1
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Dodda SR, Hossain M, Mondal S, Das S, Khator (Jain) S, Aikat K, Mukhopadhyay SS. The S-S bridge mutation between the A2 and A4 loops (T416C-I432C) of Cel7A of Aspergillus fumigatus enhances catalytic activity and thermostability. Appl Environ Microbiol 2024; 90:e0232923. [PMID: 38440989 PMCID: PMC11022540 DOI: 10.1128/aem.02329-23] [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: 12/22/2023] [Accepted: 01/28/2024] [Indexed: 03/06/2024] Open
Abstract
Disulfide bonds are important for maintaining the structural conformation and stability of the protein. The introduction of the disulfide bond is a promising strategy to increase the thermostability of the protein. In this report, cysteine residues are introduced to form disulfide bonds in the Glycoside Hydrolase family GH 7 cellobiohydrolase (GH7 CBHs) or Cel7A of Aspergillus fumigatus. Disulfide by Design 2.0 (DbD2), an online tool is used for the detection of the mutation sites. Mutations are created (D276C-G279C; DSB1, D322C-G327C; DSB2, T416C-I432C; DSB3, G460C-S465C; DSB4) inside and outside of the peripheral loops but, not in the catalytic region. The introduction of cysteine in the A2 and A4 loop of DSB3 mutant showed higher thermostability (70% activity at 70°C), higher substrate affinity (Km = 0.081 mM) and higher catalytic activity (Kcat = 9.75 min-1; Kcat/Km = 120.37 mM min-1) compared to wild-type AfCel7A (50% activity at 70°C; Km = 0.128 mM; Kcat = 4.833 min-1; Kcat/Km = 37.75 mM min-1). The other three mutants with high B factor showed loss of thermostability and catalytic activity. Molecular dynamic simulations revealed that the mutation T416C-I432C makes the tunnel wider (DSB3: 13.6 Å; Wt: 5.3 Å) at the product exit site, giving flexibility in the entrance region or mobility of the substrate in the exit region. It may facilitate substrate entry into the catalytic tunnel and release the product faster than the wild type, whereas in other mutants, the tunnel is not prominent (DSB4), the exit is lost (DSB1), and the ligand binding site is absent (DSB2). This is the first report of the gain of function of both thermostability and enzyme activity of cellobiohydrolase Cel7A by disulfide bond engineering in the loop.IMPORTANCEBioethanol is one of the cleanest renewable energy and alternatives to fossil fuels. Cost efficient bioethanol production can be achieved through simultaneous saccharification and co-fermentation that needs active polysaccharide degrading enzymes. Cellulase enzyme complex is a crucial enzyme for second-generation bioethanol production from lignocellulosic biomass. Cellobiohydrolase (Cel7A) is an important member of this complex. In this work, we engineered (disulfide bond engineering) the Cel7A to increase its thermostability and catalytic activity which is required for its industrial application.
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Affiliation(s)
- Subba Reddy Dodda
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, West Bengal, India
| | - Musaddique Hossain
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, West Bengal, India
| | - Sudipa Mondal
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, West Bengal, India
| | - Shalini Das
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, West Bengal, India
| | - Sneha Khator (Jain)
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, West Bengal, India
| | - Kaustav Aikat
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, West Bengal, India
| | - Sudit S. Mukhopadhyay
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, West Bengal, India
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2
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Chatterjee A, Puri S, Sharma PK, Deepa PR, Chowdhury S. Nature-inspired Enzyme engineering and sustainable catalysis: biochemical clues from the world of plants and extremophiles. Front Bioeng Biotechnol 2023; 11:1229300. [PMID: 37409164 PMCID: PMC10318364 DOI: 10.3389/fbioe.2023.1229300] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 06/12/2023] [Indexed: 07/07/2023] Open
Abstract
The use of enzymes to accelerate chemical reactions for the synthesis of industrially important products is rapidly gaining popularity. Biocatalysis is an environment-friendly approach as it not only uses non-toxic, biodegradable, and renewable raw materials but also helps to reduce waste generation. In this context, enzymes from organisms living in extreme conditions (extremozymes) have been studied extensively and used in industries (food and pharmaceutical), agriculture, and molecular biology, as they are adapted to catalyze reactions withstanding harsh environmental conditions. Enzyme engineering plays a key role in integrating the structure-function insights from reference enzymes and their utilization for developing improvised catalysts. It helps to transform the enzymes to enhance their activity, stability, substrates-specificity, and substrate-versatility by suitably modifying enzyme structure, thereby creating new variants of the enzyme with improved physical and chemical properties. Here, we have illustrated the relatively less-tapped potentials of plant enzymes in general and their sub-class of extremozymes for industrial applications. Plants are exposed to a wide range of abiotic and biotic stresses due to their sessile nature, for which they have developed various mechanisms, including the production of stress-response enzymes. While extremozymes from microorganisms have been extensively studied, there are clear indications that plants and algae also produce extremophilic enzymes as their survival strategy, which may find industrial applications. Typical plant enzymes, such as ascorbate peroxidase, papain, carbonic anhydrase, glycoside hydrolases and others have been examined in this review with respect to their stress-tolerant features and further improvement via enzyme engineering. Some rare instances of plant-derived enzymes that point to greater exploration for industrial use have also been presented here. The overall implication is to utilize biochemical clues from the plant-based enzymes for robust, efficient, and substrate/reaction conditions-versatile scaffolds or reference leads for enzyme engineering.
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Affiliation(s)
| | | | | | - P. R. Deepa
- *Correspondence: P. R. Deepa, ; Shibasish Chowdhury,
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3
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Yuan Y, Shen J, Salmon S. Developing Enzyme Immobilization with Fibrous Membranes: Longevity and Characterization Considerations. MEMBRANES 2023; 13:membranes13050532. [PMID: 37233593 DOI: 10.3390/membranes13050532] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/14/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023]
Abstract
Fibrous membranes offer broad opportunities to deploy immobilized enzymes in new reactor and application designs, including multiphase continuous flow-through reactions. Enzyme immobilization is a technology strategy that simplifies the separation of otherwise soluble catalytic proteins from liquid reaction media and imparts stabilization and performance enhancement. Flexible immobilization matrices made from fibers have versatile physical attributes, such as high surface area, light weight, and controllable porosity, which give them membrane-like characteristics, while simultaneously providing good mechanical properties for creating functional filters, sensors, scaffolds, and other interface-active biocatalytic materials. This review examines immobilization strategies for enzymes on fibrous membrane-like polymeric supports involving all three fundamental mechanisms of post-immobilization, incorporation, and coating. Post-immobilization offers an infinite selection of matrix materials, but may encounter loading and durability issues, while incorporation offers longevity but has more limited material options and may present mass transfer obstacles. Coating techniques on fibrous materials at different geometric scales are a growing trend in making membranes that integrate biocatalytic functionality with versatile physical supports. Biocatalytic performance parameters and characterization techniques for immobilized enzymes are described, including several emerging techniques of special relevance for fibrous immobilized enzymes. Diverse application examples from the literature, focusing on fibrous matrices, are summarized, and biocatalyst longevity is emphasized as a critical performance parameter that needs increased attention to advance concepts from lab scale to broader utilization. This consolidation of fabrication, performance measurement, and characterization techniques, with guiding examples highlighted, is intended to inspire future innovations in enzyme immobilization with fibrous membranes and expand their uses in novel reactors and processes.
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Affiliation(s)
- Yue Yuan
- Center for Nanophase Materials and Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Fiber and Polymer Science Program, Department of Textile Engineering Chemistry & Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Jialong Shen
- Fiber and Polymer Science Program, Department of Textile Engineering Chemistry & Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Sonja Salmon
- Fiber and Polymer Science Program, Department of Textile Engineering Chemistry & Science, North Carolina State University, Raleigh, NC 27695, USA
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4
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Anderson DM, Jayanthi LP, Gosavi S, Meiering EM. Engineering the kinetic stability of a β-trefoil protein by tuning its topological complexity. Front Mol Biosci 2023; 10:1021733. [PMID: 36845544 PMCID: PMC9945329 DOI: 10.3389/fmolb.2023.1021733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 01/02/2023] [Indexed: 02/11/2023] Open
Abstract
Kinetic stability, defined as the rate of protein unfolding, is central to determining the functional lifetime of proteins, both in nature and in wide-ranging medical and biotechnological applications. Further, high kinetic stability is generally correlated with high resistance against chemical and thermal denaturation, as well as proteolytic degradation. Despite its significance, specific mechanisms governing kinetic stability remain largely unknown, and few studies address the rational design of kinetic stability. Here, we describe a method for designing protein kinetic stability that uses protein long-range order, absolute contact order, and simulated free energy barriers of unfolding to quantitatively analyze and predict unfolding kinetics. We analyze two β-trefoil proteins: hisactophilin, a quasi-three-fold symmetric natural protein with moderate stability, and ThreeFoil, a designed three-fold symmetric protein with extremely high kinetic stability. The quantitative analysis identifies marked differences in long-range interactions across the protein hydrophobic cores that partially account for the differences in kinetic stability. Swapping the core interactions of ThreeFoil into hisactophilin increases kinetic stability with close agreement between predicted and experimentally measured unfolding rates. These results demonstrate the predictive power of readily applied measures of protein topology for altering kinetic stability and recommend core engineering as a tractable target for rationally designing kinetic stability that may be widely applicable.
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Affiliation(s)
| | - Lakshmi P. Jayanthi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Elizabeth M. Meiering
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada,*Correspondence: Elizabeth M. Meiering,
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5
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Veiko VP, Antipov AN, Mordkovich NN, Okorokova NA, Safonova TN, Polyakov KM. The Thermostability of Nucleoside Phosphorylases from Prokaryotes. I. The Role of the Primary Structure of the N-terminal fragment of the Protein in the Thermostability of Uridine Phosphorylases. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822060151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
AbstractMutant uridine phosphorylase genes from Shewanella oneidensis MR-1 (S. oneidensis) were constructed by site-directed mutagenesis and strains-producers of the corresponding recombinant (F5I and F5G) proteins were obtained on the basis of Escherichia coli cells. The mutant proteins were purified and their physicochemical and enzymatic properties were studied. It was shown that the N-terminal fragment of uridine phosphorylase plays an important role in the thermal stabilization of the enzyme as a whole. The role of the aminoacid (a.a.) residue phenylalanine (F5) in the formation of thermotolerance of uridine phosphorylases from gamma-proteobacteria was revealed.
