1
|
Zhao Y, Zhang W, Hong J, Yang L, Wang Y, Qu F, Xu W. Mobility capillary electrophoresis-native mass spectrometry reveals the dynamic conformational equilibrium of calmodulin and its complexes. Analyst 2024; 149:3793-3802. [PMID: 38847183 DOI: 10.1039/d4an00378k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Benefitting from the rapid evolution of artificial intelligence and structural biology, an expanding collection of high-resolution protein structures has greatly improved our understanding of protein functions. Yet, proteins are inherently flexible, and these static structures can only offer limited snapshots of their true dynamic nature. The conformational and functional changes of calmodulin (CaM) induced by Ca2+ binding have always been a focus of research. In this study, the conformational dynamics of CaM and its complexes were investigated using a mobility capillary electrophoresis (MCE) and native mass spectrometry (native MS) based method. By analyzing the ellipsoidal geometries of CaM in the solution phase at different Ca2+ concentrations, it is interesting to discover that CaM molecules, whether bound to Ca2+ or not, possess both closed and open conformations. Moreover, each individual CaM molecule actively "jumps" (equilibrium exchange) between these two distinct conformations on a timescale ranging from milli- to micro-seconds. The binding of Ca2+ ions did not affect the structural dynamics of CaM, while the binding of a peptide ligand would stabilize CaM, leading to the observation of a single, compact conformation of the resulting protein complex. A target recognition mechanism was also proposed based on these new findings, suggesting that CaM's interaction with targets may favor a conformational selection model. This enriches our understanding of the binding principles between CaM and its numerous targets.
Collapse
Affiliation(s)
- Yi Zhao
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China.
| | - Wenjing Zhang
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China.
| | - Jie Hong
- Kunshan Nier Precision Instrumentation Inc. Kunshan, Suzhou, 215316, China
| | - Lei Yang
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China.
| | - Yuanyuan Wang
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Feng Qu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
| | - Wei Xu
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China.
| |
Collapse
|
2
|
Adachi T, Mazurenko I, Mano N, Kitazumi Y, Kataoka K, Kano K, Sowa K, Lojou E. Kinetic and thermodynamic analysis of Cu2+-dependent reductive inactivation in direct electron transfer-type bioelectrocatalysis by copper efflux oxidase. Electrochim Acta 2022. [DOI: 10.1016/j.electacta.2022.140987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
3
|
Zhan J, Sun H, Dai Z, Zhang Y, Yang X. Loops constructing the substrate-binding site controlled the catalytic efficiency of Thermus thermophilus SG0.5JP17-16 laccase. Biochimie 2022; 200:60-67. [DOI: 10.1016/j.biochi.2022.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/26/2022] [Accepted: 05/19/2022] [Indexed: 11/02/2022]
|
4
|
Xiong D, Wen J, Lu G, Li T, Long M. Isolation, Purification, and Characterization of a Laccase-Degrading Aflatoxin B1 from Bacillus amyloliquefaciens B10. Toxins (Basel) 2022; 14:toxins14040250. [PMID: 35448859 PMCID: PMC9028405 DOI: 10.3390/toxins14040250] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/29/2022] [Accepted: 03/29/2022] [Indexed: 01/27/2023] Open
Abstract
Aflatoxins, widely found in feed and foodstuffs, are potentially harmful to human and animal health because of their high toxicity. In this study, a strain of Bacillus amyloliquefaciens B10 with a strong ability to degrade aflatoxin B1 (AFB1) was screened; it could degrade 2.5 μg/mL of AFB1 within 96 h. The active substances of Bacillus amyloliquefaciens B10 for the degradation of AFB1 mainly existed in the culture supernatant. A new laccase with AFB1-degrading activity was separated by ammonium sulfate precipitation, diethylaminoethyl (DEAE) and gel filtration chromatography. The results of molecular docking showed that B10 laccase and aflatoxin had a high docking score. The coding sequence of the laccase was successfully amplified from cDNA by PCR and cloned into E. coli. The purified laccase could degrade 79.3% of AFB1 within 36 h. The optimum temperature for AFB1 degradation was 40 °C, and the optimum pH was 6.0–8.0. Notably, Mg2+ and dimethyl sulfoxide (DMSO) could enhance the AFB1-degrading activity of B10 laccase. Mutation of the three key metal combined sites of B10 laccase resulted in the loss of AFB1-degrading activity, indicating that these three metal combined sites of B10 laccase play an essential role in the catalytic degradation of AFB1.
