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Stojanovski BM, Di Cera E. Codon switching of conserved Ser residues in coagulation and fibrinolytic proteases. J Thromb Haemost 2024:S1538-7836(24)00307-6. [PMID: 38821294 DOI: 10.1016/j.jtha.2024.05.021] [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: 03/13/2024] [Revised: 04/30/2024] [Accepted: 05/21/2024] [Indexed: 06/02/2024]
Abstract
BACKGROUND Unique among all amino acids, Ser is encoded by 2 sets of codons, TCN and AGY (N = any nucleotide, Y = pyrimidine), that cannot interconvert through single nucleotide substitutions. Both codons are documented at the essential residues S195 and S214 within the active site of serine proteases. However, it is not known how the codons interconverted during evolution because replacement of S195 or S214 by other amino acids typically results in loss of activity. OBJECTIVE To characterize the prevalence of codon switching among essential and non-essential Ser residues in coagulation and fibrinolytic proteases from different vertebrate lineages. METHODS TCN and AGY codon usage was analyzed in >550 sequences. RESULTS Evolutionary pressure to preserve the codon of S195 is absolute, with no evidence of interconversion. Pressure to preserve the codon of S214 is also strong, but an AGY↔TCN interconversion is observed in factor VII-inactive and protein C from ray-finned fish. In both cases, the interconversion occurred in genes that were rapidly evolving. In contrast, codon switching at nonessential Ser residues in the kringle domains of coagulation and fibrinolytic proteases is quite common and could be identified in half of the kringles analyzed. CONCLUSION Codon interconversion of essential Ser residues of coagulation and fibrinolytic proteases only occurred in genes that were rapidly evolving and that-at least in some cases-evolved following genome duplication. Interconversion is common at nonessential Ser residues as found in kringle domains.
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Affiliation(s)
- Bosko M Stojanovski
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, Missouri, USA
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, Missouri, USA.
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2
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Stojanovski BM, Pelc LA, Di Cera E. Thrombin has dual trypsin-like and chymotrypsin-like specificity. J Thromb Haemost 2024; 22:1009-1015. [PMID: 38160728 PMCID: PMC10960677 DOI: 10.1016/j.jtha.2023.12.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND The residue at the site of activation of protein C is Arg in all species except the ray-finned fish, where it is Trp. This feature raises the question of whether thrombin is the physiological activator of protein C across vertebrates. OBJECTIVES To establish if thrombin can cleave at Trp residues. METHODS The activity of wild-type thrombin and mutant D189S was tested with a library of chromogenic substrates and toward wild-type protein C and mutants carrying substitutions at the site of cleavage. RESULTS Thrombin has trypsin-like and chymotrypsin-like specificity and cleaves substrates at Arg or Trp residues. Cleavage at Arg is preferred, but cleavage at Trp is significant and comparable with that of chymotrypsin. The D189S mutant of thrombin has broad specificity and cleaves at basic and aromatic residues without significant preference. Thrombin also cleaves natural substrates at Arg or Trp residues, showing activity toward protein C across vertebrates, including the ray-finned fish. The rate of activation of protein C in the ray-finned fish is affected by the sequence preceding Trp at the scissile bond. CONCLUSION The results provide a possible solution for the paradoxical presence of a Trp residue at the site of cleavage of protein C in ray-finned fish and support thrombin as the physiological activator of protein C in all vertebrates. The dual trypsin-like and chymotrypsin-like specificity of thrombin suggests that the spectrum of physiological substrates of this enzyme is broader currently assumed.
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Affiliation(s)
- Bosko M Stojanovski
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Leslie A Pelc
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA.
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3
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Lu H, Zhao Z, Yu H, Iqbal A, Jiang P. The serine protease 2 gene regulates lipid metabolism through the LEP/ampkα1/SREBP1 pathway in bovine mammary epithelial cells. Biochem Biophys Res Commun 2024; 698:149558. [PMID: 38271832 DOI: 10.1016/j.bbrc.2024.149558] [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: 11/21/2023] [Revised: 01/12/2024] [Accepted: 01/20/2024] [Indexed: 01/27/2024]
Abstract
Molecular breeding has brought about significant transformations in the milk market and production system during the twenty-first century. The primary economic characteristic of dairy production pertains to milk fat content. Our previous transcriptome analyses revealed that serine protease 2 (PRSS2) is a candidate gene that could impact milk fat synthesis in bovine mammary epithelial cells (BMECs) of Chinese Holstein dairy cows. To elucidate the function of the PRSS2 gene in milk fat synthesis, we constructed vectors for PRSS2 overexpression and interference and assessed intracellular triglycerides (TGs), cholesterol (CHOL), and nonesterified fatty acid (NEFA) contents in BMECs. Fatty acid varieties and components were also quantified using gas chromatography‒mass spectrometry (GC‒MS) technology. The regulatory pathway mediated by PRSS2 was validated through qPCR, ELISA, and WB techniques. Based on our research findings, PRSS2 emerges as a pivotal gene that regulates the expression of associated genes, thereby making a substantial contribution to lipid metabolism via the leptin (LEP)/Adenylate-activated protein kinase, alpha 1 catalytic subunit (AMPKα1)/sterol regulatory element binding protein 1(SREBP1) pathway by inhibiting TGs and CHOL accumulation while potentially promoting NEFA synthesis in BMECs. Furthermore, the PRSS2 gene enhances intracellular medium- and long-chain fatty acid metabolism by modulating genes related to the LEP/AMPKα1/SREBP1 pathway, leading to increased contents of unsaturated fatty acids C17:1N7 and C22:4N6. This study provides a robust theoretical framework for further investigation into the underlying molecular mechanisms through which PRSS2 influences lipid metabolism in dairy cows.
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Affiliation(s)
- Huixian Lu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China; The Key Laboratory of Animal Resources and Breed Innovation in Western Guangdong Province, Guangdong Ocean University, Zhanjiang, China
| | - Zhihui Zhao
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China; The Key Laboratory of Animal Resources and Breed Innovation in Western Guangdong Province, Guangdong Ocean University, Zhanjiang, China
| | - Haibin Yu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China; The Key Laboratory of Animal Resources and Breed Innovation in Western Guangdong Province, Guangdong Ocean University, Zhanjiang, China
| | - Ambreen Iqbal
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China; The Key Laboratory of Animal Resources and Breed Innovation in Western Guangdong Province, Guangdong Ocean University, Zhanjiang, China
| | - Ping Jiang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China; The Key Laboratory of Animal Resources and Breed Innovation in Western Guangdong Province, Guangdong Ocean University, Zhanjiang, China.
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4
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Williamson G, Harris T, Bizior A, Hoskisson PA, Pritchard L, Javelle A. Biological ammonium transporters: evolution and diversification. FEBS J 2024. [PMID: 38265636 DOI: 10.1111/febs.17059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/14/2023] [Accepted: 01/09/2024] [Indexed: 01/25/2024]
Abstract
Although ammonium is the preferred nitrogen source for microbes and plants, in animal cells it is a toxic product of nitrogen metabolism that needs to be excreted. Thus, ammonium movement across biological membranes, whether for uptake or excretion, is a fundamental and ubiquitous biological process catalysed by the superfamily of the Amt/Mep/Rh transporters. A remarkable feature of the Amt/Mep/Rh family is that they are ubiquitous and, despite sharing low amino acid sequence identity, are highly structurally conserved. Despite sharing a common structure, these proteins have become involved in a diverse range of physiological process spanning all domains of life, with reports describing their involvement in diverse biological processes being published regularly. In this context, we exhaustively present their range of biological roles across the domains of life and after explore current hypotheses concerning their evolution to help to understand how and why the conserved structure fulfils diverse physiological functions.
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Affiliation(s)
- Gordon Williamson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Thomas Harris
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Adriana Bizior
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Paul Alan Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Leighton Pritchard
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Arnaud Javelle
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
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Li N, Shen B, Liu Y, Weng P, Wu Z. Heterologous expression and characterization of Bacillus velezensis SW5 serine protease involved in the hydrolysis of anchovy protein. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:3468-3478. [PMID: 36807149 DOI: 10.1002/jsfa.12514] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/13/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Bacillus velezensis SW5, with good enzyme production ability, was isolated and identified in our laboratory from fermented fish sauce. Its galactosidase has been expressed in Escherichia coli, which could hydrolyze lactose in milk. The present study aims to express a novel serine protease gene (SPr-SW5) of this strain by Bacillus subtilis WB800N, and applies the expressed enzyme in hydrolysis of anchovy to prepare antioxidant substances, aiming to alleviate the waste of low-value fish resources. RESULTS SPr-SW5 with the open reading frame of 1353 bp encodes a serine protease (SPr-SW5) with 450 amino acids. The theoretical molecular weight and isoelectric point are 47.2 kDa and 5.22, respectively. The successful expression of SPr-SW5 in B. subtilis WB800N was confirmed by a skim milk plate test. Its optimal temperature and pH were 50 °C and 8.0, respectively. SPr-SW5 activity was increased by Ca2+ and Zn2+ , but inhibited by Fe3+ . Furthermore, SPr-SW5 was tolerant to 1% Tween-40 and Tween-80; however, its activity was strongly inhibited by 10 mm phenylmethylsulfonyl fluoride. Additionally, SPr-SW5 could be capable of hydrolyzing anchovy, the hydrolysate (AHP) at 10 g L-1 , with 2,2-diphenyl-1-picrylhydrazyl and hydroxyl (·OH) scavenging rates of 73.21% and 79.71%, displaying good antioxidant activity. CONCLUSION The novel SPr-SW5 was successfully expressed in B. subtilis WB800N. It exhibited excellent temperature stability and good tolerance to several metal ions. In addition, the anchovy hydrolyzed by expressed SPr-SW5 has good antioxidant ability. Overall, this research lays a good foundation for SPr-SW5 with respect to exploration and application in the food industry as enzyme preparation. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Na Li
- Collage of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315211, People's Republic of China
| | - Biao Shen
- Zhoushan Customs District, Zhoushan, Zhejiang, 316100, People's Republic of China
| | - Yang Liu
- Collage of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315211, People's Republic of China
- Institute of Quality Standards and Testing Technology for Agro-Products, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, People's Republic of China
| | - Peifang Weng
- Collage of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315211, People's Republic of China
| | - Zufang Wu
- Collage of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315211, People's Republic of China
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Guo S, Zhao Q, Li Y, Chu S, He F, Li X, Sun N, Zong W, Liu R. Potential toxicity of bisphenol A to α-chymotrypsin and the corresponding mechanisms of their binding. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 285:121910. [PMID: 36167003 DOI: 10.1016/j.saa.2022.121910] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/16/2022] [Accepted: 09/18/2022] [Indexed: 06/16/2023]
Abstract
Bisphenol A (BPA) is an endocrine disruptor widely existing in plastics and resins, which can accumulate in animals and human bodies, posing a potential threat to the physiological and biochemical reactions of human beings or other organisms. α-Chymotrypsin is a kind of proteolytic enzyme existing in humans and animals, which can cause diseases when its activity is excessive. However, there is a lack of research on the mechanism of endocrine disruptors affecting α-chymotrypsin activity. In this study, the interaction between BPA and α-chymotrypsin was proved via multiple spectroscopic approaches, enzyme activity change, isothermal titration calorimetry and molecular docking. Results showed that α-chymotrypsin's polypeptide chains were unfolded, and protein skeletons were loosened with the exposure to BPA. α-Helix content increased and β-sheet content was decreased. The particle size of the BPA-α-chymotrypsin complex became smaller. Fluorescence sensitization may also be explained by a perturbation of the chromophore Trp 141. The thermodynamic parameters of the binding reaction were measured by isothermal titration calorimetry (ITC), which showed that there was hydrophobic interaction between BPA and α-chymotrypsin, which was consistent with the results of molecular docking. Moreover, BPA may stop near the active center of α-chymotrypsin and interact with the key residues His 57 and Ser 195. The above phenomenon explained the result that the activity of α-chymotrypsin increased to 139% when exposed to high dose BPA (40 μM). Taken together, the effects of BPA on the structure and function of α-chymotrypsin were clarified at the molecular level, which made up the gap in the mechanism of BPA on the proteolytic enzyme, and provided a reliable basis for disease avoidance and prevention.
