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Kairamkonda M, Gulati K, Jose S, Ghate M, Saxena H, Sharma M, Poluri KM. Assessing the role of zinc in the structure-stability-activity paradigm of bacteriophage T7 endolysin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2025; 341:126466. [PMID: 40424968 DOI: 10.1016/j.saa.2025.126466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2025] [Revised: 05/15/2025] [Accepted: 05/22/2025] [Indexed: 05/29/2025]
Abstract
Inorganic cofactors, such as zinc, contribute to enzymatic reactions, protein folding, and enzyme stability. T7 endolysin or T7 lysozyme (T7L), a zinc-dependent amidase involved in the lysis of bacterial cell walls, has great potential for applications in biotechnology and medicine. The present study provides an in-depth analysis of the structure stability and catalytic features of T7L, focusing on the comparison of its Apo and Holo forms using turbidimetric assay, circular dichroism, fluorescence spectroscopy, nuclear magnetic resonance (NMR) spectroscopic methods and molecular dynamics simulations. T7L Apo and T7L Holo forms showed moderate structural differences in the secondary structure; hydrophobic exposure was observed at the tertiary level. Chemical denaturation studies indicated higher stability in T7L Holo compared to the Apo form. The pH-dependent NMR analyses implied the protective role of zinc in the Holo form at lower pH levels, down to pH 5. The turbidimetric assay further revealed the affirmative role of zinc as a cofactor for its amidase activity. Molecular dynamics simulation studies further ally with these results, demonstrating the secondary conformational stability of T7L Holo compared to the Apo form. T7L Holo exhibits dynamic interactions with the solvent water, underlining the flexible arrangements of bonds that drive the enhanced catalytic function of T7L Holo. These results provide insights into protein enzymology, emphasizing the crucial influence of cofactors on enzymatic reactions and protein stability. The distinct features of structure-stability-activity between Apo and Holo forms of T7L under various conditions pave the way for the development of strategies based on T7 endolysin to combat microbial resistance.
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Affiliation(s)
- Manikyaprabhu Kairamkonda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667 Uttarakhand, India
| | - Khushboo Gulati
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667 Uttarakhand, India
| | - Sandra Jose
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667 Uttarakhand, India
| | - Mayur Ghate
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667 Uttarakhand, India
| | - Harshi Saxena
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667 Uttarakhand, India
| | - Meenakshi Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667 Uttarakhand, India
| | - Krishna Mohan Poluri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667 Uttarakhand, India; Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667 Uttarakhand, India.
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Fang H, Gao J, Yu L, Shi P, Zhao C. Engineering Pichia pastoris for Efficient De Novo Synthesis of 2'-Fucosyllactose. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2025; 73:8555-8566. [PMID: 40152696 DOI: 10.1021/acs.jafc.5c00598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2025]
Abstract
2'-Fucosyllactose (2'-FL), the most abundant in human milk oligosaccharides (HMOs), is a nutrient of great importance. As a safe organism widely used in industries, Pichia pastoris was tested here for 2'-FL production. The de novo biosynthesis pathway of 2'-FL was constructed using genome-editing technology based on CRISPR-Cas9 with an initial titer of 1.01 g/L. Introducing N-terminal SUMO or Ub tag to FucT2 and the transporter CDT2 from Neurospora crassa into P. pastoris was found to improve 2'-FL production. Then, modular metabolic engineering was conducted to improve 2'-FL production, enhancing the GTP supply module, NADPH regeneration module, and precursor supply module. Subsequently, the key enzyme FucT2 was semirationally designed to further increase 2'-FL production. Finally, the 2'-FL production by engineered P. pastoris was scaled up to the 3 L fermenter in fed-batch mode, resulting in a titer of 22.35 g/L that is the highest by P. pastoris. The results prove the effectiveness of the metabolic engineering strategies and demonstrate that P. pastoris could be a potential chassis to produce HMOs.
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Affiliation(s)
- Hao Fang
- Center for Future Foods, Muyuan Laboratory, 110 Shangding Road, Zhengzhou 450016, Henan Province, China
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, Zhejiang, China
| | - Jialun Gao
- College of Life Sciences, Northwest A&F University, 22 Xinong Road, Yangling 712100, Shaanxi, China
- Biomass Energy Center for Arid and Semi-arid Lands, Northwest A&F University, 22 Xinong Road, Yangling 712100, Shaanxi, China
| | - Liang Yu
- Department of Biological Systems Engineering, Washington State University, Pullman, Washington 99164, United States
| | - Peng Shi
- College of Life Sciences, Northwest A&F University, 22 Xinong Road, Yangling 712100, Shaanxi, China
| | - Chen Zhao
- College of Life Sciences, Northwest A&F University, 22 Xinong Road, Yangling 712100, Shaanxi, China
- Biomass Energy Center for Arid and Semi-arid Lands, Northwest A&F University, 22 Xinong Road, Yangling 712100, Shaanxi, China
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Li G, Yi S, Wang H, Qiu H, Wang W, Gao L, Xu Q, Han B, Yin X. Salidroside production through cascade biocatalysis with a thermostability-enhanced UDP-glycosyltransferase. Int J Biol Macromol 2025; 299:140261. [PMID: 39855494 DOI: 10.1016/j.ijbiomac.2025.140261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2024] [Revised: 12/24/2024] [Accepted: 01/21/2025] [Indexed: 01/27/2025]
Abstract
Salidroside is a phenylpropanoid glycoside with wide applications in the food, pharmaceutical, and cosmetic industries; however, the plant genus Rhodiola, the natural source of salidroside, has slow growth and limited distribution. In this study, we designed a novel six-enzyme biocatalytic cascade for the efficient production of salidroside, utilizing cost-effective bio-based L-Tyrosine as the starting material. A preliminary analysis revealed that the poor thermostability of the Bacillus licheniformis UDP-glycosyltransferase (EC 2.4.1.384) BlYjiC M6 is a bottleneck in the cascade. Therefore, a combined computational strategy was used to engineer it and finally obtained a mutant TSM6 (T304V/G307A/N309W/F123W/T344V/D271G) with a 134-fold longer half-life at 40 °C and a 13 °C higher Tmapp compared to M6. The integration of TSM6 into the cascade improved salidroside productivity significantly, while reducing residual intermediates. After further optimization, the whole-cell biocatalytic cascade achieved a high salidroside titer of 12.8 g·L-1 in a 5 L bioreactor, giving a productivity of 0.53 g·L-1·h-1. This study provides a green and efficient biosynthetic process for salidroside production and highlights the potential of enzyme engineering to enhance the biocatalytic cascade.
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Affiliation(s)
- Guosi Li
- Traditional Chinese Medicine Institute of Anhui Dabie Mountain, Generic Technology Research Center for Anhui Traditional Chinese Medicine Industry, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu'an 237012, Anhui, China
| | - Shanyong Yi
- Traditional Chinese Medicine Institute of Anhui Dabie Mountain, Generic Technology Research Center for Anhui Traditional Chinese Medicine Industry, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu'an 237012, Anhui, China
| | - Haijiao Wang
- Key State Laboratory of Plant Diversity and Specialty Crops, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Hulin Qiu
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519080, China
| | - Wei Wang
- Traditional Chinese Medicine Institute of Anhui Dabie Mountain, Generic Technology Research Center for Anhui Traditional Chinese Medicine Industry, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu'an 237012, Anhui, China
| | - Leilei Gao
- Traditional Chinese Medicine Institute of Anhui Dabie Mountain, Generic Technology Research Center for Anhui Traditional Chinese Medicine Industry, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu'an 237012, Anhui, China
| | - Qilin Xu
- Traditional Chinese Medicine Institute of Anhui Dabie Mountain, Generic Technology Research Center for Anhui Traditional Chinese Medicine Industry, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu'an 237012, Anhui, China
| | - Bangxing Han
- Traditional Chinese Medicine Institute of Anhui Dabie Mountain, Generic Technology Research Center for Anhui Traditional Chinese Medicine Industry, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu'an 237012, Anhui, China.
| | - Xinjian Yin
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519080, China.
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Li Y, Jiang L, Liu Y, Lin Y, Li S, Xu C, Xian M. Design Strategy of PepNzymes-SH for an Emerging Catalyst with Serine Hydrolase-Like Functionality. ACS APPLIED MATERIALS & INTERFACES 2025; 17:8821-8835. [PMID: 39874419 DOI: 10.1021/acsami.4c19978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2025]
Abstract
Serine hydrolases, as a class of green catalysts with hydrolytic and dehydrating activities, hold significant application value in the fields of biosynthesis and organic synthesis. However, practical applications face numerous challenges, including maintaining enzyme stability and managing usage costs. PepNzymes-SH, an emerging green catalytic material with enzyme-like activity, overcomes the operational limitations of natural enzymes and holds great promise as a substitute for hydrolases. Unfortunately, a systematic review of the design strategies for PepNzymes-SH is currently lacking. The core significance of this report lies in providing researchers with a comprehensive understanding and theoretical guidance through the summarization and performance evaluation of different design strategies of PepNzymes-SH. This review summarizes strategies for simulating and enhancing the stability of serine hydrolase active sites, oxyanion holes, and hydrophobic environmental structures. By comparing their catalytic activities, we assess the performance changes brought about by different strategies. Furthermore, the applications of PepNzymes-SH in the chemical, biomedicine, and environmental fields are also discussed.
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Affiliation(s)
- Yunfei Li
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Long Jiang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Yaojie Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Yu Lin
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Shuhua Li
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Chao Xu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 101408, China
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5
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Nana Teukam YG, Zipoli F, Laino T, Criscuolo E, Grisoni F, Manica M. Integrating genetic algorithms and language models for enhanced enzyme design. Brief Bioinform 2024; 26:bbae675. [PMID: 39780486 PMCID: PMC11711099 DOI: 10.1093/bib/bbae675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/24/2024] [Accepted: 12/13/2024] [Indexed: 01/11/2025] Open
Abstract
Enzymes are molecular machines optimized by nature to allow otherwise impossible chemical processes to occur. Their design is a challenging task due to the complexity of the protein space and the intricate relationships between sequence, structure, and function. Recently, large language models (LLMs) have emerged as powerful tools for modeling and analyzing biological sequences, but their application to protein design is limited by the high cardinality of the protein space. This study introduces a framework that combines LLMs with genetic algorithms (GAs) to optimize enzymes. LLMs are trained on a large dataset of protein sequences to learn relationships between amino acid residues linked to structure and function. This knowledge is then leveraged by GAs to efficiently search for sequences with improved catalytic performance. We focused on two optimization tasks: improving the feasibility of biochemical reactions and increasing their turnover rate. Systematic evaluations on 105 biocatalytic reactions demonstrated that the LLM-GA framework generated mutants outperforming the wild-type enzymes in terms of feasibility in 90% of the instances. Further in-depth evaluation of seven reactions reveals the power of this methodology to make "the best of both worlds" and create mutants with structural features and flexibility comparable with the wild types. Our approach advances the state-of-the-art computational design of biocatalysts, ultimately opening opportunities for more sustainable chemical processes.