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6
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Improving Both the Thermostability and Catalytic Efficiency of Phospholipase D from Moritella sp. JT01 through Disulfide Bond Engineering Strategy. Int J Mol Sci 2022; 23:ijms231911319. [PMID: 36232620 PMCID: PMC9570233 DOI: 10.3390/ijms231911319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/11/2022] [Accepted: 09/21/2022] [Indexed: 11/21/2022] Open
Abstract
Mining of Phospholipase D (PLD) with high activity and stability has attracted strong interest for investigation. A novel PLD from marine Moritella sp. JT01 (MsPLD) was biochemically and structurally characterized in our previous study; however, the short half-life time (t1/2) under its optimum reaction temperature seriously hampered its further applications. Herein, the disulfide bond engineering strategy was applied to improve its thermostability. Compared with wild-type MsPLD, mutant S148C-T206C/D225C-A328C with the addition of two disulfide bonds exhibited a 3.1-fold t1/2 at 35 °C and a 5.7 °C increase in melting temperature (Tm). Unexpectedly, its specific activity and catalytic efficiency (kcat/Km) also increased by 22.7% and 36.5%, respectively. The enhanced activity might be attributed to an increase in the activation entropy by displacing more water molecules by the transition state. The results of molecular dynamics simulations (MD) revealed that the introduction of double disulfide bonds rigidified the global structure of the mutant, which might cause the enhanced thermostability. Finally, the synthesis capacity of the mutant to synthesize phosphatidic acid (PA) was evaluated. The conversion rate of PA reached about 80% after 6 h reaction with wild-type MsPLD but reached 78% after 2 h with mutant S148C-T206C/D225C-A328C, which significantly reduced the time needed for the reaction to reach equilibrium. The present results pave the way for further application of MsPLD in the food and pharmaceutical industries.
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7
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Hunt for α-amylase from metagenome and strategies to improve its thermostability: a systematic review. World J Microbiol Biotechnol 2022; 38:203. [PMID: 35999473 DOI: 10.1007/s11274-022-03396-0] [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: 07/19/2022] [Accepted: 08/18/2022] [Indexed: 10/15/2022]
Abstract
With the advent of green chemistry, the use of enzymes in industrial processes serves as an alternative to the conventional chemical catalysts. A high demand for sustainable processes for catalysis has brought a significant attention to hunt for novel enzymes. Among various hydrolases, the α-amylase has a gamut of biotechnological applications owing to its pivotal role in starch-hydrolysis. Industrial demand requires enzymes with thermostability and to ameliorate this crucial property, various methods such as protein engineering, directed evolution and enzyme immobilisation strategies are devised. Besides the traditional culture-dependent approach, metagenome from uncultured bacteria serves as a bountiful resource for novel genes/biocatalysts. Exploring the extreme-niches metagenome, advancements in protein engineering and biotechnology tools encourage the mining of novel α-amylase and its stable variants to tap its robust biotechnological and industrial potential. This review outlines α-amylase and its genetics, its catalytic domain architecture and mechanism of action, and various molecular methods to ameliorate its production. It aims to impart understanding on mechanisms involved in thermostability of α-amylase, cover strategies to screen novel genes from futile habitats and some molecular methods to ameliorate its properties.
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8
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Suzuki M, Date M, Kashiwagi T, Suzuki E, Yokoyama K. Rational design of a disulfide bridge increases the thermostability of microbial transglutaminase. Appl Microbiol Biotechnol 2022; 106:4553-4562. [PMID: 35729274 DOI: 10.1007/s00253-022-12024-8] [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: 02/19/2022] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 11/02/2022]
Abstract
Microbial transglutaminase (MTG) has numerous industrial applications in the food and pharmaceutical sectors. Unfortunately, the thermostability of MTG is too low to tolerate the desired conditions used in many of these commercial processes. In a previous study, we used protein engineering to improve the thermostability of MTG. Specifically, we generated a T7C/E58C mutant of MTG from Streptomyces mobaraensis that displayed enhanced resistance to thermal inactivation. In this study, a rational structure-based approach was adopted to introduce a disulfide bridge to further increase the thermostability of MTG. In all, four new mutants, each containing a novel disulfide bond, were engineered. Of these four mutants, D3C/G283C showed the most promising thermostability with a significantly higher ∆T50 (defined as the temperature of incubation at which 50% of the initial activity remains) of + 9 °C by comparison to wild-type MTG. Indeed, D3C/G283C combined enhanced thermostability with a 2.1-fold increased half-life at 65 °C compared with the wild-type enzyme. By structure-based rational design, we were able to create an MTG variant which might be useful for expanding the scope of application in food. KEY POINTS: • Microbial transglutaminase (MTG) is an enzyme used in many food applications • The applicability of MTG to various industrial processes other than the food sector is being investigated • Improvement of thermostability was confirmed for the disulfide bridge mutant D3C/G283C.
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Affiliation(s)
- Mototaka Suzuki
- Institute for Innovation, Ajinomoto Co., Inc., 1-1, Suzuki-cho, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Masayo Date
- Institute for Innovation, Ajinomoto Co., Inc., 1-1, Suzuki-cho, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Tatsuki Kashiwagi
- Institute for Innovation, Ajinomoto Co., Inc., 1-1, Suzuki-cho, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Eiichiro Suzuki
- Institute for Innovation, Ajinomoto Co., Inc., 1-1, Suzuki-cho, Kawasaki-shi, Kanagawa, 210-8681, Japan.,Kihara Memorial Yokohama Foundation for the Advancement of Life Sciences Yokohama, Bio Industry Center, 1-6 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Keiichi Yokoyama
- Institute for Innovation, Ajinomoto Co., Inc., 1-1, Suzuki-cho, Kawasaki-shi, Kanagawa, 210-8681, Japan. .,R&B Planning Department, Ajinomoto Co., Inc, Tokyo, 104-8315, Japan.
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9
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Teufl M, Zajc CU, Traxlmayr MW. Engineering Strategies to Overcome the Stability-Function Trade-Off in Proteins. ACS Synth Biol 2022; 11:1030-1039. [PMID: 35258287 PMCID: PMC8938945 DOI: 10.1021/acssynbio.1c00512] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
In addition to its
biological function, the stability of a protein
is a major determinant for its applicability. Unfortunately, engineering
proteins for improved functionality usually results in destabilization
of the protein. This so-called stability–function trade-off
can be explained by the simple fact that the generation of a novel
protein function—or the improvement of an existing one—necessitates
the insertion of mutations, i.e., deviations from
the evolutionarily optimized wild-type sequence. In fact, it was demonstrated
that gain-of-function mutations are not more destabilizing than other
random mutations. The stability–function trade-off is a universal
phenomenon during protein evolution that has been observed with completely
different types of proteins, including enzymes, antibodies, and engineered
binding scaffolds. In this review, we discuss three types of strategies
that have been successfully deployed to overcome this omnipresent
obstacle in protein engineering approaches: (i) using highly stable
parental proteins, (ii) minimizing the extent of destabilization during
functional engineering (by library optimization and/or coselection
for stability and function), and (iii) repairing damaged mutants through
stability engineering. The implementation of these strategies in protein
engineering campaigns will facilitate the efficient generation of
protein variants that are not only functional but also stable and
therefore better-suited for subsequent applications.
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Affiliation(s)
- Magdalena Teufl
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
- CD Laboratory for Next Generation CAR T Cells, 1190 Vienna, Austria
| | - Charlotte U. Zajc
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
- CD Laboratory for Next Generation CAR T Cells, 1190 Vienna, Austria
| | - Michael W. Traxlmayr
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
- CD Laboratory for Next Generation CAR T Cells, 1190 Vienna, Austria
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10
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Cao S, Li Q, Xu Y, Tang T, Ning L, Zhu B. Evolving strategies for marine enzyme engineering: recent advances on the molecular modification of alginate lyase. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:106-116. [PMID: 37073348 PMCID: PMC10077200 DOI: 10.1007/s42995-021-00122-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 09/14/2021] [Indexed: 05/03/2023]
Abstract
Alginate, an acidic polysaccharide, is formed by β-d-mannuronate (M) and α-l-guluronate (G). As a type of polysaccharide lyase, alginate lyase can efficiently degrade alginate into alginate oligosaccharides, having potential applications in the food, medicine, and agriculture fields. However, the application of alginate lyase has been limited due to its low catalytic efficiency and poor temperature stability. In recent years, various structural features of alginate lyase have been determined, resulting in modification strategies that can increase the applicability of alginate lyase, making it important to summarize and discuss the current evidence. In this review, we summarized the structural features and catalytic mechanisms of alginate lyase. Molecular modification strategies, such as rational design, directed evolution, conserved domain recombination, and non-catalytic domain truncation, are also described in detail. Lastly, the application of alginate lyase is discussed. This comprehensive summary can inform future applications of alginate lyases.
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Affiliation(s)
- Shengsheng Cao
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 China
| | - Qian Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 China
| | - Yinxiao Xu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 China
| | - Tiancheng Tang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 China
| | - Limin Ning
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023 China
| | - Benwei Zhu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 China
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11
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Cheng JH, Zhang XY, Wang Z, Zhang X, Liu SC, Song XY, Zhang YZ, Ding JM, Chen XL, Xu F. Potential of Thermolysin-like Protease A69 in Preparation of Bovine Collagen Peptides with Moisture-Retention Ability and Antioxidative Activity. Mar Drugs 2021; 19:md19120676. [PMID: 34940675 PMCID: PMC8708487 DOI: 10.3390/md19120676] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/18/2021] [Accepted: 11/25/2021] [Indexed: 12/28/2022] Open
Abstract
Bovine bone is rich in collagen and is a good material for collagen peptide preparation. Although thermolysin-like proteases (TLPs) have been applied in different fields, the potential of TLPs in preparing bioactive collagen peptides has rarely been evaluated. Here, we characterized a thermophilic TLP, A69, from a hydrothermal bacterium Anoxybacillus caldiproteolyticus 1A02591, and evaluated its potential in preparing bioactive collagen peptides. A69 showed the highest activity at 60 °C and pH 7.0. We optimized the conditions for bovine bone collagen hydrolysis and set up a process with high hydrolysis efficiency (99.4%) to prepare bovine bone collagen peptides, in which bovine bone collagen was hydrolyzed at 60 °C for 2 h with an enzyme-substrate ratio of 25 U/g. The hydrolysate contained 96.5% peptides that have a broad molecular weight distribution below 10000 Da. The hydrolysate showed good moisture-retention ability and a high hydroxyl radical (•OH) scavenging ratio of 73.2%, suggesting that the prepared collagen peptides have good antioxidative activity. Altogether, these results indicate that the thermophilic TLP A69 has promising potential in the preparation of bioactive collagen peptides, which may have potentials in cosmetics, food and pharmaceutical industries. This study lays a foundation for the high-valued utilization of bovine bone collagen.
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Affiliation(s)
- Jun-Hui Cheng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (J.-H.C.); (X.-Y.Z.); (Z.W.); (X.-Y.S.)
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China;
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xiao-Yu Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (J.-H.C.); (X.-Y.Z.); (Z.W.); (X.-Y.S.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Zhen Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (J.-H.C.); (X.-Y.Z.); (Z.W.); (X.-Y.S.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xia Zhang
- Department of Molecular Biology, Qingdao Vland Biotech Inc., Qingdao 266102, China; (X.Z.); (S.-C.L.)
| | - Shi-Cheng Liu
- Department of Molecular Biology, Qingdao Vland Biotech Inc., Qingdao 266102, China; (X.Z.); (S.-C.L.)
| | - Xiao-Yan Song
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (J.-H.C.); (X.-Y.Z.); (Z.W.); (X.-Y.S.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China;
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Jun-Mei Ding
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, China
- Correspondence: (J.-M.D.); (X.-L.C.); (F.X.)
