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Synthesis and Immunological Evaluation of Mannosylated Desmuramyl Dipeptides Modified by Lipophilic Triazole Substituents. Int J Mol Sci 2022; 23:ijms23158628. [PMID: 35955759 PMCID: PMC9368957 DOI: 10.3390/ijms23158628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 07/30/2022] [Accepted: 08/01/2022] [Indexed: 02/05/2023] Open
Abstract
Muramyl dipeptide (N-acetylmuramyl-L-alanyl-D-isoglutamine, MDP) is the smallest peptidoglycan fragment able to trigger an immune response by activating the NOD2 receptor. Structural modification of MDP can lead to analogues with improved immunostimulating properties. The aim of this work was to prepare mannosylated desmuramyl peptides (ManDMP) containing lipophilic triazole substituents to study their immunomodulating activities in vivo. The adjuvant activity of the prepared compounds was evaluated in the mouse model using ovalbumin as an antigen and compared to the MDP and referent adjuvant ManDMPTAd. The obtained results confirm that the α-position of D-isoGln is the best position for the attachment of lipophilic substituents, especially adamantylethyl triazole. Compound 6c exhibited the strongest adjuvant activity, comparable to the MDP and better than referent ManDMPTAd.
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Maharana J, Maharana D, Bej A, Sahoo BR, Panda D, Wadavrao SB, Vats A, Pradhan SK, De S. Structural Elucidation of Inter-CARD Interfaces involved in NOD2 Tandem CARD Association and RIP2 Recognition. J Phys Chem B 2021; 125:13349-13365. [PMID: 34860029 DOI: 10.1021/acs.jpcb.1c06176] [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
Nucleotide-binding and oligomerization domain-containing protein 2 (NOD2) recognizes the muramyl dipeptide and activates the NF-κB signaling cascade following its interaction with receptor-interacting protein 2 (RIP2) via caspase recruitment domains (CARDs). The NOD2-RIP2 interaction is not understood well due to inadequate structural information. Using comparative modeling and multimicrosecond timescale molecular dynamics simulations, we have demonstrated the association of NOD2-CARDs (CARDa-CARDb) and their interaction with RIP2CARD. Our results suggest that a negatively charged interface of NOD2CARDa and positively charged type-Ia interface of NOD2CARDb are crucial for CARDa-CARDb association and the type-Ia interface of NOD2CARDa and type-Ib interface of RIP2CARD predicted to be involved in 1:1 CARD-CARD interaction. Moreover, the direct interaction of NOD2CARDb with RIP2CARD signifies the importance of both CARDs of NOD2 in RIP2-mediated CARD-CARD interaction. Altogether, the structural results could help in understanding the underlying molecular details of the NOD2-RIP2 association in higher and lower eukaryotes.
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Affiliation(s)
- Jitendra Maharana
- Department of Bioinformatics, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha 751001, India
| | - Diptimayee Maharana
- AEBN Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, West Bengal 700120, India
| | - Aritra Bej
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, West Bengal 700032, India
| | - Bikash R Sahoo
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Debashis Panda
- DBT-APSCS&T, Centre of Excellence for Bioresources and Sustainable Development, Kimin, Arunachal Pradesh 791121, India
| | - Sachin B Wadavrao
- OBC Division, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, Telangana 500007, India
| | - Ashutosh Vats
- Animal Genomics Lab., Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, Haryana 132001, India
| | - Sukanta K Pradhan
- Department of Bioinformatics, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha 751001, India
| | - Sachinandan De
- Animal Genomics Lab., Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, Haryana 132001, India
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Maršavelski A, Paurević M, Ribić R. Mannosylated adamantane-containing desmuramyl peptide recognition by the NOD2 receptor: a molecular dynamics study. Org Biomol Chem 2021; 19:7001-7012. [PMID: 34095941 DOI: 10.1039/d1ob00679g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Nucleotide-binding oligomerization domain 2 (NOD2) is an intracellular receptor that recognizes the bacterial peptidoglycan fragment muramyl dipeptide (MDP). Our group has synthesized and biologically evaluated desmuramyl peptides containing adamantane and its mannose derivatives. The most active mannosylated derivative, ManAdDMP (Man-OCH2-d-(1-Ad)Gly-l-Ala-d-isoGln), is further characterized in silico in this study. We built intact model structures of the rabbit NOD2 protein, whose crystal structure lacks seven loops, and explored the binding of ManAdDMP. Two main binding sites for ManAdDMP are located within the nucleotide-binding oligomerization domain (NOD) and C-terminal leucine-rich repeat (LRR) domains. Our analysis shows that the dipeptide isoGln moiety of ManAdDMP significantly contributes to the binding, whereas the mannose moiety interacts with modelled loop 7, which is a part of the NOD helical domain 2. The presented results point to the importance of loops 2 and 7 in ligand recognition that could be useful for further investigation of NOD2 activation/inhibition.
