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Xia YL, Du WW, Li YP, Tao Y, Zhang ZB, Liu SM, Fu YX, Zhang KQ, Liu SQ. Computational Insights into SARS-CoV-2 Main Protease Mutations and Nirmatrelvir Efficacy: The Effects of P132H and P132H-A173V. J Chem Inf Model 2024; 64:5207-5218. [PMID: 38913174 PMCID: PMC11235099 DOI: 10.1021/acs.jcim.4c00334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 06/25/2024]
Abstract
Nirmatrelvir, a pivotal component of the oral antiviral Paxlovid for COVID-19, targets the SARS-CoV-2 main protease (Mpro) as a covalent inhibitor. Here, we employed combined computational methods to explore how the prevalent Omicron variant mutation P132H, alone and in combination with A173V (P132H-A173V), affects nirmatrelvir's efficacy. Our findings suggest that P132H enhances the noncovalent binding affinity of Mpro for nirmatrelvir, whereas P132H-A173V diminishes it. Although both mutants catalyze the rate-limiting step more efficiently than the wild-type (WT) Mpro, P132H slows the overall rate of covalent bond formation, whereas P132H-A173V accelerates it. Comprehensive analysis of noncovalent and covalent contributions to the overall binding free energy of the covalent complex suggests that P132H likely enhances Mpro sensitivity to nirmatrelvir, while P132H-A173V may confer resistance. Per-residue decompositions of the binding and activation free energies pinpoint key residues that significantly affect the binding affinity and reaction rates, revealing how the mutations modulate these effects. The mutation-induced conformational perturbations alter drug-protein local contact intensities and the electrostatic preorganization of the protein, affecting noncovalent binding affinity and the stability of key reaction states, respectively. Our findings inform the mechanisms of nirmatrelvir resistance and sensitivity, facilitating improved drug design and the detection of resistant strains.
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Affiliation(s)
- Yuan-Ling Xia
- State
Key Laboratory for Conservation and Utilization of Bio-Resources in
Yunnan & School of Life Sciences, Yunnan
University, Kunming, Yunnan 650091, China
- Editorial
Office of Journal of Yunnan University (Natural Sciences Edition), Yunnan University, Kunming, Yunnan 650091, China
| | - Wen-Wen Du
- State
Key Laboratory for Conservation and Utilization of Bio-Resources in
Yunnan & School of Life Sciences, Yunnan
University, Kunming, Yunnan 650091, China
| | - Yong-Ping Li
- School
of Agriculture, Yunnan University, Kunming, Yunnan 650091, China
| | - Yan Tao
- State
Key Laboratory for Conservation and Utilization of Bio-Resources in
Yunnan & School of Life Sciences, Yunnan
University, Kunming, Yunnan 650091, China
- Yunnan
University Library, Yunnan University, Kunming, Yunnan 650091, China
| | - Zhi-Bi Zhang
- Yunnan
Key Laboratory of Stem Cell and Regenerative Medicine & Biomedical
Engineering Research Center, Kunming Medical
University, Kunming, Yunnan 650500, China
| | - Song-Ming Liu
- State
Key Laboratory for Conservation and Utilization of Bio-Resources in
Yunnan & School of Life Sciences, Yunnan
University, Kunming, Yunnan 650091, China
| | - Yun-Xin Fu
- State
Key Laboratory for Conservation and Utilization of Bio-Resources in
Yunnan & School of Life Sciences, Yunnan
University, Kunming, Yunnan 650091, China
- Human Genetics
Center and Department of Biostatistics and Data Science, School of
Public Health, The University of Texas Health
Science Center, Houston, Texas 77030, United States
| | - Ke-Qin Zhang
- State
Key Laboratory for Conservation and Utilization of Bio-Resources in
Yunnan & School of Life Sciences, Yunnan
University, Kunming, Yunnan 650091, China
| | - Shu-Qun Liu
- State
Key Laboratory for Conservation and Utilization of Bio-Resources in
Yunnan & School of Life Sciences, Yunnan
University, Kunming, Yunnan 650091, China
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2
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Deb L, Dutta P, Mandal MK, Singh SB. Antimicrobial Traits of Beauveria bassiana Against Rhizoctonia solani, the Causal Agent of Sheath Blight of Rice Under Field Conditions. PLANT DISEASE 2023:PDIS04220806RE. [PMID: 37327392 DOI: 10.1094/pdis-04-22-0806-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Beauveria bassiana, an entomopathogenic fungus, has recently drawn attention worldwide not only as a potential biocontrol agent against insect pests but also for its other beneficial roles as plant disease antagonist, endophyte, plant growth promoter, and beneficial rhizosphere colonizer. In the present study, 53 native isolates of B. bassiana were screened for antifungal ability against Rhizoctonia solani, the causal agent of sheath blight of rice. Also, the mechanisms underlying such interaction and the responsible antimicrobial traits involved were studied. Following this, potential B. bassiana isolates were assayed against the reduction of sheath blight of rice under field conditions. The results showed that B. bassiana exhibited antagonistic behavior against R. solani with a percent mycelial inhibition recorded maximum of up to 71.15%. Mechanisms behind antagonism were the production of cell-wall-degrading enzymes, mycoparasitism, and the release of secondary metabolites. The study also deciphered several antimicrobial traits and the presence of virulent genes in B. bassiana as a determinant of potential plant disease antagonists. Under field conditions, combined application of the B. bassiana microbial consortium as a seed treatment, seedling root dip, and foliar sprays showed reduced sheath blight disease incidence and severity up to 69.26 and 60.50%, respectively, along with enhanced plant-growth-promoting attributes. This is one of the few studies investigating the antagonistic abilities of the entomopathogenic fungus B. bassiana against phytopathogen R. solani and the underlying mechanisms involved.