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Affiliation(s)
- Yves Gaetan Nana Teukam
- IBM Research Europe, Säumerstrasse 4, CH-8803 Rüschlikon, Switzerland
- Institute for Complex Molecular Systems and Department of Biomedical Engineering, Eindhoven University of Technology, 5612 AZ Eindhoven, the Netherlands
| | - Federico Zipoli
- IBM Research Europe, Säumerstrasse 4, CH-8803 Rüschlikon, Switzerland
- National Center for Competence in Research-Catalysis (NCCR-Catalysis), Switzerland
| | - Teodoro Laino
- IBM Research Europe, Säumerstrasse 4, CH-8803 Rüschlikon, Switzerland
- National Center for Competence in Research-Catalysis (NCCR-Catalysis), Switzerland
| | - Emanuele Criscuolo
- Institute for Complex Molecular Systems and Department of Biomedical Engineering, Eindhoven University of Technology, 5612 AZ Eindhoven, the Netherlands
| | - Francesca Grisoni
- Institute for Complex Molecular Systems and Department of Biomedical Engineering, Eindhoven University of Technology, 5612 AZ Eindhoven, the Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Utrecht, the Netherlands
| | - Matteo Manica
- IBM Research Europe, Säumerstrasse 4, CH-8803 Rüschlikon, Switzerland
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6
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Lister JGR, Loewen ME, Loewen MC, St-Jacques AD. Rational design of disulfide bonds to increase thermostability of Rhodococcus opacus catechol 1,2 dioxygenase. Biotechnol Bioeng 2024; 121:3389-3401. [PMID: 39091151 DOI: 10.1002/bit.28808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/25/2024] [Accepted: 07/07/2024] [Indexed: 08/04/2024]
Abstract
Catechol 1,2 dioxygenase is a versatile enzyme with several potential applications. However, due to its low thermostability, its industrial potential is not being met. In this study, the thermostability of a mesophilic catechol 1,2 dioxygenase from the species Rhodococcus opacus was enhanced via the introduction of disulphide bonds into its structure. Engineered designs (56) were obtained using computational prediction applications, with a set of hypothesized selection criteria narrowing the list to 9. Following recombinant production and purification, several of the designs demonstrated substantially improved protein thermostability. Notably, variant K96C-D278C yielded improvements including a 4.6°C increase in T50, a 725% increase in half-life, a 5.5°C increase in Tm, and a >10-fold increase in total turnover number compared to wild type. Stacking of best designs was not productive. Overall, current state-of-the-art prediction algorithms were effective for design of disulfide-thermostabilized catechol 1,2 dioxygenase.
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Affiliation(s)
- Joshua G R Lister
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Matthew E Loewen
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Michele C Loewen
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
- National Research Council of Canada, Aquatic and Crop Resources Development, Ottawa, Ontario, Canada
| | - Antony D St-Jacques
- National Research Council of Canada, Aquatic and Crop Resources Development, Ottawa, Ontario, Canada
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Konermann L, Scrosati PM. Hydrogen/Deuterium Exchange Mass Spectrometry: Fundamentals, Limitations, and Opportunities. Mol Cell Proteomics 2024; 23:100853. [PMID: 39383946 PMCID: PMC11570944 DOI: 10.1016/j.mcpro.2024.100853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 09/11/2024] [Accepted: 10/02/2024] [Indexed: 10/11/2024] Open
Abstract
Hydrogen/deuterium exchange mass spectrometry (HDX-MS) probes dynamic motions of proteins by monitoring the kinetics of backbone amide deuteration. Dynamic regions exhibit rapid HDX, while rigid segments are more protected. Current data readouts focus on qualitative comparative observations (such as "residues X to Y become more protected after protein exposure to ligand Z"). At present, it is not possible to decode HDX protection patterns in an atomistic fashion. In other words, the exact range of protein motions under a given set of conditions cannot be uncovered, leaving space for speculative interpretations. Amide back exchange is an under-appreciated problem, as the widely used (m-m0)/(m100-m0) correction method can distort HDX kinetic profiles. Future data analysis strategies require a better fundamental understanding of HDX events, going beyond the classical Linderstrøm-Lang model. Combined with experiments that offer enhanced spatial resolution and suppressed back exchange, it should become possible to uncover the exact range of motions exhibited by a protein under a given set of conditions. Such advances would provide a greatly improved understanding of protein behavior in health and disease.
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Affiliation(s)
- Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada.
| | - Pablo M Scrosati
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
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Bohley M, Leroux J. Gastrointestinal Permeation Enhancers Beyond Sodium Caprate and SNAC - What is Coming Next? ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400843. [PMID: 38884149 PMCID: PMC11434117 DOI: 10.1002/advs.202400843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/13/2024] [Indexed: 06/18/2024]
Abstract
Oral peptide delivery is trending again. Among the possible reasons are the recent approvals of two oral peptide formulations, which represent a huge stride in the field. For the first time, gastrointestinal (GI) permeation enhancers (PEs) are leveraged to overcome the main limitation of oral peptide delivery-low permeability through the intestinal epithelium. Despite some success, the application of current PEs, such as salcaprozate sodium (SNAC), sodium caprylate (C8), and sodium caprate (C10), is generally resulting in relatively low oral bioavailabilities (BAs)-even for carefully selected therapeutics. With several hundred peptide-based drugs presently in the pipeline, there is a huge unmet need for more effective PEs. Aiming to provide useful insights for the development of novel PEs, this review summarizes the biological hurdles to oral peptide delivery with special emphasis on the epithelial barrier. It describes the concepts and action modes of PEs and mentions possible new targets. It further states the benchmark that is set by current PEs, while critically assessing and evaluating emerging PEs regarding translatability, safety, and efficacy. Additionally, examples of novel PEs under preclinical and clinical evaluation and future directions are discussed.
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Affiliation(s)
- Marilena Bohley
- Institute of Pharmaceutical SciencesDepartment of Chemistry and Applied BiosciencesETH ZurichZurich8093Switzerland
| | - Jean‐Christophe Leroux
- Institute of Pharmaceutical SciencesDepartment of Chemistry and Applied BiosciencesETH ZurichZurich8093Switzerland
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Benaroya H. Mitochondria and MICOS - function and modeling. Rev Neurosci 2024; 35:503-531. [PMID: 38369708 DOI: 10.1515/revneuro-2024-0004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 01/14/2024] [Indexed: 02/20/2024]
Abstract
An extensive review is presented on mitochondrial structure and function, mitochondrial proteins, the outer and inner membranes, cristae, the role of F1FO-ATP synthase, the mitochondrial contact site and cristae organizing system (MICOS), the sorting and assembly machinery morphology and function, and phospholipids, in particular cardiolipin. Aspects of mitochondrial regulation under physiological and pathological conditions are outlined, in particular the role of dysregulated MICOS protein subunit Mic60 in Parkinson's disease, the relations between mitochondrial quality control and proteins, and mitochondria as signaling organelles. A mathematical modeling approach of cristae and MICOS using mechanical beam theory is introduced and outlined. The proposed modeling is based on the premise that an optimization framework can be used for a better understanding of critical mitochondrial function and also to better map certain experiments and clinical interventions.
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Affiliation(s)
- Haym Benaroya
- Department of Mechanical and Aerospace Engineering, Rutgers University, 98 Brett Road, Piscataway, NJ 08854, USA
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10
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Zhong C, Nidetzky B. Bottom-Up Synthesized Glucan Materials: Opportunities from Applied Biocatalysis. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2400436. [PMID: 38514194 DOI: 10.1002/adma.202400436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/05/2024] [Indexed: 03/23/2024]
Abstract
Linear d-glucans are natural polysaccharides of simple chemical structure. They are comprised of d-glucosyl units linked by a single type of glycosidic bond. Noncovalent interactions within, and between, the d-glucan chains give rise to a broad variety of macromolecular nanostructures that can assemble into crystalline-organized materials of tunable morphology. Structure design and functionalization of d-glucans for diverse material applications largely relies on top-down processing and chemical derivatization of naturally derived starting materials. The top-down approach encounters critical limitations in efficiency, selectivity, and flexibility. Bottom-up approaches of d-glucan synthesis offer different, and often more precise, ways of polymer structure control and provide means of functional diversification widely inaccessible to top-down routes of polysaccharide material processing. Here the natural and engineered enzymes (glycosyltransferases, glycoside hydrolases and phosphorylases, glycosynthases) for d-glucan polymerization are described and the use of applied biocatalysis for the bottom-up assembly of specific d-glucan structures is shown. Advanced material applications of the resulting polymeric products are further shown and their important role in the development of sustainable macromolecular materials in a bio-based circular economy is discussed.
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Affiliation(s)
- Chao Zhong
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, Graz, 8010, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, Graz, 8010, Austria
- Austrian Centre of Industrial Biotechnology (acib), Krenngasse 37, Graz, 8010, Austria
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11
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Sorgenfrei FA, Sloan JJ, Weissensteiner F, Zechner M, Mehner NA, Ellinghaus TL, Schachtschabel D, Seemayer S, Kroutil W. Solvent concentration at 50% protein unfolding may reform enzyme stability ranking and process window identification. Nat Commun 2024; 15:5420. [PMID: 38926341 PMCID: PMC11208486 DOI: 10.1038/s41467-024-49774-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 06/19/2024] [Indexed: 06/28/2024] Open
Abstract
As water miscible organic co-solvents are often required for enzyme reactions to improve e.g., the solubility of the substrate in the aqueous medium, an enzyme is required which displays high stability in the presence of this co-solvent. Consequently, it is of utmost importance to identify the most suitable enzyme or the appropriate reaction conditions. Until now, the melting temperature is used in general as a measure for stability of enzymes. The experiments here show, that the melting temperature does not correlate to the activity observed in the presence of the solvent. As an alternative parameter, the concentration of the co-solvent at the point of 50% protein unfolding at a specific temperature T in shortc U 50 T is introduced. Analyzing a set of ene reductases,c U 50 T is shown to indicate the concentration of the co-solvent where also the activity of the enzyme drops fastest. Comparing possible rankings of enzymes according to melting temperature andc U 50 T reveals a clearly diverging outcome also depending on the specific solvent used. Additionally, plots ofc U 50 versus temperature enable a fast identification of possible reaction windows to deduce tolerated solvent concentrations and temperature.
