Atomistic adsorption of PETase onto large-scale PET 3D-models that mimic reality†

IF 2.9 3区 化学 Q3 CHEMISTRY, PHYSICAL
P. Paiva, E. Ippoliti, P. Carloni, P. A. Fernandes and M. J. Ramos
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引用次数: 0

Abstract

Polyethylene terephthalate (PET) has been widely used in plastic products, leading to massive PET waste accumulation in ecosystems worldwide. Efforts to find greener processes for dealing with post-consumer PET waste led to the discovery of PET-degrading enzymes such as Ideonella sakaiensis PETase (IsPETase). In silico studies have provided valuable contributions to this field, shedding light on the catalytic mechanisms and substrate interactions in many PET hydrolase enzymes. However, most of these studies have often relied on short PET oligomers, failing to replicate catalytic-relevant interactions and true substrate motions occurring during contact with a PET-degrading enzyme. A comprehensive atomistic study of PET in both its crystalline (cPET) and amorphous (aPET) states, along with investigation of the adsorption of PET-degrading enzymes onto solid PET, would greatly advance our understanding of mechanisms driving PET biodegradation. In this study, we developed large-scale computational models of cPET, comprising thousands of monomers, and conducted molecular dynamics simulations to follow the transformation of cPET into aPET. Next, these models were validated by comparison with experimentally determined data. We then studied the adsorption of IsPETase on the assembled PET models, investigated the main phenomena that differentiate the two adsorption processes, and explored them from a catalytic perspective. The results and computational PET models provided herein are envisioned to aid in the development of innovative strategies for PET waste biodegradation.

Abstract Image

PETase的原子吸附到模拟现实的大型PET 3d模型上
聚对苯二甲酸乙二醇酯(PET)在塑料制品中的广泛应用,导致了全球生态系统中大量PET废弃物的积累。寻找更环保的处理消费后PET废物的方法的努力导致了PET降解酶的发现,如酒井Ideonella sakaiensis PETase (IsPETase)。硅研究为这一领域提供了有价值的贡献,揭示了许多PET水解酶的催化机制和底物相互作用。然而,这些研究大多依赖于短PET低聚物,无法复制催化相关的相互作用以及与PET降解酶接触时发生的真实底物运动。对PET晶体(cPET)和无定形(aPET)状态的全面原子研究,以及PET降解酶在固体PET上的吸附,将极大地促进我们对PET生物降解机制的理解。在这项研究中,我们建立了cPET的大规模计算模型,包括数千个单体,并进行了分子动力学模拟,以跟踪cPET向aPET的转化。通过与实验数据的对比,验证了这些模型的正确性。然后,我们研究了IsPETase在组装PET模型上的吸附,讨论了区分两种吸附过程的主要现象,并从催化的角度对其进行了探索。本文提供的结果和计算PET模型旨在帮助开发PET废物生物降解的创新策略。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Physical Chemistry Chemical Physics
Physical Chemistry Chemical Physics 化学-物理:原子、分子和化学物理
CiteScore
5.50
自引率
9.10%
发文量
2675
审稿时长
2.0 months
期刊介绍: Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.
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