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Affiliation(s)
- Lipa Deb
- School of Crop Protection, College of Post-Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya 793103, India
| | - Pranab Dutta
- School of Crop Protection, College of Post-Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya 793103, India
| | - Mihir Kumar Mandal
- Department of Plant Pathology, University of California-Davis, Salinas, CA 93905, U.S.A
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3
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Shen JX, Du WW, Xia YL, Zhang ZB, Yu ZF, Fu YX, Liu SQ. Identification of and Mechanistic Insights into SARS-CoV-2 Main Protease Non-Covalent Inhibitors: An In-Silico Study. Int J Mol Sci 2023; 24:ijms24044237. [PMID: 36835648 PMCID: PMC9959744 DOI: 10.3390/ijms24044237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/11/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023] Open
Abstract
The indispensable role of the SARS-CoV-2 main protease (Mpro) in the viral replication cycle and its dissimilarity to human proteases make Mpro a promising drug target. In order to identify the non-covalent Mpro inhibitors, we performed a comprehensive study using a combined computational strategy. We first screened the ZINC purchasable compound database using the pharmacophore model generated from the reference crystal structure of Mpro complexed with the inhibitor ML188. The hit compounds were then filtered by molecular docking and predicted parameters of drug-likeness and pharmacokinetics. The final molecular dynamics (MD) simulations identified three effective candidate inhibitors (ECIs) capable of maintaining binding within the substrate-binding cavity of Mpro. We further performed comparative analyses of the reference and effective complexes in terms of dynamics, thermodynamics, binding free energy (BFE), and interaction energies and modes. The results reveal that, when compared to the inter-molecular electrostatic forces/interactions, the inter-molecular van der Waals (vdW) forces/interactions are far more important in maintaining the association and determining the high affinity. Given the un-favorable effects of the inter-molecular electrostatic interactions-association destabilization by the competitive hydrogen bond (HB) interactions and the reduced binding affinity arising from the un-compensable increase in the electrostatic desolvation penalty-we suggest that enhancing the inter-molecular vdW interactions while avoiding introducing the deeply buried HBs may be a promising strategy in future inhibitor optimization.
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Affiliation(s)
- Jian-Xin Shen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Wen-Wen Du
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Yuan-Ling Xia
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Zhi-Bi Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
- Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Biomedical Engineering Research Center, Kunming Medical University, Kunming 650500, China
| | - Ze-Fen Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Yun-Xin Fu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
- Human Genetics Center and Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center, Houston, TX 77030, USA
- Correspondence: (Y.-X.F.); (S.-Q.L.)
| | - Shu-Qun Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
- Correspondence: (Y.-X.F.); (S.-Q.L.)
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Pedezzi R, Evangelista DE, da Rosa Garzon NG, de Oliveira Simões FA, de Oliveira AHC, Polikarpov I, Cabral H. Biochemical and biophysical properties of a recombinant serine peptidase from Purpureocillium lilacinum. Biophys Chem 2023; 296:106978. [PMID: 36827753 DOI: 10.1016/j.bpc.2023.106978] [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: 11/22/2022] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023]
Abstract
The industrial uses of peptidases have already been consolidated; however, their range of applications is increasing. Thus, the biochemical characterization of new peptidases could increase the range of their biotechnological applications. In silico analysis identified a gene encoding a putative serine peptidase from Purpureocillium lilacinum (Pl_SerPep), annotated as a cuticle-degrading enzyme. The Pl_SerPep gene product was expressed as a recombinant in a Komagataella phaffii (previously Pichia pastoris) expression system. The enzyme (rPl_SerPep) showed optimal pH and temperature of 8.0 and 60 °C, respectively. Moreover, rPl_SerPep has a higher thermal stability than the cuticle-degrading enzymes described elsewhere. The structural analysis indicated a conformational change in the rPl_SerPep secondary structure, which would allow an increase in catalytic activity at 60 °C. Komagataella phaffii secretes rPl_SerPep with the pro peptide in its inactive form. Low-resolution small-angle X-ray scattering (SAXS) analysis showed little mobility of the pro peptide portion, which indicates the apparent stability of the inactive form of the enzyme. The presence of 20 mM guanidine in the reaction resulted in the maintenance of activity, which was apparently a consequence of pro peptide structure flexibilization.
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Affiliation(s)
- Rafael Pedezzi
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-903, Brazil
| | - Danilo Elton Evangelista
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador Sãocarlense 400, São Carlos 13566-590, SP, Brazil
| | - Nathalia Gonsales da Rosa Garzon
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-903, Brazil
| | - Flávio Antônio de Oliveira Simões
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-903, Brazil
| | | | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador Sãocarlense 400, São Carlos 13566-590, SP, Brazil
| | - Hamilton Cabral
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-903, Brazil.
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5
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Li R, Liu Z, Jiang F, Zhao Y, Yang G, Hong L. Enhancement of thermal stability of proteinase K by biocompatible cholinium-based ionic liquids. Phys Chem Chem Phys 2022; 24:13057-13065. [PMID: 35583879 DOI: 10.1039/d1cp04782e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proteinase K (PK) is a proteolytic enzyme that has been widely used in nucleic acid purification, leather production, environmental protection, and other industrial applications. However, this biocatalyst cannot tolerate high temperatures which has severely restricted its wider application. As reported in previous studies, cholinium-based ionic liquids (ILs) have gained tremendous attention serving as a promising media to stabilize and preserve proteins, DNA, and other biomolecules due to their environmentally benign nature and biocompatibility. In this work, we chose 13 different kinds of cholinium-based ILs to examine their effects on the thermal stability and enzymatic activity of PK. We found that biocompatible cholinium-based ions with appropriately chosen anions can greatly improve the thermal stability of PK, whose melting temperature (Tm) is increased from ∼74.4 °C to 87.7 °C. However, the enzymatic activity is slightly reduced in the presence of ILs. Further comparison of our results with other literature findings suggests that kosmotropic anions of cholinium-based ILs are crucial to maintain the thermal stability of proteins. However, to achieve the best performance, the choice of IL anions is protein specific.