Collapse
|
5
|
Conversion of lignin-derived 3-methoxycatechol to the natural product purpurogallin using bacterial P450 GcoAB and laccase CueO. Appl Microbiol Biotechnol 2021; 106:593-603. [PMID: 34971410 DOI: 10.1007/s00253-021-11738-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/02/2021] [Accepted: 12/11/2021] [Indexed: 01/02/2023]
Abstract
Purpurogallin is a natural benzotropolone extracted from Quercus spp, which has antioxidant, anticancer, and anti-inflammatory properties. Purpurogallin is typically synthesized from pyrogallol using enzymatic or metal catalysts, neither economically feasible nor environmentally friendly. 3-Methoxycatechol (3-MC) is a lignin-derived renewable chemical with the potential to be a substrate for the biosynthesis of purpurogallin. In this study, we designed a pathway to produce purpurogallin from 3-MC. We first characterized four bacterial laccases and identified the laccase CueO from Escherichia coli, which converts pyrogallol to purpurogallin. Then, we used CueO and the P450 GcoAB reported to convert 3-MC to pyrogallol, to construct a method for producing purpurogallin directly from 3-MC. A total of 0.21 ± 0.05 mM purpurogallin was produced from 5 mM 3-MC by whole-cell conversion. This study provides a new method to enable efficient and sustainable synthesis of purpurogallin and offers new insights into lignin valorization. KEY POINTS: • Screening four bacterial laccases for converting pyrogallol to purpurogallin. • Laccase CueO from Escherichia coli presenting the activity for purpurogallin yield. • A novel pathway for converting lignin-derived 3-methoxycatechol to purpurogallin.
Collapse
|
6
|
Yan N, Ma H, Yang CX, Liao XR, Guan ZB. Improving the decolorization activity of Bacillus pumilus W3 CotA-laccase to Congo Red by rational modification. Enzyme Microb Technol 2021; 155:109977. [PMID: 34973504 DOI: 10.1016/j.enzmictec.2021.109977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 12/16/2021] [Accepted: 12/18/2021] [Indexed: 11/19/2022]
Abstract
Congo Red (CR) is a typical azo dye with highly toxic and carcinogenic properties. This study aimed to improve the decolorization activity of Bacillus pumilus W3 CotA-laccase for azo dye CR. This work analyzed the interaction between CotA-laccase and CR based on homology modeling and molecular docking. The three amino acids (Gly323, Thr377, Thr418) in the substrate-binding pocket were rationally modified through saturation mutation. Finally, the obtained multi-site mutants T377I/T418G and G323S/T377I/T418G decolorized 76.59% and 59.37% of CR within 24 h at pH 8.0 without a mediator, which were 3.15- and 2.44-fold higher than the wild-type CotA. The catalytic efficiency of the multi-site mutants T377I/T418G and G323S/T377I/T418G to CR were increased by 2.21- and 2.01-fold compared with the wild-type CotA, respectively. The mechanism of activity enhancement of mutants was proposed by structural analysis. This evidence suggests that the mutants T377I/T418G and G323S/T377I/T418G could be used as novel bioremediation tools.
Collapse
Affiliation(s)
- Na Yan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
| | - Hui Ma
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
| | - Chun-Xue Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
| | - Xiang-Ru Liao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
| | - Zheng-Bing Guan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| |
Collapse
|
7
|
Zhang Y, Dai Z, Zhang S, Yang X. The catalytic properties of Thermus thermophilus SG0.5JP17-16 laccase were regulated by the conformational dynamics of pocket loop 6. Biochim Biophys Acta Gen Subj 2021; 1865:129872. [PMID: 33588000 DOI: 10.1016/j.bbagen.2021.129872] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/07/2021] [Accepted: 02/08/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Laccase is one member of the blue multicopper oxidase family. It can catalyze the oxidation of various substrates. The Thermus thermophilus SG0.5JP17-16 laccase (lacTT) is thermostable, pH-stable, and high tolerance to halides, and can decolorize the synthetic dyes. In lacTT, the function of the loop 6 constructing the substrate-binding pocket wasn't clear. METHODS The residues Asp394 and Asp396 located in loop 6, and were used to probe how the loop 6 influenced catalytic properties of the laccase. Site-directed mutagenesis was performed for two amino acids. Kinetic assay was utilized to characterize the catalytic efficiency of mutants. Mutants with different catalytic activities were used to decolorize the synthetic dyes to clarify the relationship between the catalytic efficiency and dye decolorization. Redox potential, structural and spectral analyses were performed to explain the differences in laccase activity between wild type and mutant enzymes. RESULTS D394M, D394E and D394R mutants with the lower laccase activity displayed a decreased decolorization efficiency, while D396A, D396M and D396E mutant enzymes with higher catalytic efficiency decolorized the synthetic dye more efficiently than the wild type enzyme. CONCLUSIONS The pocket loop 6 might experience a conformational dynamics. The D394 residue controlled this conformation change by amino acid interaction networks containing the D396 residue at the entrance of substrate channel. GENERAL SIGNIFICANCES These studies may provide clues to improve the activity of the laccase for the better use in industrial applications, and/or contribute to further understanding the mechanism of laccase oxidation on the substrate.
