna Simone, Tuffery Pierre, Pasquali Samuela, Mousseau Normand, Cragnolini Tristan, Chebaro Yassmine, St-Pierre Jean-Francois, Kalimeri Maria, Barducci Alessandro, Laurin Yoann, Tek Alex, Baaden Marc, Nguyen Phuong Hoang, Derreumaux Philippe
机构信息
Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris, France.
出版信息
Chem Soc Rev. 2014 Jul 7;43(13):4871-93. doi: 10.1039/c4cs00048j. Epub 2014 Apr 23.
Abstract
The OPEP coarse-grained protein model has been applied to a wide range of applications since its first release 15 years ago. The model, which combines energetic and structural accuracy and chemical specificity, allows the study of single protein properties, DNA-RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. Here we first review the current state of the model and the most exciting applications using advanced conformational sampling methods. We then present the current limitations and a perspective on the ongoing developments.
摘要
自15年前首次发布以来，OPEP粗粒度蛋白质模型已被广泛应用于各种领域。该模型结合了能量和结构准确性以及化学特异性，能够研究单个蛋白质特性、DNA-RNA复合物、淀粉样纤维形成以及拥挤环境中的蛋白质悬浮液。在这里，我们首先回顾该模型的当前状态以及使用先进构象采样方法的最令人兴奋的应用。然后，我们介绍当前的局限性以及对正在进行的发展的展望。
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J Chem Theory Comput. 2008 May;4(5):819-34. doi: 10.1021/ct700324x.
2
Impact of Thermostats on Folding and Aggregation Properties of Peptides Using the Optimized Potential for Efficient Structure Prediction Coarse-Grained Model.使用高效结构预测粗粒度模型的优化势函数研究恒温器对肽折叠和聚集特性的影响。
J Chem Theory Comput. 2011 May 10;7(5):1502-10. doi: 10.1021/ct100619p. Epub 2011 Apr 11.
3
Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins.流体动力学相互作用对蛋白质模拟扩散和折叠的显著影响。
J Chem Theory Comput. 2009 Feb 10;5(2):242-56. doi: 10.1021/ct800499p.
4
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J Chem Theory Comput. 2011 Aug 9;7(8):2584-92. doi: 10.1021/ct1006967. Epub 2011 Jun 29.
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