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Affiliation(s)
- Rui Li
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China. .,Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhuo Liu
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China.,Shanghai National Center for Applied Mathematics (SJTU center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fan Jiang
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China. .,Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yang Zhao
- Institute of Biothermal Science and Technology, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Guangyu Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Liang Hong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China. .,Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China.,Shanghai National Center for Applied Mathematics (SJTU center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
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6
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Jafari A, Shareghi B, Hosseini-Koupaei M, Farhadian S. Characterization of osmolyte-enzyme interactions using different spectroscopy and molecular dynamic techniques: Binding of sucrose to proteinase K. Int J Biol Macromol 2020; 151:1250-1258. [DOI: 10.1016/j.ijbiomac.2019.10.171] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 10/01/2019] [Accepted: 10/22/2019] [Indexed: 12/20/2022]
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7
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The modifier action of NiO nanoparticles on the activity, structure, and stability of proteinase K. MONATSHEFTE FUR CHEMIE 2020. [DOI: 10.1007/s00706-020-02552-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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8
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Enzymatic characteristics of a recombinant protease (rPepD) from Aspergillus niger expressed in Pichia pastoris. Protein Expr Purif 2019; 162:67-71. [PMID: 31181254 DOI: 10.1016/j.pep.2019.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/12/2019] [Accepted: 06/07/2019] [Indexed: 11/21/2022]
Abstract
The Aspergillus niger AS3.350 protease gene (pepD) was successfully cloned and expressed in Pichia pastoris KM71. The rPepD activity was 331.5 U/ml, and the optimum temperature and pH were 45 °C and 8-9 respectively. In addition, enzyme activity was significantly inhibited by PMSF, EDTA, Mg2+, Fe2+ and Zn2+ ions, and stimulated by Ca2+ which selectively bound to the T302 and D323 residues. Mutation in either or both of the residues inhibited rPepD expression, indicating that binding to Ca2+ is necessary for PepD expression and activity. The rPepD showed a wide substrate range, and was particularly selective to those with hydrophobic amino acids. The degree of rPepD-mediated hydrolysis of soy protein isolate, corn flour and gluten meal were 8.7%, 38.1% and 33.6% respectively, which was higher than that by Alcalase, indicating that rPepD has potential applications in the food processing industry.
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9
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Keppanan R, Krutmuang P, Sivaperumal S, Hussain M, Bamisile BS, Aguila LCR, Dash CK, Wang L. Synthesis of mycotoxin protein IF8 by the entomopathogenic fungus Isaria fumosorosea and its toxic effect against adult Diaphorina citri. Int J Biol Macromol 2018; 125:1203-1211. [PMID: 30227211 DOI: 10.1016/j.ijbiomac.2018.09.093] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/12/2018] [Accepted: 09/15/2018] [Indexed: 01/05/2023]
Abstract
Entomopathogenic fungi based microbial insecticides are considered as safe alternatives to chemical pesticides, which secretes several bioactive compounds to kill the host insects. In this study, we report a new approach for the synthesis and characterization of insecticide toxic protein IF8 produced by the Isaria fumosorosea 08, and to evaluate the mycotoxin level against the vector of Huanglongbing (HLB) or citrus greening disease, the Asian citrus psyllid, Diaphorina citri. Soluble toxic metabolites extracted from I. fumosorosea 08 through submerged liquid state culture had a molecular weight of 43 kDa when subjected by to sodium dodecyl sulfate-poly-acrylamide (SDS-PAGE) gel electrophoresis. The most abundant of toxic protein IF8 was determined by High-performance liquid chromatography (HPLC) and liquid chromatography electrospray ionization-mass spectroscopy (LC-ESI-MS) for the analysis of its molecular mass weight and purity. Further Matrix-assisted laser desorption ionization-time of flight (MALDI-TOFF) analysis confirmed the presence of toxic metabolites in liquid culture. Subsequently, mycotoxic effect of toxic protein IF8 was tested against D. citri at three different concentrations (1%, 2%, and 3%). The results showed the insecticidal activity of >80% when administered at three different concentrations at 48-120 hour post-application. Additionally, we also investigated the physicochemical properties and stability of IF8 by using computational biological tools. This is the first study to report the characterization of fungal mediated synthesis of the protein IF8 toxic to the insect D. citri. These results suggest the mycotoxin control of D. citri and prevention of HLB transmission by using a natural toxic compound which is eco-friendly and can be potentially used for the integrated management of D. citri.
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Affiliation(s)
- Ravindran Keppanan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China; College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | | | - Sivaramakrishnan Sivaperumal
- Department of Biotechnology and Genetic Engineering, School of Life Sciences, Bharathidasan University, Tamil Nadu, India
| | - Mubasher Hussain
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China; College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China; College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bamisope Steve Bamisile
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China; College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Luis Carlos Ramos Aguila
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China; College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chandra Kanta Dash
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China; College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liande Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China; College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
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10
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Ravindran K, Sivaramakrishnan S, Hussain M, Dash CK, Bamisile BS, Qasim M, Liande W. Investigation and molecular docking studies of Bassianolide from Lecanicillium lecanii against Plutella xylostella (Lepidoptera: Plutellidae). Comp Biochem Physiol C Toxicol Pharmacol 2018; 206-207:65-72. [PMID: 29551387 DOI: 10.1016/j.cbpc.2018.03.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/10/2018] [Accepted: 03/14/2018] [Indexed: 01/29/2023]
Abstract
Entomopathogenic fungi are rich sources of bioactive secondary metabolites that possess insecticidal properties. The present study reported a novel approach for the identification of insecticidal compounds produced by Lecanicillium lecanii 09 and to assess their toxicity against the diamondback moth Plutella xylostella L. The cyclic peptides groups of toxic substances were separated from L. lecanii 09 through submerged liquid state fermentation. The most abundant toxic metabolite, Bassianolide was purified by high-performance liquid chromatography (HPLC) and its molecular weight and purity were determined by Liquid chromatography - mass spectroscopy (LC-MS), Fourier transformed infrared spectroscopy (FT-IR), and H1 nuclear magnetic resonance (NMR) respectively. Subsequently, the toxicity of bassianolide was tested against third instar larvae of P. xylostella at three different concentrations (0.01, 0.1, 0.5 mg/ml). The results showed that higher concentration of 0.5 mg/ml had significant maximum mortality at 120 hour post inoculation. Furthermore, we investigated the ligand-target interaction of secondary metabolite binding with target insect immune receptor proteins and predicted the role of toxicity against insect host. This is the first study to report the infection process and the interaction of fungal mediated cyclicdepsipeptide compound (bassianolide) from L. lecanii 09 against the insect host P. xylostella. This novel approach provides a potential impact on biological control using natural toxic compound which acts as good inhibitor on pest insect and prevents toxicity hazards, pollution as well as ecocidal effects killing several beneficial insects.