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Affiliation(s)
- Shuqi Guo
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Qiang Zhao
- Shandong Provincial Eco-environment Monitoring Center, 3377 Jingshi Dong Lu, Jinan, Shandong 250100, PR China
| | - Yuze Li
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Shanshan Chu
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Falin He
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Xiangxiang Li
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Ning Sun
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Wansong Zong
- College of Geography and Environment, Shandong Normal University, 88# East Wenhua Road, Jinan, Shandong 250014, PR China
| | - Rutao Liu
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China.
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Ji X, Pei Q, Zhang J, Lin P, Li B, Yin H, Sun J, Su D, Qu X, Yin D. Single-cell sequencing combined with machine learning reveals the mechanism of interaction between epilepsy and stress cardiomyopathy. Front Immunol 2023; 14:1078731. [PMID: 36776884 PMCID: PMC9911815 DOI: 10.3389/fimmu.2023.1078731] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/17/2023] [Indexed: 01/28/2023] Open
Abstract
Background Epilepsy is a disorder that can manifest as abnormalities in neurological or physical function. Stress cardiomyopathy is closely associated with neurological stimulation. However, the mechanisms underlying the interrelationship between epilepsy and stress cardiomyopathy are unclear. This paper aims to explore the genetic features and potential molecular mechanisms shared in epilepsy and stress cardiomyopathy. Methods By analyzing the epilepsy dataset and stress cardiomyopathy dataset separately, the intersection of the two disease co-expressed differential genes is obtained, the co-expressed differential genes reveal the biological functions, the network is constructed, and the core modules are identified to reveal the interaction mechanism, the co-expressed genes with diagnostic validity are screened by machine learning algorithms, and the co-expressed genes are validated in parallel on the epilepsy single-cell data and the stress cardiomyopathy rat model. Results Epilepsy causes stress cardiomyopathy, and its key pathways are Complement and coagulation cascades, HIF-1 signaling pathway, its key co-expressed genes include SPOCK2, CTSZ, HLA-DMB, ALDOA, SFRP1, ERBB3. The key immune cell subpopulations localized by single-cell data are the T_cells subgroup, Microglia subgroup, Macrophage subgroup, Astrocyte subgroup, and Oligodendrocytes subgroup. Conclusion We believe epilepsy causing stress cardiomyopathy results from a multi-gene, multi-pathway combination. We identified the core co-expressed genes (SPOCK2, CTSZ, HLA-DMB, ALDOA, SFRP1, ERBB3) and the pathways that function in them (Complement and coagulation cascades, HIF-1 signaling pathway, JAK-STAT signaling pathway), and finally localized their key cellular subgroups (T_cells subgroup, Microglia subgroup, Macrophage subgroup, Astrocyte subgroup, and Oligodendrocytes subgroup). Also, combining cell subpopulations with hypercoagulability as well as sympathetic excitation further narrowed the cell subpopulations of related functions.
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Affiliation(s)
- Xuanrui Ji
- Department of Cardiology, the First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Quanwei Pei
- Department of Cardiology, the First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Junpei Zhang
- Department of Cardiology, the First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Pengqi Lin
- Department of Cardiology, the First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bin Li
- Department of Cardiology, the First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hongpeng Yin
- Department of Cardiology, the First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jingmei Sun
- Department of Cardiology, the First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Dezhan Su
- Department of Cardiology, the First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiufen Qu
- Department of Cardiology, the First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Dechun Yin
- Department of Cardiology, the First Affiliated Hospital of Harbin Medical University, Harbin, China
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Stojanovski BM, Di Cera E. Comparative sequence analysis of vitamin K-dependent coagulation factors. J Thromb Haemost 2022; 20:2837-2849. [PMID: 36156849 PMCID: PMC9669250 DOI: 10.1111/jth.15897] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/22/2022] [Accepted: 09/22/2022] [Indexed: 01/13/2023]
Abstract
BACKGROUND Prothrombin, protein C, and factors VII, IX, and X are vitamin K (VK)-dependent coagulation proteins that play an important role in the initiation, amplification, and subsequent attenuation of the coagulation response. Blood coagulation evolved in the common vertebrate ancestor as a specialization of the complement system and immune response, which in turn bear close evolutionary ties with developmental enzyme cascades. There is currently no comprehensive analysis of the evolutionary changes experienced by these coagulation proteins during the radiation of vertebrates and little is known about conservation of residues that are important for zymogen activation and catalysis. OBJECTIVES To characterize the conservation level of functionally important residues among VK-dependent coagulation proteins from different vertebrate lineages. METHODS The conservation level of residues important for zymogen activation and catalysis was analyzed in >1600 primary sequences of VK-dependent proteins. RESULTS Functionally important residues are most conserved in prothrombin and least conserved in protein C. Some of the most profound functional modifications in protein C occurred in the ancestor of bony fish when the basic residue in the activation site was replaced by an aromatic residue. Furthermore, during the radiation of placental mammals from marsupials, protein C acquired a cysteine-rich insert that introduced an additional disulfide in the EGF1 domain and evolved a proprotein convertase cleavage site in the activation peptide linker that also became significantly elongated. CONCLUSIONS Sequence variabilities at functionally important residues may lead to interspecies differences in the zymogen activation and catalytic properties of orthologous VK-dependent proteins.
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Affiliation(s)
- Bosko M. Stojanovski
- Edward A. Doisy Department of Biochemistry and Molecular BiologySaint Louis University School of MedicineSt. LouisMissouriUSA
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular BiologySaint Louis University School of MedicineSt. LouisMissouriUSA
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Elamin T, Brandstetter H, Dall E. Legumain Activity Is Controlled by Extended Active Site Residues and Substrate Conformation. Int J Mol Sci 2022; 23:12548. [PMID: 36293424 PMCID: PMC9604545 DOI: 10.3390/ijms232012548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
Legumain is a lysosomal cysteine protease with strict specificity for cleaving after asparagine residues. By sequence comparison, legumain belongs to MEROPS clan CD of the cysteine proteases, which indicates its structural and mechanistic relation to caspases. Contrasting caspases, legumain harbors a pH-dependent ligase activity in addition to the protease activity. Although we already have a significant body of knowledge on the catalytic activities of legumain, many mechanistic details are still elusive. In this study, we provide evidence that extended active site residues and substrate conformation are steering legumain activities. Biochemical experiments and bioinformatics analysis showed that the catalytic Cys189 and His148 residues are regulated by sterically close Glu190, Ser215 and Asn42 residues. While Glu190 serves as an activity brake, Ser215 and Asn42 have a favorable effect on legumain protease activity. Mutagenesis studies using caspase-9 as model enzyme additionally showed that a similar Glu190 activity brake is also implemented in the caspases. Furthermore, we show that the substrate's conformational flexibility determines whether it will be hydrolyzed or ligated by legumain. The functional understanding of the extended active site residues and of substrate prerequisites will allow us to engineer proteases with increased enzymatic activity and better ligase substrates, with relevance for biotechnological applications.
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Affiliation(s)
| | | | - Elfriede Dall
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
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10
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Tong S, Zhao W, Zhao D, Zhang W, Zhang Z. Biomaterials-Mediated Tumor Infarction Therapy. Front Bioeng Biotechnol 2022; 10:916926. [PMID: 35757801 PMCID: PMC9218593 DOI: 10.3389/fbioe.2022.916926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 05/23/2022] [Indexed: 11/19/2022] Open
Abstract
Agents for tumor vascular infarction are recently developed therapeutic agents for the vascular destruction of tumors. They can suppress the progression of the tumor by preventing the flow of nutrition and oxygen to its tissues. Agents of tumor vascular infarction can be divided into three categories according to the differences in their pathways of action: those that use the thrombin-activating pathway, fibrin-activating pathway, and platelet-activating pathway. However, poor targeting ability, low permeation, and potential side-effects restrict the development of the corresponding drugs. Biomaterials can subtly avoid these drawbacks to suppress the tumor. In this article, the authors summarize currently used biomaterials for tumor infarction therapy with the goal of identifying its mechanism, and discuss outstanding deficiencies in methods of this kind.
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Affiliation(s)
- Shizheng Tong
- Department of Orthopedics, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Wei Zhao
- Department of Orthopedics, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Duoyi Zhao
- Department of Orthopedics, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Weilin Zhang
- Department of Orthopedics, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Zhiyu Zhang
- Department of Orthopedics, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
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11
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Wang S, Ping Q, Li Y. Comprehensively understanding metabolic pathways of protein during the anaerobic digestion of waste activated sludge. CHEMOSPHERE 2022; 297:134117. [PMID: 35227742 DOI: 10.1016/j.chemosphere.2022.134117] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
The metabolic pathways of protein during anaerobic digestion (AD) of waste activated sludge (WAS) were comprehensively investigated. Results showed that 100 kinds of peptidases were involved in the hydrolysis and acidogenesis processes. Serine endopeptidases (EC 3.4.21.53) and serine-type carboxypeptidases (EC 3.4.16.4) were the key enzymes of endopeptidases and exopeptidases, respectively. The pathways of ko00250 (alanine, aspartate and glutamate metabolism), ko00260 (glycine, serine and threonine metabolism), ko00270 (cysteine and methionine metabolism), ko00280 (valine, leucine and isoleucine degradation), ko00360 (phenylalanine metabolism) and ko00310 (lysine degradation) were the critical metabolic pathways of amino acids during AD of WAS, since they have complete pathways from amino acids to vital intermediates (pyruvate or acetyl-CoA). l-aspartate, l-alanine, threonine, glycine, serine, l-cysteine were the intermediate products in the conversion of protein to pyruvate, while l-leucine, l-isoleucine, phenylalanine, lysine could be directly metabolized to acetyl-CoA. Dechloromonas and Thauera played major roles in the crucial metabolic pathways of amino acids (ko00250, ko00260, ko00280 and ko00270). These important discoveries could provide a new biological perspective for improving AD performance.
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Affiliation(s)
- Siyuan Wang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, PR China
| | - Qian Ping
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, PR China
| | - Yongmei Li
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, PR China.
