Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model,Journal of Chemical Information and Modeling

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Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model
Journal of Chemical Information and Modeling ( IF 5.6 ) Pub Date : 2017-12-01 00:00:00 , DOI: 10.1021/acs.jcim.7b00510
Bercem Dutagaci ₁ , Michael Feig ₁

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A protocol for predicting the hydrophobic length of membrane proteins using the heterogeneous dielectric generalized Born (HDGB) implicit membrane model is presented. The method involves optimal positioning in the membrane and identification of lipid-facing and inward-facing residues, followed by energy optimization of the implicit membrane model to obtain the hydrophobic length from the optimal membrane width. The latest HDGB version 3 (HDGBv3) and HDGB van der Waals (HDGBvdW) models were applied to a test set containing 15 proteins (seven β-barrel and eight α-helical proteins), for which matching membrane widths are available from experiment, and an additional set contains ten α-helical and ten β-barrel proteins without any experimental data. The results with the HDGB model compare favorably with predictions from methods used in the Orientations of Proteins in Membranes (OPM) and Protein Data Bank of Transmembrane Proteins (PDB-TM) databases.

中文翻译：

HDGB隐膜模型测定膜蛋白的疏水长度

提出了使用异质介电广义博恩（HDGB）隐式膜模型预测膜蛋白疏水长度的协议。该方法包括在膜中进行最佳定位，并确定面向脂质和面向内的残留物，然后对隐式膜模型进行能量优化，以从最佳膜宽度获得疏水长度。将最新的HDGB版本3（HDGBv3）和HDGB van der Waals（HDGBvdW）模型应用于包含15种蛋白（七个β-barrel和八个α-螺旋蛋白）的测试仪，该蛋白可从实验中获得匹配的膜宽度，并且另外一组包含十个α螺旋蛋白和十个β桶蛋白，没有任何实验数据。

更新日期：2017-12-01

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