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (J.-H.C.); (X.-Y.Z.); (Z.W.); (X.-Y.S.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Correspondence: (J.-M.D.); (X.-L.C.); (F.X.)
| | - Fei Xu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (J.-H.C.); (X.-Y.Z.); (Z.W.); (X.-Y.S.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Correspondence: (J.-M.D.); (X.-L.C.); (F.X.)
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12
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Zhang H, Zhai W, Lin L, Wang P, Xu X, Wei W, Wei D. In Silico Rational Design and Protein Engineering of Disulfide Bridges of an α‐Amylase from
Geobacillus
sp. to Improve Thermostability. STARCH-STARKE 2021. [DOI: 10.1002/star.202000274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Heng Zhang
- State Key Laboratory of Bioreactor Engineering Newworld Institute of Biotechnology East China University of Science and Technology Shanghai 200237 P. R. China
| | - Wenxin Zhai
- State Key Laboratory of Bioreactor Engineering Newworld Institute of Biotechnology East China University of Science and Technology Shanghai 200237 P. R. China
| | - Lin Lin
- Shanghai University of Medicine and Health Sciences Shanghai 200093 P. R. China
- Research Laboratory for Functional Nanomaterial National Engineering Research Center for Nanotechnology Shanghai 200241 P. R. China
| | - Ping Wang
- Weigao Shanghai R&D Center Shanghai 201203 P. R. China
| | - Xiangyang Xu
- Zaozhuang jie nuo enzyme co. ltd Zaozhuang 277100 P. R. China
| | - Wei Wei
- State Key Laboratory of Bioreactor Engineering Newworld Institute of Biotechnology East China University of Science and Technology Shanghai 200237 P. R. China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering Newworld Institute of Biotechnology East China University of Science and Technology Shanghai 200237 P. R. China
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Hydrophobicity, amphilicity, and flexibility: Relation between molecular protein properties and the macroscopic effects of surface activity. J Biotechnol 2021; 334:11-25. [PMID: 34015375 DOI: 10.1016/j.jbiotec.2021.05.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 04/16/2021] [Accepted: 05/05/2021] [Indexed: 11/24/2022]
Abstract
Their surface activity enables proteins to form and stabilize foam, which can be used for in situ product separation or foam fractionation. Thus, it would be highly desirable to predict the surface activity of proteins based on their molecular properties like hydrophobicity, amphilicity, or structure on primary, secondary, and tertiary level. Ionic strength and pH were adjusted to gain maximum surface activity. The surface activity decreased in the order α lactalbumin > β‑lactoglobulin > trypsinogen > papain. For the theoretical analysis, the database was extended by including 2 hydrophobins into the investigation, since they are known to exhibit an outstanding surface activity. No relation to the macroscopic behavior was found considering the hydrophobicity. I.e., the non-hydrophobins did not differ significantly from each other, and from the hydrophobins, one was significantly hydrophobic, and the other was significantly hydrophilic. Also, no relations were found considering the amphilicity of the secondary structure elements. However, taking into account the tertiary protein structure, it was found that for most of the proteins investigated, the presence of non-buried amphiphilic secondary structure elements in combination with a certain amount of flexibility correlates with the surface activity.
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14
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Sheydaei M, Talebi S, Salami-Kalajahi M. Synthesis, characterization, curing, thermophysical and mechanical properties of ethylene dichloride-based polysulfide polymers. JOURNAL OF MACROMOLECULAR SCIENCE PART A-PURE AND APPLIED CHEMISTRY 2020. [DOI: 10.1080/10601325.2020.1857267] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Milad Sheydaei
- Faculty of Polymer Engineering, Sahand University of Technology, Tabriz, Iran
- Institute of Polymeric Materials, Sahand University of Technology, Tabriz, Iran
| | - Saeid Talebi
- Faculty of Polymer Engineering, Sahand University of Technology, Tabriz, Iran
- Institute of Polymeric Materials, Sahand University of Technology, Tabriz, Iran
| | - Mehdi Salami-Kalajahi
- Faculty of Polymer Engineering, Sahand University of Technology, Tabriz, Iran
- Institute of Polymeric Materials, Sahand University of Technology, Tabriz, Iran
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Winter P, Stubenvoll S, Scheiblhofer S, Joubert IA, Strasser L, Briganser C, Soh WT, Hofer F, Kamenik AS, Dietrich V, Michelini S, Laimer J, Lackner P, Horejs-Hoeck J, Tollinger M, Liedl KR, Brandstetter J, Huber CG, Weiss R. In silico Design of Phl p 6 Variants With Altered Fold-Stability Significantly Impacts Antigen Processing, Immunogenicity and Immune Polarization. Front Immunol 2020; 11:1824. [PMID: 33013833 PMCID: PMC7461793 DOI: 10.3389/fimmu.2020.01824] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 07/07/2020] [Indexed: 12/18/2022] Open
Abstract
Introduction: Understanding, which factors determine the immunogenicity and immune polarizing properties of proteins, is an important prerequisite for designing better vaccines and immunotherapeutics. While extrinsic immune modulatory factors such as pathogen associated molecular patterns are well-understood, far less is known about the contribution of protein inherent features. Protein fold-stability represents such an intrinsic feature contributing to immunogenicity and immune polarization by influencing the amount of peptide-MHC II complexes (pMHCII). Here, we investigated how modulation of the fold-stability of the grass pollen allergen Phl p 6 affects its ability to stimulate immune responses and T cell polarization. Methods: MAESTRO software was used for in silico prediction of stabilizing or destabilizing point mutations. Mutated proteins were expressed in E. coli, and their thermal stability and resistance to endolysosomal proteases was determined. Resulting peptides were analyzed by mass spectrometry. The structure of the most stable mutant protein was assessed by X-ray crystallography. We evaluated the capacity of the mutants to stimulate T cell proliferation in vitro, as well as antibody responses and T cell polarization in vivo in an adjuvant-free BALB/c mouse model. Results: In comparison to wild-type protein, stabilized or destabilized mutants displayed changes in thermal stability ranging from -5 to +14°. While highly stabilized mutants were degraded very slowly, destabilization led to faster proteolytic processing in vitro. This was confirmed in BMDCs, which processed and presented the immunodominant epitope from a destabilized mutant more efficiently compared to a highly stable mutant. In vivo, stabilization resulted in a shift in immune polarization from TH2 to TH1/TH17 as indicated by higher levels of IgG2a and increased secretion of TNF-α, IFN-γ, IL-17, and IL-21. Conclusion: MAESTRO software was very efficient in detecting single point mutations that increase or reduce fold-stability. Thermal stability correlated well with the speed of proteolytic degradation and presentation of peptides on the surface of dendritic cells in vitro. This change in processing kinetics significantly influenced the polarization of T cell responses in vivo. Modulating the fold-stability of proteins thus has the potential to optimize and polarize immune responses, which opens the door to more efficient design of molecular vaccines.
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Affiliation(s)
- Petra Winter
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Stefan Stubenvoll
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | | | | | - Lisa Strasser
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Carolin Briganser
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Wai Tuck Soh
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Florian Hofer
- Center of Molecular Biosciences & Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Anna Sophia Kamenik
- Center of Molecular Biosciences & Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Valentin Dietrich
- Center of Molecular Biosciences & Institute of Organic Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Sara Michelini
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Josef Laimer
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Peter Lackner
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | | | - Martin Tollinger
- Center of Molecular Biosciences & Institute of Organic Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Klaus R Liedl
- Center of Molecular Biosciences & Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | | | - Christian G Huber
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Richard Weiss
- Department of Biosciences, University of Salzburg, Salzburg, Austria
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16
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Pereira WES, da Silva RR, de Amo GS, Ruller R, Kishi LT, Boscolo M, Gomes E, da Silva R. A Collagenolytic Aspartic Protease from Thermomucor indicae-seudaticae Expressed in Escherichia coli and Pichia pastoris. Appl Biochem Biotechnol 2020; 191:1258-1270. [PMID: 32086706 DOI: 10.1007/s12010-020-03292-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 02/13/2020] [Indexed: 01/19/2023]
Abstract
Proteases are produced by the most diverse microorganisms and have a wide spectrum of applications. However, the use of wild microorganisms, mainly fungi, for enzyme production has some drawbacks. They are subject to physiological instability due to metabolic adaptations, causing complications and impairments in the production process. Thus, the objective of this work was to promote the heterologous expression of a collagenolytic aspartic protease (ProTiN31) from Thermomucor indicae seudaticae in Escherichia coli and Pichia pastoris. The pET_28a (+) and pPICZαA vectors were synthesized containing the gene of the enzyme and transformed into E. coli and P. pastoris, respectively. The recombinant enzymes produced by E. coli and P. pastoris showed maximum activity at pH 5.0 and 50 °C, and pH 5.0 and 60 °C, respectively. The enzyme produced by P. pastoris showed better thermostability when compared to that produced by E. coli. Both enzymes were stable at pH 6.0 and 6.5 for 24 h at 4 °C, and sensitive to pepstatin A, β-mercaptoethanol, and Hg2+. Comparing the commercial collagen hydrolysate (Artrogen duo/Brazil) and gelatin degradation using protease from P. pastoris, they showed similar peptide profiles. There are its potential applications in a wide array of industrial sectors that use collagenolytic enzymes.
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Affiliation(s)
- Waldir Eduardo Simioni Pereira
- Instituto de Biociências Letras e Ciências Exatas (Ibilce), Câmpus São José do Rio Preto, Universidade Estadual Paulista (Unesp), São Paulo, Brazil
| | - Ronivaldo Rodrigues da Silva
- Instituto de Biociências Letras e Ciências Exatas (Ibilce), Câmpus São José do Rio Preto, Universidade Estadual Paulista (Unesp), São Paulo, Brazil
| | - Gabriela Salvador de Amo
- Instituto Federal de Educação, Ciência e Tecnologia de São Paulo campus Catanduva, Catanduva, São Paulo, Brazil
| | - Roberto Ruller
- Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Maurício Boscolo
- Instituto de Biociências Letras e Ciências Exatas (Ibilce), Câmpus São José do Rio Preto, Universidade Estadual Paulista (Unesp), São Paulo, Brazil
| | - Eleni Gomes
- Instituto de Biociências Letras e Ciências Exatas (Ibilce), Câmpus São José do Rio Preto, Universidade Estadual Paulista (Unesp), São Paulo, Brazil
| | - Roberto da Silva
- Instituto de Biociências Letras e Ciências Exatas (Ibilce), Câmpus São José do Rio Preto, Universidade Estadual Paulista (Unesp), São Paulo, Brazil.
