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Xu R, Pan Q, Zhu G, Ye Y, Xin M, Wang Z, Wang S, Li W, Wei Y, Guo J, Zheng L. ThermoLink: Bridging disulfide bonds and enzyme thermostability through database construction and machine learning prediction. Protein Sci 2024; 33:e5097. [PMID: 39145402 PMCID: PMC11325166 DOI: 10.1002/pro.5097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 05/27/2024] [Accepted: 06/15/2024] [Indexed: 08/16/2024]
Abstract
Disulfide bonds, covalently formed by sulfur atoms in cysteine residues, play a crucial role in protein folding and structure stability. Considering their significance, artificial disulfide bonds are often introduced to enhance protein thermostability. Although an increasing number of tools can assist with this task, significant amounts of time and resources are often wasted owing to inadequate consideration. To enhance the accuracy and efficiency of designing disulfide bonds for protein thermostability improvement, we initially collected disulfide bond and protein thermostability data from extensive literature sources. Thereafter, we extracted various sequence- and structure-based features and constructed machine-learning models to predict whether disulfide bonds can improve protein thermostability. Among all models, the neighborhood context model based on the Adaboost-DT algorithm performed the best, yielding "area under the receiver operating characteristic curve" and accuracy scores of 0.773 and 0.714, respectively. Furthermore, we also found AlphaFold2 to exhibit high superiority in predicting disulfide bonds, and to some extent, the coevolutionary relationship between residue pairs potentially guided artificial disulfide bond design. Moreover, several mutants of imine reductase 89 (IR89) with artificially designed thermostable disulfide bonds were experimentally proven to be considerably efficient for substrate catalysis. The SS-bond data have been integrated into an online server, namely, ThermoLink, available at guolab.mpu.edu.mo/thermoLink.
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Affiliation(s)
- Ran Xu
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
| | - Qican Pan
- Zelixir Biotech Company Ltd, Shanghai, China
| | | | - Yilin Ye
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
| | - Minghui Xin
- School of Physics, Shandong University, Jinan, China
| | - Zechen Wang
- School of Physics, Shandong University, Jinan, China
| | - Sheng Wang
- Zelixir Biotech Company Ltd, Shanghai, China
| | - Weifeng Li
- School of Physics, Shandong University, Jinan, China
| | - Yanjie Wei
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jingjing Guo
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
| | - Liangzhen Zheng
- Zelixir Biotech Company Ltd, Shanghai, China
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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Hu YT, Hong XZ, Li HM, Yang JK, Shen W, Wang YW, Liu YH. Modifying the amino acids in conformational motion pathway of the α-amylase of Geobacillus stearothermophilus improved its activity and stability. Front Microbiol 2023; 14:1261245. [PMID: 38143856 PMCID: PMC10740195 DOI: 10.3389/fmicb.2023.1261245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/21/2023] [Indexed: 12/26/2023] Open
Abstract
Amino acids along the conformational motion pathway of the enzyme molecule correlated to its flexibility and rigidity. To enhance the enzyme activity and thermal stability, the motion pathway of Geobacillus stearothermophilus α-amylase has been identified and molecularly modified by using the neural relational inference model and deep learning tool. The significant differences in substrate specificity, enzymatic kinetics, optimal temperature, and thermal stability were observed among the mutants with modified amino acids along the pathway. Mutants especially the P44E demonstrated enhanced hydrolytic activity and catalytic efficiency (kcat/KM) than the wild-type enzyme to 95.0% and 93.8% respectively, with the optimum temperature increased to 90°C. This mutation from proline to glutamic acid has increased the number and the radius of the bottleneck of the channels, which might facilitate transporting large starch substrates into the enzyme. The mutation could also optimize the hydrogen bonding network of the catalytic center, and diminish the spatial hindering to the substrate entry and exit from the catalytic center.
