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Razai AS, Snipas SJ, Poreba M, Fasci D, Salvesen GS. Engineering caspase 7 as an affinity reagent to capture proteolytic products. FEBS J 2020; 288:1259-1270. [PMID: 32619291 DOI: 10.1111/febs.15467] [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: 04/03/2020] [Revised: 05/19/2020] [Accepted: 06/26/2020] [Indexed: 11/29/2022]
Abstract
Many proteases recognize their substrates with high specificities, with this in mind, it should theoretically be possible to utilize the substrate binding cleft of a protease as a scaffold to engineer an affinity reagent. In this study, we sought to develop reagents that would differentiate between substrates and products of proteolysis, based on a caspase 7 scaffold. Firstly, we engineered a form of caspase 7 that can undergo conversion to a substrate binding conformation without catalysis. Seeking to generate a product-only trap, we further engineered this construct by incorporating mutations that compensate for the generation of a negative charge in the neo C terminus of a newly generated product. This was accomplished with only three substitutions within the substrate binding cleft. Moreover, the affinity of the product trap for peptides was comparable to the affinity of caspase 7 to parental substrates. Finally, generation of a hybrid fluorescent protein with the product trap provided a reagent that specifically recognized apoptotic cells and highlights the versatility of such an approach in developing affinity and imaging agents for a variety of cysteine and serine proteases.
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Affiliation(s)
- Amir S Razai
- Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Scott J Snipas
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Marcin Poreba
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.,Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wroclaw, Poland
| | - Domenico Fasci
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Guy S Salvesen
- Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
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52
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Isabela Avila-Rodríguez M, Meléndez-Martínez D, Licona-Cassani C, Manuel Aguilar-Yañez J, Benavides J, Lorena Sánchez M. Practical context of enzymatic treatment for wound healing: A secreted protease approach (Review). Biomed Rep 2020; 13:3-14. [PMID: 32440346 PMCID: PMC7238406 DOI: 10.3892/br.2020.1300] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/14/2020] [Indexed: 12/13/2022] Open
Abstract
Skin wounds have been extensively studied as their healing represents a critical step towards achieving homeostasis following a traumatic event. Dependent on the severity of the damage, wounds are categorized as either acute or chronic. To date, chronic wounds have the highest economic impact as long term increases wound care costs. Chronic wounds affect 6.5 million patients in the United States with an annual estimated expense of $25 billion for the health care system. Among wound treatment categories, active wound care represents the fastest-growing category due to its specific actions and lower costs. Within this category, proteases from various sources have been used as successful agents in debridement wound care. The wound healing process is predominantly mediated by matrix metalloproteinases (MMPs) that, when dysregulated, result in defective wound healing. Therapeutic activity has been described for animal secretions including fish epithelial mucus, maggot secretory products and snake venom, which contain secreted proteases (SPs). No further alternatives for use, sources or types of proteases used for wound healing have been found in the literature to date. Through the present review, the context of enzymatic wound care alternatives will be discussed. In addition, substrate homology of SPs and human MMPs will be compared and contrasted. The purpose of these discussions is to identify and propose the stages of wound healing in which SPs may be used as therapeutic agents to improve the wound healing process.
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Affiliation(s)
| | - David Meléndez-Martínez
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Monterrey, Nuevo León 64849, Mexico
| | | | - José Manuel Aguilar-Yañez
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Monterrey, Nuevo León 64849, Mexico
- Scicore Medical SAPI de CV, Monterrey, Nuevo León 64920, Mexico
| | - Jorge Benavides
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Monterrey, Nuevo León 64849, Mexico
| | - Mirna Lorena Sánchez
- Laboratorio de Materiales Biotecnológicos, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes-Imbice-Conicet-Cicpba, Bernal, Buenos Aires B1876BXD, Argentina
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53
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Hepsin enhances liver metabolism and inhibits adipocyte browning in mice. Proc Natl Acad Sci U S A 2020; 117:12359-12367. [PMID: 32404422 DOI: 10.1073/pnas.1918445117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Hepsin is a transmembrane serine protease primarily expressed in the liver. To date, the physiological function of hepsin remains poorly defined. Here we report that hepsin-deficient mice have low levels of blood glucose and lipids and liver glycogen, but increased adipose tissue browning and basal metabolic rates. The phenotype is caused by reduced hepatocyte growth factor activation and impaired Met signaling, resulting in decreased liver glucose and lipid metabolism and enhanced adipocyte browning. Hepsin-deficient mice exhibit marked resistance to high-fat diet-induced obesity, hyperglycemia, and hyperlipidemia. In db/db mice, hepsin deficiency ameliorates obesity and diabetes. These data indicate that hepsin is a key regulator in liver metabolism and energy homeostasis, suggesting that hepsin could be a therapeutic target for treating obesity and diabetes.
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54
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Venom serine proteinase homolog of the ectoparasitoid Scleroderma guani impairs host phenoloxidase cascade. Toxicon 2020; 183:29-35. [PMID: 32445842 DOI: 10.1016/j.toxicon.2020.05.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 11/23/2022]
Abstract
The ant-like bethylid ectoparasitoid Scleroderma guani (Hymenoptera: Bethylidae) envenomates host to suppress immune response. Yet, the roles of its venom in inhibiting melanization of the host hemolymph have not been fully characterized. Here, we demonstrated that S. guani envenomation induced strong inhibition of melanization of the hemolymph from Tenebrio molitor (Coleoptera: Tenebrionidae), permitting the successful development of parasitoid offspring. To reveal venom component associated with such function, a serine proteinase homolog (SguaSPH) rich in the venom of S. guani was characterized. It was found that one of the catalytic triad residues for serine proteinase is absent in the amino acid sequence of SguaSPH. This venom component was abundantly expressed in venom apparatus and adult stages. By enzymatic assays, SguaSPH displayed low trypsin and no chymotrypsin activity, and was able to inhibit phenoloxidase activity in the hemolymph of Ostrinia furnacalis (Lepidoptera: Crambidae). The findings suggest that SguaSPH is essential for interfering with hemolymph melanization of S. guani envenomated host via phenoloxidase cascade disruption.
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55
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Ruben EA, Gandhi PS, Chen Z, Koester SK, DeKoster GT, Frieden C, Di Cera E. 19F NMR reveals the conformational properties of free thrombin and its zymogen precursor prethrombin-2. J Biol Chem 2020; 295:8227-8235. [PMID: 32358061 PMCID: PMC7294081 DOI: 10.1074/jbc.ra120.013419] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/28/2020] [Indexed: 11/06/2022] Open
Abstract
The conformational properties of trypsin-like proteases and their zymogen forms remain controversial because of a lack of sufficient information on their free forms. Specifically, it is unclear whether the free protease is zymogen-like and shifts to its mature form upon a ligand-induced fit or exists in multiple conformations in equilibrium from which the ligand selects the optimal fit via conformational selection. Here we report the results of 19F NMR measurements that reveal the conformational properties of a protease and its zymogen precursor in the free form. Using the trypsin-like, clotting protease thrombin as a relevant model system, we show that its conformation is quite different from that of its direct zymogen precursor prethrombin-2 and more similar to that of its fully active Na+-bound form. The results cast doubts on recent hypotheses that free thrombin is zymogen-like and transitions to protease-like forms upon ligand binding. Rather, they validate the scenario emerged from previous findings of X-ray crystallography and rapid kinetics supporting a pre-existing equilibrium between open (E) and closed (E*) forms of the active site. In this scenario, prethrombin-2 is more dynamic and exists predominantly in the E* form, whereas thrombin is more rigid and exists predominantly in the E form. Ligand binding to thrombin takes place exclusively in the E form without significant changes in the overall conformation. In summary, these results disclose the structural architecture of the free forms of thrombin and prethrombin-2, consistent with an E*-E equilibrium and providing no evidence that free thrombin is zymogen-like.
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Affiliation(s)
- Eliza A Ruben
- 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
| | - Sarah K Koester
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Gregory T DeKoster
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carl Frieden
- Department of Biochemistry and Molecular Biophysics, Washington 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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56
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Queiroz FC, Vargas AMP, Oliveira MGA, Comarela GV, Silveira SA. ppiGReMLIN: a graph mining based detection of conserved structural arrangements in protein-protein interfaces. BMC Bioinformatics 2020; 21:143. [PMID: 32293241 PMCID: PMC7158050 DOI: 10.1186/s12859-020-3474-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 03/27/2020] [Indexed: 12/15/2022] Open
Abstract
Background Protein-protein interactions (PPIs) are fundamental in many biological processes and understanding these interactions is key for a myriad of applications including drug development, peptide design and identification of drug targets. The biological data deluge demands efficient and scalable methods to characterize and understand protein-protein interfaces. In this paper, we present ppiGReMLIN, a graph based strategy to infer interaction patterns in a set of protein-protein complexes. Our method combines an unsupervised learning strategy with frequent subgraph mining in order to detect conserved structural arrangements (patterns) based on the physicochemical properties of atoms on protein interfaces. To assess the ability of ppiGReMLIN to point out relevant conserved substructures on protein-protein interfaces, we compared our results to experimentally determined patterns that are key for protein-protein interactions in 2 datasets of complexes, Serine-protease and BCL-2. Results ppiGReMLIN was able to detect, in an automatic fashion, conserved structural arrangements that represent highly conserved interactions at the specificity binding pocket of trypsin and trypsin-like proteins from Serine-protease dataset. Also, for the BCL-2 dataset, our method pointed out conserved arrangements that include critical residue interactions within the conserved motif LXXXXD, pivotal to the binding specificity of BH3 domains of pro-apoptotic BCL-2 proteins towards apoptotic suppressors. Quantitatively, ppiGReMLIN was able to find all of the most relevant residues described in literature for our datasets, showing precision of at least 69% up to 100% and recall of 100%. Conclusions ppiGReMLIN was able to find highly conserved structures on the interfaces of protein-protein complexes, with minimum support value of 60%, in datasets of similar proteins. We showed that the patterns automatically detected on protein interfaces by our method are in agreement with interaction patterns described in the literature.