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17
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Chittoor B, Krishnarjuna B, Morales RAV, Norton RS. The Single Disulfide-Directed β-Hairpin Fold: Role of Disulfide Bond in Folding and Effect of an Additional Disulfide Bond on Stability. Aust J Chem 2020. [DOI: 10.1071/ch19386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Disulfide bonds play a key role in the oxidative folding, conformational stability, and functional activity of many peptides. A few disulfide-rich peptides with privileged architecture such as the inhibitor cystine knot motif have garnered attention as templates in drug design. The single disulfide-directed β-hairpin (SDH), a novel fold identified more recently in contryphan-Vc1, has been shown to possess remarkable thermal, conformational, and chemical stability and can accept a short bioactive epitope without compromising the core structure of the peptide. In this study, we demonstrated that the single disulfide bond is critical in maintaining the native fold by replacing both cysteine residues with serine. We also designed an analogue with an additional, non-native disulfide bridge by replacing Gln1 and Tyr9 with Cys. Contryphan-Vc11–22[Q1C, Y9C] was synthesised utilising orthogonal cysteine protection and its solution structure determined using solution NMR spectroscopy. This analogue maintained the overall fold of native contryphan-Vc1. Previous studies had shown that the β-hairpin core of contryphan-Vc1 was resistant to proteolysis by trypsin and α-chymotrypsin but susceptible to cleavage by pepsin. Contryphan-Vc11–22[Q1C, Y9C] proved to be completely resistant to pepsin, thus confirming our design strategy. These results highlight the role of the disulfide bond in maintaining the SDH fold and provide a basis for the design of more stable analogues for peptide epitope grafting.
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18
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Xiong X, Blakely A, Karra P, VandenBerg MA, Ghabash G, Whitby F, Zhang YW, Webber MJ, Holland WL, Hill CP, Chou DHC. Novel four-disulfide insulin analog with high aggregation stability and potency. Chem Sci 2019; 11:195-200. [PMID: 32110371 PMCID: PMC7012051 DOI: 10.1039/c9sc04555d] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/05/2019] [Indexed: 12/15/2022] Open
Abstract
A novel four-disulfide insulin analog was designed with retained bioactivity and increased fibrillation stability.
Although insulin was first purified and used therapeutically almost a century ago, there is still a need to improve therapeutic efficacy and patient convenience. A key challenge is the requirement for refrigeration to avoid inactivation of insulin by aggregation/fibrillation. Here, in an effort to mitigate this problem, we introduced a 4th disulfide bond between a C-terminal extended insulin A chain and residues near the C-terminus of the B chain. Insulin activity was retained by an analog with an additional disulfide bond between residues A22 and B22, while other linkages tested resulted in much reduced potency. Furthermore, the A22-B22 analog maintains the native insulin tertiary structure as demonstrated by X-ray crystal structure determination. We further demonstrate that this four-disulfide analog has similar in vivo potency in mice compared to native insulin and demonstrates higher aggregation stability. In conclusion, we have discovered a novel four-disulfide insulin analog with high aggregation stability and potency.
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Affiliation(s)
- Xiaochun Xiong
- Department of Biochemistry , University of Utah , Salt Lake City UT 84112 , USA . ;
| | - Alan Blakely
- Department of Biochemistry , University of Utah , Salt Lake City UT 84112 , USA . ;
| | - Prasoona Karra
- Department of Nutrition and Integrative Physiology , University of Utah , Salt Lake City UT 84112 , USA
| | - Michael A VandenBerg
- Department of Chemical & Biomolecular Engineering , University of Notre Dame , IN 46556 , USA
| | - Gabrielle Ghabash
- Department of Biochemistry , University of Utah , Salt Lake City UT 84112 , USA . ;
| | - Frank Whitby
- Department of Biochemistry , University of Utah , Salt Lake City UT 84112 , USA . ;
| | - Yi Wolf Zhang
- Department of Biochemistry , University of Utah , Salt Lake City UT 84112 , USA . ;
| | - Matthew J Webber
- Department of Chemical & Biomolecular Engineering , University of Notre Dame , IN 46556 , USA
| | - William L Holland
- Department of Nutrition and Integrative Physiology , University of Utah , Salt Lake City UT 84112 , USA
| | - Christopher P Hill
- Department of Biochemistry , University of Utah , Salt Lake City UT 84112 , USA . ;
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19
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Qiao Z, Xu M, Shao M, Zhao Y, Long M, Yang T, Zhang X, Yang S, Nakanishi H, Rao Z. Engineered disulfide bonds improve thermostability and activity of L-isoleucine hydroxylase for efficient 4-HIL production in Bacillus subtilis 168. Eng Life Sci 2019; 20:7-16. [PMID: 32625042 PMCID: PMC6999076 DOI: 10.1002/elsc.201900090] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/14/2019] [Accepted: 09/30/2019] [Indexed: 01/12/2023] Open
Abstract
4-Hydroxyisoleucine, a promising drug, has mainly been applied in the clinical treatment of type 2 diabetes in the pharmaceutical industry. l-Isoleucine hydroxylase specifically converts l-Ile to 4-hydroxyisoleucine. However, due to its poor thermostability, the industrial production of 4-hydroxyisoleucine has been largely restricted. In the present study, the disulfide bond in l-isoleucine hydroxylase protein was rationally designed to improve its thermostability to facilitate industrial application. The half-life of variant T181C was 4.03 h at 50°C, 10.27-fold the half-life of wild type (0.39 h). The specific enzyme activity of mutant T181C was 2.42 ± 0.08 U/mg, which was 3.56-fold the specific enzyme activity of wild type 0.68 ± 0.06 U/mg. In addition, molecular dynamics simulation was performed to determine the reason for the improvement of thermostability. Based on five repeated batches of whole-cell biotransformation, Bacillus subtilis 168/pMA5-ido T181C recombinant strain produced a cumulative yield of 856.91 mM (126.11 g/L) 4-hydroxyisoleucine, which is the highest level of productivity reported based on a microbial process. The results could facilitate industrial scale production of 4-hydroxyisoleucine. Rational design of disulfide bond improved l-isoleucine hydroxylase thermostability and may be suitable for protein engineering of other hydroxylases.
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Affiliation(s)
- Zhina Qiao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University Wuxi Jiangsu Province P. R. China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University Wuxi Jiangsu Province P. R. China
| | - Minglong Shao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University Wuxi Jiangsu Province P. R. China
| | - Youxi Zhao
- Beijing Key Laboratory of Biomass Waste Resource Utilization, College of Biochemical Engineering Beijing Union University Beijing P. R. China
| | - Mengfei Long
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University Wuxi Jiangsu Province P. R. China
| | - Taowei Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University Wuxi Jiangsu Province P. R. China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University Wuxi Jiangsu Province P. R. China
| | - Shangtian Yang
- Department of Chemical and Biomolecular Engineering The Ohio State University Columbus OH USA
| | - Hideki Nakanishi
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University Wuxi Jiangsu Province P. R. China
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University Wuxi Jiangsu Province P. R. China
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20
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Rational Design of Alginate Lyase from Microbulbifer sp. Q7 to Improve Thermal Stability. Mar Drugs 2019; 17:md17060378. [PMID: 31242622 PMCID: PMC6627800 DOI: 10.3390/md17060378] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 06/20/2019] [Accepted: 06/21/2019] [Indexed: 11/25/2022] Open
Abstract
Alginate lyase degrades alginate by the β-elimination mechanism to produce oligosaccharides with special bioactivities. The low thermal stability of alginate lyase limits its industrial application. In this study, introducing the disulfide bonds while using the rational design methodology enhanced the thermal stability of alginate lyase cAlyM from Microbulbifer sp. Q7. Enzyme catalytic sites, secondary structure, spatial configuration, and molecular dynamic simulation were comprehensively analyzed. When compared with cAlyM, the mutants D102C-A300C and G103C-T113C showed an increase by 2.25 and 1.16 h, respectively, in half-life time at 45 °C, in addition to increases by 1.7 °C and 0.4 °C in the melting temperature, respectively. The enzyme-specific activity and kcat/Km values of D102C-A300C were 1.8- and 1.5-times higher than those of cAlyM, respectively. The rational design strategy that was used in this study provides a valuable method for improving the thermal stability of the alginate lyase.
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21
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Ortiz CLD, Matel HD, Nellas RB. In Silico insights on enhancing thermostability and activity of a plant Fructosyltransferase from Pachysandra terminalis via introduction of disulfide bridges. J Mol Graph Model 2019; 89:250-260. [PMID: 30933883 DOI: 10.1016/j.jmgm.2019.03.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 03/18/2019] [Accepted: 03/18/2019] [Indexed: 12/18/2022]
Abstract
Drawbacks of industrially-used fructosyltransferases (FTs) such as low optimum temperature and low fructooligosaccharides (FOS) yield necessitates the search for engineered FTs that are highly thermostable and active. With the availability of the first plant FT crystal structure from Pachysandra terminalis (PDB ID: 3UGH), computer-aided protein engineering of plant FT is now feasible. To obtain insights on the effect of specific mutations i.e. disulfide bridge introduction, wild-type and mutant FTs were subjected to a 15 μs Martini Coarse-grained Molecular Dynamics (CGMD) simulations at 303 K and 334 K. We report here the five mutants, M31C-Q49C, L144C-S193C, P34C-W300C, S219C-L226C and V470C-S498C with enhanced thermostabilities and/or activities relative to the wild type. Interestingly, M31C-Q49C, which is located within the catalytic-carrying blade of the catalytic domain, has an activity enhancement at both temperatures. At 334 K, three mutations, L144C-S193C, P34C-W300C and V470C-S498C, achieved thermostability relative to the wild type. Intriguingly, both activity and stability enhancement exhibited only at 334 K can be achieved provided that the mutation is located either on the catalytic-carrying residue blade of the catalytic domain or on the non-catalytic domain. Our results suggest that V470C-S498C and L144C-S193C are promising mutants and that domain-specific approach may be exploited to customize enzyme properties.
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Affiliation(s)
| | - Hosea D Matel
- Research Center, Cavite State University, Don Severino De Las Alas Campus, Indang, Cavite, Philippines; Department of Physical Sciences, College of Arts and Sciences, Cavite State University, Don Severino De Las Alas Campus, Indang, Cavite, Philippines
| | - Ricky B Nellas
- Institute of Chemistry, College of Science, University of the Philippines Diliman, Diliman, Quezon City, Philippines.
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22
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Rouhani M, Khodabakhsh F, Norouzian D, Cohan RA, Valizadeh V. Molecular dynamics simulation for rational protein engineering: Present and future prospectus. J Mol Graph Model 2018; 84:43-53. [DOI: 10.1016/j.jmgm.2018.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/05/2018] [Accepted: 06/08/2018] [Indexed: 12/19/2022]
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23
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Nakhaee N, Asad S, Khajeh K, Arab SS, Amoozegar MA. Improving the thermal stability of azoreductase from Halomonas elongata by introducing a disulfide bond via site-directed mutagenesis. Biotechnol Appl Biochem 2018; 65:883-891. [PMID: 30132989 DOI: 10.1002/bab.1688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/11/2018] [Indexed: 11/06/2022]
Abstract
Azoreductases mainly reduce azo dyes, the largest class of colorants, to colorless aromatic amines. AzoH, a new azoreductase from the halophilic bacterium, Halomonas elongata, has been recently cloned and expressed in Escherichia coli. The aim of this study was to improve thermal stability of this enzyme by introducing new disulfide bonds. Since X-ray crystallography was not available, homology modeling and molecular dynamics was used to construct the enzyme three-dimensional structure. Potential disulfide bonds for increasing thermal stability were found using DIScover online software. Appropriate mutations (L49C/D108C) to form a disulfide bond were introduced by the Quik-Change method. Mutant protein expressed in E. coli showed increased thermal stability at 50 °C (increased half-life from 12.6 Min in AzoH to 26.66 Min in a mutated enzyme). The mutated enzyme could also tolerate 5% (w/v) NaCl and retained 30% of original activity after 24 H incubation, whereas the wild-type enzyme was completely inactivated. According to circular dichroism studies, the secondary structure was not altered by this mutation; however, a blue shift in intrinsic florescent graph revealed changes in the tertiary structure. This is the first study to improve thermal stability and salt tolerance of a halophilic azoreductase.
