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Pang P, Liu S, Hao X, Tian Y, Gong S, Miao D, Zhang Y. Exploring binding modes of the selected inhibitors to SND1 by all-atom molecular dynamics simulations. J Biomol Struct Dyn 2024; 42:5536-5550. [PMID: 37345536 DOI: 10.1080/07391102.2023.2226737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/13/2023] [Indexed: 06/23/2023]
Abstract
Breast cancer is the leading cause of cancer-related deaths in women. Previous studies have indicated that disrupting the interaction between Metadherin (MTDH) and Staphylococcal nuclease domain containing 1 (SND1) can inhibit breast cancer development. Understanding the binding mode of small molecule inhibitors with SND1 is of great significance for designing drugs targeting the MTDH-SND1 complex. In this study, we conducted all-atom molecular dynamics (MD) simulations in solution and performed binding energy calculations to gain insights into the binding mechanism of small molecules to SND1. The binding site of SND1 for small molecules is relatively rigid, and the binding of the small molecule and the mutation of key residues have little effect on the conformation of the binding site. SND1 binds more tightly to C26-A6 than to C26-A2, as C26-A2 undergoes a 180° directional change during the simulation process. The key residue mutations have a direct effect on the position and orientation of small molecule in the binding site. The key residues make primary contributions to the binding energy through van der Waals interaction and nonpolar solvation energy, although the contribution from nonpolar solvation is relatively minor. The key residue mutations also affect the formation of hydrogen bonds and ultimately the stability of the small molecule-SND1 complex.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Peilin Pang
- School of Mathematics and Physics, Hebei University of Engineering, Handan, China
| | - Senchen Liu
- School of Mathematics and Physics, Hebei University of Engineering, Handan, China
| | - Xiafei Hao
- Medical College, Hebei University of Engineering, Handan, China
| | - Yuxin Tian
- School of Mathematics and Physics, Hebei University of Engineering, Handan, China
| | - Shuyue Gong
- School of Mathematics and Physics, Hebei University of Engineering, Handan, China
| | - Dongqiang Miao
- School of Mathematics and Physics, Hebei University of Engineering, Handan, China
| | - Yanjun Zhang
- School of Mathematics and Physics, Hebei University of Engineering, Handan, China
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2
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Ramanathan P, Tigabu B, Santos RI, Ilinykh PA, Kuzmina N, Vogel OA, Thakur N, Ahmed H, Wu C, Amarasinghe GK, Basler CF, Bukreyev A. Ebolavirus Species-Specific Interferon Antagonism Mediated by VP24. Viruses 2023; 15:1075. [PMID: 37243162 PMCID: PMC10222226 DOI: 10.3390/v15051075] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Members of the Ebolavirus genus demonstrate a marked differences in pathogenicity in humans with Ebola (EBOV) being the most pathogenic, Bundibugyo (BDBV) less pathogenic, and Reston (RESTV) is not known to cause a disease in humans. The VP24 protein encoded by members of the Ebolavirus genus blocks type I interferon (IFN-I) signaling through interaction with host karyopherin alpha nuclear transporters, potentially contributing to virulence. Previously, we demonstrated that BDBV VP24 (bVP24) binds with lower affinities to karyopherin alpha proteins relative to EBOV VP24 (eVP24), and this correlated with a reduced inhibition in IFN-I signaling. We hypothesized that modification of eVP24-karyopherin alpha interface to make it similar to bVP24 would attenuate the ability to antagonize IFN-I response. We generated a panel of recombinant EBOVs containing single or combinations of point mutations in the eVP24-karyopherin alpha interface. Most of the viruses appeared to be attenuated in both IFN-I-competent 769-P and IFN-I-deficient Vero-E6 cells in the presence of IFNs. However, the R140A mutant grew at reduced levels even in the absence of IFNs in both cell lines, as well as in U3A STAT1 knockout cells. Both the R140A mutation and its combination with the N135A mutation greatly reduced the amounts of viral genomic RNA and mRNA suggesting that these mutations attenuate the virus in an IFN-I-independent attenuation. Additionally, we found that unlike eVP24, bVP24 does not inhibit interferon lambda 1 (IFN-λ1), interferon beta (IFN-β), and ISG15, which potentially explains the lower pathogenicity of BDBV relative to EBOV. Thus, the VP24 residues binding karyopherin alpha attenuates the virus by IFN-I-dependent and independent mechanisms.