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Affiliation(s)
- Frieda A Sorgenfrei
- Austrian Centre of Industrial Biotechnology c/o University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
| | - Jeremy J Sloan
- BASF SE, Carl-Bosch-Strasse 38, 67056, Ludwigshafen, Germany
| | - Florian Weissensteiner
- Austrian Centre of Industrial Biotechnology c/o University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
- Department of Chemistry, University of Graz, NAWI Graz, Heinrichstrasse 28, 8010, Graz, Austria
| | - Marco Zechner
- Austrian Centre of Industrial Biotechnology c/o University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
| | - Niklas A Mehner
- BASF SE, Carl-Bosch-Strasse 38, 67056, Ludwigshafen, Germany
| | | | | | - Stefan Seemayer
- BASF SE, Carl-Bosch-Strasse 38, 67056, Ludwigshafen, Germany.
| | - Wolfgang Kroutil
- Austrian Centre of Industrial Biotechnology c/o University of Graz, Heinrichstrasse 28, 8010, Graz, Austria.
- Department of Chemistry, University of Graz, NAWI Graz, Heinrichstrasse 28, 8010, Graz, Austria.
- BioTechMed Graz, 8010, Graz, Austria.
- Field of Excellence BioHealth, University of Graz, 8010, Graz, Austria.
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12
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Syrén PO. Ancestral terpene cyclases: From fundamental science to applications in biosynthesis. Methods Enzymol 2024; 699:311-341. [PMID: 38942509 DOI: 10.1016/bs.mie.2024.04.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Terpenes constitute one of the largest family of natural products with potent applications as renewable platform chemicals and medicines. The low activity, selectivity and stability displayed by terpene biosynthetic machineries can constitute an obstacle towards achieving expedient biosynthesis of terpenoids in processes that adhere to the 12 principles of green chemistry. Accordingly, engineering of terpene synthase enzymes is a prerequisite for industrial biotechnology applications, but obstructed by their complex catalysis that depend on reactive carbocationic intermediates that are prone to undergo bifurcation mechanisms. Rational redesign of terpene synthases can be tedious and requires high-resolution structural information, which is not always available. Furthermore, it has proven difficult to link sequence space of terpene synthase enzymes to specific product profiles. Herein, the author shows how ancestral sequence reconstruction (ASR) can favorably be used as a protein engineering tool in the redesign of terpene synthases without the need of a structure, and without excessive screening. A detailed workflow of ASR is presented along with associated limitations, with a focus on applying this methodology on terpene synthases. From selected examples of both class I and II enzymes, the author advocates that ancestral terpene cyclases constitute valuable assets to shed light on terpene-synthase catalysis and in enabling accelerated biosynthesis.
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Affiliation(s)
- Per-Olof Syrén
- School of Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden; School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
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13
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Nikolaev A, Kuzmin A, Markeeva E, Kuznetsova E, Ryzhykau YL, Semenov O, Anuchina A, Remeeva A, Gushchin I. Reengineering of a flavin-binding fluorescent protein using ProteinMPNN. Protein Sci 2024; 33:e4958. [PMID: 38501498 PMCID: PMC10949330 DOI: 10.1002/pro.4958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/12/2024] [Accepted: 02/18/2024] [Indexed: 03/20/2024]
Abstract
Recent advances in machine learning techniques have led to development of a number of protein design and engineering approaches. One of them, ProteinMPNN, predicts an amino acid sequence that would fold and match user-defined backbone structure. Its performance was previously tested for proteins composed of standard amino acids, as well as for peptide- and protein-binding proteins. In this short report, we test whether ProteinMPNN can be used to reengineer a non-proteinaceous ligand-binding protein, flavin-based fluorescent protein CagFbFP. We fixed the native backbone conformation and the identity of 20 amino acids interacting with the chromophore (flavin mononucleotide, FMN) while letting ProteinMPNN predict the rest of the sequence. The software package suggested replacing 36-48 out of the remaining 86 amino acids so that the resulting sequences are 55%-66% identical to the original one. The three designs that we tested experimentally displayed different expression levels, yet all were able to bind FMN and displayed fluorescence, thermal stability, and other properties similar to those of CagFbFP. Our results demonstrate that ProteinMPNN can be used to generate diverging unnatural variants of fluorescent proteins, and, more generally, to reengineer proteins without losing their ligand-binding capabilities.
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Affiliation(s)
- Andrey Nikolaev
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Alexander Kuzmin
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Elena Markeeva
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Elizaveta Kuznetsova
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Yury L. Ryzhykau
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
- Frank Laboratory of Neutron PhysicsJoint Institute for Nuclear ResearchDubnaRussia
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Arina Anuchina
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
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14
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Ng YK, Konermann L. Mechanism of Protein Aggregation Inhibition by Arginine: Blockage of Anionic Side Chains Favors Unproductive Encounter Complexes. J Am Chem Soc 2024; 146:8394-8406. [PMID: 38477601 DOI: 10.1021/jacs.3c14180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Aggregation refers to the assembly of proteins into nonphysiological higher order structures. While amyloid has been studied extensively, much less is known about amorphous aggregation, a process that interferes with protein expression and storage. Free arginine (Arg+) is a widely used aggregation inhibitor, but its mechanism remains elusive. Focusing on myoglobin (Mb), we recently applied atomistic molecular dynamics (MD) simulations for gaining detailed insights into amorphous aggregation (Ng J. Phys. Chem. B 2021, 125, 13099). Building on that approach, the current work for the first time demonstrates that MD simulations can directly elucidate aggregation inhibition mechanisms. Comparative simulations with and without Arg+ reproduced the experimental finding that Arg+ significantly decreased the Mb aggregation propensity. Our data reveal that, without Arg+, protein-protein encounter complexes readily form salt bridges and hydrophobic contacts, culminating in firmly linked dimeric aggregation nuclei. Arg+ promotes the dissociation of encounter complexes. These "unproductive" encounter complexes are favored because Arg+ binding to D- and E- lowers the tendency of these anionic residues to form interprotein salt bridges. Side chain blockage is mediated largely by the guanidinium group of Arg+, which binds carboxylates through H-bond-reinforced ionic contacts. Our MD data revealed Arg+ self-association into a dynamic quasi-infinite network, but we found no evidence that this self-association is important for protein aggregation inhibition. Instead, aggregation inhibition by Arg+ is similar to that mediated by free guanidinium ions. The computational strategy used here should be suitable for the rational design of aggregation inhibitors with enhanced potency.
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Affiliation(s)
- Yuen Ki Ng
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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15
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Zhao Y, Chen K, Yang H, Wang Y, Liao X. Semirational Design Based on Consensus Sequences to Balance the Enzyme Activity-Stability Trade-Off. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:6454-6462. [PMID: 38477968 DOI: 10.1021/acs.jafc.3c08620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
In this study, the phenomenon of the stability-activity trade-off, which is increasingly recognized in enzyme engineering, was explored. Typically, enhanced stability in enzymes correlates with diminished activity. Utilizing Rosa roxburghii copper-zinc superoxide dismutase (RrCuZnSOD) as a model, single-site mutations were introduced based on a semirational design derived from consensus sequences. The initial set of mutants was selected based on activity, followed by combinatorial mutation. This approach yielded two double-site mutants, D25/A115T (18,688 ± 206 U/mg) and A115T/S135P (18,095 ± 1556 U/mg), exhibiting superior enzymatic properties due to additive and synergistic effects. These mutants demonstrated increased half-lives (T1/2) at 80 °C by 1.2- and 1.6-fold, respectively, and their melting temperatures (Tm) rose by 3.4 and 2.5 °C, respectively, without any loss in activity relative to the wild type. Via an integration of structural analysis and molecular dynamics simulations, we elucidated the underlying mechanism facilitating the concurrent enhancement of both thermostability and enzymatic activity.
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Affiliation(s)
- Yang Zhao
- National Engineering Research Center for Fruit & Vegetable Processing, Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-Thermal Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Sichuan Advanced Agricultural and Industrial Institute, China Agricultural University, Chengdu 611400, China
| | - Kun Chen
- National Engineering Research Center for Fruit & Vegetable Processing, Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-Thermal Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Haixia Yang
- National Engineering Research Center for Fruit & Vegetable Processing, Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-Thermal Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yongtao Wang
- National Engineering Research Center for Fruit & Vegetable Processing, Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-Thermal Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xiaojun Liao
- National Engineering Research Center for Fruit & Vegetable Processing, Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-Thermal Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
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16
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Zhu T, Sun J, Pang H, Wu B. Computational Enzyme Redesign Enhances Tolerance to Denaturants for Peptide C-Terminal Amidation. JACS AU 2024; 4:788-797. [PMID: 38425901 PMCID: PMC10900485 DOI: 10.1021/jacsau.3c00792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 03/02/2024]
Abstract
The escalating demand for biocatalysts in pharmaceutical and biochemical applications underscores the critical imperative to enhance enzyme activity and durability under high denaturant concentrations. Nevertheless, the development of a practical computational redesign protocol for improving enzyme tolerance to denaturants is challenging due to the limitations of relying solely on model-driven approaches to adequately capture denaturant-enzyme interactions. In this study, we introduce an enzyme redesign strategy termed GRAPE_DA, which integrates multiple data-driven and model-driven computational methods to mitigate the sampling biases inherent in a single approach and comprehensively predict beneficial mutations on both the protein surface and backbone. To illustrate the methodology's effectiveness, we applied it to engineer a peptidylamidoglycolate lyase, resulting in a variant exhibiting up to a 24-fold increase in peptide C-terminal amidation activity under 2.5 M guanidine hydrochloride. We anticipate that this integrated engineering strategy will facilitate the development of enzymatic peptide synthesis and functionalization under denaturing conditions and highlight the role of engineering surface residues in governing protein stability.
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Affiliation(s)
- Tong Zhu
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinyuan Sun
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hua Pang
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bian Wu
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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17
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Nam Y, Nguyen DL, Hoang T, Kim B, Lee JH, Do H. Engineered ice-binding protein (FfIBP) shows increased stability and resistance to thermal and chemical denaturation compared to the wildtype. Sci Rep 2024; 14:3234. [PMID: 38331970 PMCID: PMC10853241 DOI: 10.1038/s41598-024-53864-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/06/2024] [Indexed: 02/10/2024] Open
Abstract
Many polar organisms produce antifreeze proteins (AFPs) and ice-binding proteins (IBPs) to protect themselves from ice formation. As IBPs protect cells and organisms, the potential of IBPs as natural or biological cryoprotective agents (CPAs) for the cryopreservation of animal cells, such as oocytes and sperm, has been explored to increase the recovery rate after freezing-thawing. However, only a few IBPs have shown success in cryopreservation, possibly because of the presence of protein denaturants, such as dimethyl sulfoxide, alcohols, or ethylene glycol, in freezing buffer conditions, rendering the IBPs inactive. Therefore, we investigated the thermal and chemical stability of FfIBP isolated from Antarctic bacteria to assess its suitability as a protein-based impermeable cryoprotectant. A molecular dynamics (MD) simulation identified and generated stability-enhanced mutants (FfIBP_CC1). The results indicated that FfIBP_CC1 displayed enhanced resistance to denaturation at elevated temperatures and chemical concentrations, compared to wildtype FfIBP, and was functional in known CPAs while retaining ice-binding properties. Given that FfIBP shares an overall structure similar to DUF3494 IBPs, which are recognized as the most widespread IBP family, these findings provide important structural information on thermal and chemical stability, which could potentially be applied to other DUF3494 IBPs for future protein engineering.