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Affiliation(s)
- Felippe C Queiroz
- Department of Computer Science, Universidade Federal de Viçosa, Av Peter Henry Rolfs, Viçosa, MG, Brazil.
| | - Adriana M P Vargas
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Av Peter Henry Rolfs, Viçosa, MG, Brazil
| | - Maria G A Oliveira
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Av Peter Henry Rolfs, Viçosa, MG, Brazil.,Instituto de Biotecnologia aplicada a Agropecuaria, BIOAGRO-UFV, Av Peter Henry Rolfs, Viçosa MG, Brazil
| | - Giovanni V Comarela
- Department of Computer Science, Universidade Federal do Espírito Santo, Av Fernando Ferrari, Vitória, ES, Brazil
| | - Sabrina A Silveira
- Department of Computer Science, Universidade Federal de Viçosa, Av Peter Henry Rolfs, Viçosa, MG, Brazil.,European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10 1SD, UK
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57
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Liu H, Heng J, Wang L, Tang X, Guo P, Li Y, Xia Q, Zhao P. Identification, characterization, and expression analysis of clip-domain serine protease genes in the silkworm, Bombyx mori. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 105:103584. [PMID: 31863792 DOI: 10.1016/j.dci.2019.103584] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 12/11/2019] [Accepted: 12/17/2019] [Indexed: 06/10/2023]
Abstract
Clip-domain serine proteases (CLIPs), characterized by regulatory module clip domains, constitute an important serine protease family identified in insects and other arthropods. They participate in host immune response and embryonic development in a cascade-activated manner. Here, we present a genome-wide identification and expression analysis of CLIP genes in the silkworm, Bombyx mori. A total of 26 CLIP genes were identified in the silkworm genome. Bioinformatics analysis indicated that these CLIPs clustered into four subfamilies (CLIPA-D), and exhibit a close evolutionary relationship with CLIPs of Manduca sexta. Tissue expression profiling revealed that silkworm CLIP genes are mainly expressed in the integument, head, fat body, and hemocytes. Temporal expression profiles showed that 15 CLIP genes were predominantly expressed during the fifth-instar larval stage, early and later period of the pupal stage, and adult stage, whereas 10 CLIP genes were mainly expressed in the wandering stage and middle to later period of the pupal stage in the integument. Pathogens and 20-hydroxyecdysone (20E) induction analysis indicated that 14 CLIP genes were positively regulated by 20E, 9 were negatively regulated by 20E but positively regulated by pathogens, and 5 were positively regulated by both factors in the integument. Together, these results suggested that silkworm CLIP genes may play multiple functions in integument development, including melanization of new cuticle, molting and immune defense. Our data provide a comprehensive understanding of CLIP genes in the silkworm integument and lays a foundation for further functional studies of CLIP genes in the silkworm.
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Affiliation(s)
- Huawei Liu
- Biological Science Research Center Southwest University, Chongqing, 400715, China; Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, 400715, China
| | - Jingya Heng
- Biological Science Research Center Southwest University, Chongqing, 400715, China
| | - Luoling Wang
- Biological Science Research Center Southwest University, Chongqing, 400715, China
| | - Xin Tang
- Biological Science Research Center Southwest University, Chongqing, 400715, China
| | - Pengchao Guo
- Biological Science Research Center Southwest University, Chongqing, 400715, China; Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, 400715, China
| | - Youshan Li
- College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, 723001, Shaanxi Province, China
| | - Qingyou Xia
- Biological Science Research Center Southwest University, Chongqing, 400715, China; Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, 400715, China
| | - Ping Zhao
- Biological Science Research Center Southwest University, Chongqing, 400715, China; Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, 400715, China.
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58
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Atkins WM. Mechanisms of promiscuity among drug metabolizing enzymes and drug transporters. FEBS J 2020; 287:1306-1322. [PMID: 31663687 PMCID: PMC7138722 DOI: 10.1111/febs.15116] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/04/2019] [Accepted: 10/29/2019] [Indexed: 12/11/2022]
Abstract
Detoxication, or 'drug-metabolizing', enzymes and drug transporters exhibit remarkable substrate promiscuity and catalytic promiscuity. In contrast to substrate-specific enzymes that participate in defined metabolic pathways, individual detoxication enzymes must cope with substrates of vast structural diversity, including previously unencountered environmental toxins. Presumably, evolution selects for a balance of 'adequate' kcat /KM values for a wide range of substrates, rather than optimizing kcat /KM for any individual substrate. However, the structural, energetic, and metabolic properties that achieve this balance, and hence optimize detoxication, are not well understood. Two features of detoxication enzymes that are frequently cited as contributions to promiscuity include the exploitation of highly reactive versatile cofactors, or cosubstrates, and a high degree of flexibility within the protein structure. This review examines these intuitive mechanisms in detail and clarifies the contributions of the classic ligand binding models 'induced fit' (IF) and 'conformational selection' (CS) to substrate promiscuity. The available literature data for drug metabolizing enzymes and transporters suggest that IF is exploited by these promiscuous detoxication enzymes, as it is with substrate-specific enzymes, but the detoxication enzymes uniquely exploit 'IFs' to retain a wide range of substrates at their active sites. In contrast, whereas CS provides no catalytic advantage to substrate-specific enzymes, promiscuous enzymes may uniquely exploit it to recruit a wide range of substrates. The combination of CS and IF, for recruitment and retention of substrates, can potentially optimize the promiscuity of drug metabolizing enzymes and drug transporters.
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Affiliation(s)
- William M. Atkins
- Department of Medicinal ChemistryUniversity of WashingtonSeattleWAUSA
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59
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Ivanov I, Verhamme IM, Sun MF, Mohammed B, Cheng Q, Matafonov A, Dickeson SK, Joseph K, Kaplan AP, Gailani D. Protease activity in single-chain prekallikrein. Blood 2020; 135:558-567. [PMID: 31800958 PMCID: PMC7033373 DOI: 10.1182/blood.2019002224] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 11/19/2019] [Indexed: 12/23/2022] Open
Abstract
Prekallikrein (PK) is the precursor of the trypsin-like plasma protease kallikrein (PKa), which cleaves kininogens to release bradykinin and converts the protease precursor factor XII (FXII) to the enzyme FXIIa. PK and FXII undergo reciprocal conversion to their active forms (PKa and FXIIa) by a process that is accelerated by a variety of biological and artificial surfaces. The surface-mediated process is referred to as contact activation. Previously, we showed that FXII expresses a low level of proteolytic activity (independently of FXIIa) that may initiate reciprocal activation with PK. The current study was undertaken to determine whether PK expresses similar activity. Recombinant PK that cannot be converted to PKa was prepared by replacing Arg371 with alanine at the activation cleavage site (PK-R371A, or single-chain PK). Despite being constrained to the single-chain precursor form, PK-R371A cleaves high-molecular-weight kininogen (HK) to release bradykinin with a catalytic efficiency ∼1500-fold lower than that of kallikrein cleavage of HK. In the presence of a surface, PK-R371A converts FXII to FXIIa with a specific activity ∼4 orders of magnitude lower than for PKa cleavage of FXII. These results support the notion that activity intrinsic to PK and FXII can initiate reciprocal activation of FXII and PK in solution or on a surface. The findings are consistent with the hypothesis that the putative zymogens of many trypsin-like proteases are actually active proteases, explaining their capacity to undergo processes such as autoactivation and to initiate enzyme cascades.
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Affiliation(s)
- Ivan Ivanov
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN
| | - Ingrid M Verhamme
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN
| | - Mao-Fu Sun
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN
| | - Bassem Mohammed
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN
| | - Qiufang Cheng
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN
| | - Anton Matafonov
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN
| | - S Kent Dickeson
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN
| | | | - Allen P Kaplan
- Department of Medicine, Medical University of South Carolina, Charleston, SC
| | - David Gailani
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN
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60
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Caro MDP, Holton N, Conti G, Venturuzzi AL, Martínez‐Zamora MG, Zipfel C, Asurmendi S, Díaz‐Ricci JC. The fungal subtilase AsES elicits a PTI-like defence response in Arabidopsis thaliana plants independently of its enzymatic activity. MOLECULAR PLANT PATHOLOGY 2020; 21:147-159. [PMID: 31769595 PMCID: PMC6988430 DOI: 10.1111/mpp.12881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Acremonium strictum elicitor subtilisin (AsES) is a 34-kDa serine-protease secreted by the strawberry fungal pathogen A. strictum. On AsES perception, a set of defence reactions is induced, both locally and systemically, in a wide variety of plant species and against pathogens of alternative lifestyles. However, it is not clear whether AsES proteolytic activity is required for triggering a defence response or if the protein itself acts as an elicitor. To investigate the necessity of the protease activity to activate the defence response, AsES coding sequences of the wild-type gene and a mutant on the active site (S226A) were cloned and expressed in Escherichia coli. Our data show that pretreatment of Arabidopsis plants with inactive proteins, i.e. inhibited with phenylmethylsulphonyl fluoride (PMSF) and mutant, resulted in an increased systemic resistance to Botrytis cinerea and expression of defence-related genes in a temporal manner that mimics the effect already reported for the native AsES protein. The data presented in this study indicate that the defence-eliciting property exhibited by AsES is not associated with its proteolytic activity. Moreover, the enhanced expression of some immune marker genes, seedling growth inhibition and the involvement of the co-receptor BAK1 observed in plants treated with AsES suggests that AsES is being recognized as a pathogen-associated molecular pattern by a leucine-rich repeat receptor. The understanding of the mechanism of action of AsES will contribute to the development of new breeding strategies to confer durable resistance in plants.
