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Chen W, Soko WC, Xie J, Bi H. Discovery of mass spectral peak markers and protein biomarkers in fish muscle exudates for rapid and precise recognition of fish species via magnetic beads (MBs) and mass spectrometry. Food Chem X 2024; 22:101509. [PMID: 38883916 PMCID: PMC11179567 DOI: 10.1016/j.fochx.2024.101509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/23/2024] [Accepted: 05/23/2024] [Indexed: 06/18/2024] Open
Abstract
In this study, muscle exudates from five fishes belonging to the family Sciaenidae, in the order Perciformes, were analyzed as models for the discovery of biomarkers by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). MagSi-weak cation exchange magnetic beads (WCX-MBs) were utilized for the enrichment of proteins from fish exudate samples, allowing protein biomarkers to be identified and subsequently used for fish species differentiation. Buffers with pH ranging from 4.0 to 9.0 can provide an environment for proteins in fish muscle exudate to bind to the WCX-MBs. The optimal enrichment based on WCX-MBs can be achieved when the exudate samples are diluted 100folds. More species-specific biomarkers in mass spectra can be identified when using WCX-MBs. The number of ions that can be considered as peak markers and can differentiate the analyzed fishes increases from 38 to 121 when using WCX-MBs to isolate peptides/protein in fish muscle exudate. Particularly, eight peak markers in mass spectra were assigned to be specific to Nibea albiflora (NA), three peak markers specific to Larimichthys crocea (LC), two peak markers specific to Miichthys miiuy (MM), seven peak markers specific to Collichthys lucidus (CL), and six peak markers specific to Larimichthys polyactis (LP). Furthermore, five proteins were identified based on the characterization of tryptic peptides and their potential to be biomarkers, of which four proteins specific to CL and one specific to LC were identified. The single-blind samples analysis demonstrated that these species-specific peak markers and protein biomarkers can be successfully utilized for corresponding fish recognition. The utilization of WCX-MBs can improve the discovery of fish species-specific biomarkers in fish muscle exudate samples. The present protocol holds potential of being a rapid and accurate identification tool for recognition of fish species.
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Affiliation(s)
- Weijiao Chen
- College of Food Science and Technology, Shanghai Ocean University (SHOU), 999 Hucheng Ring Road, Pudong New District, 201306 Shanghai, China
| | - Winnie C Soko
- College of Food Science and Technology, Shanghai Ocean University (SHOU), 999 Hucheng Ring Road, Pudong New District, 201306 Shanghai, China
| | - Jing Xie
- College of Food Science and Technology, Shanghai Ocean University (SHOU), 999 Hucheng Ring Road, Pudong New District, 201306 Shanghai, China
| | - Hongyan Bi
- College of Food Science and Technology, Shanghai Ocean University (SHOU), 999 Hucheng Ring Road, Pudong New District, 201306 Shanghai, China
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2
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Korobkin JJD, Deordieva EA, Tesakov IP, Adamanskaya EIA, Boldova AE, Boldyreva AA, Galkina SV, Lazutova DP, Martyanov AA, Pustovalov VA, Novichkova GA, Shcherbina A, Panteleev MA, Sveshnikova AN. Dissecting thrombus-directed chemotaxis and random movement in neutrophil near-thrombus motion in flow chambers. BMC Biol 2024; 22:115. [PMID: 38764040 DOI: 10.1186/s12915-024-01912-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 05/08/2024] [Indexed: 05/21/2024] Open
Abstract
BACKGROUND Thromboinflammation is caused by mutual activation of platelets and neutrophils. The site of thromboinflammation is determined by chemoattracting agents release by endothelium, immune cells, and platelets. Impaired neutrophil chemotaxis contributes to the pathogenesis of Shwachman-Diamond syndrome (SDS). In this hereditary disorder, neutrophils are known to have aberrant chemoattractant-induced F-actin properties. Here, we aim to determine whether neutrophil chemotaxis could be analyzed using our previously developed ex vivo assay of the neutrophils crawling among the growing thrombi. METHODS Adult and pediatric healthy donors, alongside with pediatric patients with SDS, were recruited for the study. Thrombus formation and granulocyte movement in hirudinated whole blood were visualized by fluorescent microscopy in fibrillar collagen-coated parallel-plate flow chambers. Alternatively, fibrinogen, fibronectin, vWF, or single tumor cells immobilized on coverslips were used. A computational model of chemokine distribution in flow chamber with a virtual neutrophil moving in it was used to analyze the observed data. RESULTS The movement of healthy donor neutrophils predominantly occurred in the direction and vicinity of thrombi grown on collagen or around tumor cells. For SDS patients or on coatings other than collagen, the movement was characterized by randomness and significantly reduced velocities. Increase in wall shear rates to 300-500 1/s led to an increase in the proportion of rolling neutrophils. A stochastic algorithm simulating leucocyte chemotaxis movement in the calculated chemoattractant field could reproduce the experimental trajectories of moving neutrophils for 72% of cells. CONCLUSIONS In samples from healthy donors, but not SDS patients, neutrophils move in the direction of large, chemoattractant-releasing platelet thrombi growing on collagen.
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Affiliation(s)
- Julia-Jessica D Korobkin
- Center for Theoretical Problems of Physico-Chemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina A Deordieva
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Ivan P Tesakov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
- Department of Oncology, Hematology, Immunology, and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Ekaterina-Iva A Adamanskaya
- Center for Theoretical Problems of Physico-Chemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Anna E Boldova
- Center for Theoretical Problems of Physico-Chemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Antonina A Boldyreva
- Center for Theoretical Problems of Physico-Chemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
| | - Sofia V Galkina
- Center for Theoretical Problems of Physico-Chemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Daria P Lazutova
- Center for Theoretical Problems of Physico-Chemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A Martyanov
- Center for Theoretical Problems of Physico-Chemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
| | | | - Galina A Novichkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Anna Shcherbina
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Mikhail A Panteleev
- Center for Theoretical Problems of Physico-Chemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
- Lomonosov Moscow State University, Moscow, Russia
| | - Anastasia N Sveshnikova
- Center for Theoretical Problems of Physico-Chemical Pharmacology, Russian Academy of Sciences, Moscow, Russia.