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Affiliation(s)
- Yewon Nam
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Dieu Linh Nguyen
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Trang Hoang
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Bogeun Kim
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea.
- Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea.
| | - Hackwon Do
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea.
- Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea.
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18
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Pijning T, Vujičić‐Žagar A, van der Laan J, de Jong RM, Ramirez‐Palacios C, Vente A, Edens L, Dijkstra BW. Structural and time-resolved mechanistic investigations of protein hydrolysis by the acidic proline-specific endoprotease from Aspergillus niger. Protein Sci 2024; 33:e4856. [PMID: 38059672 PMCID: PMC10731622 DOI: 10.1002/pro.4856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 11/16/2023] [Accepted: 12/04/2023] [Indexed: 12/08/2023]
Abstract
Proline-specific endoproteases have been successfully used in, for example, the in-situ degradation of gluten, the hydrolysis of bitter peptides, the reduction of haze during beer production, and the generation of peptides for mass spectroscopy and proteomics applications. Here we present the crystal structure of the extracellular proline-specific endoprotease from Aspergillus niger (AnPEP), a member of the S28 peptidase family with rarely observed true proline-specific endoprotease activity. Family S28 proteases have a conventional Ser-Asp-His catalytic triad, but their oxyanion-stabilizing hole shows a glutamic acid, an amino acid not previously observed in this role. Since these enzymes have an acidic pH optimum, the presence of a glutamic acid in the oxyanion hole may confine their activity to an acidic pH. Yet, considering the presence of the conventional catalytic triad, it is remarkable that the A. niger enzyme remains active down to pH 1.5. The determination of the primary cleavage site of cytochrome c along with molecular dynamics-assisted docking studies indicate that the active site pocket of AnPEP can accommodate a reverse turn of approximately 12 amino acids with proline at the S1 specificity pocket. Comparison with the structures of two S28-proline-specific exopeptidases reveals not only a more spacious active site cavity but also the absence of any putative binding sites for amino- and carboxyl-terminal residues as observed in the exopeptidases, explaining AnPEP's observed endoprotease activity.
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Affiliation(s)
- Tjaard Pijning
- Biomolecular X‐ray Crystallography, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenGroningenThe Netherlands
| | - Andreja Vujičić‐Žagar
- Biomolecular X‐ray Crystallography, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenGroningenThe Netherlands
| | | | | | | | - Andre Vente
- Taste, Texture and HealthDSM‐FirmenichDelftThe Netherlands
| | - Luppo Edens
- Taste, Texture and HealthDSM‐FirmenichDelftThe Netherlands
| | - Bauke W. Dijkstra
- Biomolecular X‐ray Crystallography, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenGroningenThe Netherlands
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19
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Wang LY, Tang H, Zhao JQ, Wang MN, Xue YP, Zheng YG. Correlation Analysis of Key Residue Sites between Computational-Aided Design Thermostability d-Amino Acid Oxidase and Ancestral Enzymes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:20177-20186. [PMID: 38064545 DOI: 10.1021/acs.jafc.3c06865] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The d-amino acid oxidase (DAAO) from Rhodotorula taiwanensis has proven to have great potential for applications due to its excellent catalytic kinetic parameters. However, its poor thermal stability has limited its performance in biocatalysis. Herein, starting from the variant SHVG of RtwDAAO, this study employed a comprehensive computational design approach for protein stability engineering, resulting in positive substitutions at specific sites (A43S, T45M, C234L, E195Y). The generated variant combination, SHVG/SMLY, exhibited a significant synergistic effect, leading to an extension of the half-life and Tmapp. The ancestral sequence reconstruction revealed the conservation of the variant sites. The association of the variant sites with the highly stable ancestral enzyme was further explored. After determining the contribution of the variant sites to thermal stability, it was applied to other homologous sequences and validated. Molecular dynamics simulations indicated that the increased hydrophobicity of the variant SHVG/SMLY was a key factor for the increased stability, with strengthened intersubunit interactions playing an important role. In addition, the physical properties of the amino acids themselves were identified as crucial factors for thermal stability generality in homologous enzymes, which is important for the rapid acquisition of a series of stable enzymes.
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Affiliation(s)
- Liu-Yu Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Heng Tang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Jin-Qiao Zhao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Meng-Nan Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, P. R. China
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20
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Musil M, Jezik A, Horackova J, Borko S, Kabourek P, Damborsky J, Bednar D. FireProt 2.0: web-based platform for the fully automated design of thermostable proteins. Brief Bioinform 2023; 25:bbad425. [PMID: 38018911 PMCID: PMC10685400 DOI: 10.1093/bib/bbad425] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/25/2023] [Accepted: 11/01/2023] [Indexed: 11/30/2023] Open
Abstract
Thermostable proteins find their use in numerous biomedical and biotechnological applications. However, the computational design of stable proteins often results in single-point mutations with a limited effect on protein stability. However, the construction of stable multiple-point mutants can prove difficult due to the possibility of antagonistic effects between individual mutations. FireProt protocol enables the automated computational design of highly stable multiple-point mutants. FireProt 2.0 builds on top of the previously published FireProt web, retaining the original functionality and expanding it with several new stabilization strategies. FireProt 2.0 integrates the AlphaFold database and the homology modeling for structure prediction, enabling calculations starting from a sequence. Multiple-point designs are constructed using the Bron-Kerbosch algorithm minimizing the antagonistic effect between the individual mutations. Users can newly limit the FireProt calculation to a set of user-defined mutations, run a saturation mutagenesis of the whole protein or select rigidifying mutations based on B-factors. Evolution-based back-to-consensus strategy is complemented by ancestral sequence reconstruction. FireProt 2.0 is significantly faster and a reworked graphical user interface broadens the tool's availability even to users with older hardware. FireProt 2.0 is freely available at http://loschmidt.chemi.muni.cz/fireprotweb.
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Affiliation(s)
- Milos Musil
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic
- Department of Information Systems, Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic
- International Clinical Research Centre, St. Anne’s University Hospital Brno, Brno, Czech Republic
| | - Andrej Jezik
- Department of Information Systems, Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic
| | - Jana Horackova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic
| | - Simeon Borko
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic
- Department of Information Systems, Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic
- International Clinical Research Centre, St. Anne’s University Hospital Brno, Brno, Czech Republic
| | - Petr Kabourek
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic
- International Clinical Research Centre, St. Anne’s University Hospital Brno, Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic
- International Clinical Research Centre, St. Anne’s University Hospital Brno, Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic
- International Clinical Research Centre, St. Anne’s University Hospital Brno, Brno, Czech Republic
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21
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Ma Z, Mu K, Zhu J, Xiao M, Wang L, Jiang X. Molecular dynamics simulations identify the topological weak spots of a protease CN2S8A. J Mol Graph Model 2023; 124:108571. [PMID: 37487372 DOI: 10.1016/j.jmgm.2023.108571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/06/2023] [Accepted: 07/19/2023] [Indexed: 07/26/2023]
Abstract
Thermophilic enzymes are highly desired in industrial applications due to their efficient catalytic activity at high temperature. However, most enzymes exhibit inferior thermostability and it remains challenging to identify the optimal sites for designing mutations to improve protein stability. To tackle this issue, we integrated topological analysis and all-atom molecular dynamics simulations to efficiently pinpoint the thermally-unstable regions in protein structures. Using a protease CN2S8A as the model, we analyzed the intramolecular hydrogen bonding interactions between adjacent secondary structure elements, and then identified the topological weak spots of CN2S8A where weak hydrogen bonding interactions were formed. To examine the role of these sites in protein structural stability, we designed three virtual mutations at different weak spots and characterized the effects of these mutations on the structural properties of CN2S8A. The results showed that all three mutations increased the protein structural stability. In conclusion, these findings provide a novel method to identify the topological weak spots of proteins, with implications in the rational design of biocatalysts with superior thermostability.
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Affiliation(s)
- Zhenyu Ma
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China
| | - Kaijie Mu
- Biomedicine Discovery Institute, Monash University, Melbourne, 3500, Australia
| | - Jingyi Zhu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Min Xiao
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xukai Jiang
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China.
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22
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Sardiña-Peña AJ, Mesa-Ramos L, Iglesias-Figueroa BF, Ballinas-Casarrubias L, Siqueiros-Cendón TS, Espinoza-Sánchez EA, Flores-Holguín NR, Arévalo-Gallegos S, Rascón-Cruz Q. Analyzing Current Trends and Possible Strategies to Improve Sucrose Isomerases' Thermostability. Int J Mol Sci 2023; 24:14513. [PMID: 37833959 PMCID: PMC10572972 DOI: 10.3390/ijms241914513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/10/2023] [Accepted: 09/10/2023] [Indexed: 10/15/2023] Open
Abstract
Due to their ability to produce isomaltulose, sucrose isomerases are enzymes that have caught the attention of researchers and entrepreneurs since the 1950s. However, their low activity and stability at temperatures above 40 °C have been a bottleneck for their industrial application. Specifically, the instability of these enzymes has been a challenge when it comes to their use for the synthesis and manufacturing of chemicals on a practical scale. This is because industrial processes often require biocatalysts that can withstand harsh reaction conditions, like high temperatures. Since the 1980s, there have been significant advancements in the thermal stabilization engineering of enzymes. Based on the literature from the past few decades and the latest achievements in protein engineering, this article systematically describes the strategies used to enhance the thermal stability of sucrose isomerases. Additionally, from a theoretical perspective, we discuss other potential mechanisms that could be used for this purpose.
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Affiliation(s)
- Amado Javier Sardiña-Peña
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
| | - Liber Mesa-Ramos
- Laboratorio de Microbiología III, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico;
| | - Blanca Flor Iglesias-Figueroa
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
| | - Lourdes Ballinas-Casarrubias
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
| | - Tania Samanta Siqueiros-Cendón
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
| | - Edward Alexander Espinoza-Sánchez
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
| | - Norma Rosario Flores-Holguín
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua 31136, Mexico;
| | - Sigifredo Arévalo-Gallegos
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
| | - Quintín Rascón-Cruz
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
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23
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Nie C, Zou Y, Liao S, Gao Q, Li Q. Peptides as carriers of active ingredients: A review. Curr Res Food Sci 2023; 7:100592. [PMID: 37766891 PMCID: PMC10519830 DOI: 10.1016/j.crfs.2023.100592] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/20/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Bioactive compounds are highly valuable in the fields of food and medicine, but their application is limited due to easy deterioration after oral or skin administration. In recent years, the use of peptides as delivery systems for bioactive compounds has been intensively researched because of their special physicochemical characteristics. Peptides can be assembled using various preparation methods and can form several composite materials such as hydrogels, micelles, emulsions and particles. The composite material properties are determined by peptides, bioactive compounds and the construction methods employed. Herein, this paper provides a comprehensive review of the peptides used for active ingredients delivery, fabrication methods for creating delivery systems, structures, targeting characteristics, functional activities and mechanism of delivery systems, as well as their absorption and metabolism, which provided theoretical basis and reference for further research and development of functional composites.