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Gomes PS, Carneiro MPD, Machado PDA, de Andrade-Neto VV, da Fonseca-Martins AM, Goundry A, Pereira da Silva JVM, Gomes DCO, Lima APCDA, Ennes-Vidal V, Sodero ACR, De-Simone SG, de Matos Guedes HL. Subtilisin of Leishmania amazonensis as Potential Druggable Target: Subcellular Localization, In Vitro Leishmanicidal Activity and Molecular Docking of PF-429242, a Subtilisin Inhibitor. Curr Issues Mol Biol 2022; 44:2089-2106. [PMID: 35678670 PMCID: PMC9164065 DOI: 10.3390/cimb44050141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 12/14/2022] Open
Abstract
Subtilisin proteases, found in all organisms, are enzymes important in the post-translational steps of protein processing. In Leishmania major and L. donovani, this enzyme has been described as essential to their survival; however, few compounds that target subtilisin have been investigated for their potential as an antileishmanial drug. In this study, we first show, by electron microscopy and flow cytometry, that subtilisin has broad localization throughout the cytoplasm and membrane of the parasite in the promastigote form with foci in the flagellar pocket. Through in silico analysis, the similarity between subtilisin of different Leishmania species and that of humans were determined, and based on molecular docking, we evaluated the interaction capacity of a serine protease inhibitor against both life cycle forms of Leishmania. The selected inhibitor, known as PF-429242, has already been used against the dengue virus, arenaviruses, and the hepatitis C virus. Moreover, it proved to have antilipogenic activity in a mouse model and caused hypolipidemia in human cells in vitro. Here, PF-429242 significantly inhibited the growth of L. amazonensis promastigotes of four different strains (IC50 values = 3.07 ± 0.20; 0.83 ± 0.12; 2.02 ± 0.27 and 5.83 ± 1.2 µM against LTB0016, PH8, Josefa and LV78 strains) whilst having low toxicity in the host macrophages (CC50 = 170.30 µM). We detected by flow cytometry that there is a greater expression of subtilisin in the amastigote form; however, PF-429242 had a low effect against this intracellular form with an IC50 of >100 µM for intracellular amastigotes, as well as against axenic amastigotes (94.12 ± 2.8 µM for the LV78 strain). In conclusion, even though PF-429242 does not affect the intracellular forms, this drug will serve as a tool to explore pharmacological and potentially leishmanicidal targets.
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Affiliation(s)
- Pollyanna Stephanie Gomes
- Laboratório de Imunologia Clínica, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz—Fiocruz, Rio de Janeiro 21040-360, Brazil; (P.S.G.); (M.P.D.C.); (P.d.A.M.); (A.M.d.F.-M.)
- Laboratório Interdisciplinar de Pesquisas Médicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
- Laboratório de Imunofarmacologia, Instituto de Biofísica Carlos Chagas Filho IBCCF, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil
- Laboratório de Imunobiotecnologia, Instituto de Microbiologia Paulo de Goés, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Monique Pacheco Duarte Carneiro
- Laboratório de Imunologia Clínica, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz—Fiocruz, Rio de Janeiro 21040-360, Brazil; (P.S.G.); (M.P.D.C.); (P.d.A.M.); (A.M.d.F.-M.)
- Laboratório de Imunobiotecnologia, Instituto de Microbiologia Paulo de Goés, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Laboratório de Bioquímica e Biologia Molecular de Proteases, Instituto de Biofísica Carlos Chagas Filho IBCCF, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (A.G.); (A.P.C.d.A.L.)
| | - Patrícia de Almeida Machado
- Laboratório de Imunologia Clínica, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz—Fiocruz, Rio de Janeiro 21040-360, Brazil; (P.S.G.); (M.P.D.C.); (P.d.A.M.); (A.M.d.F.-M.)
- Laboratório Interdisciplinar de Pesquisas Médicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
- Laboratório de Imunobiotecnologia, Instituto de Microbiologia Paulo de Goés, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Valter Viana de Andrade-Neto
- Laboratório de Bioquímica de Tripanossomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil;
| | - Alessandra Marcia da Fonseca-Martins
- Laboratório de Imunologia Clínica, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz—Fiocruz, Rio de Janeiro 21040-360, Brazil; (P.S.G.); (M.P.D.C.); (P.d.A.M.); (A.M.d.F.-M.)
- Laboratório Interdisciplinar de Pesquisas Médicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
- Laboratório de Imunofarmacologia, Instituto de Biofísica Carlos Chagas Filho IBCCF, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil
- Laboratório de Imunobiotecnologia, Instituto de Microbiologia Paulo de Goés, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Amy Goundry
- Laboratório de Bioquímica e Biologia Molecular de Proteases, Instituto de Biofísica Carlos Chagas Filho IBCCF, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (A.G.); (A.P.C.d.A.L.)
| | | | | | - Ana Paula Cabral de Araujo Lima
- Laboratório de Bioquímica e Biologia Molecular de Proteases, Instituto de Biofísica Carlos Chagas Filho IBCCF, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (A.G.); (A.P.C.d.A.L.)
| | - Vítor Ennes-Vidal
- Laboratório de Estudos Integrados em Protozoologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil;
| | - Ana Carolina Rennó Sodero
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.V.M.P.d.S.); (A.C.R.S.)
| | - Salvatore Giovanni De-Simone
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Diseases Neglected Population (INCT-IDPN), FIOCRUZ, Rio de Janeiro 21040-900, Brazil;
- Epidemiology and Molecular Systematic Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-900, Brazil
- Cellular and Molecular Biology Department, Biology Institute, Federal Fluminense University, Niterói 24020-141, Brazil
| | - Herbert L. de Matos Guedes
- Laboratório de Imunologia Clínica, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz—Fiocruz, Rio de Janeiro 21040-360, Brazil; (P.S.G.); (M.P.D.C.); (P.d.A.M.); (A.M.d.F.-M.)
- Laboratório Interdisciplinar de Pesquisas Médicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
- Laboratório de Imunofarmacologia, Instituto de Biofísica Carlos Chagas Filho IBCCF, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil
- Laboratório de Imunobiotecnologia, Instituto de Microbiologia Paulo de Goés, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
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Porfírio CTMN, Souza PFN, Ramos MV, Campos FAP, Freitas SF, Oliveira JPB, Furtado GP, Barbosa JSS, Frota TL, Nagano CS, Silva RGG, Hussain G, Freitas CDT. Serine carboxypeptidases from the carnivorous plant Nepenthes mirabilis: Partial characterization and heterologous expression. Int J Biol Macromol 2022; 198:77-86. [PMID: 34963626 DOI: 10.1016/j.ijbiomac.2021.12.104] [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: 04/19/2021] [Revised: 12/06/2021] [Accepted: 12/17/2021] [Indexed: 11/23/2022]
Abstract
This study aimed to partially characterize the three main serine carboxypeptidases (SCP3, SCP20, and SCP47) from Nepenthes mirabilis. Furthermore, one peptidase (SCP3) was chosen for further heterologous expression in Escherichia coli Shuffle®T7. SCP3 also was characterized in terms of its allergenic potential using bioinformatics tools. SCP3, SCP20, and SCP47 showed very similar 3D structures and mechanistic features to other plant serine peptidases belonging to clan SC and family S10. Although SCP3 was obtained in its soluble form, using 1% ethanol during induction with 0.5 mM IPTG at 16 °C for 18 h, it did not show proteolytic activity by zymography or in vitro analysis. SCP3 presented a few allergenic peptides and several cleavage sites for digestive enzymes. This work describes additional features of these enzymes, opening new perspectives for further studies for characterization and analysis of heterologous expression, as well as their potential biotechnological applications.
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Affiliation(s)
- Camila T M N Porfírio
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Centro de Ciências, Campus do Pici. Fortaleza, Ceará, CEP 60440-900, Brazil
| | - Pedro F N Souza
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Centro de Ciências, Campus do Pici. Fortaleza, Ceará, CEP 60440-900, Brazil.
| | - Márcio V Ramos
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Centro de Ciências, Campus do Pici. Fortaleza, Ceará, CEP 60440-900, Brazil
| | - Francisco A P Campos
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Centro de Ciências, Campus do Pici. Fortaleza, Ceará, CEP 60440-900, Brazil
| | - Samuel F Freitas
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Centro de Ciências, Campus do Pici. Fortaleza, Ceará, CEP 60440-900, Brazil
| | - João P B Oliveira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Centro de Ciências, Campus do Pici. Fortaleza, Ceará, CEP 60440-900, Brazil
| | | | - José S S Barbosa
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Centro de Ciências, Campus do Pici. Fortaleza, Ceará, CEP 60440-900, Brazil
| | - Thalia L Frota
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Centro de Ciências, Campus do Pici. Fortaleza, Ceará, CEP 60440-900, Brazil
| | - Celso S Nagano
- Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Fortaleza, CE, Brazil
| | - Rodolpho G G Silva
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Centro de Ciências, Campus do Pici. Fortaleza, Ceará, CEP 60440-900, Brazil
| | - Ghulam Hussain
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Centro de Ciências, Campus do Pici. Fortaleza, Ceará, CEP 60440-900, Brazil
| | - Cleverson D T Freitas
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Centro de Ciências, Campus do Pici. Fortaleza, Ceará, CEP 60440-900, Brazil.
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Romero A, Novoa B, Figueras A. Genomic and transcriptomic identification of the cathepsin superfamily in the Mediterranean mussel Mytilus galloprovincialis. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 127:104286. [PMID: 34619173 DOI: 10.1016/j.dci.2021.104286] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
Cathepsins are lysosomal enzymes that participate in important physiological processes, such as development, tissue remodelling, senescence and innate and adaptive immunity. The description of these proteins in molluscs is fragmented and incomplete. In the present work, we identified most of the cathepsin family members in the bivalve Mytilus galloprovincialis by screening published genomic and transcriptomic information. In this specie, the cathepsin family is composed of 41 proteins showing a high diversification of cathepsins D, L and F, not previously observed in other taxonomic groups. Specific set of cathepsins are constitutively expressed in the different mussel tissues. Transcriptomic analyses suggested coordinated activity of the different cathepsins and their sequential activation during larval development. Cathepsins also play an important role in the immune response of bivalves, and different immune pathways seem to be activated in response to Vibrio splendidus infection.
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Affiliation(s)
- Alejandro Romero
- Instituto de Investigaciones Marinas (CSIC), Eduardo Cabello 6, 36208, Vigo, Spain
| | - Beatriz Novoa
- Instituto de Investigaciones Marinas (CSIC), Eduardo Cabello 6, 36208, Vigo, Spain.
| | - Antonio Figueras
- Instituto de Investigaciones Marinas (CSIC), Eduardo Cabello 6, 36208, Vigo, Spain
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Pelc LA, Koester SK, Kukla CR, Chen Z, Di Cera E. The active site region plays a critical role in Na + binding to thrombin. J Biol Chem 2022; 298:101458. [PMID: 34861239 PMCID: PMC8695361 DOI: 10.1016/j.jbc.2021.101458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 11/23/2022] Open
Abstract
The catalytic activity of thrombin and other enzymes of the blood coagulation and complement cascades is enhanced significantly by binding of Na+ to a site >15 Å away from the catalytic residue S195, buried within the 180 and 220 loops that also contribute to the primary specificity of the enzyme. Rapid kinetics support a binding mechanism of conformational selection where the Na+-binding site is in equilibrium between open (N) and closed (N∗) forms and the cation binds selectively to the N form. Allosteric transduction of this binding step produces enhanced catalytic activity. Molecular details on how Na+ gains access to this site and communicates allosterically with the active site remain poorly defined. In this study, we show that the rate of the N∗→N transition is strongly correlated with the analogous E∗→E transition that governs the interaction of synthetic and physiologic substrates with the active site. This correlation supports the active site as the likely point of entry for Na+ to its binding site. Mutagenesis and structural data rule out an alternative path through the pore defined by the 180 and 220 loops. We suggest that the active site communicates allosterically with the Na+ site through a network of H-bonded water molecules that embeds the primary specificity pocket. Perturbation of the mobility of S195 and its H-bonding capabilities alters interaction with this network and influences the kinetics of Na+ binding and allosteric transduction. These findings have general mechanistic relevance for Na+-activated proteases and allosteric enzymes.
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Affiliation(s)
- Leslie A Pelc
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Sarah K Koester
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Cassandra R Kukla
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Zhiwei Chen
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA.
