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Li X, Rahim K, Shen X, Cui X, Du C, Zhang G. Development of a Universal One-Step Purification and Activation Method to Engineer Protein-Glutaminase through Rational Design. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10477-10486. [PMID: 38657166 DOI: 10.1021/acs.jafc.4c01406] [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: 04/26/2024]
Abstract
Cytotoxic enzymes often exist as zymogens containing prodomains to keep them in an inactive state. Protein-glutaminase (PG), which can enhance various functional characteristics of food proteins, is an enzyme containing pro-PG and mature-PG (mPG). However, poor activity and stability limit its application while tedious purification and activation steps limit its high-throughput engineering. Here, based on structural analysis, we replaced the linker sequence between pro-PG and mPG with the HRV3C protease recognition sequence and then coexpressed it with HRV3C protease in Escherichia coli to develop an efficient one-step purification and activation method for PG. We then used this method to obtain several mutants designed by a combination of computer-aided approach and beneficial point mutations. The specific activity (131.6 U/mg) of the best variant D1 was 4.14-fold that of the wild type, and t1/2 and T5010 increased by 13 min and 7 °C, respectively. D1 could effectively improve the solubility and emulsification of wheat proteins, more than twice the effect of the wild type. We also discussed the mechanism underlying the improved properties of D1. In summary, we not only provide a universal one-step purification and activation method to facilitate zymogen engineering but also obtain an excellent PG mutant.
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Affiliation(s)
- Xiaodi Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Kashif Rahim
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xingyu Shen
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xin Cui
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chao Du
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Guimin Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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Jamdar SN, Yadav P, Kulkarni BS, Sudesh, Kumar A, Makde RD. Crystal structure of a newly identified M61 family aminopeptidase with broad substrate specificity that is solely responsible for recycling acidic amino acids. FEBS J 2024. [PMID: 38646733 DOI: 10.1111/febs.17133] [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: 08/11/2023] [Revised: 02/10/2024] [Accepted: 03/25/2024] [Indexed: 04/23/2024]
Abstract
Aminopeptidases with varied substrate specificities are involved in different crucial physiological processes of cellular homeostasis. They also have wide applications in food and pharma industries. Within the bacterial cell, broad specificity aminopeptidases primarily participate in the recycling of amino acids by degrading oligopeptides generated via primary proteolysis mediated by cellular ATP-dependent proteases. However, in bacteria, a truly broad specificity enzyme, which can cleave off acidic, basic, Gly and hydrophobic amino acid residues, is extremely rare. Here, we report structure-function of a putative glycyl aminopeptidase (M61xc) from Xanthomonas campestris pv campestris (Xcc) belonging to the M61 peptidase family. The enzyme exhibits broad specificity and cleaves Ala, Leu, Asp, Glu, Met, Ser, Phe, Tyr, Gly, Arg, and Lys at the N terminus, optimally of peptides with a length of 3-7 amino acids. Further, we report the high-resolution crystal structure of M61xc in the apo form (2.1 Å) and bestatin-bound form (1.95 Å), detailing its catalytic and substrate preference mechanisms. Comparative analysis of enzyme activity in crude cell extracts from both wild-type and m61xc-knockout mutant strains of Xcc has elucidated the unique intracellular role of M61xc. This study suggests that M61xc is the exclusive enzyme in these bacteria that is responsible for liberating Asp/Glu residues from the N-termini of peptides. Also, in view of its broad specificity and peptide degradation ability, it could be considered equivalent to M1 or other oligomeric peptidases from families like M17, M18, M42 or S9, who have an important auxiliary role in post-proteasomal protein degradation in prokaryotes.