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Affiliation(s)
- Palaniappan Ramanathan
- Department of Pathology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Galveston National Laboratory, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Bersabeh Tigabu
- Department of Pathology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Galveston National Laboratory, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Rodrigo I. Santos
- Department of Pathology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Galveston National Laboratory, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Philipp A. Ilinykh
- Department of Pathology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Galveston National Laboratory, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Natalia Kuzmina
- Department of Pathology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Galveston National Laboratory, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Olivia A. Vogel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Naveen Thakur
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hamza Ahmed
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chao Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gaya K. Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Christopher F. Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexander Bukreyev
- Department of Pathology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Galveston National Laboratory, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Department of Microbiology & Immunology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
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3
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Sun M, Lin Q, Wang C, Xing J, Yan K, Liu Z, Jin Y, Cardona CJ, Xing Z. Enterovirus A71 2B Inhibits Interferon-Activated JAK/STAT Signaling by Inducing Caspase-3-Dependent Karyopherin-α1 Degradation. Front Microbiol 2022; 12:762869. [PMID: 34992585 PMCID: PMC8725996 DOI: 10.3389/fmicb.2021.762869] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Enterovirus A71 (EV-A71) is a major pathogen that causes the hand, foot, and mouth disease, which could be fatal with neurological complications in children. The underlying mechanism for the severe pathogenicity remains obscure, but impaired or aberrant innate immunity is considered to play a key role in viral pathogenesis. We reported previously that EV-A71 suppressed type I interferon (IFN) responses by inducing degradation of karyopherin-α1 (KPNA1), a component of the p-STAT1/2 complex. In this report, we showed that 2B, a non-structural protein of EV-A71, was critical to the suppression of the IFN-α-induced type I response in infected cells. Among viral proteins, 2B was the only one that was involved in the degradation of KPNA1, which impeded the formation of the p-STAT1/2/KPNA1 complex and blocked the translocation of p-STAT1/2 into the nucleus upon IFN-α stimulation. Degradation of KPNA1 induced by 2B can be inhibited in the cells pre-treated with Z-DEVD-FMK, a caspase-3 inhibitor, or siRNA targeting caspase-3, indicating that 2B-induced degradation of KPNA1 was caspase-3 dependent. The mechanism by which 2B functioned in the dysregulation of the IFN signaling was analyzed and a putative hydrophilic domain (H1) in the N-terminus of 2B was characterized to be critical for the release of cytochrome c into the cytosol for the activation of pro-caspase-3. We generated an EV-A71 infectious clone (rD1), which was deficient of the H1 domain. In rD1-infected cells, degradation of KPNA1 was relieved and the infected cells were more sensitive to IFN-α, leading to decreased viral replication, in comparison to the cells infected with the virus carrying a full length 2B. Our findings demonstrate that EV-A71 2B protein plays an important role in dysregulating JAK-STAT signaling through its involvement in promoting caspase-3 dependent degradation of KPNA1, which represents a novel strategy employed by EV-A71 to evade host antiviral innate immunity.