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Affiliation(s)
- Congyi Nie
- Guangdong Academy of Agricultural Sciences, Sericultural & Agri-Food Research Institute/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou, 510610, China
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510640, China
| | - Yuxiao Zou
- Guangdong Academy of Agricultural Sciences, Sericultural & Agri-Food Research Institute/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou, 510610, China
| | - Sentai Liao
- Guangdong Academy of Agricultural Sciences, Sericultural & Agri-Food Research Institute/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou, 510610, China
| | - Qunyu Gao
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510640, China
| | - Qian Li
- Guangdong Academy of Agricultural Sciences, Sericultural & Agri-Food Research Institute/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou, 510610, China
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24
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Jing B, Li J, Guo K, Zeng L, Sui J, Zhang Z, Wang Z, Jin H, Sun J, Xue Z, Zhao Q, Wan W, Dong X. Solvatochromic sensors detect proteome aggregation in stressed liver tissues with hepatic cancer and cirrhosis. J Mater Chem B 2023; 11:7654-7662. [PMID: 37464917 DOI: 10.1039/d3tb00984j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Protein misfolding and aggregation involve complex cellular processes with clinical implications in various diseases. However, the detection of aggregated proteomes without defined 3-D structures in a complex biological milieu is challenging. This study utilizes chromone scaffold-based environment-sensitive fluorophores P1 and P2 to detect misfolded and aggregated proteome in stressed liver cells and the liver tissues diseased patients. The reported crystallization induced emission probes (P1 and P2) exhibit both polarity and viscosity sensitivity, with emission intensity and wavelength linearly correlated to viscosity and polarity. Meanwhile, P1 and P2 selectively and generally fluoresce upon binding to various aggregated proteins. In hepatic cells, P2 outperforms P1 in detecting stress-induced global proteome aggregation. In mouse liver tissue upon drug-induced injury, the fluorescence intensity of P2 correlated with the severity of liver injury, serving as an earlier indicator for liver stress prior to ALT/AST increase. The quantification of emission wavelength reveals lower micro-environmental polarity in liver-injury tissue. In patient-derived tissues with hepatic cancer and cirrhosis, P1 and P2 also report on the presence of aggregated proteome. Together, the reported solvatochromic proteome aggregation sensors can detect hepatic proteome aggregation and analyze its local polarity in cultured cell lines, animal model tissues, and human clinical samples.
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Affiliation(s)
- Biao Jing
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.
| | - Junpeng Li
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.
| | - Kun Guo
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
| | - Lianggang Zeng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.
| | - Jidong Sui
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
| | - Zhenduo Zhang
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.
| | - Zhiming Wang
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.
| | - Hao Jin
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.
| | - Jialu Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.
| | - Zhao Xue
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
| | - Qi Zhao
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.
| | - Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.
| | - Xuepeng Dong
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China.
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25
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Jia Y, Fernandez A, Sampath J. PEGylation of Insulin and Lysozyme To Stabilize against Thermal Denaturation: A Molecular Dynamics Simulation Study. J Phys Chem B 2023; 127:6856-6866. [PMID: 37498538 DOI: 10.1021/acs.jpcb.3c01289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Biologic drugs or "biologics" (proteins derived from living organisms) are one of the fastest-growing classes of FDA-approved therapeutics. These compounds are often fragile and require conjugation to polymers for stabilization, with many proteins too ephemeral for therapeutic use. During storage or administration, proteins tend to unravel and lose their secondary structure due to changes in solution temperature, pH, and other external stressors. To enhance their lifetime, protein drugs currently in the market are conjugated with polyethylene glycol (PEG), owing to its ability to increase the stability, solubility, and pharmacokinetics of protein drugs. Here, we perform all-atom molecular dynamics simulations to study the unfolding process of egg-white lysozyme and insulin at elevated temperatures. We test the validity of two force fields─CHARMM36 and Amber ff99SB-ILDN─in the unfolding process. By calculating global and local properties, we capture residues that deteriorate first─these are the "weak links" in the proteins. Next, we conjugate both proteins with PEG and find that PEG preserves the native structure of the proteins at elevated temperatures by blocking water molecules from entering the hydrophobic core, thereby causing the secondary structure to stabilize.
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Affiliation(s)
- Yinhao Jia
- Department of Chemical Engineering, University of Florida, Gainesville, Florida 32611, United States
| | - Adam Fernandez
- Department of Chemical Engineering, University of Florida, Gainesville, Florida 32611, United States
| | - Janani Sampath
- Department of Chemical Engineering, University of Florida, Gainesville, Florida 32611, United States
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26
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Wang M, Zhang Z, Jing B, Dong X, Guo K, Deng J, Wang Z, Wan W, Jin W, Gao Z, Liu Y. Tailoring the Amphiphilicity of Fluorescent Protein Chromophores to Detect Intracellular Proteome Aggregation in Diverse Biological Samples. Anal Chem 2023; 95:11751-11760. [PMID: 37506028 DOI: 10.1021/acs.analchem.3c01903] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
The formation of amorphous misfolded and aggregated proteins is a hallmark of proteome stress in diseased cells. Given its lack of defined targeting sites, the rational design of intracellular proteome aggregation sensors has been challenging. Herein, we modulate the amphiphilicity of fluorescent protein chromophores to enable selective detection of aggregated proteins in different biological samples, including recombinant proteins, stressed live cells, intoxicated mouse liver tissue, and human hepatocellular carcinoma tissue. By tuning the number of hydroxyl groups, we optimize the selectivity of fluorescent protein chromophores toward aggregated proteins in these biological samples. In recombinant protein applications, the most hydrophobic P0 (cLogP = 5.28) offers the highest fold change (FC = 31.6), sensitivity (LLOD = 0.1 μM), and brightness (Φ = 0.20) upon binding to aggregated proteins. In contrast, P4 of balanced amphiphilicity (cLogP = 2.32) is required for selective detection of proteome stresses in live cells. In mouse and human liver histology tissues, hydrophobic P1 exhibits the best performance in staining the aggregated proteome. Overall, the amphiphilicity of fluorescent chromophores governs the sensor's performance by matching the diverse nature of different biological samples. Together with common extracellular amyloid sensors (e.g., Thioflavin T), these sensors developed herein for intracellular amorphous aggregation complement the toolbox to study protein aggregation.
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Affiliation(s)
- Mengdie Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenduo Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- The Second Hospital of Dalian Medical University, Dalian 116023, China
| | - Biao Jing
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- The Second Hospital of Dalian Medical University, Dalian 116023, China
| | - Xuepeng Dong
- The Second Hospital of Dalian Medical University, Dalian 116023, China
| | - Kun Guo
- The Second Hospital of Dalian Medical University, Dalian 116023, China
| | - Jintai Deng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- The Second Hospital of Dalian Medical University, Dalian 116023, China
| | - Zhiming Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- The Second Hospital of Dalian Medical University, Dalian 116023, China
| | - Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Wenhan Jin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Zhenming Gao
- The Second Hospital of Dalian Medical University, Dalian 116023, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
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27
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Huang Y, Wang T, Chen Y, Lin H, Chen D. Amyloid hexapeptide prevent dental caries by antibiofilm formation. J Dent 2023; 135:104596. [PMID: 37353107 DOI: 10.1016/j.jdent.2023.104596] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/11/2023] [Accepted: 06/19/2023] [Indexed: 06/25/2023] Open
Abstract
OBJECTIVES Biofilm formed by cariogenic microbes is the direct cause of dental caries, therefore, prevention of dental caries should be anti-biofilm-based. Previously, we found the amyloid hexapeptides efficiently inhibited biofilm formation by aggregating into amyloid fibrils agglutinating microbes. This study aimed to select the most stable amyloid hexapeptide GIDLKI (GI6) and study its anti-caries effect. METHODS Biofilms of multi-species bacteria, derived from mixed saliva, were cultured to evaluate the anti-biofilm formation effect of GI6. And then, the primary cariogenic bacterium Streptococcus mutans (S.mutans) was cultured in BHI with various pH, gradient concentrations of sucrose, glucose, and calcium ions to evaluate the anti-biofilm formation effects of GI6. Then models of human enamel block caries and twenty male SPF-SD rat caries induced by S. mutans biofilm were constructed, and confocal laser scanning microscopy, scanning electron microscopy, and micro-computed tomography were applied to investigate the anti-biofilm formation, anti-caries effects and use safety of GI6. RESULTS GI6 could inhibit the multi-species bacteria biofilm formation and remained effective in anti-biofilm activity against S. mutans in environments closely related to caries. GI6 suppressed S. mutans biofilm formation and thus prevented or alleviated the development of caries in human tooth blocks and rat teeth. GI6 did not affect the intestinal flora, serum biochemical parameters, and the pathological changes of various organs. CONCLUSIONS Amyloid hexapeptides, including but not limited to GI6, are novel effective anti-caries agents that can be used to prevent dental caries safely. CLINICAL SIGNIFICANCE This study explored the anti-biofilm formation and anti-caries effect of GI6 in vitro, highlighting the anti-biofilm formation therapy for dental caries and setting a foundation for the practical application of GI6 for the treatment of dental caries.
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Affiliation(s)
- Yiyi Huang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University. Guangdong Provincial Key Laboratory of Stomatology. Guangzhou, Guangdong, 510000, China
| | - Tingyu Wang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University. Guangdong Provincial Key Laboratory of Stomatology. Guangzhou, Guangdong, 510000, China
| | - Yucong Chen
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University. Guangdong Provincial Key Laboratory of Stomatology. Guangzhou, Guangdong, 510000, China
| | - Huancai Lin
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University. Guangdong Provincial Key Laboratory of Stomatology. Guangzhou, Guangdong, 510000, China.
| | - Dongru Chen
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University. Guangdong Provincial Key Laboratory of Stomatology. Guangzhou, Guangdong, 510000, China.