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Affiliation(s)
- Narjes Nakhaee
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Sedigheh Asad
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
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24
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Xu Z, Cai T, Xiong N, Zou SP, Xue YP, Zheng YG. Engineering the residues on “A” surface and C-terminal region to improve thermostability of nitrilase. Enzyme Microb Technol 2018; 113:52-58. [DOI: 10.1016/j.enzmictec.2018.03.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/28/2018] [Accepted: 03/04/2018] [Indexed: 12/29/2022]
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25
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Emruzi Z, Aminzadeh S, Karkhane AA, Alikhajeh J, Haghbeen K, Gholami D. Improving the thermostability of Serratia marcescens B4A chitinase via G191V site-directed mutagenesis. Int J Biol Macromol 2018; 116:64-70. [PMID: 29733926 DOI: 10.1016/j.ijbiomac.2018.05.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/26/2018] [Accepted: 05/03/2018] [Indexed: 11/24/2022]
Abstract
Chitinases with high thermostability are important for many industrial and biotechnological applications. This study was conducted to enhance the stability of Serratia marcescens B4A chitinase by site directed mutagenesis of G191 V. Further characterization showed that the thermal stability of the mutant showed marked increase of about 5 and 15 fold at 50 and 60 °C respectively, while the optimum temperature and pH was retained. Kinetic analysis showed decreased Km and Vmax of the mutant in comparison with the wild type chitinase of about 1.3 and 3 fold, respectively. Based on structural prediction, it was speculated that this replacement shortened an important loop concomitant with the extension of adjacent β sheets. Accordingly, a higher thermostability of G191 V up to 90 °C supporting the decreased flexibility of unfolded state was also indicated. Finally, a practical proof of kinetic and thermal stabilization of chitinase was provided through decreased flexibility and entropic stabilization of its surface loops.
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Affiliation(s)
- Zeinab Emruzi
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran, Iran
| | - Saeed Aminzadeh
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran, Iran.
| | - Ali Asghar Karkhane
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran, Iran
| | - Jahan Alikhajeh
- Departments of Physiology and Cellular Biophysics, Columbia University Medical Center, USA
| | - Kamahldin Haghbeen
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran, Iran
| | - Dariush Gholami
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran, Iran
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26
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Lakbub JC, Shipman JT, Desaire H. Recent mass spectrometry-based techniques and considerations for disulfide bond characterization in proteins. Anal Bioanal Chem 2017; 410:2467-2484. [PMID: 29256076 DOI: 10.1007/s00216-017-0772-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 11/09/2017] [Accepted: 11/17/2017] [Indexed: 12/21/2022]
Abstract
Disulfide bonds are important structural moieties of proteins: they ensure proper folding, provide stability, and ensure proper function. With the increasing use of proteins for biotherapeutics, particularly monoclonal antibodies, which are highly disulfide bonded, it is now important to confirm the correct disulfide bond connectivity and to verify the presence, or absence, of disulfide bond variants in the protein therapeutics. These studies help to ensure safety and efficacy. Hence, disulfide bonds are among the critical quality attributes of proteins that have to be monitored closely during the development of biotherapeutics. However, disulfide bond analysis is challenging because of the complexity of the biomolecules. Mass spectrometry (MS) has been the go-to analytical tool for the characterization of such complex biomolecules, and several methods have been reported to meet the challenging task of mapping disulfide bonds in proteins. In this review, we describe the relevant, recent MS-based techniques and provide important considerations needed for efficient disulfide bond analysis in proteins. The review focuses on methods for proper sample preparation, fragmentation techniques for disulfide bond analysis, recent disulfide bond mapping methods based on the fragmentation techniques, and automated algorithms designed for rapid analysis of disulfide bonds from liquid chromatography-MS/MS data. Researchers involved in method development for protein characterization can use the information herein to facilitate development of new MS-based methods for protein disulfide bond analysis. In addition, individuals characterizing biotherapeutics, especially by disulfide bond mapping in antibodies, can use this review to choose the best strategies for disulfide bond assignment of their biologic products. Graphical Abstract This review, describing characterization methods for disulfide bonds in proteins, focuses on three critical components: sample preparation, mass spectrometry data, and software tools.
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Affiliation(s)
- Jude C Lakbub
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, 1251 Wescoe Hall Dr, Lawrence, KS, 66045, USA
| | - Joshua T Shipman
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, 1251 Wescoe Hall Dr, Lawrence, KS, 66045, USA
| | - Heather Desaire
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, 1251 Wescoe Hall Dr, Lawrence, KS, 66045, USA.
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Sindhu R, Binod P, Madhavan A, Beevi US, Mathew AK, Abraham A, Pandey A, Kumar V. Molecular improvements in microbial α-amylases for enhanced stability and catalytic efficiency. BIORESOURCE TECHNOLOGY 2017; 245:1740-1748. [PMID: 28478894 DOI: 10.1016/j.biortech.2017.04.098] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 04/18/2017] [Accepted: 04/24/2017] [Indexed: 06/07/2023]
Abstract
α-Amylases is one of the most important industrial enzyme which contributes to 25% of the industrial enzyme market. Though it is produced by plant, animals and microbial source, those from microbial source seems to have potential applications due to their stability and economic viability. However a large number of α-amylases from different sources have been detailed in the literature, only few numbers of them could withstand the harsh industrial conditions. Thermo-stability, pH tolerance, calcium independency and oxidant stability and starch hydrolyzing efficiency are the crucial qualities for α-amylase in starch based industries. Microbes can be genetically modified and fine tuning can be done for the production of enzymes with desired characteristics for specific applications. This review focuses on the native and recombinant α-amylases from microorganisms, their heterologous production and the recent molecular strategies which help to improve the properties of this industrial enzyme.
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Affiliation(s)
- Raveendran Sindhu
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India.
| | - Parameswaran Binod
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India
| | - Aravind Madhavan
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India; Rajiv Gandhi Centre for Biotechnology, Jagathy, Trivandrum 695 014, India
| | - Ummalyma Sabeela Beevi
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India; Institute of Bioresources and Sustainable Development, Takyelpat, Imphal 795 001, India
| | - Anil Kuruvilla Mathew
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India
| | - Amith Abraham
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India
| | - Ashok Pandey
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India; Center of Innovative and Applied Bioprocessing, Sector 81, Mohali, Punjab, India
| | - Vinod Kumar
- Center of Innovative and Applied Bioprocessing, Sector 81, Mohali, Punjab, India
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Futami J, Miyamoto A, Hagimoto A, Suzuki S, Futami M, Tada H. Evaluation of irreversible protein thermal inactivation caused by breakage of disulphide bonds using methanethiosulphonate. Sci Rep 2017; 7:12471. [PMID: 28963503 PMCID: PMC5622167 DOI: 10.1038/s41598-017-12748-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 09/15/2017] [Indexed: 01/09/2023] Open
Abstract
Many extracellular globular proteins have evolved to possess disulphide bonds in their native conformations, which aids in thermodynamic stabilisation. However, disulphide bond breakage by heating leads to irreversible protein denaturation through disulphide-thiol exchange reactions. In this study, we demonstrate that methanethiosulphonate (MTS) specifically suppresses the heat-induced disulphide-thiol exchange reaction, thus improving the heat-resistance of proteins. In the presence of MTS, small globular proteins that contain disulphides can spontaneously refold from heat-denatured states, maintaining wild-type disulphide pairing. Because the disulphide-thiol exchange reaction is triggered by the generation of catalytic amounts of perthiol or thiol, rapid and specific perthiol/thiol protection by MTS reagents prevents irreversible denaturation. Combining MTS reagents with another additive that suppresses chemical modifications, glycinamide, further enhanced protein stabilisation. In the presence of these additives, reliable remnant activities were observed even after autoclaving. However, immunoglobulin G and biotin-binding protein, which are both composed of tetrameric quaternary structures, failed to refold from heat-denatured states, presumably due to chaperon requirements. Elucidation of the chemical modifications involved in irreversible thermoinactivation is useful for the development of preservation buffers with optimum constitutions for specific proteins. In addition, the impact of disulphide bond breakage on the thermoinactivation of proteins can be evaluated using MTS reagents.
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Affiliation(s)
- Junichiro Futami
- Department of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan.
| | - Ai Miyamoto
- Department of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Atsushi Hagimoto
- Department of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Shigeyuki Suzuki
- Department of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Midori Futami
- Department of Biomedical Engineering, Faculty of Engineering, Okayama University of Science, Okayama, 700-0005, Japan
| | - Hiroko Tada
- Division of Instrumental Analysis, Department of Instrumental Analysis and Cryogenics, Advanced Science Research Center, Okayama University, Okayama, 700-8530, Japan
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Yan S, Wu G. Bottleneck in secretion of α-amylase in Bacillus subtilis. Microb Cell Fact 2017; 16:124. [PMID: 28724440 PMCID: PMC5518135 DOI: 10.1186/s12934-017-0738-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 07/10/2017] [Indexed: 11/10/2022] Open
Abstract
Amylase plays an important role in biotechnology industries, and Gram-positive bacterium Bacillus subtilis is a major host to produce heterogeneous α-amylases. However, the secretion stress limits the high yield of α-amylase in B. subtilis although huge efforts have been made to address this secretion bottleneck. In this question-oriented review, every effort is made to answer the following questions, which look simple but are long-standing, through reviewing of literature: (1) Does α-amylase need a specific and dedicated chaperone? (2) What signal sequence does CsaA recognize? (3) Does CsaA require ATP for its operation? (4) Does an unfolded α-amylase is less soluble than a folded one? (5) Does α-amylase aggregate before transporting through Sec secretion system? (6) Is α-amylase sufficient stable to prevent itself from misfolding? (7) Does α-amylase need more disulfide bonds to be stabilized? (8) Which secretion system does PrsA pass through? (9) Is PrsA ATP-dependent? (10) Is PrsA reused after folding of α-amylase? (11) What is the fate of PrsA? (12) Is trigger factor (TF) ATP-dependent? The literature review suggests that not only the most of those questions are still open to answers but also it is necessary to calculate ATP budget in order to better understand how B. subtilis uses its energy for production and secretion.
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Affiliation(s)
- Shaomin Yan
- National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, Guangxi, China
| | - Guang Wu
- National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, Guangxi, China.
