Cutting-Edge Perspectives on Protein and Enzyme Engineering

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Biomacromolecules: Proteins, Nucleic Acids and Carbohydrates".

Deadline for manuscript submissions: 31 October 2025 | Viewed by 847

Special Issue Editors


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Guest Editor
1. Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
2. Key Laboratory of Systems Bioengineering of the Ministry of Education, Tianjin University, Tianjin 300072, China
Interests: protein materials; industrial enzyme; cell factories; protein production

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Guest Editor
Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
Interests: enzyme evolution; machine learning; protein design; unnatural amino acids

Special Issue Information

Dear Colleagues,

Protein and enzyme engineering is the process of developing useful or valuable proteins such as protein materials, industrial enzymes, and therapy proteins. It includes technologies for engineering protein, producing protein, and purifying protein. Directed evolution has emerged as a powerful strategy to engineer various protein properties. In addition, machine learning and deep learning have developed rapidly and have been applied in protein engineering such as in protein function prediction, enzymes directed evolution, and so forth. Additionally, synthetic biology provides more maneuverability for protein design and synthesis. In the process of protein engineering, unnatural amino acids may be also included, via newer methods, such as expanded genetic code, which allows for encoding novel amino acids in genetic code. For protein production and purification, the construction of efficient cell factories, development of specific chassis cells, and separation tags are current research hotspots. This Special Issue is aimed at providing an overview of the most recent advances in the field of protein and enzyme engineering.

The journal will be accepting contributions covering potential topics including, but not limited to, the following:

  • protein material;
  • protein expression system;
  • protein separation and purification;
  • enzymes directed evolution;
  • therapy proteins engineering;
  • protein computational design;
  • machine learning used for protein engineering;
  • molecular dynamics simulations of proteins;
  • unnatural amino acids incorporation;
  • protein post-translation modification;
  • protein structures and mechanisms;

Dr. Haishan Qi
Dr. Haoran Yu
Guest Editors

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Keywords

  • protein engineering
  • protein material
  • enzyme evolution
  • therapy protein
  • protein expression
  • machine learning
  • unnatural amino acids

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Published Papers (1 paper)

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Research

13 pages, 1868 KiB  
Article
Efficient Incorporation of DOPA into Proteins Free from Competition with Endogenous Translation Termination Machinery
by Youhui Yang, Yingchen Wang, Zhaoguan Wang and Hao Qi
Biomolecules 2025, 15(3), 382; https://doi.org/10.3390/biom15030382 - 6 Mar 2025
Cited by 1 | Viewed by 592
Abstract
3,4-Dihydroxy-L-phenylalanine (DOPA) is a promising noncanonical amino acid (ncAA) that introduces novel catechol chemical features into proteins, expanding their functional potential. However, the most common approach to incorporating ncAAs into proteins relies on stop codon suppression, which is often limited by the competition [...] Read more.
3,4-Dihydroxy-L-phenylalanine (DOPA) is a promising noncanonical amino acid (ncAA) that introduces novel catechol chemical features into proteins, expanding their functional potential. However, the most common approach to incorporating ncAAs into proteins relies on stop codon suppression, which is often limited by the competition of endogenous translational termination machinery. Here, we employed a special in vitro protein expression system that facilitates the efficiency of DOPA incorporation into proteins by removing essential Class I peptide release factors through targeted degradation. In the absence of both RF1 and RF2, we successfully demonstrated DOPA incorporation at all three stop codons (TAG, TAA, and TGA). By optimizing the concentration of engineered DOPA-specific aminoacyl-tRNA synthetase (DOPARS), DOPA, and DNA template, we achieved a synthesis yield of 2.24 µg of sfGFP with 100% DOPA incorporation in a 20 μL reaction system. DOPARS exhibited a dissociation constant (Kd) of 11.7 μM for DOPA but showed no detectable binding to its native counterpart, tyrosine. Additionally, DOPA was successfully incorporated into a reverse transcriptase, which interfered with its activity. This system demonstrates a fast and efficient approach for precise DOPA incorporation into proteins, paving the way for advanced protein engineering applications. Full article
(This article belongs to the Special Issue Cutting-Edge Perspectives on Protein and Enzyme Engineering)
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