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MESH Headings
- Animals
- Biological Control Agents/chemistry
- Biological Control Agents/isolation & purification
- Biological Control Agents/metabolism
- Biological Control Agents/pharmacology
- China
- Chromatography, High Pressure Liquid
- Cordyceps/chemistry
- Cordyceps/growth & development
- Cordyceps/physiology
- Fermentation
- Host-Pathogen Interactions
- Insect Proteins/antagonists & inhibitors
- Insect Proteins/chemistry
- Insect Proteins/metabolism
- Insecticides/chemistry
- Insecticides/isolation & purification
- Insecticides/metabolism
- Insecticides/pharmacology
- Larva/drug effects
- Larva/growth & development
- Larva/microbiology
- Ligands
- Models, Molecular
- Molecular Docking Simulation
- Molecular Structure
- Molecular Weight
- Moths/drug effects
- Moths/growth & development
- Moths/microbiology
- Nuclear Magnetic Resonance, Biomolecular
- Peptides, Cyclic/chemistry
- Peptides, Cyclic/isolation & purification
- Peptides, Cyclic/metabolism
- Peptides, Cyclic/pharmacology
- Spectrometry, Mass, Electrospray Ionization
- Spectroscopy, Fourier Transform Infrared
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Affiliation(s)
- Keppanan Ravindran
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sivaperumal Sivaramakrishnan
- Department of Biotechnology and Genetic Engineering, School of Life Sciences, Bharathidasan University, Tamil Nadu, India
| | - Mubasher Hussain
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China; College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chandra Kanta Dash
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bamisope Steve Bamisile
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Muhammad Qasim
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wang Liande
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
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11
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Xia YL, Sun JH, Ai SM, Li Y, Du X, Sang P, Yang LQ, Fu YX, Liu SQ. Insights into the role of electrostatics in temperature adaptation: a comparative study of psychrophilic, mesophilic, and thermophilic subtilisin-like serine proteases. RSC Adv 2018; 8:29698-29713. [PMID: 35547280 PMCID: PMC9085296 DOI: 10.1039/c8ra05845h] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 08/15/2018] [Indexed: 11/21/2022] Open
Abstract
To investigate the role of electrostatics in different temperature adaptations, we performed a comparative study on subtilisin-like serine proteases from psychrophilic Vibrio sp. PA-44 (VPR), mesophilic Engyodontium album (Tritirachium album) (PRK), and thermophilic Thermus aquaticus (AQN) using multiple-replica molecular dynamics (MD) simulations combined with continuum electrostatics calculations. The results reveal that although salt bridges are not a crucial factor in determining the overall thermostability of these three proteases, they on average provide the greatest, moderate, and least electrostatic stabilization to AQN, PRK, and VPR, respectively, at the respective organism growth temperatures. Most salt bridges in AQN are effectively stabilizing and thus contribute to maintaining the overall structural stability at 343 K, while nearly half of the salt bridges in VPR interconvert between being stabilizing and being destabilizing, likely aiding in enhancing the local conformational flexibility at 283 K. The individual salt bridges, salt-bridge networks, and calcium ions contribute differentially to local stability and flexibility of these three enzyme structures, depending on their spatial distributions and electrostatic strengths. The shared negatively charged surface potential at the active center of the three enzymes may provide the active-center flexibility necessary for nucleophilic attack and proton transfer. The differences in distributions of the electro-negative, electro-positive, and electro-neutral potentials, particularly over the back surfaces of the three proteases, may modulate/affect not only protein solubility and thermostability but also structural stability and flexibility/rigidity. These results demonstrate that electrostatics contributes to both heat and cold adaptation of subtilisin-like serine proteases through fine-tuning, either globally or locally, the structural stability and conformational flexibility/rigidity, thus providing a foundation for further engineering and mutagenesis studies. Differently charged surface patches contribute to temperature adaptation of subtilisin-like serine proteases through affecting/modulating the protein solubility and thermostability and the structural flexibility/rigidity/stability.![]()
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Affiliation(s)
- Yuan-Ling Xia
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan
- Yunnan University
- Kunming
- P. R. China
| | - Jian-Hong Sun
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan
- Yunnan University
- Kunming
- P. R. China
| | - Shi-Meng Ai
- Department of Applied Mathematics
- Yunnan Agricultural University
- Kunming
- P. R. China
| | - Yi Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan
- Yunnan University
- Kunming
- P. R. China
| | - Xing Du
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan
- Yunnan University
- Kunming
- P. R. China
| | - Peng Sang
- College of Agriculture and Biological Science
- Dali University
- Dali
- P. R. China
| | - Li-Quan Yang
- College of Agriculture and Biological Science
- Dali University
- Dali
- P. R. China
| | - Yun-Xin Fu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan
- Yunnan University
- Kunming
- P. R. China
- Human Genetics Center and Division of Biostatistics
| | - Shu-Qun Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan
- Yunnan University
- Kunming
- P. R. China
- Key Laboratory for Tumor Molecular Biology of High Education in Yunnan Province
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12
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Hosseini-Koupaei M, Shareghi B, Saboury AA, Davar F. Molecular investigation on the interaction of spermine with proteinase K by multispectroscopic techniques and molecular simulation studies. Int J Biol Macromol 2017; 94:406-414. [DOI: 10.1016/j.ijbiomac.2016.10.038] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 09/30/2016] [Accepted: 10/14/2016] [Indexed: 11/17/2022]
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13