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Ahlberg Gagner V, Jensen M, Katona G. Estimating the probability of coincidental similarity between atomic displacement parameters with machine learning. MACHINE LEARNING: SCIENCE AND TECHNOLOGY 2021. [DOI: 10.1088/2632-2153/ac022d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
High-resolution diffraction studies of macromolecules incorporate the tensor form of the anisotropic displacement parameter (ADP) of atoms from their mean position. The comparison of these parameters requires a statistical framework that can handle the experimental and modeling errors linked to structure determination. Here, a Bayesian machine learning model is introduced that approximates ADPs with the random Wishart distribution. This model allows for the comparison of random samples from a distribution that is trained on experimental structures. The comparison revealed that the experimental similarity between atoms is larger than predicted by the random model for a substantial fraction of the comparisons. Different metrics between ADPs were evaluated and categorized based on how useful they are at detecting non-accidental similarity and whether they can be replaced by other metrics. The most complementary comparisons were provided by Euclidean, Riemann and Wasserstein metrics. The analysis of ADP similarity and the positional distance of atoms in bovine trypsin revealed a set of atoms with striking ADP similarity over a long physical distance, and generally the physical distance between atoms and their ADP similarity do not correlate strongly. A substantial fraction of long- and short-range ADP similarities does not form by coincidence and are reproducibly observed in different crystal structures of the same protein.
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Structural basis of covalent inhibitory mechanism of TMPRSS2-related serine proteases by camostat. J Virol 2021; 95:e0086121. [PMID: 34160253 PMCID: PMC8428381 DOI: 10.1128/jvi.00861-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the viral pathogen causing the coronavirus disease 2019 (COVID-19) global pandemic. No effective treatment for COVID-19 has been established yet. The serine protease transmembrane protease serine 2 (TMPRSS2) is essential for viral spread and pathogenicity by facilitating the entry of SARS-CoV-2 into host cells. The protease inhibitor camostat, an anticoagulant used in the clinic, has potential anti-inflammatory and antiviral activities against COVID-19. However, the potential mechanisms of viral resistance and antiviral activity of camostat are unclear. Herein, we demonstrate high inhibitory potencies of camostat for a panel of serine proteases, indicating that camostat is a broad-spectrum inhibitor of serine proteases. In addition, we determined the crystal structure of camostat in complex with a serine protease (uPA [urokinase-type plasminogen activator]), which reveals that camostat is inserted in the S1 pocket of uPA but is hydrolyzed by uPA, and the cleaved camostat covalently binds to Ser195. We also generated a homology model of the structure of the TMPRSS2 serine protease domain. The model shows that camostat uses the same inhibitory mechanism to inhibit the activity of TMPRSS2, subsequently preventing SARS-CoV-2 spread. IMPORTANCE Serine proteases are a large family of enzymes critical for multiple physiological processes and proven diagnostic and therapeutic targets in several clinical indications. The serine protease transmembrane protease serine 2 (TMPRSS2) was recently found to mediate SARS-CoV-2 entry into the host. Camostat mesylate (FOY 305), a serine protease inhibitor active against TMPRSS2 and used for the treatment of oral squamous cell carcinoma and chronic pancreatitis, inhibits SARS-CoV-2 infection of human lung cells. However, the direct inhibition mechanism of camostat mesylate for TMPRSS2 is unclear. Herein, we demonstrate that camostat uses the same inhibitory mechanism to inhibit the activity of TMPRSS2 as uPA, subsequently preventing SARS-CoV-2 spread.
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Abstract
PURPOSE OF REVIEW To discuss the crosstalk between the complement system and hemostatic factors (coagulation cascade, platelet, endothelium, and Von Willebrand Factor), and the consequences of this interaction under physiologic and pathologic conditions. RECENT FINDINGS The complement and coagulation systems are comprised of serine proteases and are genetically related. In addition to the common ancestral genes, the complement system and hemostasis interact directly, through protein-protein interactions, and indirectly, on the surface of platelets and endothelial cells. The close interaction between the complement system and hemostatic factors is manifested both in physiologic and pathologic conditions, such as in the inflammatory response to thrombosis, thrombosis at the inflamed area, and thrombotic complications of complement disorders. SUMMARY The interaction between the complement system and hemostasis is vital for homeostasis and the protective response of the host to tissue injury, but also results in the pathogenesis of several thrombotic and inflammatory disorders.
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Denesyuk AI, Permyakov SE, Johnson MS, Permyakov EA, Uversky VN, Denessiouk K. Structural leitmotif and functional variations of the structural catalytic core in (chymo)trypsin-like serine/cysteine fold proteinases. Int J Biol Macromol 2021; 179:601-609. [PMID: 33713772 DOI: 10.1016/j.ijbiomac.2021.03.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 11/29/2022]
Abstract
Proteinases with the (chymo)trypsin-like serine/cysteine fold comprise a large superfamily performing their function through the Acid - Base - Nucleophile catalytic triad. In our previous work (Denesyuk AI, Johnson MS, Salo-Ahen OMH, Uversky VN, Denessiouk K. Int J Biol Macromol. 2020;153:399-411), we described a universal three-dimensional (3D) structural motif, NBCZone, that contains eleven amino acids: dipeptide 42 T-43 T, pentapeptide 54 T-55 T-56 T-57 T(base)-58 T, tripeptide 195 T(nucleophile)-196 T-197 T and residue 213 T (T - numeration of amino acids in trypsin). The comparison of the NBCZones among the members of the (chymo)trypsin-like protease family suggested the existence of 15 distinct groups. Within each group, the NBCZones incorporate an identical set of conserved interactions and bonds. In the present work, the structural environment of the catalytic acid at the position 102 T and the fourth member of the "catalytic tetrad" at the position 214 T was analyzed in 169 3D structures of proteinases with the (chymo)trypsin-like serine/cysteine fold. We have identified a complete Structural Catalytic Core (SCC) consisting of two classes and four groups. The proteinases belonging to different classes and groups differ from each other by the nature of the interaction between their N- and C-terminal β-barrels. Comparative analysis of the 3CLpro(s) from SARS-CoV-2 and SARS-CoV, used as an example, showed that the amino acids at positions 103 T and 179 T affect the nature of the interaction of the "catalytic acid" core (102 T-Core, N-terminal β-barrel) with the "supplementary" core (S-Core, C-terminal β-barrel), which ultimately results in the modulation of the enzymatic activity. The reported analysis represents an important standalone contribution to the analysis and systematization of the 3D structures of (chymo)trypsin-like serine/cysteine fold proteinases. The use of the developed approach for the comparison of 3D structures will allow, in the event of the appearance of new representatives of a given fold in the PDB, to quickly determine their structural homologues with the identification of possible differences.
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Affiliation(s)
- Alexander I Denesyuk
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow region 142290, Russia; Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku 20520, Finland.
| | - Sergei E Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow region 142290, Russia
| | - Mark S Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku 20520, Finland
| | - Eugene A Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow region 142290, Russia
| | - Vladimir N Uversky
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow region 142290, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku 20520, Finland
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Dyakin VV, Wisniewski TM, Lajtha A. Racemization in Post-Translational Modifications Relevance to Protein Aging, Aggregation and Neurodegeneration: Tip of the Iceberg. Symmetry (Basel) 2021; 13:455. [PMID: 34350031 PMCID: PMC8330555 DOI: 10.3390/sym13030455] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Homochirality of DNA and prevalent chirality of free and protein-bound amino acids in a living organism represents the challenge for modern biochemistry and neuroscience. The idea of an association between age-related disease, neurodegeneration, and racemization originated from the studies of fossils and cataract disease. Under the pressure of new results, this concept has a broader significance linking protein folding, aggregation, and disfunction to an organism's cognitive and behavioral functions. The integrity of cognitive function is provided by a delicate balance between the evolutionarily imposed molecular homo-chirality and the epigenetic/developmental impact of spontaneous and enzymatic racemization. The chirality of amino acids is the crucial player in the modulation the structure and function of proteins, lipids, and DNA. The collapse of homochirality by racemization is the result of the conformational phase transition. The racemization of protein-bound amino acids (spontaneous and enzymatic) occurs through thermal activation over the energy barrier or by the tunnel transfer effect under the energy barrier. The phase transition is achieved through the intermediate state, where the chirality of alpha carbon vanished. From a thermodynamic consideration, the system in the homo-chiral (single enantiomeric) state is characterized by a decreased level of entropy. The oscillating protein chirality is suggesting its distinct significance in the neurotransmission and flow of perceptual information, adaptive associative learning, and cognitive laterality. The common pathological hallmarks of neurodegenerative disorders include protein misfolding, aging, and the deposition of protease-resistant protein aggregates. Each of the landmarks is influenced by racemization. The brain region, cell type, and age-dependent racemization critically influence the functions of many intracellular, membrane-bound, and extracellular proteins including amyloid precursor protein (APP), TAU, PrP, Huntingtin, α-synuclein, myelin basic protein (MBP), and collagen. The amyloid cascade hypothesis in Alzheimer's disease (AD) coexists with the failure of amyloid beta (Aβ) targeting drug therapy. According to our view, racemization should be considered as a critical factor of protein conformation with the potential for inducing order, disorder, misfolding, aggregation, toxicity, and malfunctions.
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Affiliation(s)
- Victor V. Dyakin
- Virtual Reality Perception Lab (VRPL), The Nathan S. Kline Institute for Psychiatric Research (NKI), Orangeburg, NY 10962, USA
| | - Thomas M. Wisniewski
- Departments of Neurology, Pathology and Psychiatry, Center for Cognitive Neurology, New York University School of Medicine, New York, NY 10016, USA
| | - Abel Lajtha
- Center for Neurochemistry, The Nathan S. Kline Institute for Psychiatric Research (NKI), Orangeburg, NY 10962, USA
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Anigbo GC, Onyekwere OA, Akwukwaegbu PI, Lackson A, Bando CD, Okoye OM, Okoroafor AB, Esemaya P, Patrick C. OG. EVALUATION OF THE HAEMOSTATIC POTENTIALS OF CRUDE METHANOLIC LEAF EXTRACT OF PERSEA AMERICANA IN WISTAR RATS. ACTA CHEMICA IASI 2021. [DOI: 10.47743/achi-2021-1-0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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Wang J, Singh SK, Geng S, Zhang S, Yuan L. Genome-wide analysis of glycerol-3-phosphate O-acyltransferase gene family and functional characterization of two cutin group GPATs in Brassica napus. PLANTA 2020; 251:93. [PMID: 32246349 DOI: 10.1007/s00425-020-03384-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
Genome-wide identification, spatio-temporal expression analysis and functional characterization of selected Brassica napus GPATs highlight their roles in cuticular wax biosynthesis and defense against fungal pathogens. Glycerol-3-phosphate 1-O-acyltransferase (GPAT) is a key enzyme in the biosynthesis of glycerolipids, a major component of cellular membranes and extracellular protective layers, such as cuticles in plants. Brassica napus is an economically important crop and cultivated worldwide mostly for its edible oil. The B. napus GPATs (BnGPATs) are insufficiently characterized. Here, we performed genome-wide analysis to identify putative GPATs in B. napus and its diploid progenitors B. rapa and B oleracea. The 32 B. napus BnGPATs are phylogenetically divided into three major groups, cutin, suberin, and diverse ancient groups. Analysis of transcriptomes of different tissues and seeds at different developmental stages revealed the spatial and temporal expression profiles of BnGPATs. The yield and oil quality of B. napus are adversely affected by the necrotrophic fungus, Sclerotinia sclerotiorum. We showed that several BnGPATs, including cutin-related BnGPAT19 and 21, were upregulated in the S. sclerotiorum resistant line. RNAi-mediated suppression of BnGPAT19 and 21 in B. napus resulted in thinner cuticle, leading to rapid water and chlorophyll loss in toluidine blue staining and leaf bleaching assays. In addition, the RNAi plants also developed severe necrotic lesions following fungal inoculation compared to the wild-type plants, indicating that BnGPAT19 and 21 are likely involved in cuticular wax biosynthesis that is critical for initial pathogen defense. Taken together, we provided a comprehensive account of GPATs B. napus and characterized BnGPAT19 and 21 for their potential roles in cuticular wax biosynthesis and defense against fungal pathogens.