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.
- Lomonosov Moscow State University, Moscow, Russia.
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Martin P, Kurth EA, Budean D, Momplaisir N, Qu E, Simien JM, Orellana GE, Brautigam CA, Smrcka AV, Haglund E. Biophysical characterization of the CXC chemokine receptor 2 ligands. PLoS One 2024; 19:e0298418. [PMID: 38625857 PMCID: PMC11020491 DOI: 10.1371/journal.pone.0298418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/24/2024] [Indexed: 04/18/2024] Open
Abstract
The chemokines of the immune system act as first responders by operating as chemoattractants, directing immune cells to specific locations of inflamed tissues. This promiscuous network is comprised of 50 ligands and 18 receptors where the ligands may interact with the receptors in various oligomeric states i.e., monomers, homodimers, and heterodimers. Chemokine receptors are G-protein coupled receptors (GPCRs) present in the membrane of immune cells. The migration of immune cells occurs in response to a concentration gradient of the ligands. Chemotaxis of neutrophils is directed by CXC-ligand (CXCL) activation of the membrane bound CXC chemokine receptor 2 (CXCR2). CXCR2 plays an important role in human health and is linked to disorders such as autoimmune disorders, inflammation, and cancer. Yet, despite their important role, little is known about the biophysical characteristics controlling ligand:ligand and ligand:receptor interaction essential for biological activity. In this work, we study the homodimers of three of the CXCR2 cognate ligands, CXCL1, CXCL5, and CXCL8. The ligands share high structural integrity but a low sequence identity. We show that the sequence diversity has evolved different binding affinities and stabilities for the CXC-ligands resulting in diverse agonist/antagonist behavior. Furthermore, CXC-ligands fold through a three-state mechanism, populating a folded monomeric state before associating into an active dimer.
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Affiliation(s)
- Patrick Martin
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Emily A. Kurth
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - David Budean
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Nathalie Momplaisir
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Elaine Qu
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Jennifer M. Simien
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Grace E. Orellana
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Chad A. Brautigam
- Department of Biophysics and the Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Alan V. Smrcka
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Ellinor Haglund
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
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Zhang HQ, Jin XY, Li XP, Li MF. IL8 of Takifugu rubripes is a chemokine that interacts with peripheral blood leukocytes and promotes antibacterial defense. FISH & SHELLFISH IMMUNOLOGY 2023; 139:108918. [PMID: 37364660 DOI: 10.1016/j.fsi.2023.108918] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/14/2023] [Accepted: 06/24/2023] [Indexed: 06/28/2023]
Abstract
Interleukin 8 (IL8) is a CXC chemokine that plays a crucial role on promoting inflammatory response and immune regulation. In teleost, IL8 can induce the migration and activation of immune cells. However, the biological functions of IL8 are still unknown in Takifugu rubripes. In this study, we examined the biological characteristics of TrIL8 in T. rubripes. TrIL8 is composed of 98 residues and contained a chemokine CXC domain. We found that the TrIL8 expression was detected in diverse organs and significantly increased by Vibrio harveyi or Edwardsiella tarda challenge. The recombinant TrIL8 (rTrIL8) exhibited significantly the binding capacities to 8 tested bacteria. In addition, rTrIL8 could bind to peripheral blood leukocytes (PBL), and increased the expression of immune gene, resistance to bacterial infection, respiratory burst, acid phosphatase activity, chemotactic activity, and phagocytic activity of PBL. In the presence of rTrIL8, T. rubripes was enhanced the resistance to V. harveyi infection. These results indicated that TrIL8 is a chemokine and involved in the activation of immune cells against bacterial infection in teleost.
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Affiliation(s)
- Hong-Qiang Zhang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, 393 West Binshui Road, Xiqing District, Tianjin, 300387, China
| | - Xiao-Yan Jin
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, 393 West Binshui Road, Xiqing District, Tianjin, 300387, China
| | - Xue-Peng Li
- School of Ocean, Yantai University, Yantai, China
| | - Mo-Fei Li
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, 393 West Binshui Road, Xiqing District, Tianjin, 300387, China.
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5
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Wang G, Hu J, Zhang M, Zhang Y, Li Y, Jiang H, Wang X, Zhu J, Xu S, Wang Y, Yan X. Histopathology, immunoenzyme activity and transcriptome analysis of immune response in silver pomfret infected by cryptokaryon (Cryptorchidism irritant). FISH & SHELLFISH IMMUNOLOGY 2023; 136:108731. [PMID: 37044188 DOI: 10.1016/j.fsi.2023.108731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 03/31/2023] [Accepted: 04/02/2023] [Indexed: 06/19/2023]
Abstract
Cryptorchidism irritant (CI) infection is a major problem in the culturing process of silver pomfret (Pampus argenteus), which can result in rapid and massive death. However, there is limited information available on the immune response of silver pomfret infected by CI. To address this gap, we sampled naturally infected fish and observed milky white translucent oval CI trophozoites on the gills, body surface, and fin rays. Histological analysis showed that CI infection led to vacuolation of epithelial cells and a decrease in blood cells in the gills. We also performed transcriptome profiling of the gill, kidney complex, and spleen, generating 399,616,194 clean reads that assembled into 101,228 unigenes, which were annotated based on public databases. We detected 14,369 differentially expressed genes, and selected several key immune-related genes for further validation using RT-qPCR. The Graft-versus-host pathway and Allograft rejection pathway were enriched in the gills, leading to inflammation and ulceration. CI infection activated the immune system, increasing levels of interleukin-1 beta and MHC class II antigen, and also activated innate and acquired immune genes in silver pomfret. Furthermore, we measured the activities of five immune-related enzymes (SOD, AKP, CAT, CSH and ACP), which all increased to varying degrees after CI infection. Our findings enhance our understanding of the immune response of fish to parasitic infection and may contribute to the development of strategies to prevent high mortality in CI-stimulated fish in aquaculture.