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Du X, Sang P, Xia YL, Li Y, Liang J, Ai SM, Ji XL, Fu YX, Liu SQ. Comparative thermal unfolding study of psychrophilic and mesophilic subtilisin-like serine proteases by molecular dynamics simulations. J Biomol Struct Dyn 2016; 35:1500-1517. [PMID: 27485684 DOI: 10.1080/07391102.2016.1188155] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Molecular dynamics (MD) simulations of a subtilisin-like serine protease VPR from the psychrophilic marine bacterium Vibrio sp. PA-44 and its mesophilic homologue, proteinase K (PRK), have been performed for 20 ns at four different temperatures (300, 373, 473, and 573 K). The comparative analyses of MD trajectories reveal that at almost all temperatures, VPR exhibits greater structural fluctuations/deviations, more unstable regular secondary structural elements, and higher global flexibility than PRK. Although these two proteases follow similar unfolding pathways at high temperatures, VPR initiates unfolding at a lower temperature and unfolds faster at the same high temperatures than PRK. These observations collectively indicate that VPR is less stable and more heat-labile than PRK. Analyses of the structural/geometrical properties reveal that, when compared to PRK, VPR has larger radius of gyration (Rg), less intramolecular contacts and hydrogen bonds (HBs), more protein-solvent HBs, and smaller burial of nonpolar area and larger exposure of polar area. These suggest that the increased flexibility of VPR would be most likely caused by its reduced intramolecular interactions and more favourable protein-solvent interactions arising from the larger exposure of the polar area, whereas the enhanced stability of PRK could be ascribed to its increased intramolecular interactions arising from the better optimized hydrophobicity. The factors responsible for the significant differences in local flexibility between these two proteases were also analyzed and ascertained. This study provides insights into molecular basis of thermostability of homologous serine proteases adapted to different temperatures.
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Affiliation(s)
- Xing Du
- a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China
| | - Peng Sang
- b Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming 650032 , PR China
| | - Yuan-Ling Xia
- a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China
| | - Yi Li
- a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China
| | - Jing Liang
- a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China
| | - Shi-Meng Ai
- c Department of Applied Mathematics , Yunnan Agricultural University , Kunming 650201 , PR China
| | - Xing-Lai Ji
- a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China.,d Key Laboratory for Tumor Molecular Biology of High Education in Yunnan Province, School of Life Sciences , Yunnan University , Kunming 650223 , PR China
| | - Yun-Xin Fu
- a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China.,e Human Genetics Center and Division of Biostatistics, School of Public Health , The University of Texas Health Science Center , Houston , TX , 77030 , USA
| | - Shu-Qun Liu
- a Laboratory for Conservation and Utilization of Bio-Resources , Yunnan University , Kunming 650091 , PR China.,d Key Laboratory for Tumor Molecular Biology of High Education in Yunnan Province, School of Life Sciences , Yunnan University , Kunming 650223 , PR China
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14
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15
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Khan S, Nadir S, Wang X, Khan A, Xu J, Li M, Tao L, Khan S, Karunarathna SC. Using in silico techniques: Isolation and characterization of an insect cuticle-degrading-protease gene from Beauveria bassiana. Microb Pathog 2016; 97:189-97. [PMID: 27287496 DOI: 10.1016/j.micpath.2016.05.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/05/2016] [Accepted: 05/29/2016] [Indexed: 10/21/2022]
Abstract
Cuticle-degrading-proteases (CDPs) secreted by Beauveria spp. are pivotal biocontrol substances, possessing commercial potential for developing bio-pesticides. Therefore, a thoughtful and contemplative understanding and assessment of the structural and functional features of these proteases would markedly assist the development of biogenic pesticides. Computational molecular biology is a new facile alternative approach to the tedious experimental molecular biology; therefore, by using bioinformatics tools, we isolated and characterized an insect CDP gene from Beauveria bassiana 70 s.l. genomic DNA. The CDP gene (1240 bp with GeneBank accession no. KT804651.1) consisted of three introns and four CDS exons, and shared 74-100% sequence identity to the reference CDP genes. Its phylogenetic tree results showed a unique evolution pattern, and the predicted amino acid peptide (PAAP) consisted of 344 amino acid residues with pI, molecular weight, instability index, grand average hydropathicity value and aliphatic index of 7.2, 35.4 kDa, 24.45, -0.149, and 76.63, respectively. The gene possessed 74-89% amino acid sequence similarity to the 12 reference strains. Three motifs (Peptidase_S8 subtilase family) were detected in the PAAP, and the computed 3D structure possessed 79.09% structural identity to alkaline serine proteases. The PAAP had four (three serine proteases and one Pyridoxal-dependent decarboxylase) conserved domains, a disulfide bridge, two calcium binding sites, MY domain, and three predicted active sites in the serine family domains. These results will set the groundwork for further exploitation of proteases and understanding the mechanism of disease caused by cuticle-degrading-serine-proteases from entomopathogenic fungi.
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Affiliation(s)
- Sehroon Khan
- World Agroforestry Centre, East and Central Asia Office, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Rd, Heilongtan, Kunming 650201, Yunnan, China; Centre for Mountain Ecosystem Studies, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China.
| | - Sadia Nadir
- Department of Chemistry, Faculty of Sciences, University of Science and Technology Bannu, 28100 Bannu, Khyber Pakhtunkhwa, Pakistan; Rice Research Institute, Yunnan Agriculture University, Heilongtan, Kunming 650201, Yunnan, China
| | - Xuewen Wang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, Yunnan, China.