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Affiliation(s)
- Sahayog N Jamdar
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Pooja Yadav
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
| | | | - Sudesh
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Ashwani Kumar
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
| | - Ravindra D Makde
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
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Zhao TT, Hu HJ, Gao LX, Zhou YB, Zhu YL, Zhang C, Li J, Wang WL. Exploring the mechanism of the PTP1B inhibitors by molecular dynamics and experimental study. J Mol Graph Model 2023; 125:108585. [PMID: 37544021 DOI: 10.1016/j.jmgm.2023.108585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/08/2023]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) has proven to be an attractive target for the treatment of cancer, diabetes and other diseases. Although many PTP1B inhibitors with various scaffolds have been developed, there is still a lack of PTP1B inhibitor with high specificity and acceptable pharmacological properties. Therefore, it is urgent to develop more methods to explore complex action mode of PTP1B and ligands for designing ideal PTP1B modulators. In this work, we developed a potential molecular dynamics (MD) analytic mode to analyze the mechanism of active compounds 6a and 6e against PTP1B from different perspectives, including the stable ability, interactions and binding site of ligand and protein, the binding energy, relative movement between residues and changes in protein internal interactions. The simulated results demonstrated that compound 6a bound more stably to the active pocket of PTP1B than 6e due to its smaller molecular volume (326 Å3), matched electronegativity, and enhanced the positive correlation motion of residues, especially for WPD loop and P loop. Lastly, compound 6a as a competitive inhibitor for PTP1B was verified by enzyme kinetic assay. This work successfully studied the mechanism of compound 6a against PTP1B from various aspects, enriched the analysis of interaction mode between PTP1B and inhibitors. In summary, we hope that this work could provide more theoretical information for designing and developing more novel and ideal PTP1B inhibitors in the future.
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Affiliation(s)
- Tian-Tian Zhao
- School of Life Sciences and Health Engineering, Jiangnan University, Jiangsu, 214122, China
| | - Hao-Jie Hu
- School of Life Sciences and Health Engineering, Jiangnan University, Jiangsu, 214122, China
| | - Li-Xin Gao
- School of Life Sciences and Health Engineering, Jiangnan University, Jiangsu, 214122, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yu-Bo Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yun-Long Zhu
- Wuxi Maternal and Child Health Hospital, Wuxi School of Medicine, Jiangnan University, Jiangsu, 214002, China.
| | - Chun Zhang
- School of Life Sciences and Health Engineering, Jiangnan University, Jiangsu, 214122, China.
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Wen-Long Wang
- School of Life Sciences and Health Engineering, Jiangnan University, Jiangsu, 214122, China.
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Wang X, Chen X, Wang ZJ, Zhuang M, Zhong L, Fu C, Garcia R, Müller R, Zhang Y, Yan J, Wu D, Huo L. Discovery and Characterization of a Myxobacterial Lanthipeptide with Unique Biosynthetic Features and Anti-inflammatory Activity. J Am Chem Soc 2023. [PMID: 37466996 DOI: 10.1021/jacs.3c06014] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
The genomes of myxobacteria harbor a variety of biosynthetic gene clusters encoding numerous secondary metabolites, including ribosomally synthesized and post-translationally modified peptides (RiPPs) with diverse chemical structures and biological activities. However, the biosynthetic potential of RiPPs from myxobacteria remains barely explored. Herein, we report a novel myxobacteria lanthipeptide myxococin identified from Myxococcus fulvus. Myxococins represent the first example of lanthipeptides, of which the characteristic multiple thioether rings are installed by employing a Class II lanthipeptide synthetase MfuM and a Class I lanthipeptide cyclase MfuC in a cascaded way. Unprecedentedly, we biochemically characterized the first M61 family aminopeptidase MfuP involved in RiPP biosynthesis, demonstrating that MfuP showed the activity of an endopeptidase activity. MfuP is leader-independent but strictly selective for the multibridge structure of myxococin A and responsible for unwrapping two rings via amide bond hydrolysis, yielding myxococin B. Furthermore, the X-ray crystal structure of MfuP and structural analysis, including active-site mutations, are reported. Finally, myxococins are evaluated to exhibit anti-inflammatory activity in lipopolysaccharide-induced macrophages without detectable cytotoxicity.