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Affiliation(s)
- Guanlin Wang
- School of Marine Sciences, Ningbo University, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Jiabao Hu
- School of Marine Sciences, Ningbo University, Ningbo, China; School of Civil & Environmental Engineering and Geography Science, Ningbo University, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China.
| | - Man Zhang
- School of Marine Sciences, Ningbo University, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Youyi Zhang
- School of Marine Sciences, Ningbo University, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Yaya Li
- School of Marine Sciences, Ningbo University, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Huang Jiang
- School of Marine Sciences, Ningbo University, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Xiangbing Wang
- School of Marine Sciences, Ningbo University, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Jiajie Zhu
- School of Marine Sciences, Ningbo University, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Shanliang Xu
- School of Marine Sciences, Ningbo University, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Yajun Wang
- School of Marine Sciences, Ningbo University, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China.
| | - Xiaojun Yan
- School of Marine Sciences, Ningbo University, Ningbo, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
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Lee E, Redzic JS, Nemkov T, Saviola AJ, Dzieciatkowska M, Hansen KC, D’Alessandro A, Dinarello C, Eisenmesser EZ. Human and Bacterial Toll-Interleukin Receptor Domains Exhibit Distinct Dynamic Features and Functions. Molecules 2022; 27:4494. [PMID: 35889366 PMCID: PMC9318647 DOI: 10.3390/molecules27144494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 02/04/2023] Open
Abstract
Toll-interleukin receptor (TIR) domains have emerged as critical players involved in innate immune signaling in humans but are also expressed as potential virulence factors within multiple pathogenic bacteria. However, there has been a shortage of structural studies aimed at elucidating atomic resolution details with respect to their interactions, potentially owing to their dynamic nature. Here, we used a combination of biophysical and biochemical studies to reveal the dynamic behavior and functional interactions of a panel of both bacterial TIR-containing proteins and mammalian receptor TIR domains. Regarding dynamics, all three bacterial TIR domains studied here exhibited an inherent exchange that led to severe resonance line-broadening, revealing their intrinsic dynamic nature on the intermediate NMR timescale. In contrast, the three mammalian TIR domains studied here exhibited a range in terms of their dynamic exchange that spans multiple timescales. Functionally, only the bacterial TIR domains were catalytic towards the cleavage of NAD+, despite the conservation of the catalytic nucleophile on human TIR domains. Our development of NMR-based catalytic assays allowed us to further identify differences in product formation for gram-positive versus gram-negative bacterial TIR domains. Differences in oligomeric interactions were also revealed, whereby bacterial TIR domains self-associated solely through their attached coil-coil domains, in contrast to the mammalian TIR domains that formed homodimers and heterodimers through reactive cysteines. Finally, we provide the first atomic-resolution studies of a bacterial coil-coil domain and provide the first atomic model of the TIR domain from a human anti-inflammatory IL-1R8 protein that undergoes a slow inherent exchange.
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Affiliation(s)
- Eunjeong Lee
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, Aurora, CO 80045, USA; (E.L.); (J.S.R.); (T.N.); (A.J.S.); (M.D.); (K.C.H.); (A.D.)
| | - Jasmina S. Redzic
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, Aurora, CO 80045, USA; (E.L.); (J.S.R.); (T.N.); (A.J.S.); (M.D.); (K.C.H.); (A.D.)
| | - Travis Nemkov
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, Aurora, CO 80045, USA; (E.L.); (J.S.R.); (T.N.); (A.J.S.); (M.D.); (K.C.H.); (A.D.)
| | - Anthony J. Saviola
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, Aurora, CO 80045, USA; (E.L.); (J.S.R.); (T.N.); (A.J.S.); (M.D.); (K.C.H.); (A.D.)
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, Aurora, CO 80045, USA; (E.L.); (J.S.R.); (T.N.); (A.J.S.); (M.D.); (K.C.H.); (A.D.)
| | - Kirk C. Hansen
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, Aurora, CO 80045, USA; (E.L.); (J.S.R.); (T.N.); (A.J.S.); (M.D.); (K.C.H.); (A.D.)
| | - Angelo D’Alessandro
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, Aurora, CO 80045, USA; (E.L.); (J.S.R.); (T.N.); (A.J.S.); (M.D.); (K.C.H.); (A.D.)
| | - Charles Dinarello
- Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, Aurora, CO 80045, USA;
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Elan Z. Eisenmesser
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, Aurora, CO 80045, USA; (E.L.); (J.S.R.); (T.N.); (A.J.S.); (M.D.); (K.C.H.); (A.D.)
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7
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Redzic JS, Lee E, Born A, Issaian A, Henen MA, Nichols PJ, Blue A, Hansen KC, D'Alessandro A, Vögeli B, Eisenmesser EZ. The Inherent Dynamics and Interaction Sites of the SARS-CoV-2 Nucleocapsid N-Terminal Region. J Mol Biol 2021; 433:167108. [PMID: 34161778 PMCID: PMC8214912 DOI: 10.1016/j.jmb.2021.167108] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/16/2022]
Abstract
The nucleocapsid protein is one of four structural proteins encoded by SARS-CoV-2 and plays a central role in packaging viral RNA and manipulating the host cell machinery, yet its dynamic behavior and promiscuity in nucleotide binding has made standard structural methods to address its atomic-resolution details difficult. To begin addressing the SARS-CoV-2 nucleocapsid protein interactions with both RNA and the host cell along with its dynamic behavior, we have specifically focused on the folded N-terminal domain (NTD) and its flanking regions using nuclear magnetic resonance solution studies. Studies performed here reveal a large repertoire of interactions, which includes a temperature-dependent self-association mediated by the disordered flanking regions that also serve as binding sites for host cell cyclophilin-A while nucleotide binding is largely mediated by the central NTD core. NMR studies that include relaxation experiments have revealed the complicated dynamic nature of this viral protein. Specifically, while much of the N-terminal core domain exhibits micro-millisecond motions, a central β-hairpin shows elevated inherent flexibility on the pico-nanosecond timescale and the serine/arginine-rich region of residues 176-209 undergoes multiple exchange phenomena. Collectively, these studies have begun to reveal the complexities of the nucleocapsid protein dynamics and its preferred interaction sites with its biological targets.