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Affiliation(s)
- María del Pilar Caro
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET‐UNT, and Instituto de Química Biológica “Dr. Bernabé Bloj”, Facultad de Bioquímica, Química y Farmacia, UNTSan Miguel de TucumánArgentina
| | - Nicholas Holton
- The Sainsbury LaboratoryUniversity of East AngliaNorwich Research Park, NorwichUnited Kingdom
| | - Gabriela Conti
- Instituto de Agrobiotecnología y Biología Molecular – IABiMo – INTA – CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología AgropecuariaHurlinghamArgentina
| | - Andrea Laura Venturuzzi
- Instituto de Agrobiotecnología y Biología Molecular – IABiMo – INTA – CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología AgropecuariaHurlinghamArgentina
| | - Martin Gustavo Martínez‐Zamora
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET‐UNT, and Instituto de Química Biológica “Dr. Bernabé Bloj”, Facultad de Bioquímica, Química y Farmacia, UNTSan Miguel de TucumánArgentina
| | - Cyril Zipfel
- The Sainsbury LaboratoryUniversity of East AngliaNorwich Research Park, NorwichUnited Kingdom
- Institute of Plant and Microbial Biology and Zürich‐Basel Plant Science CenterUniversity of ZürichZürichSwitzerland
| | - Sebastian Asurmendi
- Instituto de Agrobiotecnología y Biología Molecular – IABiMo – INTA – CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología AgropecuariaHurlinghamArgentina
| | - Juan Carlos Díaz‐Ricci
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET‐UNT, and Instituto de Química Biológica “Dr. Bernabé Bloj”, Facultad de Bioquímica, Química y Farmacia, UNTSan Miguel de TucumánArgentina
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61
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Viola RE. The ammonia-lyases: enzymes that use a wide range of approaches to catalyze the same type of reaction. Crit Rev Biochem Mol Biol 2020; 54:467-483. [PMID: 31906712 DOI: 10.1080/10409238.2019.1708261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The paradigm that protein structure determines protein function has been clearly established. What is less clear is whether a specific protein structure is always required to carry out a specific function. Numerous cases are now known where there is no apparent connection between the biological function of a protein and the other members of its structural class, and where functionally related proteins can have quite diverse structures. A set of enzymes with these diverse properties, the ammonia-lyases, will be examined in this review. These are a class of enzymes that catalyze a relatively straightforward deamination reaction. However, the individual enzymes of this class possess a wide variety of different structures, utilize a diverse set of cofactors, and appear to catalyze this related reaction through a range of different mechanisms. This review aims to address a basic question: if there is not a specific protein structure and active site architecture that is both required and sufficient to define a catalyst for a given chemical reaction, then what factor(s) determine the structure and the mechanism that is selected to catalyze a particular reaction?
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Affiliation(s)
- Ronald E Viola
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH, USA
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62
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Querino Lima Afonso M, da Fonseca NJ, de Oliveira LC, Lobo FP, Bleicher L. Coevolved Positions Represent Key Functional Properties in the Trypsin-Like Serine Proteases Protein Family. J Chem Inf Model 2020; 60:1060-1068. [DOI: 10.1021/acs.jcim.9b00903] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Marcelo Querino Lima Afonso
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, Minas Gerais, Brazil 31270-901
| | - Neli J. da Fonseca
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, Minas Gerais, Brazil 31270-901
| | - Lucas Carrijo de Oliveira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, Minas Gerais, Brazil 31270-901
| | - Francisco Pereira Lobo
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, Minas Gerais, Brazil 31270-901
| | - Lucas Bleicher
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, Minas Gerais, Brazil 31270-901
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Munasinghe A, Baker SL, Lin P, Russell AJ, Colina CM. Structure-function-dynamics of α-chymotrypsin based conjugates as a function of polymer charge. SOFT MATTER 2020; 16:456-465. [PMID: 31803897 DOI: 10.1039/c9sm01842e] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The field of protein-polymer conjugates has suffered from a lack of predictive tools and design guidelines to synthesize highly active and stable conjugates. In order to develop this type of information, structure-function-dynamics relationships must be understood. These relationships depend strongly on protein-polymer interactions and how these influence protein dynamics and conformations. Probing nanoscale interactions is experimentally difficult, but computational tools, such as molecular dynamics simulations, can easily obtain atomic resolution. Atomistic molecular dynamics simulations were used to study α-chymotrypsin (CT) densely conjugated with either zwitterionic, positively charged, or negatively charged polymers. Charged polymers interacted with the protein surface to varying degrees and in different regions of the polymer, depending on their flexibilities. Specific interactions of the negatively charged polymer with CT caused structural deformations in CT's substrate binding pocket and active site while no deformations were observed for zwitterionic and positively charged polymers. Attachment of polymers displaced water molecules from CT's surface into the polymer phase and polymer hydration correlated with the Hofmeister series.
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Affiliation(s)
- Aravinda Munasinghe
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
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64
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Manne K, Narayana SVL. Structural insights into the role of the N-terminus in the activation and function of extracellular serine protease from Staphylococcus epidermidis. Acta Crystallogr D Struct Biol 2020; 76:28-40. [PMID: 31909741 PMCID: PMC6939437 DOI: 10.1107/s2059798319015055] [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: 08/27/2019] [Accepted: 11/07/2019] [Indexed: 11/10/2022] Open
Abstract
Extracellular serine protease (Esp) from Staphylococcus epidermidis is a glutamyl endopeptidase that inhibits the growth and formation of S. aureus biofilms. Previously, crystal structures of the matured and active Esp have been determined. Interestingly, many of the staphylococcal glutamyl endopeptidase zymogens, including V8 from Staphylococcus aureus and Esp from S. epidermidis, contain unusually long pro-peptide segments; however, their function is not known. With the aim of elucidating the function of these pro-peptide segments, crystal structures of the Esp zymogen (Pro-Esp) and its variants were determined. It was observed that the N-terminus of the Pro-Esp crystal structure is flexible and is not associated with the main body of the enzyme, unlike in the known active Esp structure. In addition, the loops that border the putative substrate-binding pocket of Pro-Esp are flexible and disordered; the structural components that are responsible for enzyme specificity and efficiency in serine proteases are disordered in Pro-Esp. However, the N-terminal locked Pro-Esp variants exhibit a rigid substrate-binding pocket similar to the active Esp structure and regain activity. These structural studies highlight the role of the N-terminus in stabilizing the structural components responsible for the activity and specificity of staphylococcal glutamyl endopeptidases.
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Affiliation(s)
- Kartik Manne
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Sthanam V. L. Narayana
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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65
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Role of the I16-D194 ionic interaction in the trypsin fold. Sci Rep 2019; 9:18035. [PMID: 31792294 PMCID: PMC6889508 DOI: 10.1038/s41598-019-54564-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/15/2019] [Indexed: 12/20/2022] Open
Abstract
Activity in trypsin-like proteases is the result of proteolytic cleavage at R15 followed by an ionic interaction that ensues between the new N terminus of I16 and the side chain of the highly conserved D194. This mechanism of activation, first proposed by Huber and Bode, organizes the oxyanion hole and primary specificity pocket for substrate binding and catalysis. Using the clotting protease thrombin as a relevant model, we unravel contributions of the I16-D194 ionic interaction to Na+ binding, stability of the transition state and the allosteric E*-E equilibrium of the trypsin fold. The I16T mutation abolishes the I16-D194 interaction and compromises the architecture of the oxyanion hole. The D194A mutation also abrogates the I16-D194 interaction but, surprisingly, has no effect on the architecture of the oxyanion hole that remains intact through a new H-bond established between G43 and G193. In both mutants, loss of the I16-D194 ionic interaction compromises Na+ binding, reduces stability of the transition state, collapses the 215–217 segment into the primary specific pocket and abrogates the allosteric E*-E equilibrium in favor of a rigid conformation that binds ligand at the active site according to a simple lock-and-key mechanism. These findings refine the structural role of the I16-D194 ionic interaction in the Huber-Bode mechanism of activation and reveal a functional linkage with the allosteric properties of the trypsin fold like Na+ binding and the E*-E equilibrium.
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66
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Gailani D, Emsley J. Toward a better understanding of factor XI activation. J Thromb Haemost 2019; 17:2016-2018. [PMID: 31797540 PMCID: PMC8559519 DOI: 10.1111/jth.14631] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 12/14/2022]
Affiliation(s)
- David Gailani
- The Department of Pathology, Microbiology and Immunology,
Vanderbilt University, Nashville, TN, USA
| | - Jonas Emsley
- The Center for Biomolecular Sciences, School of Pharmacy,
University of Nottingham, Nottingham, UK
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68
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Luo M, Eaton CN, Hess KR, Phillips-Piro CM, Brewer SH, Fenlon EE. Paired Spectroscopic and Crystallographic Studies of Proteases. ChemistrySelect 2019; 4:9836-9843. [PMID: 34169145 PMCID: PMC8221577 DOI: 10.1002/slct.201902049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/23/2019] [Indexed: 12/13/2022]
Abstract
The active sites of subtilisin and trypsin have been studied by paired IR spectroscopic and X-ray crystallographic studies. The active site serines of the proteases were reacted with 4-cyanobenzenesulfonyl fluoride (CBSF), an inhibitor that contains a nitrile vibrational reporter. The nitrile stretch vibration of the water-soluble inhibitor model, potassium 4-cyanobenzenesulfonate (KCBSO), and the inhibitor were calibrated by IR solvent studies in H2O/DMSO and the frequency-temperature line-slope (FTLS) method in H2O and THF. The inhibitor complexes were examined by FTLS and the slopes of the best fit lines for subtilisin-CBS and trypsin-CBS in aqueous buffer were both measured to be -3.5×10-2 cm-1/°C. These slopes were intermediate in value between that of KCBSO in aqueous buffer and CBSF in THF, which suggests that the active-site nitriles in both proteases are mostly solvated. The X-ray crystal structures of the subtilisin-CBS and trypsin-CBS complexes were solved at 1.27 and 1.32 Å, respectively. The inhibitor was modelled in two conformations in subtilisin-CBS and in one conformation in the trypsin-CBS. The crystallographic data support the FTLS data that the active-site nitrile groups are mostly solvated and participate in hydrogen bonds with water molecules. The combination of IR spectroscopy utilizing vibrational reporters paired with X-ray crystallography provides a powerful approach to studying protein structure.
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Affiliation(s)
- Meiqi Luo
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
| | - Christopher N. Eaton
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
| | - Kenneth R. Hess
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
| | | | - Scott H. Brewer
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
| | - Edward E. Fenlon
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
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69
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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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70
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Nishimiya D, Kawaguchi Y, Kodama S, Nasu H, Yano H, Yamaguchi A, Tamura M, Hashimoto R. A protein scaffold, engineered SPINK2, for generation of inhibitors with high affinity and specificity against target proteases. Sci Rep 2019; 9:11436. [PMID: 31391482 PMCID: PMC6686015 DOI: 10.1038/s41598-019-47615-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 07/19/2019] [Indexed: 12/21/2022] Open
Abstract
Proteases are one of attractive therapeutic targets to play key roles in pharmacological action. There are many protease inhibitors in nature, and most of them structurally have cystine knot motifs. Their structures are favorable for recognition of active pockets of proteases, leading to the potent inhibition. However, they also have drawbacks, such as broad cross-reactivity, on the therapeutic application. To create therapeutic proteins derived from a disulfide-rich scaffold, we selected human serine protease inhibitor Kazal type 2 (SPINK2) through a scaffold screening, as a protein scaffold with requirements for therapeutic proteins. We then constructed a diverse library of the engineered SPINK2 by introducing random mutations into its flexible loop region with the designed method. By phage panning against four serine proteases, we isolated potent inhibitors against each target with picomolar KD and sub-nanomolar Ki values. Also, they exhibited the desired specificities against target proteases without inhibiting non-target proteases. The crystal structure of kallikrein related peptidase 4 (KLK4)-engineered SPINK2 complex revealed the interface with extensive conformational complementarity. Our study demonstrates that engineered SPINK2 can serve as a scaffold to generate therapeutic molecules against target proteins with groove structures.