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Affiliation(s)
- Aleksandra Maršavelski
- Department of Chemistry, Faculty of Science, University of Zagreb, HR-10000 Zagreb, Croatia.
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Li Y, Jin L, Xia P, Sui W, Huang A, Bu G, Meng F, Kong F, Cao X, Han X, Yu G, Pan X, Yang S, Zheng C, Zeng X, Du X. Identification and functional analysis of NOD2 and its two splicing variants associated with a novel pattern of signal regulation in teleost fishes. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 120:104049. [PMID: 33609614 DOI: 10.1016/j.dci.2021.104049] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 02/14/2021] [Accepted: 02/14/2021] [Indexed: 06/12/2023]
Abstract
The nucleotide-binding oligomerization domain 2 (NOD2) has been identified as an important sensor for microorganic invasion in both mammals and teleost fishes. In this study, two splicing variants of NOD2 (NOD2-v1 and NOD2-v2) were identified as truncating the functional domains of wild-type NOD2 in the teleost fish Schizothorax prenanti. NOD2-v1 included an intron sequence that terminated within the third leucine-rich repeat (LRR) domain, while NOD2-v2 incorporated an insertion of one and half intron sequences and truncated within the second caspase activation and recruitment domain (CARD). NOD2, NOD2-v1 and NOD2-v2 genes were ubiquitously expressed. All three genes positively responded to exposure of Aeromonas hydrophila and lipopolysaccharide stimulation in varying degrees. Using luciferase activity assays in HEK293T cells, our results revealed that NOD2 activated the NF-κB signal and recognized muramyl dipeptide (MDP). NOD2-v1 exhibited deficiency in the LRR domains and could not sense MDP, but maintained the ability to activate NF-κB and enhanced NOD2-mediated MDP recognition. Given the significant change to the functional structure, NOD2-v2 lost its capacity for NF-κB activation, but interestingly repressed NOD2-mediated MDP sensing and NF-κB activation, and even NOD2-v1-induced NF-κB activation. Altogether, our study reveals a novel pattern of signal regulation by splicing variants in teleost fishes.
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Affiliation(s)
- Yunkun Li
- Department of Engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, PR China
| | - La Jin
- Department of Engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, PR China
| | - Puzhen Xia
- Department of Engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, PR China
| | - Weikai Sui
- Department of Engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, PR China
| | - Anqi Huang
- Department of Engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, PR China
| | - Guixian Bu
- Department of Engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, PR China
| | - Fengyan Meng
- Department of Engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, PR China
| | - Fanli Kong
- Department of Engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, PR China
| | - Xiaohan Cao
- Department of Engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, PR China
| | - Xingfa Han
- Department of Engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, PR China
| | - Guozhi Yu
- Department of Engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, PR China
| | - Xiaofu Pan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, PR China
| | - Shiyong Yang
- Department of Aquaculture, Sichuan Agricultural University, 625014, Sichuan, PR China
| | - Chongquan Zheng
- Yunnan Water Conservancy and Hydropower Investment Niulan River to Dianchi Lake Water Diversion Project Co.,Ltd, Kunming, 650051, PR China
| | - Xianyin Zeng
- Department of Engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, PR China.
| | - Xiaogang Du
- Department of Engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, PR China.
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Cheng WC, You TY, Teo ZZ, Sayyad AA, Maharana J, Guo CW, Liang PH, Lin CS, Meng FC. Further Insights on Structural Modifications of Muramyl Dipeptides to Study the Human NOD2 Stimulating Activity. Chem Asian J 2020; 15:3836-3844. [PMID: 32975372 DOI: 10.1002/asia.202001003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/17/2020] [Indexed: 01/02/2023]
Abstract
A series of muramyl dipeptide (MDP) analogues with structural modifications at the C4 position of MurNAc and on the d-iso-glutamine (isoGln) residue of the peptide part were synthesized. The C4-diversification of MurNAc was conveniently achieved by using CuAAC click strategy to conjugate an azido muramyl dipeptide precursor with structurally diverse alkynes. d-Glutamic acid (Glu), replaced with isoGln, was applied for the structural diversity through esterification or amidation of the carboxylic acid. In total, 26 MDP analogues were synthesized and bio-evaluated for the study of human NOD2 stimulation activity in the innate immune response. Interestingly, MDP derivatives with an ester moiety are found to be more potent than reference compound MDP itself or MDP analogues containing an amide moiety. Among the varied lengths of the alkyl chain in ester derivatives, the MDP analogue bearing the d-glutamate dodecyl (C12) ester moiety showed the best NOD2 stimulation potency.