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Affiliation(s)
- Jasmina S Redzic
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States
| | - Eunjeong Lee
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States
| | - Alexandra Born
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States
| | - Aaron Issaian
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States; Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Parker J Nichols
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States
| | - Ashley Blue
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, United States
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States.
| | - Elan Zohar Eisenmesser
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States.
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8
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Redzic JS, Duff MR, Blue A, Pitts TM, Agarwal P, Eisenmesser EZ. Modulating Enzyme Function via Dynamic Allostery within Biliverdin Reductase B. Front Mol Biosci 2021; 8:691208. [PMID: 34095235 PMCID: PMC8173106 DOI: 10.3389/fmolb.2021.691208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 04/30/2021] [Indexed: 11/17/2022] Open
Abstract
The biliverdin reductase B (BLVRB) class of enzymes catalyze the NADPH-dependent reduction of multiple flavin substrates and are emerging as critical players in cellular redox regulation. However, the role of dynamics and allostery have not been addressed, prompting studies here that have revealed a position 15 Å away from the active site within human BLVRB (T164) that is inherently dynamic and can be mutated to control global micro-millisecond motions and function. By comparing the inherent dynamics through nuclear magnetic resonance (NMR) relaxation approaches of evolutionarily distinct BLVRB homologues and by applying our previously developed Relaxation And Single Site Multiple Mutations (RASSMM) approach that monitors both the functional and dynamic effects of multiple mutations to the single T164 site, we have discovered that the most dramatic mutagenic effects coincide with evolutionary changes and these modulate coenzyme binding. Thus, evolutionarily changing sites distal to the active site serve as dynamic "dials" to globally modulate motions and function. Despite the distal dynamic and functional coupling modulated by this site, micro-millisecond motions span an order of magnitude in their apparent kinetic rates of motions. Thus, global dynamics within BLVRB are a collection of partially coupled motions tied to catalytic function.
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Affiliation(s)
- Jasmina S Redzic
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Denver, CO, United States
| | - Michael R Duff
- Biochemistry and Cellular and Molecular Biology Department, University of Tennessee, Knoxville, TN, United States
| | - Ashley Blue
- National High Magnetic Field Laboratory, Tallahassee, FL, United States
| | - Todd M Pitts
- Division of Medical Oncology, School of Medicine, University of Colorado, Aurora, CO, United States
| | - Pratul Agarwal
- Department of Physiological Sciences and High Performance Computing Center, Oklahoma State University, Stillwater, OK, United States
| | - Elan Zohar Eisenmesser
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Denver, CO, United States
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9
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Carriero MM, Henrique-Silva F, Meira CM, Gato IMQ, Caetano AR, Lobo FP, Alves AL, Varela ES, Maia AAM. Molecular characterization and gene expression analysis of the pro-inflammatory cytokines IL-1β and IL-8 in the South American fish Piaractus mesopotamicus challenged with Aeromonas dhakensis. Genet Mol Biol 2020; 43:e20200006. [PMID: 33174977 PMCID: PMC7687281 DOI: 10.1590/1678-4685-gmb-2020-0006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 08/06/2020] [Indexed: 11/24/2022] Open
Abstract
In the present study, the complete characterization of cDNA and genomic sequences of IL-1β and IL-8, as well as the expression profile of these genes in the South American fish pacu (Piaractus mesopotamicus) is provided. The full-length pmIL-1β cDNA was composed of 1208 nucleotides that would produce a precursor peptide with 273 amino acid residues. A putative caspase-1 cleavage site, similar to what is found in mammalian IL-1β, was identified producing a mature peptide with a theoretical molecular weight of 17.21 kDa. The pmIL-8 cDNA sequence consisted of 1019 nucleotides which encoded a 95-amino acid protein with a theoretical molecular weight of 10.43 kDa that showed all typical CXC chemokine features, including a 20-residue signal peptide and four conserved cysteine residues. Constitutive mRNA expression was detected for both genes in the liver, head kidney, gill, intestine, skin and spleen. After a bacterial challenge, up-regulation was detected for both pmIL-1β and pmIL-8 in the spleen and head kidney at 12 h post-infection. At 24 h post-infection there was a decrease in the expression of both genes, with pmIL-8 showing a significant down-regulation in the liver and head kidney when compared to the control groups.