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Affiliation(s)
- Jingxue Wang
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China.
| | - Sanjay Kumar Singh
- Department of Plant and Soil Sciences and the Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Siyu Geng
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China
| | - Shanshan Zhang
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China
| | - Ling Yuan
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China.
- Department of Plant and Soil Sciences and the Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA.
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Denesyuk A, Dimitriou PS, Johnson MS, Nakayama T, Denessiouk K. The acid-base-nucleophile catalytic triad in ABH-fold enzymes is coordinated by a set of structural elements. PLoS One 2020; 15:e0229376. [PMID: 32084230 PMCID: PMC7034887 DOI: 10.1371/journal.pone.0229376] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 02/05/2020] [Indexed: 01/09/2023] Open
Abstract
The alpha/beta-Hydrolases (ABH) are a structural class of proteins that are found widespread in nature and includes enzymes that can catalyze various reactions in different substrates. The catalytic versatility of the ABH fold enzymes, which has been a valuable property in protein engineering applications, is based on a similar acid-base-nucleophile catalytic mechanism. In our research, we are concerned with the structure that surrounds the key units of the catalytic machinery, and we have previously found conserved structural organizations that coordinate the catalytic acid, the catalytic nucleophile and the residues of the oxyanion hole. Here, we explore the architecture that surrounds the catalytic histidine at the active sites of enzymes from 40 ABH fold families, where we have identified six conserved interactions that coordinate the catalytic histidine next to the catalytic acid and the catalytic nucleophile. Specifically, the catalytic nucleophile is coordinated next to the catalytic histidine by two weak hydrogen bonds, while the catalytic acid is directly involved in the coordination of the catalytic histidine through by two weak hydrogen bonds. The imidazole ring of the catalytic histidine is coordinated by a CH-π contact and a hydrophobic interaction. Moreover, the catalytic triad residues are connected with a residue that is located at the core of the active site of ABH fold, which is suggested to be the fourth member of a “structural catalytic tetrad”. Besides their role in the stability of the catalytic mechanism, the conserved elements of the catalytic site are actively involved in ligand binding and affect other properties of the catalytic activity, such as substrate specificity, enantioselectivity, pH optimum and thermostability of ABH fold enzymes. These properties are regularly targeted in protein engineering applications, and thus, the identified conserved structural elements can serve as potential modification sites in order to develop ABH fold enzymes with altered activities.
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Affiliation(s)
- Alexander Denesyuk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, Russia
- * E-mail:
| | - Polytimi S. Dimitriou
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Toru Nakayama
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
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Liu H, Dang G, Zang X, Cai Z, Cui Z, Song N, Liu S. Characterization and pathogenicity of extracellular serine protease MAP3292c from Mycobacterium avium subsp. paratuberculosis. Microb Pathog 2020; 142:104055. [PMID: 32058021 DOI: 10.1016/j.micpath.2020.104055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/08/2020] [Accepted: 02/10/2020] [Indexed: 12/14/2022]
Abstract
Serine protease is the virulence factor of many pathogens. However, there are no prevailing data available for serine protease as a virulence factor derived from Mycobacterium avium subsp. paratuberculosis (MAP). The MAP3292c gene from MAP, the predicted serine protease, was expressed in Escherichia coli and characterized by biochemical methods. MAP3292c protein efficiently hydrolyzed casein at optimal temperature and pH of 41 °C and 9.0, respectively. Furthermore, divalent metal ions of Ca2+ significantly promoted the protease activity of MAP3292c, and MAP3292c had autocleavage activity between serine 86 and asparagine 87. Site-directed mutagenesis studies showed that the serine 238 residue had catalytic roles in MAP3292c. Furthermore, a BALB/c mouse model confirmed that MAP3292c significantly promoted the survival of Mycobacterium smegmatis in vivo; caused damage to the liver, spleen, and lung; and promoted the release of inflammatory cytokines IL-1β, IL-6, and TNF-α in mice. Finally, we confirmed that MAP3292c was relevant to mycobacterial pathogenicity.
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Affiliation(s)
- Hongxiu Liu
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Street, Harbin, 150069, PR China
| | - Guanghui Dang
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Street, Harbin, 150069, PR China
| | - Xinxin Zang
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Street, Harbin, 150069, PR China
| | - Zhuming Cai
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Street, Harbin, 150069, PR China
| | - Ziyin Cui
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Street, Harbin, 150069, PR China
| | - Ningning Song
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Street, Harbin, 150069, PR China
| | - Siguo Liu
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Street, Harbin, 150069, PR China.
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Residues W215, E217 and E192 control the allosteric E*-E equilibrium of thrombin. Sci Rep 2019; 9:12304. [PMID: 31444378 PMCID: PMC6707225 DOI: 10.1038/s41598-019-48839-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/13/2019] [Indexed: 01/07/2023] Open
Abstract
A pre-existing, allosteric equilibrium between closed (E*) and open (E) conformations of the active site influences the level of activity in the trypsin fold and defines ligand binding according to the mechanism of conformational selection. Using the clotting protease thrombin as a model system, we investigate the molecular determinants of the E*-E equilibrium through rapid kinetics and X-ray structural biology. The equilibrium is controlled by three residues positioned around the active site. W215 on the 215-217 segment defining the west wall of the active site controls the rate of transition from E to E* through hydrophobic interaction with F227. E192 on the opposite 190-193 segment defining the east wall of the active site controls the rate of transition from E* to E through electrostatic repulsion of E217. The side chain of E217 acts as a lever that moves the entire 215-217 segment in the E*-E equilibrium. Removal of this side chain converts binding to the active site to a simple lock-and-key mechanism and freezes the conformation in a state intermediate between E* and E. These findings reveal a simple framework to understand the molecular basis of a key allosteric property of the trypsin fold.
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26
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Dudiak BM, Maksimchuk KR, Bednar MM, Podracky CJ, Burg JM, Nguyen TM, Nwogbo FO, Valdivia RH, McCafferty DG. Insights into the Autoproteolytic Processing and Catalytic Mechanism of the Chlamydia trachomatis Virulence-Associated Protease CPAF. Biochemistry 2019; 58:3527-3536. [PMID: 31386347 DOI: 10.1021/acs.biochem.9b00522] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
CPAF (chlamydial protease-like activity factor) is a Chlamydia trachomatis protease that is translocated into the host cytosol during infection. CPAF activity results in dampened host inflammation signaling, cytoskeletal remodeling, and suppressed neutrophil activation. Although CPAF is an emerging antivirulence target, its catalytic mechanism has been unexplored to date. Steady state kinetic parameters were obtained for recombinant CPAF with vimentin-derived peptide substrates using a high-performance liquid chromatography-based discontinuous assay (kcat = 45 ± 0.6 s-1; kcat/Km = 0.37 ± 0.02 μM-1 s-1) or a new fluorescence-based continuous assay (kcat = 23 ± 0.7 s-1; kcat/Km = 0.29 ± 0.03 μM-1 s-1). Residues H105, S499, E558, and newly identified D103 were found to be indispensable for autoproteolytic processing by mutagenesis, while participation of C500 was ruled out despite its proximity to the S499 nucleophile. Pre-steady state kinetics indicated a burst kinetic profile, with fast acylation (kacyl = 110 ± 2 s-1) followed by slower, partially rate-limiting deacylation (kdeacyl = 57 ± 1 s-1). Both kcat- and kcat/Km-pH profiles showed single acidic limb ionizations with pKa values of 6.2 ± 0.1 and 6.5 ± 0.1, respectively. A forward solvent deuterium kinetic isotope effect of 2.6 ± 0.1 was observed for D2Okcatapp, but a unity effect was found for D2Okcat/Kmapp. The kcat proton inventory was linear, indicating transfer of a single proton in the rate-determining transition state, most likely from H105. Collectively, these data provide support for the classification of CPAF as a serine protease and provide a mechanistic foundation for the future design of inhibitors.
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Khavrutskii IV, Compton JR, Jurkouich KM, Legler PM. Paired Carboxylic Acids in Enzymes and Their Role in Selective Substrate Binding, Catalysis, and Unusually Shifted p Ka Values. Biochemistry 2019; 58:5351-5365. [PMID: 31192586 DOI: 10.1021/acs.biochem.9b00429] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cathepsin A (CatA, EC 3.4.16.5, UniProtKB P10619 ) is a human lysosomal carboxypeptidase. Counterintuitively, crystal structures of CatA and its homologues show a cluster of Glu and Asp residues binding the C-terminal carboxylic acid of the product or inhibitor. Each of these enzymes functions in an acidic environment and contains a highly conserved pair of Glu residues with side chain carboxyl group oxygens that are approximately 2.3-2.6 Å apart. In small molecules, carboxyl groups separated by ∼3 Å can overcome the repulsive interaction by protonation of one of the two groups. The pKa of one group increases (pKa ∼ 11) and can be as much as ∼6 pH units higher than the paired group. Consequently, at low and neutral pH, one carboxylate can carry a net negative charge while the other can remain protonated and neutral. In CatA, E69 and E149 form a Glu pair that is important to catalysis as evidenced by the 56-fold decrease in kcat/Km in the E69Q/E149Q variant. Here, we have measured the pH dependencies of log(kcat), log(Km), and log(kcat/Km) for wild type CatA and its variants and have compared the measured pKa with calculated values. We propose a substrate-assisted mechanism in which the high pKa of E149 (>8.5) favors the binding of the carboxylate form of the substrate and promotes the abstraction of the proton from H429 of the catalytic triad effectively decreasing its pKa in a low-pH environment. We also identify a similar motif consisting of a pair of histidines in S-formylglutathione hydrolase.
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Affiliation(s)
- Ilja V Khavrutskii
- Armed Forces Radiobiology Research Institute , Uniformed Services University , Bethesda , Maryland 20889-5648 , United States
| | - Jaimee R Compton
- U.S. Naval Research Laboratory , 4555 Overlook Avenue , Washington, D.C. 20375 , United States
| | - Kayla M Jurkouich
- Department of Biomedical Engineering , Case Western Reserve University , Cleveland , Ohio 44106 , United States
| | - Patricia M Legler
- U.S. Naval Research Laboratory , 4555 Overlook Avenue , Washington, D.C. 20375 , United States
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Ding M, Fan J, Wang W, Wang H, Liu H. Molecular characterization, expression and antimicrobial activity of complement factor D in Megalobrama amblycephala. FISH & SHELLFISH IMMUNOLOGY 2019; 89:43-51. [PMID: 30890434 DOI: 10.1016/j.fsi.2019.03.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 02/23/2019] [Accepted: 03/12/2019] [Indexed: 06/09/2023]
Abstract
Complement factor D (Df) is a serine protease, which can activate the alternative pathway by cleaving complement factor B, and involves in the innate defense against pathogens infection in teleost. In this study, we cloned, characterized the Df gene from blunt snout bream (Megalobrama amblycephala) (Mamdf), and examined its expression pattern and antimicrobial activity. The open reading frame (ORF) of Mamdf was 753 bp, encoding 250 amino acids with a molecular mass of 27.2 kDa. Mamdf consisted of a single serine protease trypsin superfamily domain, 3 substrate binding sites and 3 active sites, but no potential N-glycosylation site. Pairwise alignment showed that Mamdf shared the highest identity (94%) with grass carp (Ctenopharyngodon idellus). Phylogenetic analysis indicated that Mamdf and other vertebrate Df had a common ancestral origin. Mamdf structured with 4 introns and 5 exons. The Mamdf mRNA expressed relatively high at the intestine appearance stage during early development and constitutively expressed in various tissues with the highest expression in the kidney in healthy adults. After challenged with Aeromonas hydrophila, significant changes of Mamdf at both mRNA and protein levels in the kidney, spleen, liver and head-kidney were observed. The recombinant Mamdf protein showed antimicrobial activity against both gram-positive bacteria and gram-negative bacteria. The above results suggested the immune function of Mamdf, and would benefit further detailed Df function research in the immune process in teleost.