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Affiliation(s)
- Daisuke Nishimiya
- DAIICHI SANKYO CO., LTD., Biologics Division, Modality Research Laboratories, 1-2-58, Hiromachi, Shinagawa-ku, Tokyo, 140-8710, Japan.
| | - Yoshirou Kawaguchi
- DAIICHI SANKYO CO., LTD., Biologics Division, Modality Research Laboratories, 1-2-58, Hiromachi, Shinagawa-ku, Tokyo, 140-8710, Japan
| | - Shiho Kodama
- DAIICHI SANKYO CO., LTD., Biologics Division, Modality Research Laboratories, 1-2-58, Hiromachi, Shinagawa-ku, Tokyo, 140-8710, Japan
| | - Hatsumi Nasu
- DAIICHI SANKYO CO., LTD., Biologics Division, Modality Research Laboratories, 1-2-58, Hiromachi, Shinagawa-ku, Tokyo, 140-8710, Japan
| | - Hidenori Yano
- DAIICHI SANKYO CO., LTD., Biologics Division, Modality Research Laboratories, 1-2-58, Hiromachi, Shinagawa-ku, Tokyo, 140-8710, Japan
| | - Aya Yamaguchi
- DAIICHI SANKYO CO., LTD., Biologics Division, Modality Research Laboratories, 1-2-58, Hiromachi, Shinagawa-ku, Tokyo, 140-8710, Japan
| | - Masakazu Tamura
- DAIICHI SANKYO CO., LTD., Biologics Division, Modality Research Laboratories, 1-2-58, Hiromachi, Shinagawa-ku, Tokyo, 140-8710, Japan
| | - Ryuji Hashimoto
- DAIICHI SANKYO CO., LTD., Biologics Division, Modality Research Laboratories, 1-2-58, Hiromachi, Shinagawa-ku, Tokyo, 140-8710, Japan
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71
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Zhou S, Wang L. Unraveling the structural and chemical features of biological short hydrogen bonds. Chem Sci 2019; 10:7734-7745. [PMID: 31588321 PMCID: PMC6764281 DOI: 10.1039/c9sc01496a] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/30/2019] [Indexed: 02/06/2023] Open
Abstract
Short hydrogen bonds are ubiquitous in biological macromolecules and exhibit distinctive proton potential energy surfaces and proton sharing properties.
The three-dimensional architecture of biomolecules often creates specialized structural elements, notably short hydrogen bonds that have donor–acceptor separations below 2.7 Å. In this work, we statistically analyze 1663 high-resolution biomolecular structures from the Protein Data Bank and demonstrate that short hydrogen bonds are prevalent in proteins, protein–ligand complexes and nucleic acids. From these biological macromolecules, we characterize the preferred location, connectivity and amino acid composition in short hydrogen bonds and hydrogen bond networks, and assess their possible functional importance. Using electronic structure calculations, we further uncover how the interplay of the structural and chemical features determines the proton potential energy surfaces and proton sharing conditions in biological short hydrogen bonds.
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Affiliation(s)
- Shengmin Zhou
- Department of Chemistry and Chemical Biology , Institute for Quantitative Biomedicine , Rutgers University , Piscataway , NJ 08854 , USA .
| | - Lu Wang
- Department of Chemistry and Chemical Biology , Institute for Quantitative Biomedicine , Rutgers University , Piscataway , NJ 08854 , USA .
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72
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Abstract
Calnexin is a chaperone protein that plays a critical role in glycoprotein folding in the endoplasmic reticulum (ER). The function of calnexin depends on its binding to monoglucosylated oligosaccharides on nascent glycoproteins, whereas the generation of monoglucosylated oligosaccharides depends on the activity of α-glucosidases I and II, which trim off terminal glucose residues sequentially from triglucosylated N-glycans. This biochemical mechanism can be exploited to study calnexin-assisted folding and subsequent ER exiting of glycoproteins in cells. In our investigation of the intracellular trafficking of N-glycosylated serine proteases, we used an inhibitor of α-glucosidases I and II to block the trimming of triglucosylated oligosaccharides, thereby inhibiting calnexin-assisted glycoprotein folding. The study helped us to discover a key role of calnexin in the folding, ER exiting, and extracellular expression of N-glycosylated serine proteases such as corin, enteropeptidase, and prothrombin. A similar approach of glucosidase inhibition can be used to study the calnexin/calreticulin-dependent folding and intracellular trafficking of other N-glycosylated proteins.
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Affiliation(s)
- Hao Wang
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qingyu Wu
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Soochow University, Suzhou, China.,Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, USA
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73
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Sampedro LJG, Grimaldos NAG, Pereañez JA, Montoya JEZ. LIPIDS AS COMPETITIVE INHIBITORS OF SUBTILISIN CARLSBERG IN THE ENZYMATIC HYDROLYSIS OF PROTEINS IN RED TILAPIA (Oreochromis sp.) VISCERA: INSIGHTS FROM KINETIC MODELS AND A MOLECULAR DOCKING STUDY. BRAZILIAN JOURNAL OF CHEMICAL ENGINEERING 2019. [DOI: 10.1590/0104-6632.20190362s20180346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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74
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Salah Eldein E, Abdalla M, Eltayb WA, El-Arabey AA, Ganash M, Alshammari FD, Barreto G, Ashraf GM. Molecular cloning, expression, purification, and functional characterization of SP-22 gene from Bombyx mori. J Cell Biochem 2019; 120:15594-15603. [PMID: 31099441 DOI: 10.1002/jcb.28826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 11/09/2022]
Abstract
Serine protease (SPs) is one of the immune enzyme's molecules that play a main role in the variation of a physiological process by controlling protease actions in vertebrates. For example, signaling cells, protector and improvement, which are included in melanization, are utilized to cascade with the meddling pathogens and defense the harmed tissue in insects. In this study, we explore the biochemical process of (SP-22) from Bombyx mori. Reverse-transcription polymerase chain reaction (RT-PCR) discloses that BmSP-22 is expressed in all tissues including the fat body. The formative expression profile of BmSP-22 reveal that BmSP-22 messenger RNA is expressed constitutively in larvae. Injection of recombinant BmSP-22 into B. mori larvae reduces significantly the transcript levels of antimicrobial peptides in the fat body. Our results suggest that BmSP-22 plays an important role in the innate immunity of B. mori and possibly in other insects.
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Affiliation(s)
- Elshareef Salah Eldein
- College of Life Science, Anhui Agricultural University, Hefei, China.,Institute of Africa City of Technology Khartoum, Khartoum, Sudan
| | - Mohnad Abdalla
- Qingdao Institute of Bioenergy and Bioprocess Technology, Qingdao Shi, Shandong Sheng, People's Republic of China
| | - Wafa Ali Eltayb
- Biotechnology Department, Faculty of Science and Technology, Shendi University, Nher Anile, Sudan
| | - Amr Ahmed El-Arabey
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
| | - Magdah Ganash
- Department of Biology, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Fawaz D Alshammari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Kingdom of Saudi Arabia
| | - George Barreto
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile.,Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá D.C., Colombia
| | - Ghulam Md Ashraf
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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75
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Proust L, Sourabié A, Pedersen M, Besançon I, Haudebourg E, Monnet V, Juillard V. Insights Into the Complexity of Yeast Extract Peptides and Their Utilization by Streptococcus thermophilus. Front Microbiol 2019; 10:906. [PMID: 31133999 PMCID: PMC6524704 DOI: 10.3389/fmicb.2019.00906] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/09/2019] [Indexed: 11/23/2022] Open
Abstract
Streptococcus thermophilus, an extensively used lactic starter, is generally produced in yeast extract-based media containing a complex mixture of peptides whose exact composition remains elusive. In this work, we aimed at investigating the peptide content of a commercial yeast extract (YE) and identifying dynamics of peptide utilization during the growth of the industrial S. thermophilus N4L strain, cultivated in 1 l bioreactors under pH-regulation. To reach that goal, we set up a complete analytical workflow based on mass spectrometry (peptidomics). About 4,600 different oligopeptides ranging from 6 to more than 30 amino acids in length were identified during the time-course of the experiment. Due to the low spectral abundance of individual peptides, we performed a clustering approach to decipher the rules of peptide utilization during fermentation. The physicochemical characteristics of consumed peptides perfectly matched the known affinities of the oligopeptide transport system of S. thermophilus. Moreover, by analyzing such a large number of peptides, we were able to establish that peptide net charge is the major factor for oligopeptide transport in S. thermophilus N4L.
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Affiliation(s)
- Lucas Proust
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- Procelys, Lesaffre Group, Maisons-Alfort, France
| | | | | | | | - Eloi Haudebourg
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Véronique Monnet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Vincent Juillard
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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76
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Nutho B, Mulholland AJ, Rungrotmongkol T. Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations Support a Concerted Reaction Mechanism for the Zika Virus NS2B/NS3 Serine Protease with Its Substrate. J Phys Chem B 2019; 123:2889-2903. [PMID: 30845796 DOI: 10.1021/acs.jpcb.9b02157] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Zika virus (ZIKV) is mainly transmitted to humans by Aedes species mosquitoes and is associated with serious pathological disorders including microcephaly in newborns and Guillain-Barré syndrome in adults. Currently, there is no vaccine or anti-ZIKV drug available for preventing or controlling ZIKV infection. An attractive drug target for ZIKV treatment is a two-compartment (NS2B/NS3) serine protease that processes viral polyprotein during infection. Here, conventional molecular dynamics simulations of the ZIKV protease in complex with peptide substrate (TGKRS) sequence at the C-terminus of NS2B show that the substrate is in the active conformation for the cleavage reaction by ZIKV protease. Hybrid quantum mechanics/molecular mechanics (QM/MM) umbrella sampling simulations (PM6/ff14SB) of acylation results reveal that proton transfer from S135 to H51 and nucleophilic attack on the substrate by S135 are concerted. The rate-limiting step involves the formation of a tetrahedral intermediate. In addition, the single-point energy QM/MM calculations, precisely at the level of coupled cluster theory (LCCSD(T)/(aug)-cc-pVTZ), were performed to correct the potential energy profiles for the first step of the acylation process. The average computed activation barrier at this level of theory is 16.3 kcal mol-1. Therefore, the computational approaches presented here are helpful for further designing of NS2B/NS3 inhibitors based on transition-state analogues.