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Affiliation(s)
- Mateus Maldonado Carriero
- Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Pirassununga, SP, Brazil
| | - Flavio Henrique-Silva
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
| | - Caroline Munhoz Meira
- Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Pirassununga, SP, Brazil
| | - Igor Mateus Queiroz Gato
- Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Pirassununga, SP, Brazil
| | - Alexandre Rodrigues Caetano
- Embrapa Recursos Genéticos e Biotecnologia, Empresa Brasileira de Pesquisa Agropecuária, Brasília, DF, Brazil
| | - Francisco Pereira Lobo
- Embrapa Informática na Agricultura, Empresa Brasileira de Pesquisa Agropecuária, Campinas, SP, Brazil
| | - Anderson Luis Alves
- Embrapa Pesca e Aquicultura, Empresa Brasileira de Pesquisa Agropecuária, Palmas, TO, Brazil
| | - Eduardo Sousa Varela
- Embrapa Pesca e Aquicultura, Empresa Brasileira de Pesquisa Agropecuária, Palmas, TO, Brazil
| | - Antonio Augusto Mendes Maia
- Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Pirassununga, SP, Brazil
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10
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Navarro J. Fine-Tuning of GPCR-Chemokine Interactions. Design and Identification of Chemokine Analogues as Receptor Agonists, Biased Agonists, and Antagonists. Biochemistry 2019; 58:1432-1439. [PMID: 30726064 DOI: 10.1021/acs.biochem.8b01266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chemokines play important roles in immune defense by directing migration of leukocytes and serve as key promoters of tumorigenesis and metastasis. This study explores the molecular mechanisms of recognition and activation of two homologous chemokine receptors, CXCR1 and CXCR2, using CXCL8 analogues with residue substitutions in the conserved Glu4Leu5Arg6 (ELR) triad. Analysis of the binding of CXCL8 analogues to CXCR1 is consistent with the two-site model for signal recognition of CXCR1, whereas analysis of the binding of CXCL8 analogues to CXCR2 supported a single-site model for signal recognition of CXCR2. The CXCL8-Arg6His analogue stimulated calcium release, phosphorylation of ERK1/2, and chemotaxis in cells expressing CXCR1. However, CXCL8-Arg6His failed to stimulate calcium release and chemotaxis in cells expressing CXCR2, although it stimulated phosphorylation of ERK1/2, indicating that CXCL8-Arg6His operated as a classical CXCR2 biased agonist. The CXCL8-Glu4AlaLeu5AlaArg6His analogue was inactive in cells expressing CXCR1 and CXCR2. These findings suggest that the Glu4Leu5 motif in CXCL8 is essential for activation of CXCR1 and CXCR2. Importantly, CXCL8-Glu4AlaLeu5AlaArg6His blocked specifically the calcium release and chemotaxis of cells expressing CXCR1 but not of cells expressing CXCR2. CXCL8-Glu4AlaLeu5AlaArg6His was identified as the first specific CXCR1 antagonist. The binding of CXCL8-ELR6H to CXCR1 created a Zn2+ coordination site at the receptor activation domain responsible for calcium release, as ZnCl2 specifically blocked CXCL8-Arg6His-induced calcium release without affecting CXCL8-induced calcium release. This work provides the basis for further exploration of the activation mechanisms of chemokine receptors and will assist in the design of the next generation of modulators of CXCR1 and CXCR2.
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Affiliation(s)
- Javier Navarro
- Department of Neuroscience, Cell Biology and Anatomy, School of Medicine, Sealy Center for Structural Biology and Molecular Biophysics , University of Texas Medical Branch , Galveston , Texas 77555 , United States
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11
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Interleukin-37 monomer is the active form for reducing innate immunity. Proc Natl Acad Sci U S A 2019; 116:5514-5522. [PMID: 30819901 DOI: 10.1073/pnas.1819672116] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Interleukin-37 (IL-37), a member of the IL-1 family of cytokines, is a fundamental suppressor of innate and acquired immunities. Here, we used an integrative approach that combines biophysical, biochemical, and biological studies to elucidate the unique characteristics of IL-37. Our studies reveal that single amino acid mutations at the IL-37 dimer interface that result in the stable formation of IL-37 monomers also remain monomeric at high micromolar concentrations and that these monomeric IL-37 forms comprise higher antiinflammatory activities than native IL-37 on multiple cell types. We find that, because native IL-37 forms dimers with nanomolar affinity, higher IL-37 only weakly suppresses downstream markers of inflammation whereas lower concentrations are more effective. We further show that IL-37 is a heparin binding protein that modulates this self-association and that the IL-37 dimers must block the activity of the IL-37 monomer. Specifically, native IL-37 at 2.5 nM reduces lipopolysaccharide (LPS)-induced vascular cell adhesion molecule (VCAM) protein levels by ∼50%, whereas the monomeric D73K mutant reduced VCAM by 90% at the same concentration. Compared with other members of the IL-1 family, both the N and the C termini of IL-37 are extended, and we show they are disordered in the context of the free protein. Furthermore, the presence of, at least, one of these extended termini is required for IL-37 suppressive activity. Based on these structural and biological studies, we present a model of IL-37 interactions that accounts for its mechanism in suppressing innate inflammation.
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12
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Joseph PRB, Spyracopoulos L, Rajarathnam K. Dynamics-Derived Insights into Complex Formation between the CXCL8 Monomer and CXCR1 N-Terminal Domain: An NMR Study. Molecules 2018; 23:E2825. [PMID: 30384436 PMCID: PMC6278376 DOI: 10.3390/molecules23112825] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 10/19/2018] [Accepted: 10/25/2018] [Indexed: 11/29/2022] Open
Abstract
Interleukin-8 (CXCL8), a potent neutrophil-activating chemokine, exerts its function by activating the CXCR1 receptor that belongs to class A G protein-coupled receptors (GPCRs). Receptor activation involves interactions between the CXCL8 N-terminal loop and CXCR1 N-terminal domain (N-domain) residues (Site-I) and between the CXCL8 N-terminal and CXCR1 extracellular/transmembrane residues (Site-II). CXCL8 exists in equilibrium between monomers and dimers, and it is known that the monomer binds CXCR1 with much higher affinity and that Site-I interactions are largely responsible for the differences in monomer vs. dimer affinity. Here, using backbone 15N-relaxation nuclear magnetic resonance (NMR) data, we characterized the dynamic properties of the CXCL8 monomer and the CXCR1 N-domain in the free and bound states. The main chain of CXCL8 appears largely rigid on the picosecond time scale as evident from high order parameters (S²). However, on average, S² are higher in the bound state. Interestingly, several residues show millisecond-microsecond (ms-μs) dynamics only in the bound state. The CXCR1 N-domain is unstructured in the free state but structured with significant dynamics in the bound state. Isothermal titration calorimetry (ITC) data indicate that both enthalpic and entropic factors contribute to affinity, suggesting that increased slow dynamics in the bound state contribute to affinity. In sum, our data indicate a critical and complex role for dynamics in driving CXCL8 monomer-CXCR1 Site-I interactions.
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Affiliation(s)
- Prem Raj B Joseph
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77555, USA.
- Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Leo Spyracopoulos
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
| | - Krishna Rajarathnam
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77555, USA.
- Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX 77555, USA.
