Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico.
Departamento de Ciencias de la Alimentación, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana Unidad Lerma, Avenida de las Garzas 10, Colonia El Panteón, Lerma de Villada, Estado de México 52005, Mexico.
J Agric Food Chem. 2022 Feb 2;70(4):934-943. doi: 10.1021/acs.jafc.1c06110. Epub 2022 Jan 6.
tools, such as molecular docking, are widely applied to study interactions and binding affinity of biological activity of proteins and peptides. However, restricted sampling of both ligand and receptor conformations and use of approximated scoring functions can produce results that do not correlate with actual experimental binding affinities. Molecular dynamics simulations (MDS) can provide valuable information in deciphering functional mechanisms of proteins/peptides and other biomolecules, overcoming the rigid sampling limitations in docking analysis. This review will discuss the information related to the traditional use of models, such as molecular docking, and its application for studying food proteins and bioactive peptides, followed by an in-depth introduction to the theory of MDS and description of why these molecular simulation techniques are important in the theoretical prediction of structural and functional dynamics of food proteins and bioactive peptides. Applications, limitations, and future prospects of MDS will also be discussed.
工具，如分子对接，广泛应用于研究蛋白质和肽的生物活性的相互作用和结合亲和力。然而，配体和受体构象的受限采样和使用近似评分函数可能会产生与实际实验结合亲和力不相关的结果。分子动力学模拟（MDS）可以在破译蛋白质/肽和其他生物分子的功能机制方面提供有价值的信息，克服对接分析中刚性采样的限制。本文综述了传统使用模型（如分子对接）的相关信息，及其在研究食品蛋白质和生物活性肽中的应用，接着深入介绍了 MDS 的理论，并描述了为什么这些分子模拟技术在食品蛋白质和生物活性肽的结构和功能动力学的理论预测中非常重要。还讨论了 MDS 的应用、局限性和未来前景。