| | - Afsar Khan
- Department of Chemistry, COMSATS Institute of Information Technology, Abbottabad 22060, Pakistan
| | - Jianchu Xu
- World Agroforestry Centre, East and Central Asia Office, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Rd, Heilongtan, Kunming 650201, Yunnan, China; Centre for Mountain Ecosystem Studies, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | - Meng Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, Yunnan, China
| | - Lihong Tao
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, Yunnan, China
| | - Siraj Khan
- School of Software, Beijing Institute of Technology, Beijing, China
| | - Samantha C Karunarathna
- World Agroforestry Centre, East and Central Asia Office, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Rd, Heilongtan, Kunming 650201, Yunnan, China
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16
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Sang P, Yang Q, Du X, Yang N, Yang LQ, Ji XL, Fu YX, Meng ZH, Liu SQ. Effect of the Solvent Temperatures on Dynamics of Serine Protease Proteinase K. Int J Mol Sci 2016; 17:254. [PMID: 26907253 DOI: 10.3390/ijms17020254] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 01/21/2016] [Accepted: 02/06/2016] [Indexed: 11/16/2022] Open
Abstract
To obtain detailed information about the effect of the solvent temperatures on protein dynamics, multiple long molecular dynamics (MD) simulations of serine protease proteinase K with the solute and solvent coupled to different temperatures (either 300 or 180 K) have been performed. Comparative analyses demonstrate that the internal flexibility and mobility of proteinase K are strongly dependent on the solvent temperatures but weakly on the protein temperatures. The constructed free energy landscapes (FELs) at the high solvent temperatures exhibit a more rugged surface, broader spanning range, and higher minimum free energy level than do those at the low solvent temperatures. Comparison between the dynamic hydrogen bond (HB) numbers reveals that the high solvent temperatures intensify the competitive HB interactions between water molecules and protein surface atoms, and this in turn exacerbates the competitive HB interactions between protein internal atoms, thus enhancing the conformational flexibility and facilitating the collective motions of the protein. A refined FEL model was proposed to explain the role of the solvent mobility in facilitating the cascade amplification of microscopic motions of atoms and atomic groups into the global collective motions of the protein.
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Affiliation(s)
- Peng Sang
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
- Laboratory of Molecular Cardiology, Department of Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming 650032, China.
| | - Qiong Yang
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
| | - Xing Du
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
| | - Nan Yang
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
| | - Li-Quan Yang
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
- College of Agriculture and Biological Science, Dali University, Dali 671003, China.
| | - Xing-Lai Ji
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
| | - Yun-Xin Fu
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
- Human Genetics Center, School of Public Health, the University of Texas Health Science Center, Houston, TX 77030, USA.
| | - Zhao-Hui Meng
- Laboratory of Molecular Cardiology, Department of Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming 650032, China.
| | - Shu-Qun Liu
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
- Laboratory of Molecular Cardiology, Department of Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming 650032, China.
- Key Laboratory for Tumor molecular biology of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming 650091, China.
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17
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Hosseini-Koupaei M, Shareghi B, Saboury AA, Davar F, Raisi F. The effect of spermidine on the structure, kinetics and stability of proteinase K: spectroscopic and computational approaches. RSC Adv 2016. [DOI: 10.1039/c6ra20975k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Polyamines (such as spermidine) are low molecular weight compounds which can be used as cosolvents in biological and industrial applications.
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Affiliation(s)
| | - Behzad Shareghi
- Department of Biology
- Faculty of Science
- University of Shahrekord
- Shahrekord
- Iran
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics
- University of Tehran
- Tehran
- Iran
- Center of Excellence in Biothermodynamics
| | - Fatemeh Davar
- Department of Chemistry
- Isfahan University of Technology
- Isfahan
- Iran
| | - Fatame Raisi
- Young Researchers and Elites Club
- Islamic Azad University
- Shahrekord
- Iran
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18
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Sánchez-Pérez LDC, Barranco-Florido JE, Rodríguez-Navarro S, Cervantes-Mayagoitia JF, Ramos-López MÁ. Enzymes of Entomopathogenic Fungi, Advances and Insights. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/aer.2014.22007] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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19
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Yang LQ, Sang P, Tao Y, Fu YX, Zhang KQ, Xie YH, Liu SQ. Protein dynamics and motions in relation to their functions: several case studies and the underlying mechanisms. J Biomol Struct Dyn 2013; 32:372-93. [PMID: 23527883 PMCID: PMC3919177 DOI: 10.1080/07391102.2013.770372] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Proteins are dynamic entities in cellular solution with functions governed essentially by their dynamic personalities. We review several dynamics studies on serine protease proteinase K and HIV-1 gp120 envelope glycoprotein to demonstrate the importance of investigating the dynamic behaviors and molecular motions for a complete understanding of their structure–function relationships. Using computer simulations and essential dynamic (ED) analysis approaches, the dynamics data obtained revealed that: (i) proteinase K has highly flexible substrate-binding site, thus supporting the induced-fit or conformational selection mechanism of substrate binding; (ii) Ca2+ removal from proteinase K increases the global conformational flexibility, decreases the local flexibility of substrate-binding region, and does not influence the thermal motion of catalytic triad, thus explaining the experimentally determined decreased thermal stability, reduced substrate affinity, and almost unchanged catalytic activity upon Ca2+ removal; (iii) substrate binding affects the large concerted motions of proteinase K, and the resulting dynamic pocket can be connected to substrate binding, orientation, and product release; (iv) amino acid mutations 375 S/W and 423 I/P of HIV-1 gp120 have distinct effects on molecular motions of gp120, facilitating 375 S/W mutant to assume the CD4-bound conformation, while 423 I/P mutant to prefer for CD4-unliganded state. The mechanisms underlying protein dynamics and protein–ligand binding, including the concept of the free energy landscape (FEL) of the protein–solvent system, how the ruggedness and variability of FEL determine protein's dynamics, and how the three ligand-binding models, the lock-and-key, induced-fit, and conformational selection are rationalized based on the FEL theory are discussed in depth.