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28
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Haidar Y, Konermann L. Effects of Hydrogen/Deuterium Exchange on Protein Stability in Solution and in the Gas Phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37314114 DOI: 10.1021/jasms.3c00130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Mass spectrometry (MS)-based techniques are widely used for probing protein structure and dynamics in solution. H/D exchange (HDX)-MS is one of the most common approaches in this context. HDX is often considered to be a "benign" labeling method, in that it does not perturb protein behavior in solution. However, several studies have reported that D2O pushes unfolding equilibria toward the native state. The origin, and even the existence of this protein stabilization remain controversial. Here we conducted thermal unfolding assays in solution to confirm that deuterated proteins in D2O are more stable, with 2-4 K higher melting temperatures than unlabeled proteins in H2O. Previous studies tentatively attributed this phenomenon to strengthened H-bonds after deuteration, an effect that may arise from the lower zero-point vibrational energy of the deuterated species. Specifically, it was proposed that strengthened water-water bonds (W···W) in D2O lower the solubility of nonpolar side chains. The current work takes a broader view by noting that protein stability in solution also depends on water-protein (W···P) and protein-protein (P···P) H-bonds. To help unravel these contributions, we performed collision-induced unfolding (CIU) experiments on gaseous proteins generated by native electrospray ionization. CIU profiles of deuterated and unlabeled proteins were indistinguishable, implying that P···P contacts are insensitive to deuteration. Thus, protein stabilization in D2O is attributable to solvent effects, rather than alterations of intraprotein H-bonds. Strengthening of W···W contacts represents one possible explanation, but the stabilizing effect of D2O can also originate from weakened W···P bonds. Future work will be required to elucidate which of these two scenarios is correct, or if both contribute to protein stabilization in D2O. In any case, the often-repeated adage that "D-bonds are more stable than H-bonds" does not apply to intramolecular contacts in native proteins.
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Affiliation(s)
- Yousef Haidar
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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29
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Sardiña-Peña AJ, Ballinas-Casarrubias L, Siqueiros-Cendón TS, Espinoza-Sánchez EA, Flores-Holguín NR, Iglesias-Figueroa BF, Rascón-Cruz Q. Thermostability improvement of sucrose isomerase PalI NX-5: a comprehensive strategy. Biotechnol Lett 2023:10.1007/s10529-023-03388-6. [PMID: 37199887 DOI: 10.1007/s10529-023-03388-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 03/29/2023] [Accepted: 04/27/2023] [Indexed: 05/19/2023]
Abstract
OBJECTIVE To increase the thermal stability of sucrose isomerase from Erwinia rhapontici NX-5, we designed a comprehensive strategy that combines different thermostabilizing elements. RESULTS We identified 19 high B value amino acid residues for site-directed mutagenesis. An in silico evaluation of the influence of post-translational modifications on the thermostability was also carried out. The sucrose isomerase variants were expressed in Pichia pastoris X33. Thus, for the first time, we report the expression and characterization of glycosylated sucrose isomerases. The designed mutants K174Q, L202E and K174Q/L202E, showed an increase in their optimal temperature of 5 °C, while their half-lives increased 2.21, 1.73 and 2.89 times, respectively. The mutants showed an increase in activity of 20.3% up to 25.3%. The Km values for the K174Q, L202E, and K174Q/L202E mutants decreased by 5.1%, 7.9%, and 9.4%, respectively; furthermore, the catalytic efficiency increased by up to 16%. CONCLUSIONS With the comprehensive strategy followed, we successfully obtain engineered mutants more suitable for industrial applications than their counterparts: native (this research) and wild-type from E. rhapontici NX-5, without compromising the catalytic activity of the molecule.
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Affiliation(s)
- A J Sardiña-Peña
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, C. P. 31125, Chihuahua, México
| | - L Ballinas-Casarrubias
- Laboratorio de Química Analítica III, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, C. P. 31125, Chihuahua, México
| | - T S Siqueiros-Cendón
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, C. P. 31125, Chihuahua, México
| | - E A Espinoza-Sánchez
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, C. P. 31125, Chihuahua, México
| | - N R Flores-Holguín
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua, México
| | - B F Iglesias-Figueroa
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, C. P. 31125, Chihuahua, México
| | - Q Rascón-Cruz
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, C. P. 31125, Chihuahua, México.
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30
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Priyadarshi A, Devi HM, Swaminathan R. Disruption of Spatial Proximities among Charged Groups in Equilibrium-Denatured States of Proteins Tracked Using Protein Charge Transfer Spectra. Biochemistry 2023. [PMID: 37162303 DOI: 10.1021/acs.biochem.3c00006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The absorption and luminescence originating from protein charge transfer spectra (ProCharTS) depend on the proximity between multiple charged groups in a protein. This makes ProCharTS absorbance/luminescence intensity a sensitive probe for detecting changes in the protein structure, which alter the proximity among charged groups in the protein. In this work, ProCharTS absorbance of charge-rich proteins like human serum albumin (HSA), α3C, and α3W was used to monitor structural changes upon chemical denaturant-induced protein unfolding under equilibrium conditions. The denaturation midpoints were estimated using nonlinear regression analysis. For HSA, absorbance at 325 and 340 nm estimated the GdnHCl-induced denaturation midpoints to be 0.80 and 0.61 M, respectively. A similar analysis of α3C and α3W ProCharTS absorbance yielded denaturation midpoints of 0.88 and 0.86 M at 325 nm and 0.96 and 0.66 M at 340 nm, respectively. A previously reported molten globule-like state in the GdnHCl-induced HSA unfolding pathway was detected by the increase in HSA ProCharTS absorbance at 0.5 M GdnHCl. To validate the above results, protein unfolding was additionally monitored using conventional methods like circular dichroism (CD), Trp, and dansyl fluorescence. Our results suggest that disruption of charged amino acid sidechain contacts as revealed by ProCharTS occurs at lower denaturant concentrations compared to the loss of secondary/folded structure monitored by CD and fluorescence. Further, HSA ProCharTS absorbance at 315-340 nm revealed that tertiary contacts among charged residues were disrupted at lower GdnHCl concentrations compared to sequence adjacent contacts. Our data underscore the utility of ProCharTS as a novel label-free tool to track unfolding in charge-rich proteins.
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Affiliation(s)
- Anurag Priyadarshi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
| | - Himanshi Maniram Devi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
| | - Rajaram Swaminathan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
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31
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Das D, Yadav P, Mitra S, Ainavarapu SRK. Metal-binding and circular permutation-dependent thermodynamic and kinetic stability of azurin. Proteins 2023; 91:634-648. [PMID: 36511110 DOI: 10.1002/prot.26454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 11/18/2022] [Accepted: 11/25/2022] [Indexed: 12/15/2022]
Abstract
Native topology is known to determine the folding kinetics and the energy landscape of proteins. Furthermore, the circular permutation (CP) of proteins alters the order of the secondary structure connectivity while retaining the three-dimensional structure, making it an elegant and powerful approach to altering native topology. Previous studies elucidated the influence of CP in proteins with different folds such as Greek key β-barrel, β-sandwich, β-α-β, and all α-Greek key. CP mainly affects the protein stability and unfolding kinetics, while folding kinetics remains mostly unaltered. However, the effect of CP on metalloproteins is yet to be elaborately studied. The active site of metalloproteins poses an additional complexity in studying protein folding. Here, we investigate a CP variant (cpN42) of azurin-in both metal-free and metal-bound (holo) forms. As observed earlier in other proteins, apo-forms of wild-type (WT) and cpN42 fold with similar rates. In contrast, zinc-binding accelerates the folding of WT but decelerates the folding of cpN42. On zinc-binding, the spontaneous folding rate of WT increases by >250 times that of cpN42, which is unprecedented and the highest for any CP to date. On the other hand, zinc-binding reduces the spontaneous unfolding rate of cpN42 by ~100 times, making the WT and CP azurins unfold at similar rates. Our study demonstrates metal binding as a novel way to modulate the unfolding and folding rates of CPs compared to their WT counterparts. We hope our study increases the understanding of the effect of CP on the folding mechanism and energy landscape of metalloproteins.
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Affiliation(s)
- Debanjana Das
- Department of Chemical Sciences, Dr. Homi Bhabha Road, Colaba, Tata Institute of Fundamental Research, Mumbai, India
| | - Priya Yadav
- Department of Chemical Sciences, Dr. Homi Bhabha Road, Colaba, Tata Institute of Fundamental Research, Mumbai, India
| | - Soumyajit Mitra
- Department of Chemical Sciences, Dr. Homi Bhabha Road, Colaba, Tata Institute of Fundamental Research, Mumbai, India
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences, Dr. Homi Bhabha Road, Colaba, Tata Institute of Fundamental Research, Mumbai, India
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32
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Li B, Sun Y, Zhu X, Qian S, Pu J, Guo Y, Wu H, Zhang L, Xin Y. Aggregation Interface and Rigid Spots Sustain the Stable Framework of a Thermophilic N-Demethylase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:5614-5629. [PMID: 37000489 DOI: 10.1021/acs.jafc.3c00877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Enzymes from thermophilic microorganisms usually show high thermostability, which is of great potential in industrial application; to understand the structural logic of these enzymes is helpful for the construction of robust biocatalysts. In this study, based on the crystal structure of an N-demethylase─TrSOX─with outstanding thermostability from Thermomicrobium roseum, substitutions were introduced on the aggregation interface and rigid spots to reduce the aggregation ratio and the rigidity. Four substitutions on the aggregation interface─V162S, M308S, F170S, and V306S─considerably reduced the thermostability and slightly enhanced the catalytic efficiency. In addition, the thermostable framework was considerably disrupted in several multiple P → G substitutions in several local motifs (P129G/P134G, P237G/P259G, and P259G/P276G). These structural fluctuations were in good accordance with whole-structure or partial root-mean-square deviation, radius of gyration H-bonds, and solvent-accessible surface area values in molecular dynamics simulation. Furthermore, these key spots were introduced into an unstable homolog from Bacillus sp., resulting in a dramatical increase in the half-life at 60 °C from <10 to 1440 min. These results could help understand the natural stable framework of thermophilic enzymes, which could be references for the construction of robust enzymes in industrial applications.
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Affiliation(s)
- Bingjie Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Yuqian Sun
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Xinyi Zhu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Siyu Qian
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Jiayang Pu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Yuwen Guo
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Haobo Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Liang Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Research Center for Cereal Fermentation and Food Bio Manufacturing, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Yu Xin
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Research Center for Cereal Fermentation and Food Bio Manufacturing, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
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33
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Rosace A, Bennett A, Oeller M, Mortensen MM, Sakhnini L, Lorenzen N, Poulsen C, Sormanni P. Automated optimisation of solubility and conformational stability of antibodies and proteins. Nat Commun 2023; 14:1937. [PMID: 37024501 PMCID: PMC10079162 DOI: 10.1038/s41467-023-37668-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 03/24/2023] [Indexed: 04/08/2023] Open
Abstract
Biologics, such as antibodies and enzymes, are crucial in research, biotechnology, diagnostics, and therapeutics. Often, biologics with suitable functionality are discovered, but their development is impeded by developability issues. Stability and solubility are key biophysical traits underpinning developability potential, as they determine aggregation, correlate with production yield and poly-specificity, and are essential to access parenteral and oral delivery. While advances for the optimisation of individual traits have been made, the co-optimization of multiple traits remains highly problematic and time-consuming, as mutations that improve one property often negatively impact others. In this work, we introduce a fully automated computational strategy for the simultaneous optimisation of conformational stability and solubility, which we experimentally validate on six antibodies, including two approved therapeutics. Our results on 42 designs demonstrate that the computational procedure is highly effective at improving developability potential, while not affecting antigen-binding. We make the method available as a webserver at www-cohsoftware.ch.cam.ac.uk.