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Affiliation(s)
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol BS8 1TS , U.K
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77
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Whittington AC, Mason AJ, Rokyta DR. A Single Mutation Unlocks Cascading Exaptations in the Origin of a Potent Pitviper Neurotoxin. Mol Biol Evol 2019; 35:887-898. [PMID: 29329419 DOI: 10.1093/molbev/msx334] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Evolutionary innovations and complex phenotypes seemingly require an improbable amount of genetic change to evolve. Rattlesnakes display two dramatically different venom phenotypes. Type I venoms are hemorrhagic with low systemic toxicity and high expression of tissue-destroying snake venom metalloproteinases. Type II venoms are highly neurotoxic and lack snake venom metalloproteinase expression and associated hemorrhagic activity. This dichotomy hinges on Mojave toxin (MTx), a phospholipase A2 (PLA2) based β-neurotoxin expressed in Type II venoms. MTx is comprised of a nontoxic acidic subunit that undergoes extensive proteolytic processing and allosterically regulates activity of a neurotoxic basic subunit. Evolution of the acidic subunit presents an evolutionary challenge because the need for high expression of a nontoxic venom component and the proteolytic machinery required for processing suggests genetic changes of seemingly little immediate benefit to fitness. We showed that MTx evolved through a cascading series of exaptations unlocked by a single nucleotide change. The evolution of one new cleavage site in the acidic subunit unmasked buried cleavage sites already present in ancestral PLA2s, enabling proteolytic processing. Snake venom serine proteases, already present in the venom to disrupt prey hemostasis, possess the requisite specificities for MTx acidic subunit proteolysis. The dimerization interface between MTx subunits evolved by exploiting a latent, but masked, hydrophobic interaction between ancestral PLA2s. The evolution of MTx through exaptation of existing functional and structural features suggests complex phenotypes that depend on evolutionary innovations can arise from minimal genetic change enabled by prior evolution.
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Affiliation(s)
- A Carl Whittington
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Andrew J Mason
- Department of Biology, University of Central Florida, Orlando, FL
- Department of Biological Sciences, Clemson University, Clemson, SC
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL
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78
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Byun S, Park HJ, Joo JC, Kim YH. Enzymatic Synthesis of D-pipecolic Acid by Engineering the Substrate Specificity of Trypanosoma cruzi Proline Racemase and Its Molecular Docking Study. BIOTECHNOL BIOPROC E 2019. [DOI: 10.1007/s12257-018-0367-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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79
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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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80
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A mechanism for hereditary angioedema with normal C1 inhibitor: an inhibitory regulatory role for the factor XII heavy chain. Blood 2018; 133:1152-1163. [PMID: 30591525 DOI: 10.1182/blood-2018-06-860270] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 12/13/2018] [Indexed: 12/29/2022] Open
Abstract
The plasma proteins factor XII (FXII) and prekallikrein (PK) undergo reciprocal activation to the proteases FXIIa and kallikrein by a process that is enhanced by surfaces (contact activation) and regulated by the serpin C1 inhibitor. Kallikrein cleaves high-molecular-weight kininogen (HK), releasing the vasoactive peptide bradykinin. Patients with hereditary angioedema (HAE) experience episodes of soft tissue swelling as a consequence of unregulated kallikrein activity or increased prekallikrein activation. Although most HAE cases are caused by reduced plasma C1-inhibitor activity, HAE has been linked to lysine/arginine substitutions for Thr309 in FXII (FXII-Lys/Arg309). Here, we show that FXII-Lys/Arg309 is susceptible to cleavage after residue 309 by coagulation proteases (thrombin and FXIa), resulting in generation of a truncated form of FXII (δFXII). The catalytic efficiency of δFXII activation by kallikrein is 15-fold greater than for full-length FXII. The enhanced rate of reciprocal activation of PK and δFXII in human plasma and in mice appears to overwhelm the normal inhibitory function of C1 inhibitor, leading to increased HK cleavage. In mice given human FXII-Lys/Arg309, induction of thrombin generation by infusion of tissue factor results in enhanced HK cleavage as a consequence of δFXII formation. The effects of δFXII in vitro and in vivo are reproduced when wild-type FXII is bound by an antibody to the FXII heavy chain (HC; 15H8). The results contribute to our understanding of the predisposition of patients carrying FXII-Lys/Arg309 to angioedema after trauma, and reveal a regulatory function for the FXII HC that normally limits PK activation in plasma.
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81
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Cao X, Jiang H. Building a platform for predicting functions of serine protease-related proteins in Drosophila melanogaster and other insects. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018; 103:53-69. [PMID: 30367934 PMCID: PMC6358214 DOI: 10.1016/j.ibmb.2018.10.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/19/2018] [Accepted: 10/21/2018] [Indexed: 05/15/2023]
Abstract
Serine proteases (SPs) and serine protease homologs (SPHs) play essential roles in insect physiological processes including digestion, defense and development. Studies of insect genomes, transcriptomes and proteomes have generated a vast amount of information on these proteins, dwarfing the biological data acquired from a few model species. The large number and high diversity of homologous sequences makes it a challenge to use the limited functional information for making predictions across a broad taxonomic group of insects. In this work, we have extensively updated the framework of knowledge on the SP-related proteins in Drosophila melanogaster by identifying 52 new SPs/SPHs, classifying the 257 proteins into four groups (CLIP, gut, single- and multi-domain SPs/SPHs), and detecting inherent connections among phylogenetic relationships, genomic locations and expression profiles for 99 of the genes. Information on the existence of specific proteins in eggs, larvae, pupae and adults is presented to facilitate future research. More importantly, we have developed an approach to reveal close homologous or orthologous relationships among SPs/SPHs from D. melanogaster, Anopheles gambiae, Apis mellifera, Manduca sexta, and Tribolium castaneum thus inspiring functional studies in these and other holometabolous insects. This approach is useful for tackling similar problems on large and diverse protein families in other groups of organisms.
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Affiliation(s)
- Xiaolong Cao
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Haobo Jiang
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA.
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82
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Li S, Xu X, Shakeel M, Xu J, Zheng Z, Zheng J, Yu X, Zhao Q, Jin F. Bacillus thuringiensis Suppresses the Humoral Immune System to Overcome Defense Mechanism of Plutella xylostella. Front Physiol 2018; 9:1478. [PMID: 30498450 PMCID: PMC6249373 DOI: 10.3389/fphys.2018.01478] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 09/28/2018] [Indexed: 12/30/2022] Open
Abstract
Background: Plutella xylostella has become a notorious pest of cruciferous crops all over the world. Delta-endotoxins of Bacillus thuringiensis are widely used insecticidal proteins for controlling P. xylostella. However, the interaction mechanism of B. thuringiensis with the immune system of P. xylostella, at the genomic level, is still unclear. This study explored the immune response of P. xylostella to B. thuringiensis, at different time intervals, 6 h, 12 h, 18 h, 24 h, and 36 h, by using RNA-Sequencing (RNA-Seq) and RT-qPCR. Results: In total, 167 immunity-related genes were identified and placed into different families, including pattern recognition receptors (PRRs), signal modulators, immune pathways (Toll, IMD, and JAK/STAT), and immune effectors. It is worth mentioning that the analyses of the differentially expressed immunity-related genes revealed that most of the differentially expressed genes (DEGs) (87, 56, 76, 67, and 73 genes) were downregulated in P. xylostella following B. thuringiensis oral infection at 6 h, 12 h, 18 h, 24 h, and 36 h. Interestingly, our RNA-Seq analysis also revealed reduced expression of antimicrobial peptides, that play a vital role in the humoral immune system of P. xylostella. Conclusion: This study demonstrates that B. thuringiensis plays a novel role in controlling P. xylostella, by suppressing the immune system.
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Affiliation(s)
- Shuzhong Li
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Xiaoxia Xu
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Muhammad Shakeel
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Jin Xu
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Zhihua Zheng
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Jinlong Zheng
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Xiaoqiang Yu
- Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Qian Zhao
- Beijing Genomics Institute, Shenzhen, China
| | - Fengliang Jin
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
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83
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Xu P, Huang M. Small Peptides as Modulators of Serine Proteases. Curr Med Chem 2018; 27:3686-3705. [PMID: 30332941 DOI: 10.2174/0929867325666181016163630] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/26/2018] [Accepted: 10/09/2018] [Indexed: 02/08/2023]
Abstract
Serine proteases play critical roles in many physiological and pathological processes, and are proven diagnostic and therapeutic targets in a number of clinical indications. Suppression of the aberrant proteolytic activities of these proteases has been clinically used for the treatments of relevant diseases. Polypeptides with 10-20 residues are of great interests as medicinal modulators of serine proteases, because these peptides demonstrate the characteristics of both small molecule drugs and macromolecular drugs. In this review, we summarized the recent development of peptide-based inhibitors against serine proteases with potent inhibitory and high specificity comparable to monoclonal antibodies. In addition, we also discussed the strategies of enhancing plasma half-life and bioavailability of peptides in vivo, which is the main hurdle that limits the clinical translation of peptide-based drugs. This review advocates new avenue for the development of effective serine protease inhibitors and highlights the prospect of the medicinal use of these inhibitors.