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Affiliation(s)
- Ming Ding
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jun Fan
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Weimin Wang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huanling Wang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hong Liu
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
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29
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Anti-inflammatory activity of a serine protease produced from Bacillus pumilus SG2. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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30
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Dahms SO, Demir F, Huesgen PF, Thorn K, Brandstetter H. Sirtilins - the new old members of the vitamin K-dependent coagulation factor family. J Thromb Haemost 2019; 17:470-481. [PMID: 30644641 PMCID: PMC6850207 DOI: 10.1111/jth.14384] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Indexed: 12/04/2022]
Abstract
Essentials Blood coagulation is driven by vitamin K (VK)-dependent proteases. We have identified and characterized 'sirtilin' as an additional VK-dependent protease. Sirtilins emerged early in the evolution of the coagulation system of vertebrates. Ubiquitous occurrence might indicate an important functional role of sirtilins. SUMMARY: Background Vitamin K (VK)-dependent proteases are major players in blood coagulation, including both the initiation and the regulation of the cascade. Five different members of this protease family have been described, comprising the following coagulation factors: factor VII, FIX, FX, protein C (PC), and prothrombin (FII). FVII, FIX, FX and PC share a typical domain architecture, with an N-terminal γ-carboxyglutamate (Gla) domain, two epidermal growth factor-like (EGF) domains, and a C-terminal trypsin-like serine protease (SP) domain. Objectives We have identified uncharacterized proteins in snake genomes showing the typical Gla-EGF1-EGF2-SP domain architecture but relatively low sequence conservation compared to known VK-dependent proteases. On the basis of sequence analysis, we hypothesized that these proteins are functional members of the VK-dependent protease family. Methods/results Using phylogenetic analyses, we confirmed the so-called 'sirtilins' as an additional VK-dependent protease class. These proteases were found in several vertebrates, including jawless fish, cartilaginous fish, bony fish, reptiles, birds, and marsupials, but not in other mammals. The recombinant zymogen form of Thamnophis sirtalis sirtilin was produced by in vitro renaturation, and was activated with human activated FXI. The activated form of sirtilin proteolytically cleaved peptide and protein substrates, including prothrombin. Mass spectrometry-based substrate profiling of sirtilin revealed a narrower sequence specificity than those of FIX and FX. Conclusions The ubiquitous occurrence of sirtilins in many vertebrate classes might indicate an important functional role. Understanding the detailed functions of sirtilins might contribute to a deeper understanding of the evolution and function of the vertebrate coagulation system.
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Affiliation(s)
- Sven O. Dahms
- Department of BiosciencesUniversity of SalzburgSalzburgAustria
| | - Fatih Demir
- ZEA‐3 AnalyticsCentral Institute for Engineering, Electronics and AnalyticsForschungszentrum JülichJülichGermany
| | - Pitter F. Huesgen
- ZEA‐3 AnalyticsCentral Institute for Engineering, Electronics and AnalyticsForschungszentrum JülichJülichGermany
| | - Karina Thorn
- Haemophilia ResearchNovo Nordisk A/SMåløvDenmark
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Smith G, Kelly JE, Macias-Muñoz A, Butts CT, Martin RW, Briscoe AD. Evolutionary and structural analyses uncover a role for solvent interactions in the diversification of cocoonases in butterflies. Proc Biol Sci 2019; 285:rspb.2017.2037. [PMID: 29298934 DOI: 10.1098/rspb.2017.2037] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 12/01/2017] [Indexed: 01/22/2023] Open
Abstract
Multi-omic approaches promise to supply the power to detect genes underlying disease and fitness-related phenotypes. Optimal use of the resulting profusion of data requires detailed investigation of individual candidate genes, a challenging proposition. Here, we combine transcriptomic and genomic data with molecular modelling of candidate enzymes to characterize the evolutionary history and function of the serine protease cocoonase. Heliconius butterflies possess the unique ability to feed on pollen; recent work has identified cocoonase as a candidate gene in pollen digestion. Cocoonase was first described in moths, where it aids in eclosure from the cocoon and is present as a single copy gene. In heliconiine butterflies it is duplicated and highly expressed in the mouthparts of adults. At least six copies of cocoonase are present in Heliconius melpomene and copy number varies across H. melpomene sub-populations. Most cocoonase genes are under purifying selection, however branch-site analyses suggest cocoonase 3 genes may have evolved under episodic diversifying selection. Molecular modelling of cocoonase proteins and examination of their predicted structures revealed that the active site region of each type has a similar structure to trypsin, with the same predicted substrate specificity across types. Variation among heliconiine cocoonases instead lies in the outward-facing residues involved in solvent interaction. Thus, the neofunctionalization of cocoonase duplicates appears to have resulted from the need for these serine proteases to operate in diverse biochemical environments. We suggest that cocoonase may have played a buffering role in feeding during the diversification of Heliconius across the neotropics by enabling these butterflies to digest protein from a range of biochemical milieux.
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Affiliation(s)
- G Smith
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA .,School of Biological Sciences, Bangor University, Brambell Laboratories, Bangor, Gwynedd, UK
| | - J E Kelly
- Department of Chemistry, University of California, Irvine, CA 92697, USA
| | - A Macias-Muñoz
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
| | - C T Butts
- Department of Sociology, University of California, Irvine, CA 92697, USA.,Department of Statistics, University of California, Irvine, CA 92697, USA.,Department of Electrical Engineering and Computer Science, University of California, Irvine, CA 92697, USA
| | - R W Martin
- Department of Chemistry, University of California, Irvine, CA 92697, USA.,Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - A D Briscoe
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
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32
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Landi N, Ragucci S, Russo R, Pedone PV, Chambery A, Di Maro A. Structural insights into nucleotide and protein sequence of Ageritin: a novel prototype of fungal ribotoxin. J Biochem 2018; 165:415-422. [DOI: 10.1093/jb/mvy113] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/10/2018] [Indexed: 02/02/2023] Open
Affiliation(s)
- Nicola Landi
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DISTABIF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, I Caserta, Italy
| | - Sara Ragucci
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DISTABIF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, I Caserta, Italy
| | - Rosita Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DISTABIF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, I Caserta, Italy
| | - Paolo V Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DISTABIF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, I Caserta, Italy
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DISTABIF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, I Caserta, Italy
| | - Antimo Di Maro
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DISTABIF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, I Caserta, Italy
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Ullah A, Masood R, Ali I, Ullah K, Ali H, Akbar H, Betzel C. Thrombin-like enzymes from snake venom: Structural characterization and mechanism of action. Int J Biol Macromol 2018; 114:788-811. [PMID: 29604354 DOI: 10.1016/j.ijbiomac.2018.03.164] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/08/2018] [Accepted: 03/23/2018] [Indexed: 01/15/2023]
Abstract
Snake venom thrombin-like enzymes (SVTLEs) constitute the major portion (10-24%) of snake venom and these are the second most abundant enzymes present in the crude venom. During envenomation, these enzymes had shown prominently the various pathological effects, such as disturbance in hemostatic system, fibrinogenolysis, fibrinolysis, platelet aggregation, thrombosis, neurologic disorders, activation of coagulation factors, coagulant, procoagulant etc. These enzymes also been used as a therapeutic agent for the treatment of various diseases such as congestive heart failure, ischemic stroke, thrombotic disorders etc. Although the crystal structures of five SVTLEs are available in the Protein Data Bank (PDB), there is no single article present in the literature that has described all of them. The current work describes the structural aspects, structure-based mechanism of action, processing and inhibition of these enzymes. The sequence analysis indicates that these enzymes show a high sequence identity (57-85%) with each other and low sequence identity with trypsin (36-43%), human alpha-thrombin (29-36%) and other snake venom serine proteinases (57-85%). Three-dimensional structural analysis indicates that the loops surrounding the active site are variable both in amino acids composition and length that may convey variable substrate specificity to these enzymes. The surface charge distributions also vary in these enzymes. Docking analysis with suramin shows that this inhibitor preferably binds to the C-terminal region of these enzymes and causes the destabilization of their three-dimensional structure.
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Affiliation(s)
- Anwar Ullah
- Department of Biosciences, COMSATS Institute of Information Technology Park Road, Islamabad 45550, Pakistan.
| | - Rehana Masood
- Department of Biochemistry, Shaheed Benazir Bhutto Women University, Peshawar 25000, Pakistan
| | - Ijaz Ali
- Department of Biosciences, COMSATS Institute of Information Technology Park Road, Islamabad 45550, Pakistan
| | - Kifayat Ullah
- Department of Biosciences, COMSATS Institute of Information Technology Park Road, Islamabad 45550, Pakistan
| | - Hamid Ali
- Department of Biosciences, COMSATS Institute of Information Technology Park Road, Islamabad 45550, Pakistan
| | - Haji Akbar
- Department of Biosciences, COMSATS Institute of Information Technology Park Road, Islamabad 45550, Pakistan
| | - Christian Betzel
- Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
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Jaiswal RK, Varshney AK, Yadava PK. Diversity and functional evolution of the plasminogen activator system. Biomed Pharmacother 2018; 98:886-898. [PMID: 29571259 DOI: 10.1016/j.biopha.2018.01.029] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 12/29/2017] [Accepted: 01/03/2018] [Indexed: 01/08/2023] Open
Abstract
The urokinase plasminogen activator system is a family of serine proteases which consists of uPA (urokinase plasminogen activator), uPAR (urokinase type plasminogen activator receptor) and PAI-1 (plasminogen activator inhibitor 1). In addition to their significant roles in activation, these proteases act as key regulators of the tumor microenvironment and are involved in the metastatic process in many cancers. High levels of uPA system proteases in many human cancer predicts poor patient prognosis and strongly indicated a key role of uPA system in cancer metastasis. Individual components of uPA system are found to be differentially expressed in cancer cells compared to normal cells and therefore are potential therapeutic targets. In this review, we present the molecular and cellular mechanisms underlying the role of uPA system in cancer progression. Epithelial to mesenchymal transitions (EMT) is the main cause of the cancer cell metastasis. We have also attempted to relate the role of uPA signaling in EMT of cancer cells.