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Affiliation(s)
- Yu-Ting Hu
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Xi-Zhi Hong
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Hui-Min Li
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Jiang-Ke Yang
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Wei Shen
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Ya-Wei Wang
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Yi-Han Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
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Zhu M, Zhai W, Song R, Lin L, Wei W, Wei D. Enhanced Thermostability of Geobacillus stearothermophilus α-Amylase by Rational Design of Disulfide Bond and Application in Corn Starch Liquefaction and Bread Quality Improvement. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18928-18942. [PMID: 38053503 DOI: 10.1021/acs.jafc.3c06761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
α-Amylase (EC 3.2.1.1) from Geobacillus stearothermophilus (generally recognized as safe) exhibited thermal inactivation, hampering its further application in starch-based industries. To address this, we performed structural analyses based on molecular dynamics targeting the flexible regions of α-amylase. Subsequently, we rationally designed a thermostable mutant, AmyS1, by introducing disulfide bonds to stabilize the flexible regions. AmyS1 showed excellent thermostability without any stability-activity trade-off, giving a 40-fold longer T1/2 (1359 min) at 90 °C. Thermostability mechanism analysis revealed that the introduction of disulfide bonds in AmyS1 refined weak spots and reconfigured the protein's force network. Moreover, AmyS1 exhibited improved pH compatibility and enhanced corn starch liquefaction at 100 °C with a 5.1-fold increased product concentration. Baking tests confirmed that AmyS1 enhanced bread quality and extended the shelf life. Therefore, mutant AmyS1 is a robust candidate for the starch-based industry.
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Affiliation(s)
- Mengyu Zhu
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Wenxin Zhai
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Runfei Song
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Lin Lin
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China
- Research Laboratory for Functional Nanomaterial, National Engineering Research Center for Nanotechnology, Shanghai 200241, China
| | - Wei Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
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Zhang H, Dou Z, Bi W, Yang C, Wu X, Wang L. Multi-omics study of sulfur metabolism affecting functional microbial community succession during aerobic solid-state fermentation. BIORESOURCE TECHNOLOGY 2023; 387:129664. [PMID: 37573975 DOI: 10.1016/j.biortech.2023.129664] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/05/2023] [Accepted: 08/09/2023] [Indexed: 08/15/2023]
Abstract
Microbial-mediated sulfur metabolism is closely related to carbon and nitrogen metabolism in natural biological systems. In this study, the effects of sulfur metabolism on microbial communities and functional enzyme succession were investigated based on integrated multi-omics by adding sulfur-containing compounds to aerobic fermentation systems. Sulfur powder was oxidized to S2O32- and subsequently to SO42- by the microbial sulfur-oxidizing system, which lowered the pH to 7.5 on day 7. The decrease in pH resulted in Planifilum (secreted S8, M17 and M32 proteases) losing its competitive advantage, whereas Novibacillus (secreted M14 and M19 metalloproteases) became dominant. Structural proteomics indicated that the surface of Novibacillus proteases has more negatively charged amino acid residues that help maintain protein stability at low pH. These findings aid understanding of the effects of sulfur metabolism on fermentation and the mechanism of microbial adaptation after pH reduction, providing new perspectives on the optimization of fermentation processes.
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Affiliation(s)
- Hong Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Zhixin Dou
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Wenhui Bi
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China; Faculty of Food Science and Engineering, Shandong Agricultural and Engineering University, Jinan, Shandong 250100, China
| | - Chuanlun Yang
- Shandong Chambroad Holding Group Co., Ltd., Boxing 256599, China
| | - Xiuyun Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
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Li X, Zheng D, Wu J, Jin Z, Svensson B, Bai Y. Increasing γ-CD conversion rates by improving thermostability of Bacillus sp. FJAT-44876 γ-CGTase. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.102204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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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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Chen H, Ma L, Dai H, Fu Y, Wang H, Zhang Y. Advances in Rational Protein Engineering toward Functional Architectures and Their Applications in Food Science. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:4522-4533. [PMID: 35353517 DOI: 10.1021/acs.jafc.2c00232] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein biomolecules including enzymes, cagelike proteins, and specific peptides have been continuously exploited as functional biomaterials applied in catalysis, nutrient delivery, and food preservation in food-related areas. However, natural proteins usually function well in physiological conditions, not industrial conditions, or may possess undesirable physical and chemical properties. Currently, rational protein design as a valuable technology has attracted extensive attention for the rational engineering or fabrication of ideal protein biomaterials with novel properties and functionality. This article starts with the underlying knowledge of protein folding and assembly and is followed by the introduction of the principles and strategies for rational protein design. Basic strategies for rational protein engineering involving experienced protein tailoring, computational prediction, computation redesign, and de novo protein design are summarized. Then, we focus on the recent progress of rational protein engineering or design in the application of food science, and a comprehensive summary ranging from enzyme manufacturing to cagelike protein nanocarriers engineering and antimicrobial peptides preparation is given. Overall, this review highlights the importance of rational protein engineering in food biomaterial preparation which could be beneficial for food science.