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13
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Blevins MA, Zhang C, Zhang L, Li H, Li X, Norris DA, Huang M, Zhao R. CPP-E1A fusion peptides inhibit CtBP-mediated transcriptional repression. Mol Oncol 2018; 12:1358-1373. [PMID: 29879296 PMCID: PMC6068344 DOI: 10.1002/1878-0261.12330] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 05/17/2018] [Accepted: 05/18/2018] [Indexed: 12/29/2022] Open
Abstract
The carboxyl‐terminal binding proteins (CtBP) are transcriptional corepressors that regulate the expression of multiple epithelial‐specific and pro‐apoptotic genes. Overexpression of CtBP occurs in many human cancers where they promote the epithelial‐to‐mesenchymal transition, stem cell‐like features, and cell survival, while knockdown of CtBP in tumor cells results in p53‐independent apoptosis. CtBPs are recruited to their target genes by binding to a conserved PXDLS peptide motif present in multiple DNA‐binding transcription factors. Disrupting the interaction between CtBP and its transcription factor partners may be a means of altering CtBP‐mediated transcriptional repression and a potential approach for cancer therapies. However, small molecules targeting protein–protein interactions have traditionally been difficult to identify. In this study, we took advantage of the fact that CtBP binds to a conserved peptide motif to explore the feasibility of using peptides containing the PXDLS motif fused to cell‐penetrating peptides (CPP) to inhibit CtBP function. We demonstrate that these peptides disrupt the ability of CtBP to interact with its protein partner, E1A, in an AlphaScreen assay. Moreover, these peptides can enter both lung carcinoma and melanoma cells, disrupt the interaction between CtBP and a transcription factor partner, and inhibit CtBP‐mediated transcriptional repression. Finally, the constitutive expression of one such peptide, Pep1‐E1A‐WT, in a melanoma cell line reverses CtBP‐mediated oncogenic phenotypes including proliferation, migration, and sphere formation and limits tumor growth in vivo. Together, our results suggest that CPP‐fused PXDLS‐containing peptides can potentially be developed into a research tool or therapeutic agent targeting CtBP‐mediated transcriptional events in various biological pathways.
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Affiliation(s)
- Melanie A Blevins
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Caiguo Zhang
- Department of Dermatology, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Lingdi Zhang
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Hong Li
- Department of Dermatology, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Xueni Li
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - David A Norris
- Department of Dermatology, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Mingxia Huang
- Department of Dermatology, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
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14
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Park SH, Berkamp S, Radoicic J, De Angelis AA, Opella SJ. Interaction of Monomeric Interleukin-8 with CXCR1 Mapped by Proton-Detected Fast MAS Solid-State NMR. Biophys J 2018; 113:2695-2705. [PMID: 29262362 DOI: 10.1016/j.bpj.2017.09.041] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/17/2017] [Accepted: 09/21/2017] [Indexed: 12/01/2022] Open
Abstract
The human chemokine interleukin-8 (IL-8; CXCL8) is a key mediator of innate immune and inflammatory responses. This small, soluble protein triggers a host of biological effects upon binding and activating CXCR1, a G protein-coupled receptor, located in the cell membrane of neutrophils. Here, we describe 1H-detected magic angle spinning solid-state NMR studies of monomeric IL-8 (1-66) bound to full-length and truncated constructs of CXCR1 in phospholipid bilayers under physiological conditions. Cross-polarization experiments demonstrate that most backbone amide sites of IL-8 (1-66) are immobilized and that their chemical shifts are perturbed upon binding to CXCR1, demonstrating that the dynamics and environments of chemokine residues are affected by interactions with the chemokine receptor. Comparisons of spectra of IL-8 (1-66) bound to full-length CXCR1 (1-350) and to N-terminal truncated construct NT-CXCR1 (39-350) identify specific chemokine residues involved in interactions with binding sites associated with N-terminal residues (binding site-I) and extracellular loop and helical residues (binding site-II) of the receptor. Intermolecular paramagnetic relaxation enhancement broadening of IL-8 (1-66) signals results from interactions of the chemokine with CXCR1 (1-350) containing Mn2+ chelated to an unnatural amino acid assists in the characterization of the receptor-bound form of the chemokine.
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Affiliation(s)
- Sang Ho Park
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Sabrina Berkamp
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Jasmina Radoicic
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Anna A De Angelis
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Stanley J Opella
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California.
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15
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Berkamp S, Park SH, De Angelis AA, Marassi FM, Opella SJ. Structure of monomeric Interleukin-8 and its interactions with the N-terminal Binding Site-I of CXCR1 by solution NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2017; 69:111-121. [PMID: 29143165 PMCID: PMC5869024 DOI: 10.1007/s10858-017-0128-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 08/18/2017] [Indexed: 06/07/2023]
Abstract
The structure of monomeric human chemokine IL-8 (residues 1-66) was determined in aqueous solution by NMR spectroscopy. The structure of the monomer is similar to that of each subunit in the dimeric full-length protein (residues 1-72), with the main differences being the location of the N-loop (residues 10-22) relative to the C-terminal α-helix and the position of the side chain of phenylalanine 65 near the truncated dimerization interface (residues 67-72). NMR was used to analyze the interactions of monomeric IL-8 (1-66) with ND-CXCR1 (residues 1-38), a soluble polypeptide corresponding to the N-terminal portion of the ligand binding site (Binding Site-I) of the chemokine receptor CXCR1 in aqueous solution, and with 1TM-CXCR1 (residues 1-72), a membrane-associated polypeptide that includes the same N-terminal portion of the binding site, the first trans-membrane helix, and the first intracellular loop of the receptor in nanodiscs. The presence of neither the first transmembrane helix of the receptor nor the lipid bilayer significantly affected the interactions of IL-8 with Binding Site-I of CXCR1.
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Affiliation(s)
- Sabrina Berkamp
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, San Diego, CA, 92093-0307, USA
| | - Sang Ho Park
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, San Diego, CA, 92093-0307, USA
| | - Anna A De Angelis
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, San Diego, CA, 92093-0307, USA
| | - Francesca M Marassi
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, San Diego, CA, 92037, USA
| | - Stanley J Opella
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, San Diego, CA, 92093-0307, USA.