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Affiliation(s)
- Angelo Rosace
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield road, CB2 1EW, Cambridge, UK
- Master in Bioinformatics for Health Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Anja Bennett
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield road, CB2 1EW, Cambridge, UK
- Department of Mammalian Expression, Global Research Technologies, Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Måløv, Denmark
- BRIC, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Marc Oeller
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield road, CB2 1EW, Cambridge, UK
| | - Mie M Mortensen
- Department of Purification Technologies, Global Research Technologies, Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Måløv, Denmark
- Faculty of Engineering and Science, Department of Biotechnology, Chemistry and Environmental Engineering, University of Aalborg, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Laila Sakhnini
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield road, CB2 1EW, Cambridge, UK
- Department of Biophysics and Injectable Formulation 2, Global Research Technologies, Novo Nordisk A/S, Måløv, 2760, Denmark
| | - Nikolai Lorenzen
- Department of Biophysics and Injectable Formulation 2, Global Research Technologies, Novo Nordisk A/S, Måløv, 2760, Denmark
| | - Christian Poulsen
- Department of Mammalian Expression, Global Research Technologies, Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Måløv, Denmark
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield road, CB2 1EW, Cambridge, UK.
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34
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Chen Q, Xiao H, Li ZP, Pei XQ, Yang W, Liu Y, Wu ZL. Stereo-complementary epoxidation of 4-vinyl-2,3-dihydrobenzofuran using mutants of SeStyA with enhanced stability and enantioselectivity. MOLECULAR CATALYSIS 2023. [DOI: 10.1016/j.mcat.2023.113055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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35
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Hecko S, Schiefer A, Badenhorst CPS, Fink MJ, Mihovilovic MD, Bornscheuer UT, Rudroff F. Enlightening the Path to Protein Engineering: Chemoselective Turn-On Probes for High-Throughput Screening of Enzymatic Activity. Chem Rev 2023; 123:2832-2901. [PMID: 36853077 PMCID: PMC10037340 DOI: 10.1021/acs.chemrev.2c00304] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Many successful stories in enzyme engineering are based on the creation of randomized diversity in large mutant libraries, containing millions to billions of enzyme variants. Methods that enabled their evaluation with high throughput are dominated by spectroscopic techniques due to their high speed and sensitivity. A large proportion of studies relies on fluorogenic substrates that mimic the chemical properties of the target or coupled enzymatic assays with an optical read-out that assesses the desired catalytic efficiency indirectly. The most reliable hits, however, are achieved by screening for conversions of the starting material to the desired product. For this purpose, functional group assays offer a general approach to achieve a fast, optical read-out. They use the chemoselectivity, differences in electronic and steric properties of various functional groups, to reduce the number of false-positive results and the analytical noise stemming from enzymatic background activities. This review summarizes the developments and use of functional group probes for chemoselective derivatizations, with a clear focus on screening for enzymatic activity in protein engineering.
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Affiliation(s)
- Sebastian Hecko
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Astrid Schiefer
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Christoffel P S Badenhorst
- Institute of Biochemistry, Dept. of Biotechnology & Enzyme Catalysis, University of Greifswald, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
| | - Michael J Fink
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
| | - Marko D Mihovilovic
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Uwe T Bornscheuer
- Institute of Biochemistry, Dept. of Biotechnology & Enzyme Catalysis, University of Greifswald, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
| | - Florian Rudroff
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
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36
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Lee JM, Park BS, Oh MK. Production of 2’-Fucosyllactose using ⍺1,2-fucosyltransferase from a GRAS bacterial strain. Enzyme Microb Technol 2023; 167:110232. [PMID: 37028251 DOI: 10.1016/j.enzmictec.2023.110232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/25/2023] [Accepted: 03/26/2023] [Indexed: 03/30/2023]
Abstract
2'-Fucosyllactose (2'-FL) is a major oligosaccharide found in human breast milk. It is produced from GDP-L-fucose and D-lactose by ⍺1,2-fucosyltransferase (⍺1,2-fucT), but the enzyme has been identified mostly in pathogens. In this study, an ⍺1,2-fucT was isolated from a Generally Recognized as Safe (GRAS) Bacillus megaterium strain. The enzyme was successfully expressed in metabolically-engineered Escherichia coli. Furthermore, replacement of non-conserved amino acid residues with conserved ones in the protein led to an increase in the rate of 2'-FL production. As a result, fed-batch fermentation of E. coli produced 30 g/L of 2'-FL from glucose and lactose. Thus, the overproduction of 2'-FL using a novel enzyme from a GRAS bacteria strain was successfully demonstrated.
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Affiliation(s)
- Jun-Min Lee
- Department of Chemical & Biological Engineering, Korea University, Seoul 136-763, South Korea
| | - Bu-Soo Park
- Department of Chemical & Biological Engineering, Korea University, Seoul 136-763, South Korea
| | - Min-Kyu Oh
- Department of Chemical & Biological Engineering, Korea University, Seoul 136-763, South Korea.
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37
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Zhu W, Qin L, Xu Y, Lu H, Wu Q, Li W, Zhang C, Li X. Three Molecular Modification Strategies to Improve the Thermostability of Xylanase XynA from Streptomyces rameus L2001. Foods 2023; 12:foods12040879. [PMID: 36832954 PMCID: PMC9957083 DOI: 10.3390/foods12040879] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/07/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
Glycoside hydrolase family 11 (GH11) xylanases are the preferred candidates for the production of functional oligosaccharides. However, the low thermostability of natural GH11 xylanases limits their industrial applications. In this study, we investigated the following three strategies to modify the thermostability of xylanase XynA from Streptomyces rameus L2001 mutation to reduce surface entropy, intramolecular disulfide bond construction, and molecular cyclization. Changes in the thermostability of XynA mutants were analyzed using molecular simulations. All mutants showed improved thermostability and catalytic efficiency compared with XynA, except for molecular cyclization. The residual activities of high-entropy amino acid-replacement mutants Q24A and K104A increased from 18.70% to more than 41.23% when kept at 65 °C for 30 min. The catalytic efficiencies of Q24A and K143A increased to 129.99 and 92.26 mL/s/mg, respectively, compared with XynA (62.97 mL/s/mg) when using beechwood xylan as the substrate. The mutant enzyme with disulfide bonds formed between Val3 and Thr30 increased the t1/260 °C by 13.33-fold and the catalytic efficiency by 1.80-fold compared with the wild-type XynA. The high thermostabilities and hydrolytic activities of XynA mutants will be useful for enzymatic production of functional xylo-oligosaccharides.
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Affiliation(s)
- Weijia Zhu
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Liqin Qin
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Youqiang Xu
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Hongyun Lu
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Qiuhua Wu
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Weiwei Li
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber of Commerce, Beijing 100048, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Chengnan Zhang
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber of Commerce, Beijing 100048, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Xiuting Li
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber of Commerce, Beijing 100048, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing 100048, China
- Correspondence:
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38
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Yang T, Villois A, Kunka A, Grigolato F, Arosio P, Prokop Z, deMello A, Stavrakis S. Droplet-Based Microfluidic Temperature-Jump Platform for the Rapid Assessment of Biomolecular Kinetics. Anal Chem 2022; 94:16675-16684. [DOI: 10.1021/acs.analchem.2c03009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Tianjin Yang
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, 8093Zürich, Switzerland
| | - Alessia Villois
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, 8093Zürich, Switzerland
| | - Antonín Kunka
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91Brno, Czech Republic
| | - Fulvio Grigolato
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, 8093Zürich, Switzerland
| | - Paolo Arosio
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, 8093Zürich, Switzerland
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00Brno, Czech Republic
| | - Andrew deMello
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, 8093Zürich, Switzerland
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, 8093Zürich, Switzerland
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39
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Niu C, Fu J, Zheng F, Liu C, Wang J, Li Q. Enhanced acidic stability of a Bacillus 1,3-1,4-β-glucanase through pH-based molecular dynamics simulation for efficient application in brewing industry. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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40
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Tajoddin NN, Konermann L. Structural Dynamics of a Thermally Stressed Monoclonal Antibody Characterized by Temperature-Dependent H/D Exchange Mass Spectrometry. Anal Chem 2022; 94:15499-15509. [DOI: 10.1021/acs.analchem.2c03931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nastaran N. Tajoddin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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41
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Enhanced thermal stability of the β-galactosidase BgaB from Bacillus circulans by cyclization mediated via SpyTag/SpyCatcher interaction and its use in galacto-oligosaccharides synthesis. Int J Biol Macromol 2022; 222:2341-2352. [DOI: 10.1016/j.ijbiomac.2022.10.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/22/2022] [Accepted: 10/04/2022] [Indexed: 11/05/2022]
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42
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Oliveira MLG, Castelli EC, Veiga‐Castelli LC, Pereira ALE, Marcorin L, Carratto TMT, Souza AS, Andrade HS, Simões AL, Donadi EA, Courtin D, Sabbagh A, Giuliatti S, Mendes‐Junior CT. Genetic diversity of the
LILRB1
and
LILRB2
coding regions in an admixed Brazilian population sample. HLA 2022; 100:325-348. [DOI: 10.1111/tan.14725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/02/2022] [Accepted: 06/24/2022] [Indexed: 11/27/2022]
Affiliation(s)
| | - Erick C. Castelli
- Pathology Department, School of Medicine São Paulo State University (UNESP) Botucatu State of São Paulo Brazil
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine São Paulo State University (UNESP) Botucatu State of São Paulo Brazil
| | - Luciana C. Veiga‐Castelli
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Alison Luis E. Pereira
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Letícia Marcorin
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Thássia M. T. Carratto
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Andreia S. Souza
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine São Paulo State University (UNESP) Botucatu State of São Paulo Brazil
| | - Heloisa S. Andrade
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine São Paulo State University (UNESP) Botucatu State of São Paulo Brazil
| | - Aguinaldo L. Simões
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Eduardo A. Donadi
- Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | | | | | - Silvana Giuliatti
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Celso Teixeira Mendes‐Junior
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
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43
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Qing R, Hao S, Smorodina E, Jin D, Zalevsky A, Zhang S. Protein Design: From the Aspect of Water Solubility and Stability. Chem Rev 2022; 122:14085-14179. [PMID: 35921495 PMCID: PMC9523718 DOI: 10.1021/acs.chemrev.1c00757] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 12/13/2022]
Abstract
Water solubility and structural stability are key merits for proteins defined by the primary sequence and 3D-conformation. Their manipulation represents important aspects of the protein design field that relies on the accurate placement of amino acids and molecular interactions, guided by underlying physiochemical principles. Emulated designer proteins with well-defined properties both fuel the knowledge-base for more precise computational design models and are used in various biomedical and nanotechnological applications. The continuous developments in protein science, increasing computing power, new algorithms, and characterization techniques provide sophisticated toolkits for solubility design beyond guess work. In this review, we summarize recent advances in the protein design field with respect to water solubility and structural stability. After introducing fundamental design rules, we discuss the transmembrane protein solubilization and de novo transmembrane protein design. Traditional strategies to enhance protein solubility and structural stability are introduced. The designs of stable protein complexes and high-order assemblies are covered. Computational methodologies behind these endeavors, including structure prediction programs, machine learning algorithms, and specialty software dedicated to the evaluation of protein solubility and aggregation, are discussed. The findings and opportunities for Cryo-EM are presented. This review provides an overview of significant progress and prospects in accurate protein design for solubility and stability.