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Affiliation(s)
- Peng Xu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Mingdong Huang
- College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
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84
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Wang H, Li S, Wang J, Chen S, Sun XL, Wu Q. N-glycosylation in the protease domain of trypsin-like serine proteases mediates calnexin-assisted protein folding. eLife 2018; 7:e35672. [PMID: 29889025 PMCID: PMC6021170 DOI: 10.7554/elife.35672] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 06/08/2018] [Indexed: 12/24/2022] Open
Abstract
Trypsin-like serine proteases are essential in physiological processes. Studies have shown that N-glycans are important for serine protease expression and secretion, but the underlying mechanisms are poorly understood. Here, we report a common mechanism of N-glycosylation in the protease domains of corin, enteropeptidase and prothrombin in calnexin-mediated glycoprotein folding and extracellular expression. This mechanism, which is independent of calreticulin and operates in a domain-autonomous manner, involves two steps: direct calnexin binding to target proteins and subsequent calnexin binding to monoglucosylated N-glycans. Elimination of N-glycosylation sites in the protease domains of corin, enteropeptidase and prothrombin inhibits corin and enteropeptidase cell surface expression and prothrombin secretion in transfected HEK293 cells. Similarly, knocking down calnexin expression in cultured cardiomyocytes and hepatocytes reduced corin cell surface expression and prothrombin secretion, respectively. Our results suggest that this may be a general mechanism in the trypsin-like serine proteases with N-glycosylation sites in their protease domains.
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Affiliation(s)
- Hao Wang
- Molecular CardiologyCleveland ClinicClevelandUnited States
- Department of ChemistryCleveland State UniversityClevelandUnited States
| | - Shuo Li
- Molecular CardiologyCleveland ClinicClevelandUnited States
| | - Juejin Wang
- Molecular CardiologyCleveland ClinicClevelandUnited States
| | - Shenghan Chen
- Molecular CardiologyCleveland ClinicClevelandUnited States
| | - Xue-Long Sun
- Molecular CardiologyCleveland ClinicClevelandUnited States
- Department of ChemistryCleveland State UniversityClevelandUnited States
- Chemical and Biomedical EngineeringCleveland State UniversityClevelandUnited States
- Center for Gene Regulation of Health and DiseaseCleveland State UniversityClevelandUnited States
| | - Qingyu Wu
- Molecular CardiologyCleveland ClinicClevelandUnited States
- Department of ChemistryCleveland State UniversityClevelandUnited States
- Cyrus Tang Hematology CenterState Key Laboratory of Radiation Medicine and Prevention, Soochow UniversitySuzhouChina
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85
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Yang J, Vrettou C, Connelley T, Morrison WI. Identification and annotation of bovine granzyme genes reveals a novel granzyme encoded within the trypsin-like locus. Immunogenetics 2018; 70:585-597. [PMID: 29947943 PMCID: PMC6096847 DOI: 10.1007/s00251-018-1062-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 05/09/2018] [Indexed: 11/26/2022]
Abstract
Granzymes are a family of serine proteases found in the lytic granules of cytotoxic T lymphocytes and natural killer (NK) cells, which are involved in killing of susceptible target cells. Most information on granzymes and their enzymatic specificities derive from studies in humans and mice. Although granzymes shared by both species show a high level of conservation, the complement of granzyme genes differs between the species. The aim of this study was to identify granzyme genes expressed in cattle, determine their genomic locations and analyse their sequences to predict likely functional specificities. Orthologues of the five granzyme genes found in humans (A, B, H, K and M) were identified, as well a novel gene designated granzyme O, most closely related to granzyme A. An orthologue of granzyme O was found in pigs and a non-function version was detected in the human genome. Use of specific PCRs demonstrated that all of these genes, including granzyme O, are expressed in activated subsets of bovine lymphocytes, with particularly high levels in CD8 T cells. Consistent with findings in humans and mice, the granzyme-encoding genes were located on three distinct genomic loci, which correspond to different proteolytic enzymatic activities, namely trypsin-like, chymotrypsin-like and metase-like. Analysis of amino acid sequences indicated that the granzyme proteins have broadly similar enzymatic specificities to their human and murine counterparts but indicated that granzyme B has a different secondary specificity. These findings provide the basis for further work to examine their role in the cytotoxic activity of bovine CD8 T cells.
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Affiliation(s)
- Jie Yang
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH8 9YL, UK.,Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, Royal Free Hospital, London, NW3 2QG, UK
| | - Christina Vrettou
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH8 9YL, UK
| | - Tim Connelley
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH8 9YL, UK
| | - W Ivan Morrison
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH8 9YL, UK.
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86
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Wang YH, Chang MM, Wang XL, Zheng AH, Zou Z. The immune strategies of mosquito Aedes aegypti against microbial infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 83:12-21. [PMID: 29217264 DOI: 10.1016/j.dci.2017.12.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/30/2017] [Accepted: 12/03/2017] [Indexed: 06/07/2023]
Abstract
Yellow fever mosquito Aedes aegypti transmits many devastating arthropod-borne viruses (arboviruses), such as dengue virus, yellow fever virus, Chikungunya virus, and Zika virus, which cause great concern to human health. Mosquito control is an effective method to block the spread of infectious diseases. Ae. aegypti uses its innate immune system to fight against arboviruses, parasites, and fungi. In this review, we briefly summarize the recent findings in the immune response of Ae. aegypti against arboviral and entomopathogenic infections. This review enriches our understanding of the mosquito immune system and provides evidence to support the development of novel mosquito control strategies.
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Affiliation(s)
- Yan-Hong Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Meng-Meng Chang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xue-Li Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ai-Hua Zheng
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhen Zou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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87
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Wang RX, Tong XL, Gai TT, Li CL, Qiao L, Hu H, Han MJ, Xiang ZH, Lu C, Dai FY. A serine protease homologue Bombyx mori scarface induces a short and fat body shape in silkworm. INSECT MOLECULAR BIOLOGY 2018; 27:319-332. [PMID: 29441628 DOI: 10.1111/imb.12373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Body shape is one of the most prominent and basic characteristics of any organism. In insects, abundant variations in body shape can be observed both within and amongst species. However, the molecular mechanism underlying body shape fine-tuning is very complex and has been largely unknown until now. In the silkworm Bombyx mori, the tubby (tub) mutant has an abnormal short fat body shape and the abdomen of tub larvae expands to form a fusiform body shape. Morphological investigation revealed that the body length was shorter and the body width was wider than that of the Dazao strain. Thus, this mutant is a good model for studying the molecular mechanisms of body shape fine-tuning. Using positional cloning, we identified a gene encoding the serine protease homologue, B. mori scarface (Bmscarface), which is associated with the tub phenotype. Sequence analysis revealed a specific 312-bp deletion from an exon of Bmscarface in the tub strain. In addition, recombination was not observed between the tub and Bmscarface loci. Moreover, RNA interference of Bmscarface resulted in the tub-like phenotype. These results indicate that Bmscarface is responsible for the tub mutant phenotype. This is the first study to report that mutation of a serine protease homologue can induce an abnormal body shape in insects.
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Affiliation(s)
- R-X Wang
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - X-L Tong
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - T-T Gai
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - C-L Li
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - L Qiao
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - H Hu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - M-J Han
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - Z-H Xiang
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - C Lu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - F-Y Dai
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
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88
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Waldner BJ, Kraml J, Kahler U, Spinn A, Schauperl M, Podewitz M, Fuchs JE, Cruciani G, Liedl KR. Electrostatic recognition in substrate binding to serine proteases. J Mol Recognit 2018; 31:e2727. [PMID: 29785722 PMCID: PMC6175425 DOI: 10.1002/jmr.2727] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 04/11/2018] [Accepted: 04/11/2018] [Indexed: 12/16/2022]
Abstract
Serine proteases of the Chymotrypsin family are structurally very similar but have very different substrate preferences. This study investigates a set of 9 different proteases of this family comprising proteases that prefer substrates containing positively charged amino acids, negatively charged amino acids, and uncharged amino acids with varying degree of specificity. Here, we show that differences in electrostatic substrate preferences can be predicted reliably by electrostatic molecular interaction fields employing customized GRID probes. Thus, we are able to directly link protease structures to their electrostatic substrate preferences. Additionally, we present a new metric that measures similarities in substrate preferences focusing only on electrostatics. It efficiently compares these electrostatic substrate preferences between different proteases. This new metric can be interpreted as the electrostatic part of our previously developed substrate similarity metric. Consequently, we suggest, that substrate recognition in terms of electrostatics and shape complementarity are rather orthogonal aspects of substrate recognition. This is in line with a 2‐step mechanism of protein‐protein recognition suggested in the literature.
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Affiliation(s)
- Birgit J Waldner
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Johannes Kraml
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Ursula Kahler
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Alexander Spinn
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Michael Schauperl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Maren Podewitz
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Julian E Fuchs
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Gabriele Cruciani
- Laboratory of Chemometrics, Department of Chemistry, University of Perugia, Perugia, Italy
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
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89
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Bongard J, Lorenz M, Vetter IR, Stege P, Porfetye AT, Schmitz AL, Kaschani F, Wolf A, Koch U, Nussbaumer P, Klebl B, Kaiser M, Ehrmann M. Identification of Noncatalytic Lysine Residues from Allosteric Circuits via Covalent Probes. ACS Chem Biol 2018; 13:1307-1312. [PMID: 29658704 DOI: 10.1021/acschembio.8b00101] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Covalent modifications of nonactive site lysine residues by small molecule probes has recently evolved into an important strategy for interrogating biological systems. Here, we report the discovery of a class of bioreactive compounds that covalently modify lysine residues in DegS, the rate limiting protease of the essential bacterial outer membrane stress response pathway. These modifications lead to an allosteric activation and allow the identification of novel residues involved in the allosteric activation circuit. These findings were validated by structural analyses via X-ray crystallography and cell-based reporter systems. We anticipate that our findings are not only relevant for a deeper understanding of the structural basis of allosteric activation in DegS and other HtrA serine proteases but also pinpoint an alternative use of covalent small molecules for probing essential biochemical mechanisms.