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Affiliation(s)
- Xiaotong Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
- Helmholtz International Lab for Anti-Infectives, Shandong University, Qingdao 266237, P. R. China
| | - Xiaoyu Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
- Helmholtz International Lab for Anti-Infectives, Shandong University, Qingdao 266237, P. R. China
| | - Zong-Jie Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
- Helmholtz International Lab for Anti-Infectives, Shandong University, Qingdao 266237, P. R. China
| | - Mengwei Zhuang
- Department of Diagnostics, Medical Integration and Practice Center, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Lin Zhong
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, Chin
| | - Chengzhang Fu
- Helmholtz International Laboratory, Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- Helmholtz International Lab for Anti-Infectives, Campus E8 1, 66123 Saarbrücken, Germany
| | - Ronald Garcia
- Helmholtz International Laboratory, Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- Helmholtz International Lab for Anti-Infectives, Campus E8 1, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Helmholtz International Laboratory, Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- Helmholtz International Lab for Anti-Infectives, Campus E8 1, 66123 Saarbrücken, Germany
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
- Helmholtz International Lab for Anti-Infectives, Shandong University, Qingdao 266237, P. R. China
| | - Jie Yan
- Department of Diagnostics, Medical Integration and Practice Center, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Dalei Wu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
- Helmholtz International Lab for Anti-Infectives, Shandong University, Qingdao 266237, P. R. China
| | - Liujie Huo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
- Helmholtz International Lab for Anti-Infectives, Shandong University, Qingdao 266237, P. R. China
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Li Y, Ma Y, Xia Y, Zhang T, Sun S, Gao J, Yao H, Wang H. Discovery and biosynthesis of tricyclic copper-binding ribosomal peptides containing histidine-to-butyrine crosslinks. Nat Commun 2023; 14:2944. [PMID: 37221219 DOI: 10.1038/s41467-023-38517-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/12/2023] [Indexed: 05/25/2023] Open
Abstract
Cyclic peptide natural products represent an important class of bioactive compounds and clinical drugs. Enzymatic side-chain macrocyclization of ribosomal peptides is a major strategy developed by nature to generate these chemotypes, as exemplified by the superfamily of ribosomally synthesized and post-translational modified peptides. Despite the diverse types of side-chain crosslinks in this superfamily, the participation of histidine residues is rare. Herein, we report the discovery and biosynthesis of bacteria-derived tricyclic lanthipeptide noursin, which is constrained by a tri amino acid labionin crosslink and an unprecedented histidine-to-butyrine crosslink, named histidinobutyrine. Noursin displays copper-binding ability that requires the histidinobutyrine crosslink and represents the first copper-binding lanthipeptide. A subgroup of lanthipeptide synthetases, named LanKCHbt, were identified to catalyze the formation of both the labionin and the histidinobutyrine crosslinks in precursor peptides and produce noursin-like compounds. The discovery of the histidinobutyrine-containing lanthipeptides expands the scope of post-translational modifications, structural diversity and bioactivity of ribosomally synthesized and post-translational modified peptides.
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Affiliation(s)
- Yuqing Li
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Yeying Ma
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Yinzheng Xia
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Tao Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Shuaishuai Sun
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Jiangtao Gao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China.
| | - Hongwei Yao
- Institute of Molecular Enzymology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, 215123, China.
| | - Huan Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China.
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6
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Synthetic biology-inspired cell engineering in diagnosis, treatment, and drug development. Signal Transduct Target Ther 2023; 8:112. [PMID: 36906608 PMCID: PMC10007681 DOI: 10.1038/s41392-023-01375-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 01/31/2023] [Accepted: 02/15/2023] [Indexed: 03/13/2023] Open
Abstract
The fast-developing synthetic biology (SB) has provided many genetic tools to reprogram and engineer cells for improved performance, novel functions, and diverse applications. Such cell engineering resources can play a critical role in the research and development of novel therapeutics. However, there are certain limitations and challenges in applying genetically engineered cells in clinical practice. This literature review updates the recent advances in biomedical applications, including diagnosis, treatment, and drug development, of SB-inspired cell engineering. It describes technologies and relevant examples in a clinical and experimental setup that may significantly impact the biomedicine field. At last, this review concludes the results with future directions to optimize the performances of synthetic gene circuits to regulate the therapeutic activities of cell-based tools in specific diseases.
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Recent Developments in Zn-Based Biodegradable Materials for Biomedical Applications. J Funct Biomater 2022; 14:jfb14010001. [PMID: 36662048 PMCID: PMC9865652 DOI: 10.3390/jfb14010001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Zn-based biodegradable alloys or composites have the potential to be developed to next-generation orthopedic implants as alternatives to conventional implants to avoid revision surgeries and to reduce biocompatibility issues. This review summarizes the current research status on Zn-based biodegradable materials. The biological function of Zn, design criteria for orthopedic implants, and corrosion behavior of biodegradable materials are briefly discussed. The performance of many novel zinc-based biodegradable materials is evaluated in terms of biodegradation, biocompatibility, and mechanical properties. Zn-based materials perform a significant role in bone metabolism and the growth of new cells and show medium degradation without the release of excessive hydrogen. The addition of alloying elements such as Mg, Zr, Mn, Ca, and Li into pure Zn enhances the mechanical properties of Zn alloys. Grain refinement by the application of post-processing techniques is effective for the development of many suitable Zn-based biodegradable materials.
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McEwan IJ. Breaking apart condensates. Nat Chem Biol 2022; 18:1292-1293. [PMID: 36229684 DOI: 10.1038/s41589-022-01161-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Iain J McEwan
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland, UK.
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