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Affiliation(s)
- Menghuai Sun
- Medical School and Jiangsu Provincial Key Laboratory of Medicine, Nanjing University, Nanjing, China.,Nanjing Children's Hospital, Nanjing Medical University, Nanjing, China.,Department of Gastroenterology, Beijing Children's Hospital, Capital Medical, University, National Center for Children's Health, China
| | - Qian Lin
- Nanjing Children's Hospital, Nanjing Medical University, Nanjing, China
| | - Chunyang Wang
- Clinical Medical College, Xi'an Medical University, Xi'an, China
| | - Jiao Xing
- Nanjing Children's Hospital, Nanjing Medical University, Nanjing, China
| | - Kunlong Yan
- Nanjing Children's Hospital, Nanjing Medical University, Nanjing, China
| | - Zhifeng Liu
- Nanjing Children's Hospital, Nanjing Medical University, Nanjing, China
| | - Yu Jin
- Medical School and Jiangsu Provincial Key Laboratory of Medicine, Nanjing University, Nanjing, China.,Nanjing Children's Hospital, Nanjing Medical University, Nanjing, China
| | - Carol J Cardona
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, University of Minnesota at Twin Cities, Saint Paul, MN, United States
| | - Zheng Xing
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, University of Minnesota at Twin Cities, Saint Paul, MN, United States
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Wang Y, Liu M, Li J, Wei H, Zhang K. Experimental and in silico studies of competitive inhibition of family GH10 Aspergillus fumigatus xylanase A by Oryza sativa xylanase inhibitor protein. Int J Biol Macromol 2021; 193:1391-1399. [PMID: 34742846 DOI: 10.1016/j.ijbiomac.2021.10.201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 10/07/2021] [Accepted: 10/26/2021] [Indexed: 11/25/2022]
Abstract
The family GH10 Aspergillus fumigatus xylanase A (AfXylA10) gene, afxyla10 was cloned and recombinantly expressed in Pichia pastoris X33. The optimum temperature and pH of reAfXylA10 was 53 °C and 7.0, and Mn2+ remarkably activated the catalytic activity. The recombinant Oryza sativa xylanase inhibitor protein, rePOsXIP significantly inhibited reAfXylA10 with inhibition constant (Ki) of 177.94 nM via competitive inhibition and decreased the concentration of hydrolysate from beechwood xylan. Optimal inhibition of rePOsXIP on reAfXylA10 occurred at 45 °C for 40 min. The fluorescence of reAfXylA10 was statically quenched by rePOsXIP, indicating the formation of reAfXylA10-rePOsXIP complex during their interaction. Furthermore, molecular dynamics (MD) simulations were performed to obtain the detailed information on enzyme-inhibitor interaction. The binding free energy (ΔG) of AfXylA10-OsXIP complex was -30 ± 9 kcal/mol by MM-PBSA calculation, and the α-7 helix of OsXIP anchored in the catalytic cleft of AfXylA10 by competition with the xylan substrate. K239OsXIP stably interacted with the catalytic site E140AfXylA10 through hydrogen bond and vdW interaction. Intermolecular hydrogen bonds T104AfXylA10/V99AfXylA10-Q5OsXIP, R256AfXylA10-E235OsXIP, D155AfXylA10-Y243OsXIP and D145AfXylA10-R194OsXIP on the upper of the TIM barrel were essential for strengthening the stability of complex. Therefore, these non-covalent interactions (NCI) played key role in the interaction between AfXylA10 and OsXIP.
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Affiliation(s)
- Yuting Wang
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Mingqi Liu
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China.
| | - Jiayi Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huiwen Wei
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Keer Zhang
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
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5
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Wang D, Huang M, Gao D, Chen K, Xinxie, Xu W, Li X. Screening anti-TMV agents targeting tobacco mosaic virus helicase protein. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2020; 166:104449. [PMID: 32448412 DOI: 10.1016/j.pestbp.2019.07.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/29/2019] [Accepted: 07/13/2019] [Indexed: 06/11/2023]
Abstract
Tobacco mosaic virus helicase (TMV-Hel) plays important roles in viral multiplication. TMV-Hel is a potential target of anti-TMV agents. Our previous studies expressed and purified TMV-Hel as target protein for cytosinpeptidemycin. In this study, we preform molecular docking to study the binding sites of commercial antiviral agents with TMV-Hel. Then we verify the interactions between the potential anti-TMV agents and TMV-Hel in vitro using Microscale Thermophoresis experiment and study the inhibiting expression of TMV-Hel with the potential anti-TMV agents in vivo using Western-blot (WB) method. The results showed that ribavirin bound to TMV-Hel with a dissociation constant of 1.55 μM by direct interaction with eight binding sites, which was consistent with the docking studies. Ribavirin inhibited the expression of TMV-Hel in Nicotiana benthamiana. Docking studies combined Microscale Thermophoresis and WB experiment provided a new method to screen anti-TMV agents targeting TMV-Hel.
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Affiliation(s)
- Dongmei Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China
| | - Maoxi Huang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China
| | - Di Gao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China
| | - Kai Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China
| | - Xinxie
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Weiming Xu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China.
| | - Xiangyang Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China.