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Affiliation(s)
- Wei-Chieh Cheng
- Genomics Research Center, Academia Sinica, No. 128, Academia Road Sec. 2, Nangang District, Taipei, 115, Taiwan.,Department of Chemistry, National Cheng-Kung University, No.1, University Road, Tainan, 701, Taiwan.,Department of Applied Chemistry, National Chiayi University, No. 300, Syuefu Road, Chiayi, 600, Taiwan.,Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, No.100, Shin-Chuan 1st Road, Kaohsiung, 807, Taiwan
| | - Ting-Yun You
- Genomics Research Center, Academia Sinica, No. 128, Academia Road Sec. 2, Nangang District, Taipei, 115, Taiwan
| | - Zhen-Zhuo Teo
- Genomics Research Center, Academia Sinica, No. 128, Academia Road Sec. 2, Nangang District, Taipei, 115, Taiwan.,School of Pharmacy, National Taiwan University, No. 17, Xuzhou Road, Taipei, 106, Taiwan
| | - Ashik A Sayyad
- Genomics Research Center, Academia Sinica, No. 128, Academia Road Sec. 2, Nangang District, Taipei, 115, Taiwan
| | - Jitendra Maharana
- Institute of Biological Chemistry Academia Sinica, No. 128, Academia Road Sec. 2, Nangang District, Taipei, 115, Taiwan.,Taiwan International Graduate Program (TIGP), Chemical biology and molecular Biophysics (CBMB), Academia Sinica, No. 128, Academia Road Sec. 2, Nangang District, Taipei, 115, Taiwan.,Institute of Bioinformatics and Structural Biology, National Tsing Hua University, No. 101, Sec. 2, Guangfu Rd., Hsinchu, 300, Taiwan
| | - Chih-Wei Guo
- Genomics Research Center, Academia Sinica, No. 128, Academia Road Sec. 2, Nangang District, Taipei, 115, Taiwan
| | - Pi-Hui Liang
- School of Pharmacy, National Taiwan University, No. 17, Xuzhou Road, Taipei, 106, Taiwan
| | - Chung-Shun Lin
- Genomics Research Center, Academia Sinica, No. 128, Academia Road Sec. 2, Nangang District, Taipei, 115, Taiwan
| | - Fan-Chun Meng
- Genomics Research Center, Academia Sinica, No. 128, Academia Road Sec. 2, Nangang District, Taipei, 115, Taiwan
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Sahoo BR. Structure of fish Toll-like receptors (TLR) and NOD-like receptors (NLR). Int J Biol Macromol 2020; 161:1602-1617. [PMID: 32755705 PMCID: PMC7396143 DOI: 10.1016/j.ijbiomac.2020.07.293] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/26/2020] [Accepted: 07/27/2020] [Indexed: 12/23/2022]
Abstract
Innate immunity driven by pattern recognition receptor (PRR) protects the host from invading pathogens. Aquatic animals like fish where the adaptive immunity is poorly developed majorly rely on their innate immunity modulated by PRRs like toll-like receptors (TLR) and NOD-like receptors (NLR). However, current development to improve the fish immunity via TLR/NLR signaling is affected by a poor understanding of its mechanistic and structural features. This review discusses the structure of fish TLRs/NLRs and its interaction with pathogen associated molecular patterns (PAMPs) and downstream signaling molecules. Over the past one decade, significant progress has been done in studying the structure of TLRs/NLRs in higher eukaryotes; however, structural studies on fish innate immune receptors are undermined. Several novel TLR genes are identified in fish that are absent in higher eukaryotes, but the function is still poorly understood. Unlike the fundamental progress achieved in developing antagonist/agonist to modulate human innate immunity, analogous studies in fish are nearly lacking due to structural inadequacy. This underlies the importance of exploring the structural and mechanistic details of fish TLRs/NLRs at an atomic and molecular level. This review outlined the mechanistic and structural basis of fish TLR and NLR activation.
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Sandall CF, Ziehr BK, MacDonald JA. ATP-Binding and Hydrolysis in Inflammasome Activation. Molecules 2020; 25:molecules25194572. [PMID: 33036374 PMCID: PMC7583971 DOI: 10.3390/molecules25194572] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/02/2020] [Accepted: 10/03/2020] [Indexed: 02/06/2023] Open
Abstract
The prototypical model for NOD-like receptor (NLR) inflammasome assembly includes nucleotide-dependent activation of the NLR downstream of pathogen- or danger-associated molecular pattern (PAMP or DAMP) recognition, followed by nucleation of hetero-oligomeric platforms that lie upstream of inflammatory responses associated with innate immunity. As members of the STAND ATPases, the NLRs are generally thought to share a similar model of ATP-dependent activation and effect. However, recent observations have challenged this paradigm to reveal novel and complex biochemical processes to discern NLRs from other STAND proteins. In this review, we highlight past findings that identify the regulatory importance of conserved ATP-binding and hydrolysis motifs within the nucleotide-binding NACHT domain of NLRs and explore recent breakthroughs that generate connections between NLR protein structure and function. Indeed, newly deposited NLR structures for NLRC4 and NLRP3 have provided unique perspectives on the ATP-dependency of inflammasome activation. Novel molecular dynamic simulations of NLRP3 examined the active site of ADP- and ATP-bound models. The findings support distinctions in nucleotide-binding domain topology with occupancy of ATP or ADP that are in turn disseminated on to the global protein structure. Ultimately, studies continue to reveal how the ATP-binding and hydrolysis properties of NACHT domains in different NLRs integrate with signaling modules and binding partners to control innate immune responses at the molecular level.