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Affiliation(s)
- Rishi Kumar Jaiswal
- Applied Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Akhil Kumar Varshney
- Applied Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Pramod Kumar Yadava
- Applied Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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Sun Y, Wang Y, Liu W, Zhou JL, Zeng J, Wang XH, Jiang YR, Li DH, Qin L. Upregulation of a Trypsin-Like Serine Protease Gene in Antheraea pernyi (Lepidoptera: Saturniidae) Strains Exposed to Different Pathogens. JOURNAL OF ECONOMIC ENTOMOLOGY 2017; 110:941-948. [PMID: 28369437 DOI: 10.1093/jee/tox096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Indexed: 06/07/2023]
Abstract
Antheraea pernyi Guérin-Méneville is used for silk production and as a food resource. Its infection by exogenous pathogens, including microsporidia, fungi, bacteria, and virus, can lead to silkworm diseases, causing major economic losses. A trypsin-like serine protease gene (TLS) was found in A. pernyi transcriptome data resulting from two different infection experiments. The cDNA sequence of ApTLS was 1,020 bp in length and contained an open reading frame of 774 bp encoding a 257-amino acid protein (GenBank KF779933). The present study investigated the expression patterns of ApTLS after exposure to different pathogens, and in four different A. pernyi strains. Semiquantitative RT-PCR indicated that ApTLS was expressed in all developmental stages and was most expressed in the midgut. Quantitative real-time PCR indicated ApTLS was upregulated in the midgut of A. pernyi exposed to nucleopolyhedrovirus (ApNPV), Nosema pernyi, Enterococcus pernyi, and Beauveria bassiana infections, and the highest gene expression level was found under ApNPV infection. The strain Shenhuang No. 2 presented the lowest infection rate and the highest ApTLS gene expression level when exposed to ApNPV. Thus, ApTLS seems to be involved in innate defense reactions in A. pernyi.
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Affiliation(s)
- Ying Sun
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Liaoning Engineering and Technology Resource Center for Insect Resource, Shenyang 110866, China (; ; ; ; ; ; )
| | - Yong Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Liaoning Engineering and Technology Resource Center for Insect Resource, Shenyang 110866, China (; ; ; ; ; ; )
| | - Wei Liu
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Jing-Lin Zhou
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Liaoning Engineering and Technology Resource Center for Insect Resource, Shenyang 110866, China (; ; ; ; ; ; )
| | - Jun Zeng
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Liaoning Engineering and Technology Resource Center for Insect Resource, Shenyang 110866, China (; ; ; ; ; ; )
| | - Xiao-Hui Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Liaoning Engineering and Technology Resource Center for Insect Resource, Shenyang 110866, China (; ; ; ; ; ; )
| | - Yi-Ren Jiang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Liaoning Engineering and Technology Resource Center for Insect Resource, Shenyang 110866, China (; ; ; ; ; ; )
| | - Dong-Hua Li
- Yanbian Academy of Agricultural Sciences, Yanbian 133400, China
| | - Li Qin
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Liaoning Engineering and Technology Resource Center for Insect Resource, Shenyang 110866, China ( ; ; ; ; ; ; )
- Corresponding author, e-mail:
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Li YL, Hou MZ, Shen GM, Lu XP, Wang Z, Jia FX, Wang JJ, Dou W. Functional analysis of five trypsin-like protease genes in the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae). PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2017; 136:52-57. [PMID: 28187831 DOI: 10.1016/j.pestbp.2016.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 08/11/2016] [Accepted: 08/14/2016] [Indexed: 06/06/2023]
Abstract
Insect midgut proteases catalyze the release of free amino acids from dietary proteins and are essential for insect normal development. To date, digestive proteases as potential candidates have made great progress in pest control. To clarify the function of trypsin-like protease genes in the digestive system of Bactrocera dorsalis, a serious pest of a wide range of tropical and subtropical fruit and vegetable crops, five trypsin genes (BdTry1, BdTry2, BdTry3, BdTry4 and BdTry5) were identified from transcriptome dataset, and the effects of feeding condition on their expression levels were examined subsequently. RNA interference (RNAi) was applied to further explore their function on the growth of B. dorsalis. The results showed that all the BdTrys in starving midgut expressed at a minimal level but up-regulated upon feeding (except BdTry3). Besides, RNAi by feeding dsRNAs to larvae proved to be an effective method to cause gene silencing and the mixed dsRNAs of the five BdTrys slowed larvae growth of B. dorsalis. The current data suggest that trypsin genes are actively involved in digestion process of B. dorsalis larvae and thereafter play crucial roles in their development.
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Affiliation(s)
- Ya-Li Li
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, PR China
| | - Ming-Zhe Hou
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, PR China
| | - Guang-Mao Shen
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, PR China
| | - Xue-Ping Lu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, PR China
| | - Zhe Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, PR China
| | - Fu-Xian Jia
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, PR China
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, PR China
| | - Wei Dou
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, PR China.
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da Silva RR. Bacterial and Fungal Proteolytic Enzymes: Production, Catalysis and Potential Applications. Appl Biochem Biotechnol 2017; 183:1-19. [DOI: 10.1007/s12010-017-2427-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/24/2017] [Indexed: 11/29/2022]
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Riley BT, Ilyichova O, Costa MGS, Porebski BT, de Veer SJ, Swedberg JE, Kass I, Harris JM, Hoke DE, Buckle AM. Direct and indirect mechanisms of KLK4 inhibition revealed by structure and dynamics. Sci Rep 2016; 6:35385. [PMID: 27767076 PMCID: PMC5073354 DOI: 10.1038/srep35385] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 09/28/2016] [Indexed: 11/09/2022] Open
Abstract
The kallikrein-related peptidase (KLK) family of proteases is involved in many aspects of human health and disease. One member of this family, KLK4, has been implicated in cancer development and metastasis. Understanding mechanisms of inactivation are critical to developing selective KLK4 inhibitors. We have determined the X-ray crystal structures of KLK4 in complex with both sunflower trypsin inhibitor-1 (SFTI-1) and a rationally designed SFTI-1 derivative to atomic (~1 Å) resolution, as well as with bound nickel. These structures offer a structural rationalization for the potency and selectivity of these inhibitors, and together with MD simulation and computational analysis, reveal a dynamic pathway between the metal binding exosite and the active site, providing key details of a previously proposed allosteric mode of inhibition. Collectively, this work provides insight into both direct and indirect mechanisms of inhibition for KLK4 that have broad implications for the enzymology of the serine protease superfamily, and may potentially be exploited for the design of therapeutic inhibitors.
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Affiliation(s)
- Blake T Riley
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Olga Ilyichova
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Mauricio G S Costa
- Programa de Computação Científica, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Benjamin T Porebski
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Simon J de Veer
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland 4059, Australia
| | - Joakim E Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Itamar Kass
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Jonathan M Harris
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland 4059, Australia
| | - David E Hoke
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Ashley M Buckle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
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Use of protease inhibitory gold nanoparticles as a compatibility enhancer for Bt and deltamethrin: A novel approach for pest control. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2016. [DOI: 10.1016/j.bcab.2016.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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40
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Pozzi N, Bystranowska D, Zuo X, Di Cera E. Structural Architecture of Prothrombin in Solution Revealed by Single Molecule Spectroscopy. J Biol Chem 2016; 291:18107-16. [PMID: 27435675 DOI: 10.1074/jbc.m116.738310] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Indexed: 01/29/2023] Open
Abstract
The coagulation factor prothrombin has a complex spatial organization of its modular assembly that comprises the N-terminal Gla domain, kringle-1, kringle-2, and the C-terminal protease domain connected by three intervening linkers. Here we use single molecule Förster resonance energy transfer to access the conformational landscape of prothrombin in solution and uncover structural features of functional significance that extend recent x-ray crystallographic analysis. Prothrombin exists in equilibrium between two alternative conformations, open and closed. The closed conformation predominates (70%) and features an unanticipated intramolecular collapse of Tyr(93) in kringle-1 onto Trp(547) in the protease domain that obliterates access to the active site and protects the zymogen from autoproteolytic conversion to thrombin. The open conformation (30%) is more susceptible to chymotrypsin digestion and autoactivation, and features a shape consistent with recent x-ray crystal structures. Small angle x-ray scattering measurements of prothrombin wild type stabilized 70% in the closed conformation and of the mutant Y93A stabilized 80% in the open conformation directly document two envelopes that differ 50 Å in length. These findings reveal important new details on the conformational plasticity of prothrombin in solution and the drastic structural difference between its alternative conformations. Prothrombin uses the intramolecular collapse of kringle-1 onto the active site in the closed form to prevent autoactivation. The open-closed equilibrium also defines a new structural framework for the mechanism of activation of prothrombin by prothrombinase.
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Affiliation(s)
- Nicola Pozzi
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104 and
| | - Dominika Bystranowska
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104 and
| | - Xiaobing Zuo
- the X-Ray Science Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Enrico Di Cera
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104 and
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41
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An Integrated In Silico Approach for the Structural and Functional Exploration of Lipocalin 2 and its Functional Insights with Metalloproteinase 9 and Lipoprotein Receptor-Related Protein 2. Appl Biochem Biotechnol 2015; 176:712-29. [DOI: 10.1007/s12010-015-1606-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 04/06/2015] [Indexed: 12/17/2022]
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42
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Sherlin D, Anishetty S. Mechanistic insights from molecular dynamic simulation of Rv0045c esterase in Mycobacterium tuberculosis. J Mol Model 2015; 21:90. [DOI: 10.1007/s00894-015-2630-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 02/22/2015] [Indexed: 11/29/2022]
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Pelc LA, Chen Z, Gohara DW, Vogt AD, Pozzi N, Di Cera E. Why Ser and not Thr brokers catalysis in the trypsin fold. Biochemistry 2015; 54:1457-64. [PMID: 25664608 DOI: 10.1021/acs.biochem.5b00014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Although Thr is equally represented as Ser in the human genome and as a nucleophile is as good as Ser, it is never found in the active site of the large family of trypsin-like proteases that utilize the Asp/His/Ser triad. The molecular basis of the preference of Ser over Thr in the trypsin fold was investigated with X-ray structures of the thrombin mutant S195T free and bound to an irreversible active site inhibitor. In the free form, the methyl group of T195 is oriented toward the incoming substrate in a conformation seemingly incompatible with productive binding. In the bound form, the side chain of T195 is reoriented for efficient substrate acylation without causing steric clash within the active site. Rapid kinetics prove that this change is due to selection of an active conformation from a preexisting ensemble of reactive and unreactive rotamers whose relative distribution determines the level of activity of the protease. Consistent with these observations, the S195T substitution is associated with a weak yet finite activity that allows identification of an unanticipated important role for S195 as the end point of allosteric transduction in the trypsin fold. The S195T mutation abrogates the Na(+)-dependent enhancement of catalytic activity in thrombin, activated protein C, and factor Xa and significantly weakens the physiologically important allosteric effects of thrombomodulin on thrombin and of cofactor Va on factor Xa. The evolutionary selection of Ser over Thr in trypsin-like proteases was therefore driven by the need for high catalytic activity and efficient allosteric regulation.
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Affiliation(s)
- Leslie A Pelc
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine , St. Louis, Missouri 63104, United States
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The catalytic triad of testes-specific protease 50 (TSP50) is essential for its function in cell proliferation. Cell Signal 2014; 26:2266-75. [PMID: 25049081 DOI: 10.1016/j.cellsig.2014.07.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 06/22/2014] [Accepted: 07/04/2014] [Indexed: 12/12/2022]
Abstract
Testes-specific protease 50 (TSP50) is a novelly identified pro-oncogene and it shares a similar enzymatic structure with many serine proteases. Our previous results suggested that TSP50 could promote tumorigenesis through degradation of IκBα protein and activating NF-κB signaling, and the threonine mutation in its catalytic triad could depress TSP50-mediated cell proliferation. However, whether the two other residues in the catalytic triad of TSP50 play a role in maintaining protease activity and tumorigenesis, and the mechanisms involved in this process remain unclear. Here, we constructed and characterized three catalytic triad mutants of TSP50 and found that all the mutants could significantly depress TSP50-induced cell proliferation and colony formation in vitro and tumor formation in vivo, and the aspartic acid at position 206 in the catalytic triad played a more crucial role than threonine and histidine in this process. Mechanistic studies revealed that the mutants in the catalytic triad abolished the enzyme activity of TSP50, but did not change the cellular localization. Furthermore, our data indicated that all the three mutants suppressed activation of NF-κB signal by preventing the interaction between TSP50 and the NF-κB:IκBα complex. Most importantly, we demonstrated that TSP50 could interact with IκBα protein and cleave it directly as a new protease in vitro.
