Depto. Física Aplicada, Instituto de Física, Universidade de São Paulo (IF/USP), Rua do Matão 1371, São Paulo, SP, 05508-090, Brazil.
Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, 13563-120, Brazil.
Eur Biophys J. 2021 Jul;50(5):687-697. doi: 10.1007/s00249-021-01499-4. Epub 2021 Feb 4.
Circular dichroism (CD) spectroscopy is a well-established biophysical technique used to investigate the structure of molecules. The analysis of a protein CD spectrum depends on the quality of the original CD data, which can be affected by the sample purity, background absorption of the additives/solvent/buffer, the choice of the parameters used for data collection, etc. In this paper, the CD spectrum of myoglobin was used as a model to exploit how variations on each data collection parameter could affect the final protein CD spectrum and, the subsequent effect of them on the quantitative analysis of protein secondary structure. Bioinformatics analysis carried out with SESCA package and PDBMD2CD server predicted a theoretical myoglobin CD spectrum, and a Monte Carlo-like model was implemented to estimate the uncertainty in secondary structure predictions performed with CDSSTR, Selcon 3 and ContinLL algorithms. An inappropriate choice of data collection parameters can lead to a misinterpretation of the CD data in terms of the protein structural content.
圆二色性（CD）光谱学是一种成熟的生物物理技术，用于研究分子结构。蛋白质 CD 光谱的分析取决于原始 CD 数据的质量，而原始 CD 数据的质量可能会受到样品纯度、添加剂/溶剂/缓冲液的背景吸收、数据收集参数的选择等因素的影响。在本文中，肌红蛋白的 CD 光谱被用作模型，以探讨每个数据收集参数的变化如何影响最终的蛋白质 CD 光谱，以及它们对蛋白质二级结构定量分析的后续影响。SESCA 包和 PDBMD2CD 服务器进行的生物信息学分析预测了理论肌红蛋白 CD 光谱，并实现了蒙特卡罗样模型来估计 CDSSTR、Selcon 3 和 ContinLL 算法进行的二级结构预测的不确定性。数据收集参数的不当选择可能导致对 CD 数据中蛋白质结构含量的错误解释。