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Scheiblhofer S, Laimer J, Machado Y, Weiss R, Thalhamer J. Influence of protein fold stability on immunogenicity and its implications for vaccine design. Expert Rev Vaccines 2017; 16:479-489. [PMID: 28290225 PMCID: PMC5490637 DOI: 10.1080/14760584.2017.1306441] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION In modern vaccinology and immunotherapy, recombinant proteins more and more replace whole organisms to induce protective or curative immune responses. Structural stability of proteins is of crucial importance for efficient presentation of antigenic peptides on MHC, which plays a decisive role for triggering strong immune reactions. Areas covered: In this review, we discuss structural stability as a key factor for modulating the potency of recombinant vaccines and its importance for antigen proteolysis, presentation, and stimulation of B and T cells. Moreover, the impact of fold stability on downstream events determining the differentiation of T cells into effector cells is reviewed. We summarize studies investigating the impact of protein fold stability on the outcome of the immune response and provide an overview on computational methods to estimate the effects of point mutations on protein stability. Expert commentary: Based on this information, the rational design of up-to-date vaccines is discussed. A model for predicting immunogenicity of proteins based on their conformational stability at different pH values is proposed.
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Affiliation(s)
- Sandra Scheiblhofer
- a Department of Molecular Biology , University of Salzburg , Salzburg , Austria
| | - Josef Laimer
- a Department of Molecular Biology , University of Salzburg , Salzburg , Austria
| | - Yoan Machado
- a Department of Molecular Biology , University of Salzburg , Salzburg , Austria
| | - Richard Weiss
- a Department of Molecular Biology , University of Salzburg , Salzburg , Austria
| | - Josef Thalhamer
- a Department of Molecular Biology , University of Salzburg , Salzburg , Austria
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Legler PM, Compton JR, Hale ML, Anderson GP, Olson MA, Millard CB, Goldman ER. Stability of isolated antibody-antigen complexes as a predictive tool for selecting toxin neutralizing antibodies. MAbs 2016; 9:43-57. [PMID: 27660893 PMCID: PMC5240650 DOI: 10.1080/19420862.2016.1236882] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ricin is an A-B ribosome inactivating protein (RIP) toxin composed of an A-chain subunit (RTA) that contains a catalytic N-glycosidase and a B-chain (RTB) lectin domain that binds cell surface glycans. Ricin exploits retrograde transport to enter into the Golgi and the endoplasmic reticulum, and then dislocates into the cytoplasm where it can reach its substrate, the rRNA. A subset of isolated antibodies (Abs) raised against the RTA subunit protect against ricin intoxication, and RTA-based vaccine immunogens have been shown to provide long-lasting protective immunity against the holotoxin. Anti-RTA Abs are unlikely to cross a membrane and reach the cytoplasm to inhibit the enzymatic activity of the A-chain. Moreover, there is not a strict correlation between the apparent binding affinity (Ka) of anti-RTA Abs and their ability to successfully neutralize ricin toxicity. Some anti-RTA antibodies are toxin-neutralizing, whereas others are not. We hypothesize that neutralizing anti-RTA Abs may interfere selectively with conformational change(s) or partial unfolding required for toxin internalization. To test this hypothesis, we measured the melting temperatures (Tm) of neutralizing single-domain Ab (sdAb)-antigen (Ag) complexes relative to the Tm of the free antigen (Tm-shift = Tmcomplex – TmAg), and observed increases in the Tmcomplex of 9–20 degrees. In contrast, non-neutralizing sdAb-Ag complexes shifted the TmComplex by only 6–7 degrees. A strong linear correlation (r2 = 0.992) was observed between the magnitude of the Tm-shift and the viability of living cells treated with the sdAb and ricin holotoxin. The Tm-shift of the sdAb-Ag complex provided a quantitative biophysical parameter that could be used to predict and rank-order the toxin-neutralizing activities of Abs. We determined the first structure of an sdAb-RTA1-33/44-198 complex, and examined other sdAb-RTA complexes. We found that neutralizing sdAb bound to regions involved in the early stages of unfolding. These Abs likely interfere with steps preceding or following endocytosis that require conformational changes. This method may have utility for the characterization or rapid screening of other Ab that act to prevent conformational changes or unfolding as part of their mechanism of action.
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Affiliation(s)
| | | | - Martha L Hale
- c US Army Medical Research Institute of Infectious Diseases , Frederick , MD , USA
| | | | - Mark A Olson
- c US Army Medical Research Institute of Infectious Diseases , Frederick , MD , USA
| | - Charles B Millard
- c US Army Medical Research Institute of Infectious Diseases , Frederick , MD , USA
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Niu C, Zhu L, Xu X, Li Q. Rational Design of Disulfide Bonds Increases Thermostability of a Mesophilic 1,3-1,4-β-Glucanase from Bacillus terquilensis. PLoS One 2016; 11:e0154036. [PMID: 27100881 PMCID: PMC4839689 DOI: 10.1371/journal.pone.0154036] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/07/2016] [Indexed: 11/19/2022] Open
Abstract
1,3-1,4-β-glucanase is an important biocatalyst in brewing industry and animal feed industry, while its low thermostability often reduces its application performance. In this study, the thermostability of a mesophilic β-glucanase from Bacillus terquilensis was enhanced by rational design and engineering of disulfide bonds in the protein structure. Protein spatial configuration was analyzed to pre-exclude the residues pairs which negatively conflicted with the protein structure and ensure the contact of catalytic center. The changes in protein overall and local flexibility among the wild-type enzyme and the designated mutants were predicted to select the potential disulfide bonds for enhancement of thermostability. Two residue pairs (N31C-T187C and P102C-N125C) were chosen as engineering targets and both of them were proved to significantly enhance the protein thermostability. After combinational mutagenesis, the double mutant N31C-T187C/P102C-N125C showed a 48.3% increase in half-life value at 60°C and a 4.1°C rise in melting temperature (Tm) compared to wild-type enzyme. The catalytic property of N31C-T187C/P102C-N125C mutant was similar to that of wild-type enzyme. Interestingly, the optimal pH of double mutant was shifted from pH6.5 to pH6.0, which could also increase its industrial application. By comparison with mutants with single-Cys substitutions, the introduction of disulfide bonds and the induced new hydrogen bonds were proved to result in both local and overall rigidification and should be responsible for the improved thermostability. Therefore, the introduction of disulfide bonds for thermostability improvement could be rationally and highly-effectively designed by combination with spatial configuration analysis and molecular dynamics simulation.
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Affiliation(s)
- Chengtuo Niu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of biotechnology, Jiangnan University, Wuxi, China
| | - Linjiang Zhu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of biotechnology, Jiangnan University, Wuxi, China
| | - Xin Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of biotechnology, Jiangnan University, Wuxi, China
| | - Qi Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of biotechnology, Jiangnan University, Wuxi, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- * E-mail:
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Hibi T, Kume A, Kawamura A, Itoh T, Fukada H, Nishiya Y. Hyperstabilization of Tetrameric Bacillus sp. TB-90 Urate Oxidase by Introducing Disulfide Bonds through Structural Plasticity. Biochemistry 2016; 55:724-32. [PMID: 26739254 DOI: 10.1021/acs.biochem.5b01119] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacillus sp. TB-90 urate oxidase (BTUO) is one of the most thermostable homotetrameric enzymes. We previously reported [Hibi, T., et al. (2014) Biochemistry 53, 3879-3888] that specific binding of a sulfate anion induced thermostabilization of the enzyme, because the bound sulfate formed a salt bridge with two Arg298 residues, which stabilized the packing between two β-barrel dimers. To extensively characterize the sulfate-binding site, Arg298 was substituted with cysteine by site-directed mutagenesis. This substitution markedly increased the protein melting temperature by ∼ 20 °C compared with that of the wild-type enzyme, which was canceled by reduction with dithiothreitol. Calorimetric analysis of the thermal denaturation suggested that the hyperstabilization resulted from suppression of the dissociation of the tetramer into the two homodimers. The crystal structure of R298C at 2.05 Å resolution revealed distinct disulfide bond formation between the symmetrically related subunits via Cys298, although the Cβ distance between Arg298 residues of the wild-type enzyme (5.4 Å apart) was too large to predict stable formation of an engineered disulfide cross-link. Disulfide bonding was associated with local disordering of interface loop II (residues 277-300), which suggested that the structural plasticity of the loop allowed hyperstabilization by disulfide formation. Another conformational change in the C-terminal region led to intersubunit hydrogen bonding between Arg7 and Asp312, which probably promoted mutant thermostability. Knowledge of the disulfide linkage of flexible loops at the subunit interface will help in the development of new strategies for enhancing the thermostabilization of multimeric proteins.
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Affiliation(s)
- Takao Hibi
- Department of Bioscience, Fukui Prefectural University , Fukui 910-1195, Japan
| | - Asami Kume
- Department of Bioscience, Fukui Prefectural University , Fukui 910-1195, Japan
| | - Akie Kawamura
- Department of Bioscience, Fukui Prefectural University , Fukui 910-1195, Japan
| | - Takafumi Itoh
- Department of Bioscience, Fukui Prefectural University , Fukui 910-1195, Japan
| | - Harumi Fukada
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University , Sakai, Osaka 599-8531, Japan
| | - Yoshiaki Nishiya
- Tsuruga Institute for Biotechnology, Toyobo Company Ltd. , Tsuruga, Fukui 914-0047, Japan
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Rana A, Akhter Y. A multi-subunit based, thermodynamically stable model vaccine using combined immunoinformatics and protein structure based approach. Immunobiology 2015; 221:544-57. [PMID: 26707618 DOI: 10.1016/j.imbio.2015.12.004] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 12/03/2015] [Accepted: 12/06/2015] [Indexed: 10/22/2022]
Abstract
Immunizations with the conventional vaccines have failed to effectively inhibit the incidences and further dissemination of the infections. To address it, we have implemented protein structure based strategies to design an efficient multi-epitope subunit vaccine against Mycobacterium avium subsp. paratuberculosis (MAP). Previously reported immunodominant peptide epitope sequences from MAP1611 protein were conjugated together with a stretch of conserved amino acid residues of heparin-binding hemagglutinin, reported as a TLR4 agonist and was employed as an adjuvant to polarize the cellular responses toward host protective Th1 responses. These three types of component peptides were combined with the help of relevant linkers for efficient separation to improve and intensify the antigen processing and presentation. The primary structures of these multi peptides were 3-dimensional homology modeled to yield the final chimeric vaccine. Further, its conformational correctness and stability enhancement was assessed using molecular dynamics (MD) simulations. Finally, disulfide engineering in the most flexible regions of the molecule yielded three potential mutants, Y593C-E610C, Q631C-A634C and a double mutant Q631C-A634C/Y593C-E610C. The double mutant represents thermodynamically most stable version among them. It is potentially highly antigenic, soluble and non-allergen molecule interacting with the TLR receptor expressed on the immune cells. This vaccine contains both T-cell and several B-cell epitopes and an adjuvant which potentially possess protective cellular and humoral immune responses triggering properties. The presented vaccine strategy will be proven a promising pathogen specific candidate with wide therapeutic application against MAP which may be extended to other prevalent infections in future.