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Affiliation(s)
- Jens Bongard
- Microbiology, Faculty of Biology, Zentrum für Medizinische Biotechnologie (ZMB), Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Marian Lorenz
- Microbiology, Faculty of Biology, Zentrum für Medizinische Biotechnologie (ZMB), Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Ingrid R. Vetter
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Patricia Stege
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Arthur T. Porfetye
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Anna Laura Schmitz
- Chemical Biology, Faculty of Biology, Zentrum für Medizinische Biotechnologie (ZMB), Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Farnusch Kaschani
- Chemical Biology, Faculty of Biology, Zentrum für Medizinische Biotechnologie (ZMB), Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Alex Wolf
- Lead Discovery Center GmbH, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
| | - Uwe Koch
- Lead Discovery Center GmbH, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
| | - Peter Nussbaumer
- Lead Discovery Center GmbH, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
| | - Bert Klebl
- Lead Discovery Center GmbH, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
| | - Markus Kaiser
- Chemical Biology, Faculty of Biology, Zentrum für Medizinische Biotechnologie (ZMB), Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Michael Ehrmann
- Microbiology, Faculty of Biology, Zentrum für Medizinische Biotechnologie (ZMB), Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
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90
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Quan ML, Pinto DJP, Smallheer JM, Ewing WR, Rossi KA, Luettgen JM, Seiffert DA, Wexler RR. Factor XIa Inhibitors as New Anticoagulants. J Med Chem 2018; 61:7425-7447. [PMID: 29775297 DOI: 10.1021/acs.jmedchem.8b00173] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
With the introduction of thrombin and factor Xa inhibitors to the oral anticoagulant market, significant improvements in both efficacy and safety have been achieved. Early clinical and preclinical data suggest that inhibitors of factor XIa can provide a still safer alternative, with expanded efficacy for arterial indications. This Perspective provides an overview of target rationale and details of the discovery and development of inhibitors of factor XIa as next generation antithrombotic agents.
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Affiliation(s)
- Mimi L Quan
- Research and Development , Bristol-Myers Squibb Company , P.O. Box 5400, Princeton , New Jersey 08543 , United States
| | - Donald J P Pinto
- Research and Development , Bristol-Myers Squibb Company , P.O. Box 5400, Princeton , New Jersey 08543 , United States
| | - Joanne M Smallheer
- Research and Development , Bristol-Myers Squibb Company , P.O. Box 5400, Princeton , New Jersey 08543 , United States
| | - William R Ewing
- Research and Development , Bristol-Myers Squibb Company , P.O. Box 5400, Princeton , New Jersey 08543 , United States
| | - Karen A Rossi
- Research and Development , Bristol-Myers Squibb Company , P.O. Box 5400, Princeton , New Jersey 08543 , United States
| | - Joseph M Luettgen
- Research and Development , Bristol-Myers Squibb Company , P.O. Box 5400, Princeton , New Jersey 08543 , United States
| | - Dietmar A Seiffert
- Research and Development , Bristol-Myers Squibb Company , P.O. Box 5400, Princeton , New Jersey 08543 , United States
| | - Ruth R Wexler
- Research and Development , Bristol-Myers Squibb Company , P.O. Box 5400, Princeton , New Jersey 08543 , United States
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91
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Martins A, Pfirrmann T, Heessen S, Sundqvist G, Bulone V, Andréasson C, Ljungdahl PO. Ssy5 is a signaling serine protease that exhibits atypical biogenesis and marked S1 specificity. J Biol Chem 2018; 293:8362-8378. [PMID: 29661936 DOI: 10.1074/jbc.ra118.002457] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/06/2018] [Indexed: 11/06/2022] Open
Abstract
Ssy5 is a signaling endoprotease that plays a key role in regulating central metabolism, cellular aging, and morphological transitions important for growth and survival of yeast (Saccharomyces cerevisiae) cells. In response to extracellular amino acids, Ssy5 proteolytically activates the transcription factors Stp1 and Stp2, leading to enhanced Ssy1-Ptr3-Ssy5 (SPS) sensor-regulated gene expression. Ssy5 comprises a catalytic (Cat) domain and an extensive regulatory prodomain. Ssy5 is refractory to both broad-spectrum and serine protease-specific inhibitors, confounding its classification as a protease, and no information about Ssy5's cleavage-site preferences and its mechanism of substrate selection is available. Here, using mutational and inhibition experiments, we investigated the biogenesis and catalytic properties of Ssy5 and conclusively show that it is a serine protease. Atypical for the majority of serine proteases, Ssy5's prodomain was obligatorily required in cis during biogenesis for the maturation of the proteolytic activity of the Cat domain. Autolysis and Stp1 and Stp2 cleavage occurred between a cysteine (at the P1 site) and a serine or alanine (at the P'1 site) and required residues with short side chains at the P1 site. Substitutions in the Cat domain affecting substrate specificity revealed that residues Phe-634, His-661, and Gly-671 in the S1-binding pocket of this domain are important for Ssy5 catalytic function. This study confirms that the signaling protease Ssy5 is a serine protease and provides a detailed understanding of the biogenesis and intrinsic properties of this key enzyme in yeast.
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Affiliation(s)
- António Martins
- From the Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University SE-106 91 Stockholm, Sweden
| | - Thorsten Pfirrmann
- From the Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University SE-106 91 Stockholm, Sweden
| | - Stijn Heessen
- From the Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University SE-106 91 Stockholm, Sweden
| | - Gustav Sundqvist
- the Division of Glycoscience, AlbaNova University Centre, Royal Institute of Technology (KTH), SE-106 91 Stockholm, Sweden, and
| | - Vincent Bulone
- the Division of Glycoscience, AlbaNova University Centre, Royal Institute of Technology (KTH), SE-106 91 Stockholm, Sweden, and.,the ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Urrbra 5064, South Australia, Australia
| | - Claes Andréasson
- From the Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University SE-106 91 Stockholm, Sweden
| | - Per O Ljungdahl
- From the Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University SE-106 91 Stockholm, Sweden,
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92
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Cinar G, Ozdemir A, Hamsici S, Gunay G, Dana A, Tekinay AB, Guler MO. Local delivery of doxorubicin through supramolecular peptide amphiphile nanofiber gels. Biomater Sci 2018; 5:67-76. [PMID: 27819087 DOI: 10.1039/c6bm00656f] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Peptide amphiphiles (PAs) self-assemble into supramolecular nanofiber gels that provide a suitable environment for encapsulation of both hydrophobic and hydrophilic molecules. The PA gels have significant advantages for controlled delivery applications due to their high capacity to retain water, biocompatibility, and biodegradability. In this study, we demonstrate injectable supramolecular PA nanofiber gels for drug delivery applications. Doxorubicin (Dox), as a widely used chemotherapeutic drug for breast cancer treatment, was encapsulated within the PA gels prepared at different concentrations. Physical and chemical properties of the gels were characterized, and slow release of the Dox molecules through the supramolecular PA nanofiber gels was studied. In addition, the diffusion constants of the drug molecules within the PA nanofiber gels were estimated using fluorescence recovery after the photobleaching (FRAP) method. The PA nanofiber gels did not show any cytotoxicity and the encapsulation strategy enhanced the activity of drug molecules on cellular viability through prolonged release compared to direct administration under in vitro conditions. Moreover, the local in vivo injection of the Dox encapsulated PA nanofiber gels (Dox/PA) to the tumor site demonstrated the lowest tumor growth rate compared to the direct Dox injection and increased the apoptotic cells within the tumor tissue for local drug release through the PA nanofiber gels under in vivo conditions.
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Affiliation(s)
- Goksu Cinar
- Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center (UNAM), Bilkent University, Ankara, 06800, Turkey.
| | - Ayse Ozdemir
- Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center (UNAM), Bilkent University, Ankara, 06800, Turkey.
| | - Seren Hamsici
- Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center (UNAM), Bilkent University, Ankara, 06800, Turkey.
| | - Gokhan Gunay
- Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center (UNAM), Bilkent University, Ankara, 06800, Turkey.
| | - Aykutlu Dana
- Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center (UNAM), Bilkent University, Ankara, 06800, Turkey.
| | - Ayse B Tekinay
- Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center (UNAM), Bilkent University, Ankara, 06800, Turkey.
| | - Mustafa O Guler
- Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center (UNAM), Bilkent University, Ankara, 06800, Turkey.
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93
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94
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Chakraborty P, Acquasaliente L, Pelc LA, Di Cera E. Interplay between conformational selection and zymogen activation. Sci Rep 2018; 8:4080. [PMID: 29511224 PMCID: PMC5840343 DOI: 10.1038/s41598-018-21728-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 02/09/2018] [Indexed: 11/09/2022] Open
Abstract
Trypsin-like proteases are synthesized as zymogens and activated through a mechanism that folds the active site for efficient binding and catalysis. Ligand binding to the active site is therefore a valuable source of information on the changes that accompany zymogen activation. Using the physiologically relevant transition of the clotting zymogen prothrombin to the mature protease thrombin, we show that the mechanism of ligand recognition follows selection within a pre-existing ensemble of conformations with the active site accessible (E) or inaccessible (E*) to binding. Prothrombin exists mainly in the E* conformational ensemble and conversion to thrombin produces two dominant changes: a progressive shift toward the E conformational ensemble triggered by removal of the auxiliary domains upon cleavage at R271 and a drastic drop of the rate of ligand dissociation from the active site triggered by cleavage at R320. Together, these effects produce a significant (700-fold) increase in binding affinity. Limited proteolysis reveals how the E*-E equilibrium shifts during prothrombin activation and influences exposure of the sites of cleavage at R271 and R320. These new findings on the molecular underpinnings of prothrombin activation are relevant to other zymogens with modular assembly involved in blood coagulation, complement and fibrinolysis.
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Affiliation(s)
- Pradipta Chakraborty
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Laura Acquasaliente
- 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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95
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Dorau R, Görbe T, Svedendahl Humble M. Improved Enantioselectivity of Subtilisin Carlsberg towards Secondary Alcohols by Protein Engineering. Chembiochem 2018; 19:338-346. [PMID: 29105250 DOI: 10.1002/cbic.201700408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Indexed: 11/07/2022]
Abstract
Generally, the catalytic activity of subtilisin Carlsberg (SC) for transacylation reactions with secondary alcohols in organic solvent is low. Enzyme immobilization and protein engineering was performed to improve the enantioselectivity of SC towards secondary alcohols. Possible amino-acid residues for mutagenesis were found by combining available literature data with molecular modeling. SC variants were created by site-directed mutagenesis and were evaluated for a model transacylation reaction containing 1-phenylethanol in THF. Variants showing high E values (>100) were found. However, the conversions were still low. A second mutation was made, and both the E values and conversions were increased. Relative to that shown by the wild type, the most successful variant, G165L/M221F, showed increased conversion (up to 36 %), enantioselectivity (E values up to 400), substrate scope, and stability in THF.