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16
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Thompson S, Martínez-Burgo B, Sepuru KM, Rajarathnam K, Kirby JA, Sheerin NS, Ali S. Regulation of Chemokine Function: The Roles of GAG-Binding and Post-Translational Nitration. Int J Mol Sci 2017; 18:ijms18081692. [PMID: 28771176 PMCID: PMC5578082 DOI: 10.3390/ijms18081692] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/28/2017] [Accepted: 07/30/2017] [Indexed: 12/12/2022] Open
Abstract
The primary function of chemokines is to direct the migration of leukocytes to the site of injury during inflammation. The effects of chemokines are modulated by several means, including binding to G-protein coupled receptors (GPCRs), binding to glycosaminoglycans (GAGs), and through post-translational modifications (PTMs). GAGs, present on cell surfaces, bind chemokines released in response to injury. Chemokines bind leukocytes via their GPCRs, which directs migration and contributes to local inflammation. Studies have shown that GAGs or GAG-binding peptides can be used to interfere with chemokine binding and reduce leukocyte recruitment. Post-translational modifications of chemokines, such as nitration, which occurs due to the production of reactive species during oxidative stress, can also alter their biological activity. This review describes the regulation of chemokine function by GAG-binding ability and by post-translational nitration. These are both aspects of chemokine biology that could be targeted if the therapeutic potential of chemokines, like CXCL8, to modulate inflammation is to be realised.
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Affiliation(s)
- Sarah Thompson
- Applied Immunobiology and Transplantation Group, Institute of Cellular Medicine, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, UK.
| | - Beatriz Martínez-Burgo
- Applied Immunobiology and Transplantation Group, Institute of Cellular Medicine, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, UK.
| | - Krishna Mohan Sepuru
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA.
| | - Krishna Rajarathnam
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA.
| | - John A Kirby
- Applied Immunobiology and Transplantation Group, Institute of Cellular Medicine, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, UK.
| | - Neil S Sheerin
- Applied Immunobiology and Transplantation Group, Institute of Cellular Medicine, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, UK.
| | - Simi Ali
- Applied Immunobiology and Transplantation Group, Institute of Cellular Medicine, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, UK.
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17
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Wang GL, Wang MC, Zhang XW, Chang MX, Xie HX, Nie P. Molecular cloning, biological effect, and tissue distribution of interleukin-8 protein in mandarin fish (Siniperca chuasti) upon Flavobacterium columnare infection. FISH & SHELLFISH IMMUNOLOGY 2017; 66:112-119. [PMID: 28478260 DOI: 10.1016/j.fsi.2017.05.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 04/28/2017] [Accepted: 05/02/2017] [Indexed: 06/07/2023]
Abstract
Interleukin-8 (IL-8), a CXC-type chemokine, plays a key role in acute inflammation by recruiting neutrophils in mammals. In the present study, the open reading frame (ORF) of IL-8, encoding 99 amino acids was cloned in mandarin fish, and its function in inflammation was investigated. The IL-8 contains four conserved cysteine residues, with the first two forming the CXC signature motif. The genomic sequence of mandarin fish IL-8 has four exons and three introns, a typical gene organization of the CXC chemokine. Bioactive recombinant IL-8 (rIL-8) exhibited a chemotactic effect on head kidney leukocytes in vitro, and activates the transcription of the inflammatory genes, IL-8 and IL-1β. When mandarin fish was challenged intraperitoneally with the pathogenic bacterium Flavobacterium columnare G4, the steady-state protein level of IL-8 was up-regulated in trunk kidney and head kidney. These results suggest that IL-8 is a functional CXC chemokine in mandarin fish, and plays a key role in the inflammatory responses towards bacterial infection.
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Affiliation(s)
- Gai Ling Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China; School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian, Henan Province, 463000, China
| | - Ming Cheng Wang
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian, Henan Province, 463000, China
| | - Xiao Wen Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China
| | - Ming Xian Chang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China
| | - Hai Xia Xie
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China.
| | - Pin Nie
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China
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18
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Pawlick RL, Wink J, Pepper AR, Bruni A, Abualhassen N, Rafiei Y, Gala-Lopez B, Bral M, Shapiro AJ. Reparixin, a CXCR1/2 inhibitor in islet allotransplantation. Islets 2016; 8:115-24. [PMID: 27328412 PMCID: PMC5029202 DOI: 10.1080/19382014.2016.1199303] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Quality of life in Type 1 diabetic patients may be improved with islet transplantation, but lifelong immunosuppression is required to prevent rejection. Allo-immune response is a key player in graft dysfunction and although the adaptive immune response is well characterized, the effect of the innate immune reaction after transplantation is only recently becoming appreciated. In this study, we address how the innate response affects long-term outcomes in a murine islet allotransplant model. CTLA-4 Ig treatment is known to significantly prolong kidney subcapsular islet allograft survival and enhance glucose tolerance. The combination of CTLA-4 Ig with reparixin, which blocks against inflammatory neutrophil infiltration, yielded no long-term graft survival in an intrahepatic allotransplant model but had similar long-term graft survival in the kidney subcapsular model. Seven days after transplant, serum blood IFN-γ levels were significantly lower in the CTLA-4 Ig with reparixin treatment group compared to controls. IL-12p70 cytokine levels were increased with combination treatment, a positive modulation of the inflammatory response to the allograft. Furthermore, KC GRO, also known as CXCL1, was decreased in serum 7 d after transplant. Histologically, we found that immune cell infiltrate, CD4+ and CD8+ T cell populations along with both CXCR1+ and CXCR2+ cell populations were decreased within the CTLA-4 Ig and reparixin islet transplant graft. Overall these data provide insight into the down regulation of T-cell recruitment by CTLA-4 Ig and decreased neutrophil activation and recruitment with reparixin after long-term islet graft survival.
