Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy.
Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.
Int J Mol Sci. 2023 Mar 28;24(7):6368. doi: 10.3390/ijms24076368.
Molecular modeling techniques have become indispensable in many fields of molecular sciences in which the details related to mechanisms and reactivity need to be studied at an atomistic level. This review article provides a collection of computational modeling works on a topic of enormous interest and urgent relevance: the properties of metalloenzymes involved in the degradation and valorization of natural biopolymers and synthetic plastics on the basis of both circular biofuel production and bioremediation strategies. In particular, we will focus on lytic polysaccharide monooxygenase, laccases, and various heme peroxidases involved in the processing of polysaccharides, lignins, rubbers, and some synthetic polymers. Special attention will be dedicated to the interaction between these enzymes and their substrate studied at different levels of theory, starting from classical molecular docking and molecular dynamics techniques up to techniques based on quantum chemistry.
分子建模技术在许多分子科学领域中已经不可或缺,这些领域需要在原子水平上研究与机制和反应性相关的细节。本文综述了一系列关于一个极富趣味和现实意义的主题的计算建模工作:涉及天然生物聚合物和合成塑料降解和增值的金属酶的性质,这些工作是基于循环生物燃料生产和生物修复策略的。具体来说,我们将重点介绍参与多糖、木质素、橡胶和一些合成聚合物处理的溶菌多糖单加氧酶、漆酶和各种血红素过氧化物酶。特别关注这些酶与其底物之间的相互作用,研究将从经典的分子对接和分子动力学技术一直到基于量子化学的技术,在不同的理论水平上进行。