We have developed a computational method of atomistically refining the structural ensemble of intrinsically disordered peptides (IDPs) facilitated by experimental measurements using circular dichroism spectroscopy (CD). A major challenge surrounding this approach stems from the deconvolution of experimental CD spectra into secondary structure features of the IDP ensemble. Currently available algorithms for CD deconvolution were designed to analyze the spectra of proteins with stable secondary structures. Herein, our work aims to minimize any bias from the peptide deconvolution analysis by implementing a non-negative linear least-squares fitting algorithm in conjunction with a CD reference data set that contains soluble and denatured proteins (SDP48). The non-negative linear least-squares method yields the best results for deconvolution of proteins with higher disordered content than currently available methods, according to a validation analysis of a set of protein spectra with Protein Data Bank entries. We subsequently used this analysis to deconvolute our experimental CD data to refine our computational model of the peptide secondary structure ensemble produced by all-atom molecular dynamics simulations with implicit solvent. We applied this approach to determine the ensemble structures of a set of short IDPs, that mimic the calmodulin binding domain of calcium/calmodulin-dependent protein kinase II and its 1-amino-acid and 3-amino-acid mutants. Our study offers a, to our knowledge, novel way to solve the ensemble secondary structures of IDPs in solution, which is important to advance the understanding of their roles in regulating signaling pathways through the formation of complexes with multiple partners.

中文翻译：

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分子动力学根据圆二色性解卷积光谱对固有无序肽的集合精化

我们开发了一种计算方法，通过使用圆二色光谱 (CD) 的实验测量促进了内在无序肽 (IDP) 的结构集合的原子化。围绕这种方法的一个主要挑战源于将实验 CD 光谱解卷积为 IDP 集合的二级结构特征。目前可用的 CD 解卷积算法旨在分析具有稳定二级结构的蛋白质的光谱。在此，我们的工作旨在通过实施非负线性最小二乘拟合算法以及包含可溶性和变性蛋白质 (SDP48) 的 CD 参考数据集来最小化肽解卷积分析的任何偏差。根据一组蛋白质光谱与蛋白质数据库条目的验证分析，非负线性最小二乘法比目前可用的方法对具有更高无序含量的蛋白质的解卷积产生最佳结果。我们随后使用此分析对我们的实验 CD 数据进行解卷积，以改进我们的肽二级结构集合的计算模型，该模型由具有隐式溶剂的全原子分子动力学模拟产生。我们应用这种方法来确定一组短 IDP 的整体结构，模拟钙/钙调蛋白依赖性蛋白激酶 II 及其 1-氨基酸和 3-氨基酸突变体的钙调蛋白结合域。据我们所知，我们的研究提供了一种新颖的方法来解决溶液中 IDP 的整体二级结构，