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Affiliation(s)
- Robin Dorau
- Division of Industrial Biotechnology, School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, 106 91, Stockholm, Sweden
- Division of Microbiology and Production, National Food Institute, Technical University of Denmark, Kemitorvet, Bygning 201, 2800, Kgs. Lyngby, Denmark
| | - Tamás Görbe
- Department of Organic Chemistry, Stockholm University, Arrhenius Laboratory, 106 91, Stockholm, Sweden
| | - Maria Svedendahl Humble
- Division of Industrial Biotechnology, School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, 106 91, Stockholm, Sweden
- Pharem Biotech AB, Biovation Park, Forskargatan 20 J, 151 36, Stockholm, Sweden
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96
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Böttcher-Friebertshäuser E, Garten W, Klenk HD. Membrane-Anchored Serine Proteases: Host Cell Factors in Proteolytic Activation of Viral Glycoproteins. ACTIVATION OF VIRUSES BY HOST PROTEASES 2018. [PMCID: PMC7122464 DOI: 10.1007/978-3-319-75474-1_8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Over one third of all known proteolytic enzymes are serine proteases. Among these, the trypsin-like serine proteases comprise one of the best characterized subfamilies due to their essential roles in blood coagulation, food digestion, fibrinolysis, or immunity. Trypsin-like serine proteases possess primary substrate specificity for basic amino acids. Most of the well-characterized trypsin-like proteases such as trypsin, plasmin, or urokinase are soluble proteases that are secreted into the extracellular environment. At the turn of the millennium, a number of novel trypsin-like serine proteases have been identified that are anchored in the cell membrane, either by a transmembrane domain at the N- or C-terminus or via a glycosylphosphatidylinositol (GPI) linkage. Meanwhile more than 20 membrane-anchored serine proteases (MASPs) have been identified in human and mouse, and some of them have emerged as key regulators of mammalian development and homeostasis. Thus, the MASP corin and TMPRSS6/matriptase-2 have been demonstrated to be the activators of the atrial natriuretic peptide (ANP) and key regulator of hepcidin expression, respectively. Furthermore, MASPs have been recognized as host cell factors activating respiratory viruses including influenza virus as well as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) coronaviruses. In particular, transmembrane protease serine S1 member 2 (TMPRSS2) has been shown to be essential for proteolytic activation and consequently spread and pathogenesis of a number of influenza A viruses in mice and as a factor associated with severe influenza virus infection in humans. This review gives an overview on the physiological functions of the fascinating and rapidly evolving group of MASPs and a summary of the current knowledge on their role in proteolytic activation of viral fusion proteins.
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Affiliation(s)
| | - Wolfgang Garten
- 0000 0004 1936 9756grid.10253.35Institut für Virologie, Philipps Universität, Marburg, Germany
| | - Hans Dieter Klenk
- 0000 0004 1936 9756grid.10253.35Institut für Virologie, Philipps-Universität, Marburg, Germany
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97
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Flanagan ML, Arguello AE, Colman DE, Kim J, Krejci JN, Liu S, Yao Y, Zhang Y, Gorin DJ. A DNA-conjugated small molecule catalyst enzyme mimic for site-selective ester hydrolysis. Chem Sci 2018; 9:2105-2112. [PMID: 29732115 PMCID: PMC5911826 DOI: 10.1039/c7sc04554a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/10/2018] [Indexed: 12/19/2022] Open
Abstract
The challenge of site-selectivity must be overcome in many chemical research contexts, including selective functionalization in complex natural products and labeling of one biomolecule in a living system. Synthetic catalysts incorporating molecular recognition domains can mimic naturally-occurring enzymes to direct a chemical reaction to a particular instance of a functional group. We propose that DNA-conjugated small molecule catalysts (DCats), prepared by tethering a small molecule catalyst to a DNA aptamer, are a promising class of reagents for site-selective transformations. Specifically, a DNA-imidazole conjugate able to increase the rate of ester hydrolysis in a target ester by >100-fold compared with equimolar untethered imidazole was developed. Other esters are unaffected. Furthermore, DCat-catalyzed hydrolysis follows enzyme-like kinetics and a stimuli-responsive variant of the DCat enables programmable "turn on" of the desired reaction.
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Affiliation(s)
- Moira L Flanagan
- Smith College , Department of Chemistry , Northampton , MA 01063 , USA .
| | - A Emilia Arguello
- Smith College , Department of Chemistry , Northampton , MA 01063 , USA .
| | - Drew E Colman
- Smith College , Department of Chemistry , Northampton , MA 01063 , USA .
| | - Jiyeon Kim
- Smith College , Department of Chemistry , Northampton , MA 01063 , USA .
| | - Jesse N Krejci
- Smith College , Department of Chemistry , Northampton , MA 01063 , USA .
| | - Shimu Liu
- Smith College , Department of Chemistry , Northampton , MA 01063 , USA .
| | - Yueyu Yao
- Smith College , Department of Chemistry , Northampton , MA 01063 , USA .
| | - Yu Zhang
- Smith College , Department of Chemistry , Northampton , MA 01063 , USA .
| | - David J Gorin
- Smith College , Department of Chemistry , Northampton , MA 01063 , USA .
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98
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Jiang L, Zhang X, Zhou Y, Chen Y, Luo Z, Li J, Yuan C, Huang M. Halogen bonding for the design of inhibitors by targeting the S1 pocket of serine proteases. RSC Adv 2018; 8:28189-28197. [PMID: 35542712 PMCID: PMC9083945 DOI: 10.1039/c8ra03145b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/24/2018] [Indexed: 12/14/2022] Open
Abstract
BrBA binds to the S1 pocket of urokinase with Br facing the base of the pocket by halogen bonds, while iodine of IBA binds to the S1 in the opposite way.
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Affiliation(s)
| | - Xu Zhang
- Center for Life Science
- School of Life Sciences
- Yunnan University
- Kunming 650021
- China
| | - Yang Zhou
- College of Chemistry
- Fuzhou University
- Fuzhou 350116
- China
| | - Yayu Chen
- College of Chemistry
- Fuzhou University
- Fuzhou 350116
- China
| | - Zhipu Luo
- Synchrotron Radiation Research Section
- NCI
- Argonne National Laboratory
- USA
| | - Jinyu Li
- College of Chemistry
- Fuzhou University
- Fuzhou 350116
- China
| | - Cai Yuan
- College of Biological Science and Engineering
- Fuzhou University
- Fuzhou 350116
- China
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99
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Affiliation(s)
- I. W. Hamley
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, United Kingdom
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100
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Antunes AA, Jesus LDOP, Manfredi MA, de Souza AA, Machado MFM, E Silva PM, Icimoto MY, Juliano MA, Juliano L, Judice WADS. Thermodynamic analysis of Kex2 activity: The acylation and deacylation steps are potassium- and substrate-dependent. Biophys Chem 2017; 235:29-39. [PMID: 29432900 DOI: 10.1016/j.bpc.2017.11.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/30/2017] [Accepted: 11/30/2017] [Indexed: 01/15/2023]
Abstract
Kex2 is the prototype of a large family of eukaryotic subtilisin-related proprotein-processing proteases that cleave at sites containing pairs of basic residues. Here, we studied the effects of KCl on the individual rate constants of association, dissociation, acylation and deacylation and determined the thermodynamic parameters at each step of the Kex2 reaction. Potassium bound Kex2 with KD=20.3mM. The order in which potassium entered the reaction system modified the effect of activation or inhibition, which depended on the size of the substrate. A possible allosteric potassium binding site at the S6 subsite was involved in activation, and a distant site located between the catalytic domain and the P-domain was involved in inhibition. Potassium decreased the energetic barriers of almost all steps of catalysis. The acylation of Ac-PMYKR-AMC in the absence of potassium was the rate-limiting step. Therefore, for substrates containing a P1-Arg, the deacylation step is not necessarily the rate-limiting event, and other residues at the P' positions may participate in controlling the acylation and deacylation steps. Thus, it is reasonable to conclude that potassium is involved in the processing of the α-mating factor that promotes Ca2+ mobilization by activating a high-affinity Ca2+-influx system to increase the cytosolic [Ca2+], resulting in the activation of channels that are essential for the survival of Saccharomyces cerevisiae cells.
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Affiliation(s)
- Alyne Alexandrino Antunes
- Centro Interdisciplinar de Investigação Bioquímica, Universidade de Mogi das Cruzes - UMC, Av. Cândido Xavier de Almeida e Souza, 200, Sala 1S-15, Vila Partênio, CEP: 08780-911 Mogi das Cruzes, SP, Brazil
| | - Larissa de Oliveira Passos Jesus
- Centro Interdisciplinar de Investigação Bioquímica, Universidade de Mogi das Cruzes - UMC, Av. Cândido Xavier de Almeida e Souza, 200, Sala 1S-15, Vila Partênio, CEP: 08780-911 Mogi das Cruzes, SP, Brazil
| | - Marcella Araújo Manfredi
- Centro Interdisciplinar de Investigação Bioquímica, Universidade de Mogi das Cruzes - UMC, Av. Cândido Xavier de Almeida e Souza, 200, Sala 1S-15, Vila Partênio, CEP: 08780-911 Mogi das Cruzes, SP, Brazil
| | - Aline Aparecida de Souza
- Centro Interdisciplinar de Investigação Bioquímica, Universidade de Mogi das Cruzes - UMC, Av. Cândido Xavier de Almeida e Souza, 200, Sala 1S-15, Vila Partênio, CEP: 08780-911 Mogi das Cruzes, SP, Brazil
| | - Maurício Ferreira Marcondes Machado
- Centro Interdisciplinar de Investigação Bioquímica, Universidade de Mogi das Cruzes - UMC, Av. Cândido Xavier de Almeida e Souza, 200, Sala 1S-15, Vila Partênio, CEP: 08780-911 Mogi das Cruzes, SP, Brazil
| | - Pamela Moraes E Silva
- Centro Interdisciplinar de Investigação Bioquímica, Universidade de Mogi das Cruzes - UMC, Av. Cândido Xavier de Almeida e Souza, 200, Sala 1S-15, Vila Partênio, CEP: 08780-911 Mogi das Cruzes, SP, Brazil
| | - Marcelo Yudi Icimoto
- Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio, 100, São Paulo, SP 04044-020, Brazil
| | - Maria Aparecida Juliano
- Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio, 100, São Paulo, SP 04044-020, Brazil
| | - Luiz Juliano
- Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio, 100, São Paulo, SP 04044-020, Brazil
| | - Wagner Alves de Souza Judice
- Centro Interdisciplinar de Investigação Bioquímica, Universidade de Mogi das Cruzes - UMC, Av. Cândido Xavier de Almeida e Souza, 200, Sala 1S-15, Vila Partênio, CEP: 08780-911 Mogi das Cruzes, SP, Brazil.
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