Discrimination of native loop conformations in membrane proteins: Decoy library design and evaluation of effective energy scoring functions
Discrimination of native loop conformations in membrane proteins: Decoy library design and evaluation of effective energy scoring functions
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DOI：
10.1002/prot.10404
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发表时间：
2003-09-01
影响因子：
2.9
通讯作者：
Woolf, TB
中科院分区：
文献类型：
--
作者：
Forrest, LR;Woolf, TB
最近对几种重要膜蛋白晶体结构的确定为对其跨膜区域的比较建模开辟了道路。然而，正确预测环区结构的能力仍然是一个相当大的挑战，这可能是至关重要的，例如在配体结合中。为了应对这一挑战，准确的评分方法必须区分未知环结构的候选构象。据报道，球状蛋白的环预测取得了一些成功。然而，膜蛋白环与脂质双层的接近性使人们对相同评分方法对该问题的适用性产生怀疑。在这项工作中，我们利用两种膜蛋白的结构，通过分子动力学和蒙特卡罗技术在一定温度范围内生成非天然折叠的“诱饵库”。我们引入了一种新的诱饵库生成方法，通过构建覆盖范围广泛的 C(α-均方根偏差 (RMSD) 与天然结构的构象平坦分布；这消除了后续评分阶段中可能存在的偏差。然后，我们使用有效能量函数对这些诱饵构象进行评分，使用越来越多的 CPU 密集型隐式溶剂模型，包括 (1) 具有恒定或距离依赖电介质的简单库仑静电；(2) 原子溶剂化参数；(3) 有效能量函数(EEF1) Lazaridis 和 Karplus；(4) 广义 Born/分析连续溶剂；以及 (5) 有限差分泊松-玻尔兹曼能量函数 我们表明，在均匀环境的假设下，可以使用有效能量来实现类天然膜蛋白环的区分；因此，相邻脂质双层的缺失不会影响评分能力。有趣的是，使用可电离侧链的不带电状态有助于预测，特别是对于最简单的能量函数 (C) 2003 Wiley-Liss, Inc.。
The recent determination of crystal structures for several important membrane proteins opens the way for comparative modeling of their membrane-spanning regions. However, the ability to predict correctly the structures of loop regions, which may be critical, for example, in ligand binding, remains a considerable challenge. To meet this challenge, accurate scoring methods have to discriminate between candidate conformations of an unknown loop structure. Some success in loop prediction has been reported for globular proteins; however, the proximity of membrane protein loops to the lipid bilayer casts doubt on the applicability of the same scoring methods to this problem. In this work, we develop "decoy libraries" of non-native folds generated, using the structures of two membrane proteins, with molecular dynamics and Monte Carlo techniques over a range of temperatures. We introduce a new approach for decoy library generation by constructing a flat distribution of conformations covering a wide range of C(alpha-root-mean-square deviation (RMSD) from the native structure; this removes possible bias in subsequent scoring stages. We then score these decoy conformations with effective energy functions, using increasingly more cpu-intensive implicit solvent models, including (1) simple Coulombic electrostatics with constant or distance-dependent dielectrics; (2) atomic solvation parameters; (3) the effective energy function (EEF1) of Lazaridis and Karplus; (4) generalized Born/Analytical Continuum Solvent; and (5) finite-difference Poisson-Boltzmann energy functions. We show that distinction of native-like membrane protein loops may be achieved using effective energies with the assumption of a homogenous environment; thus, the absence of the adjacent lipid bilayer does not affect the scoring ability. In particular, the Analytical Continuum Solvent and finite-difference Poisson-Boltzmann energy functions are seen to be the most powerful scoring functions. Interestingly, the use of the uncharged states of ionizable sidechains is shown to aid prediction, particularly for the simplest energy functions. (C) 2003 Wiley-Liss, Inc.