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Affiliation(s)
- Aarti Rana
- School of Life Sciences, Central University of Himachal Pradesh, Kangra, Himachal Pradesh 176206, India
| | - Yusuf Akhter
- School of Life Sciences, Central University of Himachal Pradesh, Kangra, Himachal Pradesh 176206, India.
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35
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Schmidt S, Genz M, Balke K, Bornscheuer UT. The effect of disulfide bond introduction and related Cys/Ser mutations on the stability of a cyclohexanone monooxygenase. J Biotechnol 2015; 214:199-211. [DOI: 10.1016/j.jbiotec.2015.09.026] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 09/16/2015] [Accepted: 09/22/2015] [Indexed: 01/30/2023]
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Rational Substitution of Surface Acidic Residues for Enhancing the Thermostability of Thermolysin. Appl Biochem Biotechnol 2015; 178:725-38. [DOI: 10.1007/s12010-015-1905-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/21/2015] [Indexed: 11/26/2022]
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Vinther TN, Kjeldsen TB, Jensen KJ, Hubálek F. The road to the first, fully active and more stable human insulin variant with an additional disulfide bond. J Pept Sci 2015; 21:797-806. [DOI: 10.1002/psc.2822] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/14/2015] [Accepted: 08/19/2015] [Indexed: 12/21/2022]
Affiliation(s)
| | | | - Knud J. Jensen
- Faculty of Science, Department of Chemistry; University of Copenhagen; DK-1871 Frederiksberg Denmark
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38
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Naderi M, Moosavi-Movahedi AA, Hosseinkhani S, Nazari M, Bohlooli M, Hong J, Hadi-Alijanvand H, Sheibani N. Implication of disulfide bridge induced thermal reversibility, structural and functional stability for luciferase. Protein Pept Lett 2015; 22:23-30. [PMID: 25159509 DOI: 10.2174/0929866521666140827112816] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 08/18/2014] [Accepted: 08/18/2014] [Indexed: 11/22/2022]
Abstract
Firefly luciferase is a relatively unstable protein and commonly loses its activity at room temperature because of structural changes. The structural and functional stability of this protein is critical for its enzymatic applications. Different approaches are applied to increase the stability of this enzyme such as designing of covalent cross-links (disulfide bonds). In this study, luciferase mutants containing one or two disulfide bonds were compared to the native protein for their for their structural, thermodynamic, and functional properties. Mutant forms of P. Pyralis luciferase A²⁹⁶C-A³²⁶C and A²⁹⁶C-A³²⁶C/P⁴⁵¹C-V⁴⁶⁹C were used. Thermodynamic and biophysical studies were carried out using UV-Vis, fluorescence, circular dichroism, luminescence spectroscopy and differential scanning calorimetry (DSC). We observed that both mutant forms of the protein were more stable than the wild-type enzyme. However, the single disulfide bond containing mutant was structurally and functionally more stable than the mutant protein containing two disulfide bonds. Furthermore, the enzymatic activity of the single disulfide bond containing mutant protein was 7-folds greater than the wild type and the double disulfide bond proteins. The A²⁹⁶C-A³²⁶C mutation also increased the reversibility and disaggregation of the protein. The enhanced activity of the single disulfide bond mutant protein was contributed to the expansion of its active site cleft, which was confirmed by bioinformatics tools.
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Affiliation(s)
| | | | | | | | | | | | | | - Nader Sheibani
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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Yin X, Hu D, Li JF, He Y, Zhu TD, Wu MC. Contribution of Disulfide Bridges to the Thermostability of a Type A Feruloyl Esterase from Aspergillus usamii. PLoS One 2015; 10:e0126864. [PMID: 25969986 PMCID: PMC4429965 DOI: 10.1371/journal.pone.0126864] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 04/08/2015] [Indexed: 11/18/2022] Open
Abstract
The contribution of disulfide bridges to the thermostability of a type A feruloyl esterase (AuFaeA) from Aspergillus usamii E001 was studied by introducing an extra disulfide bridge or eliminating a native one from the enzyme. MODIP and DbD, two computational tools that can predict the possible disulfide bridges in proteins for thermostability improvement, and molecular dynamics (MD) simulations were used to design the extra disulfide bridge. One residue pair A126-N152 was chosen, and the respective amino acid residues were mutated to cysteine. The wild-type AuFaeA and its variants were expressed in Pichia pastoris GS115. The temperature optimum of the recombinant (re-) AuFaeAA126C-N152C was increased by 6°C compared to that of re-AuFaeA. The thermal inactivation half-lives of re-AuFaeAA126C-N152C at 55 and 60°C were 188 and 40 min, which were 12.5- and 10-folds longer than those of re-AuFaeA. The catalytic efficiency (kcat/Km) of re-AuFaeAA126C-N152C was similar to that of re-AuFaeA. Additionally, after elimination of each native disulfide bridge in AuFaeA, a great decrease in expression level and at least 10°C decrease in thermal stability of recombinant AuEaeA variants were also observed.
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Affiliation(s)
- Xin Yin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Die Hu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Jian-Fang Li
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Yao He
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Tian-Di Zhu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Min-Chen Wu
- Wuxi Medical School, Jiangnan University, Wuxi, China
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40
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Zhang S, Wang Y, Song X, Hong J, Zhang Y, Yao L. Improving Trichoderma reesei Cel7B Thermostability by Targeting the Weak Spots. J Chem Inf Model 2014; 54:2826-33. [DOI: 10.1021/ci500339v] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Shujun Zhang
- Laboratory
of Biofuels, Qingdao
Institute of Bioenergy and Bioprocess Technology Chinese Academy of Sciences, Qingdao, 266061, China
| | - Yefei Wang
- Laboratory
of Biofuels, Qingdao
Institute of Bioenergy and Bioprocess Technology Chinese Academy of Sciences, Qingdao, 266061, China
| | - Xiangfei Song
- Laboratory
of Biofuels, Qingdao
Institute of Bioenergy and Bioprocess Technology Chinese Academy of Sciences, Qingdao, 266061, China
| | - Jingbo Hong
- Laboratory
of Biofuels, Qingdao
Institute of Bioenergy and Bioprocess Technology Chinese Academy of Sciences, Qingdao, 266061, China
| | - Yu Zhang
- Laboratory
of Biofuels, Qingdao
Institute of Bioenergy and Bioprocess Technology Chinese Academy of Sciences, Qingdao, 266061, China
| | - Lishan Yao
- Laboratory
of Biofuels, Qingdao
Institute of Bioenergy and Bioprocess Technology Chinese Academy of Sciences, Qingdao, 266061, China
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41
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Gilbreth RN, Chacko BM, Grinberg L, Swers JS, Baca M. Stabilization of the third fibronectin type III domain of human tenascin-C through minimal mutation and rational design. Protein Eng Des Sel 2014; 27:411-8. [PMID: 24996411 DOI: 10.1093/protein/gzu024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Non-antibody scaffolds are increasingly used to generate novel binding proteins for both research and therapeutic applications. Our group has developed the tenth fibronectin type III domain of human tenascin-C (TNfn3) as one such scaffold. As a scaffold, TNfn3 must tolerate extensive mutation to introduce novel binding sites. However, TNfn3's marginal stability (T(m) ∼ 59°C, ΔG(unfolding) = 5.7 kcal/mol) stands as a potential obstacle to this process. To address this issue, we sought to engineer highly stable TNfn3 variants. We used two parallel strategies. Using insights gained from structural analysis of other FN3 family members, we (1) rationally designed stabilizing point mutations or (2) introduced novel stabilizing disulfide bonds. Both strategies yielded highly stable TNfn3 variants with T(m) values as high as 83°C and ΔG(unfolding) values as high as 9.4 kcal/mol. Notably, only three or four mutations were required to achieve this level of stability with either approach. These results validate our rational design strategies and illustrate that substantial stability increases can be achieved with minimal mutation. One TNfn3 variant reported here has now been successfully used as a scaffold to develop two promising therapeutic molecules. We anticipate that other variants described will exhibit similar utility.
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Affiliation(s)
- R N Gilbreth
- Department of Antibody Discovery and Protein Engineering, MedImmune LLC, Gaithersburg, MD 20878, USA
| | - B M Chacko
- Department of Antibody Discovery and Protein Engineering, MedImmune LLC, Gaithersburg, MD 20878, USA
| | - L Grinberg
- Department of Antibody Discovery and Protein Engineering, MedImmune LLC, Gaithersburg, MD 20878, USA
| | - J S Swers
- Department of Antibody Discovery and Protein Engineering, MedImmune LLC, Gaithersburg, MD 20878, USA
| | - M Baca
- Department of Antibody Discovery and Protein Engineering, MedImmune LLC, Gaithersburg, MD 20878, USA
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42
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Involvement of Val 315 located in the C-terminal region of thermolysin in its expression in Escherichia coli and its thermal stability. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:330-8. [DOI: 10.1016/j.bbapap.2013.10.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 10/12/2013] [Accepted: 10/29/2013] [Indexed: 11/19/2022]
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43
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Dombkowski AA, Sultana KZ, Craig DB. Protein disulfide engineering. FEBS Lett 2013; 588:206-12. [PMID: 24291258 DOI: 10.1016/j.febslet.2013.11.024] [Citation(s) in RCA: 174] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 11/15/2013] [Accepted: 11/18/2013] [Indexed: 11/29/2022]
Abstract
Improving the stability of proteins is an important goal in many biomedical and industrial applications. A logical approach is to emulate stabilizing molecular interactions found in nature. Disulfide bonds are covalent interactions that provide substantial stability to many proteins and conform to well-defined geometric conformations, thus making them appealing candidates in protein engineering efforts. Disulfide engineering is the directed design of novel disulfide bonds into target proteins. This important biotechnological tool has achieved considerable success in a wide range of applications, yet the rules that govern the stabilizing effects of disulfide bonds are not fully characterized. Contrary to expectations, many designed disulfide bonds have resulted in decreased stability of the modified protein. We review progress in disulfide engineering, with an emphasis on the issue of stability and computational methods that facilitate engineering efforts.