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Affiliation(s)
- Li-Quan Yang
- a Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education , Yunnan University , Kunming , 650091 , P.R. China
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20
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Larriba E, Martín-Nieto J, Lopez-Llorca LV. Gene cloning, molecular modeling, and phylogenetics of serine protease P32 and serine carboxypeptidase SCP1 from nematophagous fungi Pochonia rubescens and Pochonia chlamydosporia. Can J Microbiol 2012; 58:815-27. [PMID: 22690687 DOI: 10.1139/w2012-054] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The fungi Pochonia chlamydosporia and Pochonia rubescens are parasites of nematode eggs and thus are biocontrol agents of nematodes. Proteolytic enzymes such as the S8 proteases VCP1 and P32, secreted during the pathogenesis of nematode eggs, are major virulence factors in these fungi. Recently, expression of these enzymes and of SCP1, a new putative S10 carboxypeptidase, was detected during endophytic colonization of barley roots by these fungi. In our study, we cloned the genomic and mRNA sequences encoding P32 from P. rubescens and SCP1 from P. chlamydosporia. P32 showed a high homology with the serine proteases Pr1A from the entomopathogenic fungus Metarhizium anisopliae and VCP1 from P. chlamydosporia (86% and 76% identity, respectively). However, the catalytic pocket of P32 showed differences in the amino acids of the substrate-recognition sites compared with the catalytic pockets of Pr1A and VCP1 proteases. Phylogenetic analysis of P32 suggests a common ancestor with protease Pr1A. SCP1 displays the characteristic features of a member of the S10 family of serine proteases. Phylogenetic comparisons show that SCP1 and other carboxypeptidases from filamentous fungi have an origin different from that of yeast vacuolar serine carboxypeptidases. Understanding protease genes from nematophagous fungi is crucial for enhancing the biocontrol potential of these organisms.
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Affiliation(s)
- Eduardo Larriba
- Department of Marine Sciences and Applied Biology, University of Alicante, Spain.
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21
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Liang L, Liu S, Yang J, Meng Z, Lei L, Zhang K. Comparison of homology models and crystal structures of cuticle-degrading proteases from nematophagous fungi: structural basis of nematicidal activity. FASEB J 2011; 25:1894-902. [PMID: 21350115 DOI: 10.1096/fj.10-175653] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Cuticle-degrading proteases secreted by nematophagous fungi can degrade nematode cuticle during infection. Alkaline proteases from nematode-parasitic fungi show stronger nematicidal activity in vitro than neutral proteases from nematode-trapping fungi. Sequence alignment of these proteases revealed that the active-site residues were much conserved. Disulfide bridges in alkaline proteases not only contribute to the thermal stability of enzyme structure but also increase the flexibility of S1 and S4 pockets located at the substrate-binding site. Molecular electrostatic potential surfaces of these proteases change gradually from negative to positive while arranging in the order from neutral to alkaline proteases, possibly contributing to the distinct extent of substrate (nematode cuticle) attraction by proteases. The differences in flexibility of substrate-binding site and in electrostatic surface potential distribution between neutral and alkaline cuticle-degrading proteases are associated with the changes of their catalytic activities and nematicidal activities with fungal species. Our results indicate that nematode-parasitic and nematode-trapping fungi have evolved for distinct adaptation under selective pressure.
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Affiliation(s)
- Lianming Liang
- Laboratory for Conservation and Utilization of Bioresources, Yunnan University, Kunming 650091, China
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22
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Liang L, Yang J, Li J, Mo Y, Li L, Zhao X, Zhang KQ. Cloning and homology modeling of a serine protease gene (PrC) from the nematophagous fungus Clonostachys rosea. ANN MICROBIOL 2010. [DOI: 10.1007/s13213-010-0166-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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23
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Tao Y, Rao ZH, Liu SQ. Insight derived from molecular dynamics simulation into substrate-induced changes in protein motions of proteinase K. J Biomol Struct Dyn 2010; 28:143-58. [PMID: 20645649 DOI: 10.1080/073911010010524953] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Because of the significant industrial, agricultural and biotechnological importance of serine protease proteinase K, it has been extensively investigated using experimental approaches such as X-ray crystallography, site-directed mutagenesis and kinetic measurement. However, detailed aspects of enzymatic mechanism such as substrate binding, release and relevant regulation remain unstudied. Molecular dynamics (MD) simulations of the proteinase K alone and in complex with the peptide substrate AAPA were performed to investigate the effect of substrate binding on the dynamics/molecular motions of proteinase K. The results indicate that during simulations the substrate-complexed proteinase K adopt a more compact and stable conformation than the substrate-free form. Further essential dynamics (ED) analysis reveals that the major internal motions are confined within a subspace of very small dimension. Upon substrate binding, the overall flexibility of the protease is reduced; and the noticeable displacements are observed not only in substrate-binding regions but also in regions opposite the substrate-binding groove/pockets. The dynamic pockets caused by the large concerted motions are proposed to be linked to the substrate recognition, binding, orientation and product release; and the significant displacements in regions opposite the binding groove/pockets are considered to play a role in modulating the dynamics of enzyme-substrate interaction. Our simulation results complement the biochemical and structural studies, highlighting the dynamic mechanism of the functional properties of proteinase K.
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Affiliation(s)
- Yan Tao
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, Yunnan, P R China
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24
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Liu SQ, Tao Y, Meng ZH, Fu YX, Zhang KQ. The effect of calciums on molecular motions of proteinase K. J Mol Model 2010; 17:289-300. [DOI: 10.1007/s00894-010-0724-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Accepted: 04/19/2010] [Indexed: 10/19/2022]
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25
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Molecular cloning and homology modelling of a subtilisin-like serine protease from the marine fungus, Engyodontium album BTMFS10. World J Microbiol Biotechnol 2010; 26:1269-79. [DOI: 10.1007/s11274-009-0298-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2009] [Accepted: 12/22/2009] [Indexed: 10/20/2022]
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26
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Liang L, Meng Z, Ye F, Yang J, Liu S, Sun Y, Guo Y, Mi Q, Huang X, Zou C, Rao Z, Lou Z, Zhang KQ. The crystal structures of two cuticle-degrading proteases from nematophagous fungi and their contribution to infection against nematodes. FASEB J 2009; 24:1391-400. [PMID: 20007510 DOI: 10.1096/fj.09-136408] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Cuticle-degrading proteases are involved in the breakdown of cuticle/eggshells of nematodes or insects, a hard physical barrier against fungal infections. Understanding the 3-dimensional structures of these proteins can provide crucial information for improving the effectiveness of these fungi in biocontrol applications, e.g., by targeted protein engineering. However, the structures of these proteases remain unknown. Here, we report the structures of two cuticle-degrading proteases from two species of nematophagous fungi. The two structures were solved with X-ray crystallography to resolutions of 1.65 A (Ver112) and 2.1 A (PL646), respectively. Crystal structures of PL646 and Ver112 were found to be very similar to each other, and similar to that of proteinase K from another fungus Tritirachium album. Differences between the structures were found among residues of the substrate binding sites (S1 and S4). Experimental studies showed that the enzymes differed in hydrolytic activity to synthetic peptide substrates. Our analyses of the hydrophobic/hydrophilic and electrostatic features of these two proteins suggest that their surfaces likely play important roles during fungal infection against nematodes. The two crystal structures provide a solid basis for investigating the relationship between structure and function of cuticle-degrading proteases.