Collapse
Affiliation(s)
- Yi Zhang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, People's Republic of China
| | - Zhuojun Dai
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, People's Republic of China
| | - Shumin Zhang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, People's Republic of China
| | - Xiaorong Yang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, People's Republic of China.
| |
Collapse
|
8
|
Mutations in the coordination spheres of T1 Cu affect Cu 2+-activation of the laccase from Thermus thermophilus. Biochimie 2021; 182:228-237. [PMID: 33535124 DOI: 10.1016/j.biochi.2021.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/15/2020] [Accepted: 01/11/2021] [Indexed: 02/01/2023]
Abstract
Thermus thermophilus laccase belongs to the sub-class of multicopper oxidases that is activated by the extra binding of copper to a methionine-rich domain allowing an electron pathway from the substrate to the conventional first electron acceptor, the T1 Cu. In this work, two key amino acid residues in the 1st and 2nd coordination spheres of T1 Cu are mutated in view of tuning their redox potential and investigating their influence on copper-related activity. Evolution of the kinetic parameters after copper addition highlights that both mutations play a key role influencing the enzymatic activity in distinct unexpected ways. These results clearly indicate that the methionine rich domain is not the only actor in the cuprous oxidase activity of CueO-like enzymes.
Collapse
|
9
|
Borges PT, Brissos V, Hernandez G, Masgrau L, Lucas MF, Monza E, Frazão C, Cordeiro TN, Martins LO. Methionine-Rich Loop of Multicopper Oxidase McoA Follows Open-to-Close Transitions with a Role in Enzyme Catalysis. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01623] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Patrícia T. Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Vânia Brissos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Guillem Hernandez
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Laura Masgrau
- Zymvol Biomodeling, Carrer Roc Boronat, 117, 08018 Barcelona, Spain
- Department of Chemistry, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | | | - Emanuele Monza
- Zymvol Biomodeling, Carrer Roc Boronat, 117, 08018 Barcelona, Spain
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Tiago N. Cordeiro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Lígia O. Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| |
Collapse
|
10
|
Zhu Y, Zhan J, Zhang Y, Lin Y, Yang X. The K428 residue from Thermus thermophilus SG0.5JP17-16 laccase plays the substantial role in substrate binding and oxidation. J Biomol Struct Dyn 2020; 39:1312-1320. [DOI: 10.1080/07391102.2020.1729864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yanyun Zhu
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, People’s Republic Of China
| | - Jiangbo Zhan
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, People’s Republic Of China
| | - Yi Zhang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, People’s Republic Of China
| | - Ying Lin
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, People’s Republic Of China
| | - Xiaorong Yang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, People’s Republic Of China
| |
Collapse
|
11
|
Simić S, Jeremic S, Djokic L, Božić N, Vujčić Z, Lončar N, Senthamaraikannan R, Babu R, Opsenica IM, Nikodinovic-Runic J. Development of an efficient biocatalytic system based on bacterial laccase for the oxidation of selected 1,4-dihydropyridines. Enzyme Microb Technol 2020; 132:109411. [DOI: 10.1016/j.enzmictec.2019.109411] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/14/2019] [Accepted: 08/17/2019] [Indexed: 01/17/2023]
|
12
|
Abstract
There is a high number of well characterized, commercially available laccases with different redox potentials and low substrate specificity, which in turn makes them attractive for a vast array of biotechnological applications. Laccases operate as batteries, storing electrons from individual substrate oxidation reactions to reduce molecular oxygen, releasing water as the only by-product. Due to society’s increasing environmental awareness and the global intensification of bio-based economies, the biotechnological industry is also expanding. Enzymes such as laccases are seen as a better alternative for use in the wood, paper, textile, and food industries, and they are being applied as biocatalysts, biosensors, and biofuel cells. Almost 140 years from the first description of laccase, industrial implementations of these enzymes still remain scarce in comparison to their potential, which is mostly due to high production costs and the limited control of the enzymatic reaction side product(s). This review summarizes the laccase applications in the last decade, focusing on the published patents during this period.
Collapse
|