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45
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Fan J, Han P, Chen X, Hu Q, Ye M. Comparative proteomic analysis of Bombyx mori hemocytes treated with destruxin A. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2014; 86:33-45. [PMID: 24719308 DOI: 10.1002/arch.21160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Destruxin A (DA), a cyclodepsipeptidic secondary metabolite of the entomopathogenic fungus, Metarhizium anisopliae, is an important anti-immunity agent against insect hemocytes. To understand the mechanism of the molecular responses to DA, fifth-instar larvae of the silkworm, Bombyx mori, were injected with 2 μg of DA. The proteomics of hemocytes were then investigated using two-dimensional electrophoresis and mass spectrometry, and validated qPCR. As a result, a total of 47 differently expressed protein spots were detected and 22 proteins in 26 spots were identified. There are eight immunity-related proteins, including three downregulated proteins (antitrypsin isoform 3, p50 protein, and calreticulin precursor) and five upregulated proteins (C-type lectin 10 precursor, serine proteinase-like protein, paralytic peptide, PPO-1, and PPO-2). Four resistance- and/or stress-related proteins (arginine kinase, carboxylesterase clade H, member 1, aminoacylase, and thiol peroxiredoxin) were upregulated. Ten proteins with other or unknown functions were also recorded. Five selected proteins were verified with qPCR. These results provide new insights into the molecular mechanism of host immune response to DA challenge.
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Affiliation(s)
- Jiqiao Fan
- Department of Pesticide Science, College of Natural Resource and Environment, South China Agricultural University, Guangzhou, China
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46
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Molecular Targets of β-Lactam-Based Antimicrobials: Beyond the Usual Suspects. Antibiotics (Basel) 2014; 3:128-42. [PMID: 27025739 PMCID: PMC4790389 DOI: 10.3390/antibiotics3020128] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 02/24/2014] [Accepted: 02/25/2014] [Indexed: 12/20/2022] Open
Abstract
The common practice in antibacterial drug development has been to rapidly make an attempt to find ever-more stable and broad-spectrum variants for a particular antibiotic, once a drug resistance for that antibiotic is detected. We are now facing bacterial resistance toward our clinically relevant antibiotics of such a magnitude that the conversation for antimicrobial drug development ought to include effective new antibiotics with alternative mechanisms of action. The electrophilic β-lactam ring is amenable for the inhibition of different enzyme classes by a suitable decoration of the core scaffold. Monocyclic β-lactams lacking an ionizable group at the lactam nitrogen exhibit target preferences toward bacterial enzymes important for resistance and virulence. The present review intends to draw attention to the versatility of the β-lactams as antimicrobials with "unusual" molecular targets.
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Xiong C, Fang F, Chen L, Yang Q, He J, Zhou D, Shen B, Ma L, Sun Y, Zhang D, Zhu C. Trypsin-catalyzed deltamethrin degradation. PLoS One 2014; 9:e89517. [PMID: 24594869 PMCID: PMC3940599 DOI: 10.1371/journal.pone.0089517] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 01/21/2014] [Indexed: 12/02/2022] Open
Abstract
To explore if trypsin could catalyze the degradation of non-protein molecule deltamethrin, we compared in vitro hydrolytic reactions of deltamethrin in the presence and absence of trypsin with ultraviolet-visible (UV/Vis) spectrophotometry and gas chromatography-mass spectrometry (GC/MS). In addition, acute oral toxicity of the degradation products was determined in Wistar rats. The results show that the absorption peak of deltamethrin is around 264 nm, while the absorption peaks of deltamethrin degradation products are around 250 nm and 296 nm. In our GC setting, the retention time of undegraded deltamethrin was 37.968 min, while those of deltamethrin degradation products were 15.289 min and 18.730 min. The LD50 of deltamethrin in Wistar rats is 55 mg/kg, while that of deltamethrin degradation products is 3358 mg/kg in female rats and 1045 mg/kg in male rates (61-fold and 19-fold reductions in toxicity), suggesting that trypsin could directly degrade deltamethrin, which significantly reduces the toxicity of deltamethrin. These results expand people's understanding of the functions of proteases and point to potential applications of trypsin as an attractive agent to control residual pesticides in the environment and on agricultural products.
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Affiliation(s)
- Chunrong Xiong
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, China
- Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, China
| | - Fujin Fang
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, China
- Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, China
| | - Lin Chen
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, China
- Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, China
| | - Qinggui Yang
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, China
- Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, China
| | - Ji He
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, China
- Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, China
| | - Dan Zhou
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, China
- Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, China
| | - Bo Shen
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, China
- Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, China
| | - Lei Ma
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, China
- Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, China
| | - Yan Sun
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, China
- Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, China
| | - Donghui Zhang
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, China
- Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, China
- * E-mail:
| | - Changliang Zhu
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, China
- Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing, Jiangsu, China
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48
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Fuchs JE, von Grafenstein S, Huber RG, Kramer C, Liedl KR. Substrate-driven mapping of the degradome by comparison of sequence logos. PLoS Comput Biol 2013; 9:e1003353. [PMID: 24244149 PMCID: PMC3828135 DOI: 10.1371/journal.pcbi.1003353] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 10/05/2013] [Indexed: 12/27/2022] Open
Abstract
Sequence logos are frequently used to illustrate substrate preferences and specificity of proteases. Here, we employed the compiled substrates of the MEROPS database to introduce a novel metric for comparison of protease substrate preferences. The constructed similarity matrix of 62 proteases can be used to intuitively visualize similarities in protease substrate readout via principal component analysis and construction of protease specificity trees. Since our new metric is solely based on substrate data, we can engraft the protease tree including proteolytic enzymes of different evolutionary origin. Thereby, our analyses confirm pronounced overlaps in substrate recognition not only between proteases closely related on sequence basis but also between proteolytic enzymes of different evolutionary origin and catalytic type. To illustrate the applicability of our approach we analyze the distribution of targets of small molecules from the ChEMBL database in our substrate-based protease specificity trees. We observe a striking clustering of annotated targets in tree branches even though these grouped targets do not necessarily share similarity on protein sequence level. This highlights the value and applicability of knowledge acquired from peptide substrates in drug design of small molecules, e.g., for the prediction of off-target effects or drug repurposing. Consequently, our similarity metric allows to map the degradome and its associated drug target network via comparison of known substrate peptides. The substrate-driven view of protein-protein interfaces is not limited to the field of proteases but can be applied to any target class where a sufficient amount of known substrate data is available.
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Affiliation(s)
- Julian E. Fuchs
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Susanne von Grafenstein
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Roland G. Huber
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Christian Kramer
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
- * E-mail:
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49
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Chandrasekaran M, Chandrasekar R, Sa T, Sathiyabama M. Serine protease identification (in vitro) and molecular structure predictions (in silico) from a phytopathogenic fungus, Alternaria solani. J Basic Microbiol 2013; 54 Suppl 1:S210-8. [PMID: 24122785 DOI: 10.1002/jobm.201300433] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 08/23/2013] [Indexed: 11/10/2022]
Abstract
Serine proteases are involved in an enormous number of biological processes. The present study aims at characterizing three-dimensional (3D) molecular architecture of serine proteases from early blight pathogen, Alternaria solani that are hypothesized to be markers of phytopathogenicity. A serine protease was purified to homogeneity and MALDI-TOF-MS/MS analysis revealed that protease produced by A. solani belongs to alkaline serine proteases (AsP). AsP is made up of 403 amino acid residues with molecular weight of 42.1 kDa (Isoelectric point - 6.51) and its molecular formula was C1859 H2930 N516 O595 S4 . AsP structure model was built based on its comparative homology with serine protease using the program, MODELER. AsP had 16 β-sheets and 10 α-helices, with Ser(350) (G347-G357), Asp(158) (D158-H169), and His(193) (H193-G203) in separate turn/coil structures. Biological metal binding region situated near 6th-helix and His(193) residue is responsible for metal binding site. Also, calcium ion (Ca(2+)) is coordinated by the carboxyl groups of Lys(84), Ile(85), Lys(86), Asp(87), Phe(88), Ala(89), Ala(90) (K84-A90) for first Ca(2+) binding site and carbonyl oxygen atom of Lys(244), Gly(245), Arg(246), Thr(247), Lys(248), Lys(249), and Ala(250) (K244-A250), for second Ca(2+) binding site. Moreover, Ramachandran plot analysis of protein residues falling into most favored secondary structures were determined (83.3%). The predicted molecular 3D structural model was further verified using PROCHECK, ERRAT, and VADAR servers to confirm the geometry and stereo-chemical parameters of the molecular structural design. The functional analysis of AsP 3D molecular structure predictions familiar in the current study may provide a new perspective in the understanding and identification of antifungal protease inhibitor designing.
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Affiliation(s)
- Murugesan Chandrasekaran
- Department of Plant Science, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India; Department of Environmental and Biological Chemistry, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
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Koumandou VL, Scorilas A. Evolution of the plasma and tissue kallikreins, and their alternative splicing isoforms. PLoS One 2013; 8:e68074. [PMID: 23874499 PMCID: PMC3707919 DOI: 10.1371/journal.pone.0068074] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 05/25/2013] [Indexed: 12/14/2022] Open
Abstract
Kallikreins are secreted serine proteases with important roles in human physiology. Human plasma kallikrein, encoded by the KLKB1 gene on locus 4q34-35, functions in the blood coagulation pathway, and in regulating blood pressure. The human tissue kallikrein and kallikrein-related peptidases (KLKs) have diverse expression patterns and physiological roles, including cancer-related processes such as cell growth regulation, angiogenesis, invasion, and metastasis. Prostate-specific antigen (PSA), the product of the KLK3 gene, is the most widely used biomarker in clinical practice today. A total of 15 KLKs are encoded by the largest contiguous cluster of protease genes in the human genome (19q13.3-13.4), which makes them ideal for evolutionary analysis of gene duplication events. Previous studies on the evolution of KLKs have traced mammalian homologs as well as a probable early origin of the family in aves, amphibia and reptilia. The aim of this study was to address the evolutionary and functional relationships between tissue KLKs and plasma kallikrein, and to examine the evolution of alternative splicing isoforms. Sequences of plasma and tissue kallikreins and their alternative transcripts were collected from the NCBI and Ensembl databases, and comprehensive phylogenetic analysis was performed by Bayesian as well as maximum likelihood methods. Plasma and tissue kallikreins exhibit high sequence similarity in the trypsin domain (>50%). Phylogenetic analysis indicates an early divergence of KLKB1, which groups closely with plasminogen, chymotrypsin, and complement factor D (CFD), in a monophyletic group distinct from trypsin and the tissue KLKs. Reconstruction of the earliest events leading to the diversification of the tissue KLKs is not well resolved, indicating rapid expansion in mammals. Alternative transcripts of each KLK gene show species-specific divergence, while examination of sequence conservation indicates that many annotated human KLK isoforms are missing the catalytic triad that is crucial for protease activity.
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Affiliation(s)
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, University of Athens, Athens, Greece
- * E-mail:
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