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Affiliation(s)
- Rui Qing
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The
David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Shilei Hao
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Key
Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China
| | - Eva Smorodina
- Department
of Immunology, University of Oslo and Oslo
University Hospital, Oslo 0424, Norway
| | - David Jin
- Avalon GloboCare
Corp., Freehold, New Jersey 07728, United States
| | - Arthur Zalevsky
- Laboratory
of Bioinformatics Approaches in Combinatorial Chemistry and Biology, Shemyakin−Ovchinnikov Institute of Bioorganic
Chemistry RAS, Moscow 117997, Russia
| | - Shuguang Zhang
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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44
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Zhu H, Tian F, Sun L, Zhu Y, Qiu Q, Dai L. Computational Design of Extraordinarily Stable Peptide Structures through Side-Chain-Locked Knots. J Phys Chem Lett 2022; 13:7741-7748. [PMID: 35969173 DOI: 10.1021/acs.jpclett.2c02385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Extraordinarily stable protein and peptide structures are critically demanded in many applications. Typical approaches to enhance protein and peptide stability are strengthening certain interactions. Here, we develop a very different approach: stabilizing peptide structures through side-chain-locked knots. More specifically, a peptide core consists of a knot, which is prevented from unknotting and unfolding by large side chains of amino acids at knot boundaries. These side chains impose free energy barriers for unknotting. The free energy barriers are quantified using all-atom and coarse-grained simulations. The barriers become infinitely high for large side chains and tight knot cores, resulting in stable peptide structures, which never unfold unless one chemical bond is broken. The extraordinary stability is essentially kinetic stability. Our new approach lifts the thermodynamic restriction in designing peptide structures, provides extra freedom in selecting sequence and structural motifs that are thermodynamically unstable, and should expand the functionality of peptides. This work also provides a bottom-up understanding of how knotting enhances protein stability.
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Affiliation(s)
- Haoqi Zhu
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
| | - Fujia Tian
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
| | - Liang Sun
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
| | - Yongjian Zhu
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
| | - Qiyuan Qiu
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
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45
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Bolivar JM, Woodley JM, Fernandez-Lafuente R. Is enzyme immobilization a mature discipline? Some critical considerations to capitalize on the benefits of immobilization. Chem Soc Rev 2022; 51:6251-6290. [PMID: 35838107 DOI: 10.1039/d2cs00083k] [Citation(s) in RCA: 180] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Enzyme immobilization has been developing since the 1960s and although many industrial biocatalytic processes use the technology to improve enzyme performance, still today we are far from full exploitation of the field. One clear reason is that many evaluate immobilization based on only a few experiments that are not always well-designed. In contrast to many other reviews on the subject, here we highlight the pitfalls of using incorrectly designed immobilization protocols and explain why in many cases sub-optimal results are obtained. We also describe solutions to overcome these challenges and come to the conclusion that recent developments in material science, bioprocess engineering and protein science continue to open new opportunities for the future. In this way, enzyme immobilization, far from being a mature discipline, remains as a subject of high interest and where intense research is still necessary to take full advantage of the possibilities.
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Affiliation(s)
- Juan M Bolivar
- FQPIMA group, Chemical and Materials Engineering Department, Faculty of Chemical Sciences, Complutense University of Madrid, Madrid, 28040, Spain
| | - John M Woodley
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, 2800 Kgs Lyngby, Denmark.
| | - Roberto Fernandez-Lafuente
- Departamento de Biocatálisis. ICP-CSIC, C/Marie Curie 2, Campus UAM-CSIC Cantoblanco, Madrid 28049, Spain. .,Center of Excellence in Bionanoscience Research, External Scientific Advisory Academic, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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46
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Ruan Y, Zhang R, Xu Y. Directed evolution of maltogenic amylase from Bacillus licheniformis R-53: Enhancing activity and thermostability improves bread quality and extends shelf life. Food Chem 2022; 381:132222. [DOI: 10.1016/j.foodchem.2022.132222] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 01/06/2022] [Accepted: 01/20/2022] [Indexed: 11/24/2022]
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Hueting DA, Vanga SR, Syrén PO. Thermoadaptation in an Ancestral Diterpene Cyclase by Altered Loop Stability. J Phys Chem B 2022; 126:3809-3821. [PMID: 35583961 PMCID: PMC9169049 DOI: 10.1021/acs.jpcb.1c10605] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Thermostability is
the key to maintain the structural integrity
and catalytic activity of enzymes in industrial biotechnological processes,
such as terpene cyclase-mediated generation of medicines, chiral synthons,
and fine chemicals. However, affording a large increase in the thermostability
of enzymes through site-directed protein engineering techniques can
constitute a challenge. In this paper, we used ancestral sequence
reconstruction to create a hyperstable variant of the ent-copalyl diphosphate synthase PtmT2, a terpene cyclase involved in
the assembly of antibiotics. Molecular dynamics simulations on the
μs timescale were performed to shed light on possible molecular
mechanisms contributing to activity at an elevated temperature and
the large 40 °C increase in melting temperature observed for
an ancestral variant of PtmT2. In silico analysis
revealed key differences in the flexibility of a loop capping the
active site, between extant and ancestral proteins. For the modern
enzyme, the loop collapses into the active site at elevated temperatures,
thus preventing biocatalysis, whereas the loop remains in a productive
conformation both at ambient and high temperatures in the ancestral
variant. Restoring a Pro loop residue introduced in the ancestral
variant to the corresponding Gly observed in the extant protein led
to reduced catalytic activity at high temperatures, with only moderate
effects on the melting temperature, supporting the importance of the
flexibility of the capping loop in thermoadaptation. Conversely, the
inverse Gly to Pro loop mutation in the modern enzyme resulted in
a 3-fold increase in the catalytic rate. Despite an overall decrease
in maximal activity of ancestor compared to wild type, its increased
thermostability provides a robust backbone amenable for further enzyme
engineering. Our work cements the importance of loops in enzyme catalysis
and provides a molecular mechanism contributing to thermoadaptation
in an ancestral enzyme.
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Affiliation(s)
- David A Hueting
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm 114 28, Sweden.,School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm 114 28, Sweden
| | - Sudarsana R Vanga
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm 114 28, Sweden.,School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm 114 28, Sweden
| | - Per-Olof Syrén
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm 114 28, Sweden.,School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm 114 28, Sweden
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48
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Thermostabilizing ketoreductase ChKRED20 by consensus mutagenesis at dimeric interfaces. Enzyme Microb Technol 2022; 158:110052. [DOI: 10.1016/j.enzmictec.2022.110052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/15/2022] [Accepted: 04/17/2022] [Indexed: 11/19/2022]
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49
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Zhao Y, Zhao L, Zhang W, Rao L, Wang Y, Liao X. Production of a Novel Superoxide Dismutase by Escherichia coli and Pichia pastoris and Analysis of the Thermal Stability of the Enzyme. Front Nutr 2022; 9:850824. [PMID: 35356736 PMCID: PMC8959677 DOI: 10.3389/fnut.2022.850824] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 01/31/2022] [Indexed: 12/25/2022] Open
Abstract
Previously, a new copper-zinc SOD (CuZnSOD) isolated from chestnut rose (Rosa roxburghii) with good stability was described. In this study, the biosynthetic approach was used to create recombinant CuZnSOD. RACE PCR was also used to amplify the full-length CuZnSOD gene from chestnut rose, and the ORF segment was expressed in E. coli BL21 and P. pastoris GS115. For characterization, the enzyme was isolated in two steps in E. coli and one step in P. pastoris. The biochemical properties of the two recombinant enzymes were similar, and their optimal reaction pH and temperature were 6.0 and 50°C, respectively. According to molecular dynamics simulation, the CuZnSOD showed high stability from 70 to 90°C, and eight amino acids are important for enzyme thermal stability at high temperatures. This study set the stage for industrial manufacture by filling gaps in the link between conformational changes and the thermal stability of the new CuZnSOD.
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Affiliation(s)
- Yang Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- National Engineering Research Center for Fruit and Vegetable Processing, Beijing, China
- Key Laboratory of Fruit and Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Key Laboratory for Food Non-thermal Processing, Beijing, China
| | - Liang Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- National Engineering Research Center for Fruit and Vegetable Processing, Beijing, China
- Key Laboratory of Fruit and Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Key Laboratory for Food Non-thermal Processing, Beijing, China
| | - Weiwei Zhang
- Department of Applied Physics, China Agricultural University, Beijing, China
| | - Lei Rao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- National Engineering Research Center for Fruit and Vegetable Processing, Beijing, China
- Key Laboratory of Fruit and Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Key Laboratory for Food Non-thermal Processing, Beijing, China
| | - Yongtao Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- National Engineering Research Center for Fruit and Vegetable Processing, Beijing, China
- Key Laboratory of Fruit and Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Key Laboratory for Food Non-thermal Processing, Beijing, China
- Yongtao Wang
| | - Xiaojun Liao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- National Engineering Research Center for Fruit and Vegetable Processing, Beijing, China
- Key Laboratory of Fruit and Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Key Laboratory for Food Non-thermal Processing, Beijing, China
- *Correspondence: Xiaojun Liao
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50
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ElGamacy M. Accelerating therapeutic protein design. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 130:85-118. [PMID: 35534117 DOI: 10.1016/bs.apcsb.2022.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein structures provide for defined microenvironments that can support complex pharmacological functions, otherwise unachievable by small molecules. The advent of therapeutic proteins has thus greatly broadened the range of manageable disorders. Leveraging the knowledge and recent advances in de novo protein design methods has the prospect of revolutionizing how protein drugs are discovered and developed. This review lays out the main challenges facing therapeutic proteins discovery and development, and how present and future advancements of protein design can accelerate the protein drug pipelines.
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Affiliation(s)
- Mohammad ElGamacy
- University Hospital Tübingen, Division of Translational Oncology, Tübingen, Germany; Max Planck Institute for Biology, Tübingen, Germany.
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