In Silico Identification of Potential Sites for a Plastic-Degrading Enzyme by a Reverse Screening through the Protein Sequence Space and Molecular Dynamics Simulations

บทความในวารสาร

ผู้เขียน/บรรณาธิการ

กลุ่มสาขาการวิจัยเชิงกลยุทธ์

รายละเอียดสำหรับงานพิมพ์

รายชื่อผู้แต่ง: Charupanit, Krit; Tipmanee, Varomyalin; Sutthibutpong, Thana; Limsakul, Praopim;

ผู้เผยแพร่: MDPI

ปีที่เผยแพร่ (ค.ศ.): 2022

วารสาร: Molecules (1420-3049)

Volume number: 27

Issue number: 10

นอก: 1420-3049

eISSN: 1420-3049

URL: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85130542847&doi=10.3390%2fmolecules27103353&partnerID=40&md5=ff9f8e6907c8387aed96481b5e3c92c6

ภาษา: English-Great Britain (EN-GB)

ดูในเว็บของวิทยาศาสตร์ | ดูบนเว็บไซต์ของสำนักพิมพ์ | บทความในเว็บของวิทยาศาสตร์

บทคัดย่อ

The accumulation of polyethylene terephthalate (PET) seriously harms the environment because of its high resistance to degradation. The recent discovery of the bacteria-secreted biodegradation enzyme, PETase, sheds light on PET recycling; however, the degradation efficiency is far from practical use. Here, in silico alanine scanning mutagenesis (ASM) and site-saturation mutagenesis (SSM) were employed to construct the protein sequence space from binding energy of the PETase–PET interaction to identify the number and position of mutation sites and their appropriate side-chain properties that could improve the PETase–PET interaction. The binding mechanisms of the potential PETase variant were investigated through atomistic molecular dynamics simulations. The results show that up to two mutation sites of PETase are preferable for use in protein engineering to enhance the PETase activity, and the proper side chain property depends on the mutation sites. The predicted variants agree well with prior experimental studies. Particularly, the PETase variants with S238C or Q119F could be a potential candidate for improving PETase. Our combination of in silico ASM and SSM could serve as an alternative protocol for protein engineering because of its simplicity and reliability. In addition, our findings could lead to PETase improvement, offering an important contribution towards a sustainable future. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.

คำสำคัญ

alanine scanning mutagenesis, PETase, site-saturation mutagenesis