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Affiliation(s)
- Hai Chen
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Liang Ma
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Hongjie Dai
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Yu Fu
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Hongxia Wang
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Yuhao Zhang
- College of Food Science, Southwest University, Chongqing 400715, China
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Ban X, Xi S, Jiang H, Gu Z, Li C, Cheng L, Hong Y, Li Z. The amino acid on the top of the active groove allosterically modulates product specificity of the 1,4-α-glucan branching enzyme. Food Chem 2022; 384:132458. [PMID: 35219229 DOI: 10.1016/j.foodchem.2022.132458] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 01/02/2023]
Abstract
The 1,4-α-glucan branching enzymes (GBEs, EC 2.4.1.18) catalyse the formation of α-1,6 branching points in starch, presenting several potential applications in modifying starch. Previous study proved that W285 is considered to act as a "switch" to stop extension of substrates in the structure of GBE from Cyanothece sp. (cceBE). In the structure of GBE from Rhodothermus obamensis STB05 (RoGBE), the amino acid 160 site is structurally similar to the W285 in cceBE. In order to explore the role of this site in RoGBE, several engineered mutants individually substituted with Arg, Phe and Ala at G160 were studied in our research. The results show that substitution with Arg and Phe increased branching activity significantly, and the ratio of short glucan chains among all oligosaccharides increased. Finally, we proposed that the G160 is a 'door model' to elucidate introduced mutagenesis that triggers and controls the length of binding glucan chains of starch.
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Affiliation(s)
- Xiaofeng Ban
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Shixia Xi
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Haimin Jiang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhengbiao Gu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; The Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, China
| | - Caiming Li
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Li Cheng
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yan Hong
- The Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhaofeng Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, China.
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Yu Z, Yu H, Xu J, Wang Z, Wang Z, Kang T, Chen K, Pu Z, Wu J, Yang LR, Xu G. Enhancing Thermostability of Lipase from Pseudomonas alcaligenes for producing L-menthol by the CREATE Strategy. Catal Sci Technol 2022. [DOI: 10.1039/d2cy00082b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Lipase from Pseudomonas alcaligenes (PaL) catalyzes the hydrolysis of racemic menthol propionate to produce L-menthol, one of the most important flavoring agents in food, cosmetics and pharmaceuticals industries. However,...
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Identification of difructose dianhydride I synthase/hydrolase from an oral bacterium establishes a novel glycoside hydrolase family. J Biol Chem 2021; 297:101324. [PMID: 34688653 PMCID: PMC8605356 DOI: 10.1016/j.jbc.2021.101324] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/07/2021] [Accepted: 10/07/2021] [Indexed: 11/30/2022] Open
Abstract
Fructooligosaccharides and their anhydrides are widely used as health-promoting foods and prebiotics. Various enzymes acting on β-D-fructofuranosyl linkages of natural fructan polymers have been used to produce functional compounds. However, enzymes that hydrolyze and form α-D-fructofuranosyl linkages have been less studied. Here, we identified the BBDE_2040 gene product from Bifidobacterium dentium (α-D-fructofuranosidase and difructose dianhydride I synthase/hydrolase from Bifidobacterium dentium [αFFase1]) as an enzyme with α-D-fructofuranosidase and α-D-arabinofuranosidase activities and an anomer-retaining manner. αFFase1 is not homologous with any known enzymes, suggesting that it is a member of a novel glycoside hydrolase family. When caramelized fructose sugar was incubated with αFFase1, conversions of β-D-Frup-(2→1)-α-D-Fruf to α-D-Fruf-1,2′:2,1′-β-D-Frup (diheterolevulosan II) and β-D-Fruf-(2→1)-α-D-Fruf (inulobiose) to α-D-Fruf-1,2′:2,1′-β-D-Fruf (difructose dianhydride I [DFA I]) were observed. The reaction equilibrium between inulobiose and DFA I was biased toward the latter (1:9) to promote the intramolecular dehydrating condensation reaction. Thus, we named this enzyme DFA I synthase/hydrolase. The crystal structures of αFFase1 in complex with β-D-Fruf and β-D-Araf were determined at the resolutions of up to 1.76 Å. Modeling of a DFA I molecule in the active site and mutational analysis also identified critical residues for catalysis and substrate binding. The hexameric structure of αFFase1 revealed the connection of the catalytic pocket to a large internal cavity via a channel. Molecular dynamics analysis implied stable binding of DFA I and inulobiose to the active site with surrounding water molecules. Taken together, these results establish DFA I synthase/hydrolase as a member of a new glycoside hydrolase family (GH172).
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