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Affiliation(s)
- Rena L. Pawlick
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - John Wink
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Andrew R. Pepper
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Antonio Bruni
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | | | - Yasmin Rafiei
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Boris Gala-Lopez
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Mariusz Bral
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - A.M. James Shapiro
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
- Clinical Islet Transplant Program, University of Alberta, Edmonton, AB, Canada
- CONTACT: Dr. A.M. James Shapiro , Canada Research Chair in Transplantation Surgery and Regenerative Medicine, 2000 College Plaza, 8215 112th St., Edmonton, AB, Canada T6G 2C8
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19
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Jiang SJ, Liou JW, Chang CC, Chung Y, Lin LF, Hsu HJ. Peptides derived from CXCL8 based on in silico analysis inhibit CXCL8 interactions with its receptor CXCR1. Sci Rep 2015; 5:18638. [PMID: 26689258 PMCID: PMC4686899 DOI: 10.1038/srep18638] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 11/23/2015] [Indexed: 12/11/2022] Open
Abstract
Chemokine CXCL8 is crucial for regulation of inflammatory and immune responses via activating its cognate receptor CXCR1. In this study, molecular docking and binding free energy calculations were combined to predict the initial binding event of CXCL8 to CXCR1 for peptide drug design. The simulations reveal that in the initial binding, the N-loop of CXCL8 interacts with the N-terminus of CXCR1, which is dominated by electrostatic interactions. The derived peptides from the binding region of CXCL8 are synthesized for further confirmation. Surface plasmon resonance analyses indicate that the CXCL8 derived peptide with 14 residues is able to bind to the receptor CXCR1 derived peptide with equilibrium KD of 252 μM while the peptide encompassing a CXCL8 K15A mutation hardly binds to CXCR1 derived peptide (KD = 1553 μM). The cell experiments show that the designed peptide inhibits CXCL8-induced and LPS-activated monocytes adhesion and transmigration. However, when the peptides were mutated on two lysine residues (K15 and K20), the inhibition effects were greatly reduced indicating these two amino acids are key residues for the initial binding of CXCL8 to CXCR1. This study demonstrates that in silico prediction based functional peptide design can be effective for developing anti-inflammation drugs.
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Affiliation(s)
- Shinn-Jong Jiang
- Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien 97004, Taiwan
| | - Je-Wen Liou
- Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien 97004, Taiwan
- Institute of Medical Sciences, Tzu Chi University, Hualien 97004, Taiwan
| | - Chun-Chun Chang
- Institute of Medical Sciences, Tzu Chi University, Hualien 97004, Taiwan
- Department of Laboratory Medicine, Tzu Chi Medical Center, Hualien 97004, Taiwan
| | - Yi Chung
- Department of Life Sciences, Tzu Chi University, Hualien 97004, Taiwan
| | - Lee-Fong Lin
- Department of Life Sciences, Tzu Chi University, Hualien 97004, Taiwan
| | - Hao-Jen Hsu
- Department of Life Sciences, Tzu Chi University, Hualien 97004, Taiwan
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Eisenmesser EZ, Capodagli GC, Armstrong GS, Holliday MJ, Isern NG, Zhang F, Pegan SD. Inherent dynamics within the Crimean-Congo Hemorrhagic fever virus protease are localized to the same region as substrate interactions. Protein Sci 2015; 24:651-60. [PMID: 25564798 DOI: 10.1002/pro.2637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 12/29/2014] [Accepted: 12/30/2014] [Indexed: 12/12/2022]
Abstract
Crimean-Congo Hemorrhagic fever virus (CCHFV) is one of several lethal viruses that encodes for a viral ovarian tumor domain (vOTU), which serves to cleave and remove ubiquitin (Ub) and interferon stimulated gene product 15 (ISG15) from numerous proteins involved in cellular signaling. Such manipulation of the host cell machinery serves to downregulate the host response and, therefore, complete characterization of these proteases is important. While several structures of the CCHFV vOTU protease have been solved, both free and bound to Ub and ISG15, few structural differences have been found and little insight has been gained as to the structural plasticity of this protease. Therefore, we have used NMR relaxation experiments to probe the dynamics of CCHFV vOTU, both alone and in complex with Ub, discovering a highly dynamic protease that exhibits conformational exchange within the same regions found to engage its Ub substrate. These experiments reveal a structural plasticity around the N-terminal regions of CCHFV vOTU, which are unique to vOTUs, and provide a rationale for engaging multiple substrates with the same binding site.
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Affiliation(s)
- Elan Z Eisenmesser
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Aurora, Colorado, 80224
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Joseph PRB, Rajarathnam K. Solution NMR characterization of WT CXCL8 monomer and dimer binding to CXCR1 N-terminal domain. Protein Sci 2014; 24:81-92. [PMID: 25327289 DOI: 10.1002/pro.2590] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 09/03/2014] [Accepted: 10/10/2014] [Indexed: 01/24/2023]
Abstract
Chemokine CXCL8 and its receptor CXCR1 are key mediators in combating infection and have also been implicated in the pathophysiology of various diseases including chronic obstructive pulmonary disease (COPD) and cancer. CXCL8 exists as monomers and dimers but monomer alone binds CXCR1 with high affinity. CXCL8 function involves binding two distinct CXCR1 sites - the N-terminal domain (Site-I) and the extracellular/transmembrane domain (Site-II). Therefore, higher monomer affinity could be due to stronger binding at Site-I or Site-II or both. We have now characterized the binding of a human CXCR1 N-terminal domain peptide (hCXCR1Ndp) to WT CXCL8 under conditions where it exists as both monomers and dimers. We show that the WT monomer binds the CXCR1 N-domain with much higher affinity and that binding is coupled to dimer dissociation. We also characterized the binding of two CXCL8 monomer variants and a trapped dimer to two different hCXCR1Ndp constructs, and observe that the monomer binds with ∼10- to 100-fold higher affinity than the dimer. Our studies also show that the binding constants of monomer and dimer to the receptor peptides, and the dimer dissociation constant, can vary significantly as a function of pH and buffer, and so the ability to observe WT monomer peaks is critically dependent on NMR experimental conditions. We conclude that the monomer is the high affinity CXCR1 agonist, that Site-I interactions play a dominant role in determining monomer vs. dimer affinity, and that the dimer plays an indirect role in regulating monomer function.
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Affiliation(s)
- Prem Raj B Joseph
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, 77555
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