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Affiliation(s)
- Alan A Dombkowski
- Carman and Ann Adams Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | - Kazi Zakia Sultana
- Department of Computer Science & Engineering, Chittagong University of Engineering & Technology, Chittagong 4349, Bangladesh
| | - Douglas B Craig
- Carman and Ann Adams Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI 48201, USA
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44
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In silico rational design and systems engineering of disulfide bridges in the catalytic domain of an alkaline α-amylase from Alkalimonas amylolytica to improve thermostability. Appl Environ Microbiol 2013; 80:798-807. [PMID: 24212581 DOI: 10.1128/aem.03045-13] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
High thermostability is required for alkaline α-amylases to maintain high catalytic activity under the harsh conditions used in textile production. In this study, we attempted to improve the thermostability of an alkaline α-amylase from Alkalimonas amylolytica through in silico rational design and systems engineering of disulfide bridges in the catalytic domain. Specifically, 7 residue pairs (P35-G426, Q107-G167, G116-Q120, A147-W160, G233-V265, A332-G370, and R436-M480) were chosen as engineering targets for disulfide bridge formation, and the respective residues were replaced with cysteines. Three single disulfide bridge mutants-P35C-G426C, G116C-Q120C, and R436C-M480C-of the 7 showed significantly enhanced thermostability. Combinational mutations were subsequently assessed, and the triple mutant P35C-G426C/G116C-Q120C/R436C-M480C showed a 6-fold increase in half-life at 60°C and a 5.2°C increase in melting temperature compared with the wild-type enzyme. Interestingly, other biochemical properties of this mutant also improved: the optimum temperature increased from 50°C to 55°C, the optimum pH shifted from 9.5 to 10.0, the stable pH range extended from 7.0 to 11.0 to 6.0 to 12.0, and the catalytic efficiency (kcat/Km) increased from 1.8 × 10(4) to 2.4 × 10(4) liters/g · min. The possible mechanism responsible for these improvements was explored through comparative analysis of the model structures of wild-type and mutant enzymes. The disulfide bridge engineering strategy used in this work may be applied to improve the thermostability of other industrial enzymes.
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45
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Branigan E, Pliotas C, Hagelueken G, Naismith JH. Quantification of free cysteines in membrane and soluble proteins using a fluorescent dye and thermal unfolding. Nat Protoc 2013; 8:2090-7. [PMID: 24091556 PMCID: PMC3836627 DOI: 10.1038/nprot.2013.128] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cysteine is an extremely useful site for selective attachment of labels to proteins for many applications, including the study of protein structure in solution by electron paramagnetic resonance (EPR), fluorescence spectroscopy and medical imaging. The demand for quantitative data for these applications means that it is important to determine the extent of the cysteine labeling. The efficiency of labeling is sensitive to the 3D context of cysteine within the protein. Where the label or modification is not directly measurable by optical or magnetic spectroscopy, for example, in cysteine modification to dehydroalanine, assessing labeling efficiency is difficult. We describe a simple assay for determining the efficiency of modification of cysteine residues, which is based on an approach previously used to determine membrane protein stability. The assay involves a reaction between the thermally unfolded protein and a thiol-specific coumarin fluorophore that is only fluorescent upon conjugation with thiols. Monitoring fluorescence during thermal denaturation of the protein in the presence of the dye identifies the temperature at which the maximum fluorescence occurs; this temperature differs among proteins. Comparison of the fluorescence intensity at the identified temperature between modified, unmodified (positive control) and cysteine-less protein (negative control) allows for the quantification of free cysteine. We have quantified both site-directed spin labeling and dehydroalanine formation. The method relies on a commonly available fluorescence 96-well plate reader, which rapidly screens numerous samples within 1.5 h and uses <100 μg of material. The approach is robust for both soluble and detergent-solubilized membrane proteins.
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Affiliation(s)
- Emma Branigan
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, UK
| | - Christos Pliotas
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, UK
| | - Gregor Hagelueken
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, UK
| | - James H Naismith
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, UK
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46
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The role of disulfide bond in hyperthermophilic endocellulase. Extremophiles 2013; 17:593-9. [PMID: 23624891 PMCID: PMC3691470 DOI: 10.1007/s00792-013-0542-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 04/11/2013] [Indexed: 12/03/2022]
Abstract
The hyperthermophilic endocellulase, EGPh (glycosyl hydrolase family 5) from Pyrococcus horikoshii possesses 4 cysteine residues forming 2 disulfide bonds, as identified by structural analysis. One of the disulfide bonds is located at the proximal region of the active site in EGPh, which exhibits a distinct pattern from that of the thermophilic endocellulase EGAc (glycosyl hydrolase family 5) of Acidothermus cellulolyticus despite the structural similarity between the two endocellulases. The structural similarity between EGPh and EGAc suggests that EGPh possesses a structure suitable for changing the position of the disulfide bond corresponding to that in EGAc. Introduction of this alternative disulfide bond in EGPh, while removing the original disulfide bond, did not result in a loss of enzymatic activity but the EGPh was no longer hyperthermostable. These results suggest that the contribution of disulfide bond to hyperthermostability at temperature higher than 100 °C is restrictive, and that its impact is dependent on the specific structural environment of the hyperthermophilic proteins. The data suggest that the structural position and environment of the disulfide bond has a greater effect on high-temperature thermostability of the enzyme than on the potential energy of the dihedral angle that contributes to disulfide bond cleavage.
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47
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Pirie CM, De Mey M, Prather KLJ, Ajikumar PK. Integrating the protein and metabolic engineering toolkits for next-generation chemical biosynthesis. ACS Chem Biol 2013; 8:662-72. [PMID: 23373985 DOI: 10.1021/cb300634b] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Through microbial engineering, biosynthesis has the potential to produce thousands of chemicals used in everyday life. Metabolic engineering and synthetic biology are fields driven by the manipulation of genes, genetic regulatory systems, and enzymatic pathways for developing highly productive microbial strains. Fundamentally, it is the biochemical characteristics of the enzymes themselves that dictate flux through a biosynthetic pathway toward the product of interest. As metabolic engineers target sophisticated secondary metabolites, there has been little recognition of the reduced catalytic activity and increased substrate/product promiscuity of the corresponding enzymes compared to those of central metabolism. Thus, fine-tuning these enzymatic characteristics through protein engineering is paramount for developing high-productivity microbial strains for secondary metabolites. Here, we describe the importance of protein engineering for advancing metabolic engineering of secondary metabolism pathways. This pathway integrated enzyme optimization can enhance the collective toolkit of microbial engineering to shape the future of chemical manufacturing.
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Affiliation(s)
- Christopher M. Pirie
- Manus Biosynthesis Inc., Suite 102, 790 Memorial Drive, Cambridge, Massachusetts 02139,
United States
| | - Marjan De Mey
- Manus Biosynthesis Inc., Suite 102, 790 Memorial Drive, Cambridge, Massachusetts 02139,
United States
- Centre of
Expertise−Industrial Biotechnology and Biocatalysis, Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - Kristala L. Jones Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
| | - Parayil Kumaran Ajikumar
- Manus Biosynthesis Inc., Suite 102, 790 Memorial Drive, Cambridge, Massachusetts 02139,
United States
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48
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Vinther TN, Norrman M, Ribel U, Huus K, Schlein M, Steensgaard DB, Pedersen TÅ, Pettersson I, Ludvigsen S, Kjeldsen T, Jensen KJ, Hubálek F. Insulin analog with additional disulfide bond has increased stability and preserved activity. Protein Sci 2013; 22:296-305. [PMID: 23281053 DOI: 10.1002/pro.2211] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 12/04/2012] [Accepted: 12/07/2012] [Indexed: 11/10/2022]
Abstract
Insulin is a key hormone controlling glucose homeostasis. All known vertebrate insulin analogs have a classical structure with three 100% conserved disulfide bonds that are essential for structural stability and thus the function of insulin. It might be hypothesized that an additional disulfide bond may enhance insulin structural stability which would be highly desirable in a pharmaceutical use. To address this hypothesis, we designed insulin with an additional interchain disulfide bond in positions A10/B4 based on Cα-Cα distances, solvent exposure, and side-chain orientation in human insulin (HI) structure. This insulin analog had increased affinity for the insulin receptor and apparently augmented glucodynamic potency in a normal rat model compared with HI. Addition of the disulfide bond also resulted in a 34.6°C increase in melting temperature and prevented insulin fibril formation under high physical stress even though the C-terminus of the B-chain thought to be directly involved in fibril formation was not modified. Importantly, this analog was capable of forming hexamer upon Zn addition as typical for wild-type insulin and its crystal structure showed only minor deviations from the classical insulin structure. Furthermore, the additional disulfide bond prevented this insulin analog from adopting the R-state conformation and thus showing that the R-state conformation is not a prerequisite for binding to insulin receptor as previously suggested. In summary, this is the first example of an insulin analog featuring a fourth disulfide bond with increased structural stability and retained function.
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Affiliation(s)
- Tine N Vinther
- Diabetes Research Unit, Novo Nordisk A/S, Novo Nordisk Park, Måløv DK-2760, Denmark
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49
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Singh RK, Tiwari MK, Singh R, Lee JK. From protein engineering to immobilization: promising strategies for the upgrade of industrial enzymes. Int J Mol Sci 2013; 14:1232-77. [PMID: 23306150 PMCID: PMC3565319 DOI: 10.3390/ijms14011232] [Citation(s) in RCA: 268] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 11/14/2012] [Accepted: 12/24/2012] [Indexed: 11/16/2022] Open
Abstract
Enzymes found in nature have been exploited in industry due to their inherent catalytic properties in complex chemical processes under mild experimental and environmental conditions. The desired industrial goal is often difficult to achieve using the native form of the enzyme. Recent developments in protein engineering have revolutionized the development of commercially available enzymes into better industrial catalysts. Protein engineering aims at modifying the sequence of a protein, and hence its structure, to create enzymes with improved functional properties such as stability, specific activity, inhibition by reaction products, and selectivity towards non-natural substrates. Soluble enzymes are often immobilized onto solid insoluble supports to be reused in continuous processes and to facilitate the economical recovery of the enzyme after the reaction without any significant loss to its biochemical properties. Immobilization confers considerable stability towards temperature variations and organic solvents. Multipoint and multisubunit covalent attachments of enzymes on appropriately functionalized supports via linkers provide rigidity to the immobilized enzyme structure, ultimately resulting in improved enzyme stability. Protein engineering and immobilization techniques are sequential and compatible approaches for the improvement of enzyme properties. The present review highlights and summarizes various studies that have aimed to improve the biochemical properties of industrially significant enzymes.
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Affiliation(s)
- Raushan Kumar Singh
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 143-701, Korea.
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50
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Wang H, Andersen KK, Sehgal P, Hagedorn J, Westh P, Borch K, Otzen DE. pH Regulation of the Kinetic Stability of the Lipase from Thermomyces lanuginosus. Biochemistry 2012; 52:264-76. [DOI: 10.1021/bi301258e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- H. Wang
- Interdisciplinary Nanoscience
Centre (iNANO), Center for Insoluble Protein Structures (inSPIN),
Department of Molecular Biology and Genetics, University of Aarhus, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - K. K. Andersen
- Interdisciplinary Nanoscience
Centre (iNANO), Center for Insoluble Protein Structures (inSPIN),
Department of Molecular Biology and Genetics, University of Aarhus, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - P. Sehgal
- Department of Biophysics and
Biomedicine, University of Aarhus, 1180
Ole Worms Allé 6, 8000 Aarhus C, Denmark
| | - J. Hagedorn
- Abbott Products GmbH, Hans-Böckler Allee 20, 30173 Hannover, Germany
| | - P. Westh
- NSM Functional Biomaterials, Roskilde University, P.O. Box 260, 4000 Roskilde, Denmark
| | - K. Borch
- Novozymes A/S, DK-2880 Bagsværd, Denmark
| | - D. E. Otzen
- Interdisciplinary Nanoscience
Centre (iNANO), Center for Insoluble Protein Structures (inSPIN),
Department of Molecular Biology and Genetics, University of Aarhus, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
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