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Affiliation(s)
- Lianming Liang
- Laboratory for Conservation and Utilization of Bioresources, Yunnan University, 2 North Cuihu Road, Kunming 650091, China
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27
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Liu SQ, Meng ZH, Fu YX, Zhang KQ. Insights derived from molecular dynamics simulation into the molecular motions of serine protease proteinase K. J Mol Model 2009; 16:17-28. [PMID: 19466463 DOI: 10.1007/s00894-009-0518-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2009] [Accepted: 04/07/2009] [Indexed: 10/20/2022]
Abstract
Serine protease proteinase K, a member of the subtilisin family of enzymes, is of significant industrial, agricultural and biotechnological importance. Despite the wealth of structural information about proteinase K provided by static X-ray structures, a full understanding of the enzymatic mechanism requires further insight into the dynamic properties of this enzyme. Molecular dynamics simulations and essential dynamics (ED) analysis were performed to investigate the molecular motions in proteinase K. The results indicate that the internal core of proteinase K is relatively rigid, whereas the surface-exposed loops, most notably the substrate-binding regions, exhibit considerable conformational fluctuations. Further ED analysis reveals that the large concerted motions in the substrate-binding regions cause opening/closing of the substrate-binding pockets, thus supporting the proposed induced-fit mechanism of substrate binding. The distinct electrostatic/hydrogen-bonding interactions between Asp39 and His69 and between His69 and Ser224 within the catalytic triad lead to different thermal motions and orientations of these three catalytic residues, which can be related to their different functional roles in the catalytic process. Statistical analyses of the geometrical/functional properties as well as evolutionary conservation of the glycines in proteinase K-like proteins reveal that glycines may play an important role in determining the folding architecture and structural flexibility of this class of enzymes. Our simulation study complements the biochemical and structural studies and provides new insights into the dynamic structural basis of the functional properties of this class of enzymes.
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Affiliation(s)
- Shu-Qun Liu
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, 650091 Yunnan, P. R. China
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28
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Li J, Jia Z, Zhou W, Wei Q. Calcineurin regulatory subunit B is a unique calcium sensor that regulates calcineurin in both calcium-dependent and calcium-independent manner. Proteins 2009; 77:612-23. [DOI: 10.1002/prot.22474] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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29
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Ye F, Liang L, Mi Q, Yang J, Lou Z, Sun Y, Guo Y, Meng Z, Zhang K. Preliminary crystallographic study of two cuticle-degrading proteases from the nematophagous fungi Lecanicillium psalliotae and Paecilomyces lilacinus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:271-4. [PMID: 19255481 PMCID: PMC2650454 DOI: 10.1107/s1744309109003595] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2008] [Accepted: 01/29/2009] [Indexed: 11/11/2022]
Abstract
Cuticle-degrading proteases are extracellular subtilisin-like serine proteases that are secreted by entomopathogenic and nematophagous fungi. These proteases can digest the host cuticle during invasion of an insect or nematode and serve as a group of important virulence factors during the infection of nematodes by nematophagous fungi. To elucidate the mechanism of interaction between the proteases and the nematode cuticle, two cuticle-degrading proteases, Ver112 from Lecanicillium psalliotae (syn. Verticillium psalliotae) and PL646 from Paecilomyces lilacinus, were studied. The Ver112 protein and the complex between PL646 and the substrate-like tetrapeptide inhibitor methoxysuccinyl-Ala-Ala-Pro-Val-chloromethyl ketone (MSU-AAPV) were crystallized using the hanging-drop vapour-diffusion method at 289 K. The crystals were analyzed by X-ray diffraction to resolutions of 1.65 and 2.2 A, respectively. These analyses identified that crystals of Ver112 belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 43.7, b = 67.8, c = 76.3 A, alpha = beta = gamma = 90 degrees . In contrast, crystals of the PL646-MSU-AAPV complex belonged to space group P2(1), with unit-cell parameters a = 65.1, b = 62.5, c = 67.6 A, beta = 92.8 degrees .
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Affiliation(s)
- Fengping Ye
- Laboratory for Conservation and Utilization of Bio-resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, People’s Republic of China
| | - Lianming Liang
- Laboratory for Conservation and Utilization of Bio-resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, People’s Republic of China
| | - Qili Mi
- Laboratory for Conservation and Utilization of Bio-resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, People’s Republic of China
| | - Jinkui Yang
- Laboratory for Conservation and Utilization of Bio-resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, People’s Republic of China
| | - Zhiyong Lou
- Tsinghua–Nankai–IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Yuna Sun
- Tsinghua–Nankai–IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Yu Guo
- Tsinghua–Nankai–IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Zhaohui Meng
- Laboratory for Conservation and Utilization of Bio-resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, People’s Republic of China
- Laboratory of Molecular Cardiology, Department of Cardiology, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, People’s Republic of China
| | - Keqin Zhang
- Laboratory for Conservation and Utilization of Bio-resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, People’s Republic of China
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