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6
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Li X, Chen K, Gao D, Wang D, Huang M, Zhu H, Kang J. Binding studies between cytosinpeptidemycin and the superfamily 1 helicase protein of tobacco mosaic virus. RSC Adv 2018; 8:18952-18958. [PMID: 35539684 PMCID: PMC9080650 DOI: 10.1039/c8ra01466c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/14/2018] [Indexed: 11/21/2022] Open
Abstract
Tobacco mosaic virus (TMV) helicases play important roles in viral multiplication and interactions with host organisms. They can also be targeted by antiviral agents. Cytosinpeptidemycin has a good control effect against TMV. However, the mechanism of action is unclear. In this study, we expressed and purified TMV superfamily 1 helicase (TMV-Hel) and analyzed its three-dimensional structure. Furthermore, the binding interactions of TMV-Hel and cytosinpeptidemycin were studied. Microscale thermophoresis and isothermal titration calorimetry experiments showed that cytosinpeptidemycin bound to TMV-Hel with a dissociation constant of 0.24–0.44 μM. Docking studies provided further insights into the interaction of cytosinpeptidemycin with the His375 of TMV-Hel. Mutational and Microscale thermophoresis analyses showed that cytosinpeptidemycin bound to a TMV-Hel mutant (H375A) with a dissociation constant of 14.5 μM. Thus, His375 may be the important binding site for cytosinpeptidemycin. The data are important for designing and synthesizing new effective antiphytoviral agents. Tobacco mosaic virus (TMV) helicases play important roles in viral multiplication and interactions with host organisms.![]()
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Affiliation(s)
- Xiangyang Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Guizhou University
- Guiyang 550025
| | - Kai Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Guizhou University
- Guiyang 550025
| | - Di Gao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Guizhou University
- Guiyang 550025
| | - Dongmei Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Guizhou University
- Guiyang 550025
| | - Maoxi Huang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Guizhou University
- Guiyang 550025
| | - Hengmin Zhu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Guizhou University
- Guiyang 550025
| | - Jinxin Kang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Guizhou University
- Guiyang 550025
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Nan Y, Wu C, Zhang YJ. Interplay between Janus Kinase/Signal Transducer and Activator of Transcription Signaling Activated by Type I Interferons and Viral Antagonism. Front Immunol 2017; 8:1758. [PMID: 29312301 PMCID: PMC5732261 DOI: 10.3389/fimmu.2017.01758] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 11/27/2017] [Indexed: 12/13/2022] Open
Abstract
Interferons (IFNs), which were discovered a half century ago, are a group of secreted proteins that play key roles in innate immunity against viral infection. The major signaling pathway activated by IFNs is the Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway, which leads to the expression of IFN-stimulated genes (ISGs), including many antiviral effectors. Viruses have evolved various strategies with which to antagonize the JAK/STAT pathway to influence viral virulence and pathogenesis. In recent years, notable progress has been made to better understand the JAK/STAT pathway activated by IFNs and antagonized by viruses. In this review, recent progress in research of the JAK/STAT pathway activated by type I IFNs, non-canonical STAT activation, viral antagonism of the JAK/STAT pathway, removing of the JAK/STAT antagonist from viral genome for attenuation, and the potential pathogenesis roles of tyrosine phosphorylation-independent non-canonical STATs activation during virus infection are discussed in detail. We expect that this review will provide new insight into the understanding the complexity of the interplay between JAK/STAT signaling and viral antagonism.
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Affiliation(s)
- Yuchen Nan
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China.,Molecular Virology Laboratory, VA-MD Regional College of Veterinary Medicine, Maryland Pathogen Research Institute, University of Maryland, College Park, MD, United States
| | - Chunyan Wu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yan-Jin Zhang
- Molecular Virology Laboratory, VA-MD Regional College of Veterinary Medicine, Maryland Pathogen Research Institute, University of Maryland, College Park, MD, United States
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Banerjee A, Pal A, Pal D, Mitra P. Ebolavirus interferon antagonists—protein interaction perspectives to combat pathogenesis. Brief Funct Genomics 2017; 17:392-401. [DOI: 10.1093/bfgp/elx034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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