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NOD2/c-Jun NH 2-Terminal Kinase Triggers Mycoplasma ovipneumoniae-Induced Macrophage Autophagy. J Bacteriol 2020; 202:JB.00689-19. [PMID: 32778560 PMCID: PMC7515247 DOI: 10.1128/jb.00689-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 07/29/2020] [Indexed: 02/07/2023] Open
Abstract
Mycoplasma ovipneumoniae belongs to Mycoplasma, a genus containing the smallest self-replicating microorganisms, and causes infectious pleuropneumonia in goats and sheep. Nucleotide-binding oligomerization domain-containing protein (NOD2), an intracellular pattern recognition receptor, interacts with muramyl dipeptide (MDP) to recognize bacterial peptidoglycans and is involved in autophagy induction. However, there have been no reports about NOD recognition of mycoplasmas or M. ovipneumoniae-induced autophagy. In this study, we sought to determine the role of NOD2 in M. ovipneumoniae-induced autophagy using Western blotting, immunofluorescence, real-time PCR (RT-PCR), and color-changing unit (CCU) analysis. M. ovipneumoniae infection markedly increased NOD2 but did not increase NOD1 expression in RAW 264.7 cells. Treating RAW 264.7 cells with MDP significantly increased colocalization of M. ovipneumoniae and LC3, whereas treatment with NOD inhibitor, NOD-IN-1, decreased colocalization of M. ovipneumoniae and LC3. Furthermore, suppressing NOD2 expression with small interfering RNA (siRNA)-NOD2 failed to trigger M. ovipneumoniae-induced autophagy by detecting autophagy markers Atg5, beclin1, and LC3-II. In addition, M. ovipneumoniae infection significantly increased the phosphorylated c-Jun NH2-terminal kinase (p-JNK)/JNK, p-Bcl-2/Bcl-2, beclin1, Atg5, and LC3-II ratios in RAW 264.7 cells. Treatment with JNK inhibitor, SP600126, or siRNA-NOD2 did not increase this reaction. These findings suggested that M. ovipneumoniae infection activated NOD2, and both NOD2 and JNK pathway activation promoted M. ovipneumoniae-induced autophagy. This study provides new insight into the NOD2 reorganization mechanism and the pathogenesis of M. ovipneumoniae infection.IMPORTANCE M. ovipneumoniae, which lacks a cell wall, causes infectious pleuropneumonia in goats and sheep. In the present study, we focused on the interaction between NOD and M. ovipneumoniae, as well as its association with autophagy. We showed for the first time that NOD2 was activated by M. ovipneumoniae even when peptidoglycans were not present. We also observed that both NOD2 and JNK pathway activation promoted M. ovipneumoniae-induced autophagy.
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Qu F, Xu W, Deng Z, Xie Y, Tang J, Chen Z, Luo W, Xiong D, Zhao D, Fang J, Zhou Z, Liu Z. Fish c-Jun N-Terminal Kinase (JNK) Pathway Is Involved in Bacterial MDP-Induced Intestinal Inflammation. Front Immunol 2020; 11:459. [PMID: 32292404 PMCID: PMC7134542 DOI: 10.3389/fimmu.2020.00459] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/28/2020] [Indexed: 01/01/2023] Open
Abstract
The c-Jun NH2-terminal kinases (JNKs) are an evolutionarily conserved family of serine/threonine protein kinases that play critical roles in the pathological process in species ranging from insects to mammals. However, the function of JNKs in bacteria-induced intestinal inflammation is still poorly understood. In this study, a fish JNK (CiJNK) pathway was identified, and its potential roles in bacterial muramyl dipeptide (MDP)-induced intestinal inflammation were investigated in Ctenopharyngodon idella. The present CiJNK was found to possess a conserved dual phosphorylation motif (TPY) in a serine/threonine protein kinase (S_TKc) domain and to contain several potential immune-related transcription factor binding sites, including nuclear factor kappa B (NF-κB), activating protein 1 (AP-1), and signal transducer and activator of downstream transcription 3 (STAT3), in its 5′ flanking regions. Quantitative real-time PCR results revealed that the mRNA levels of the JNK pathway genes in the intestine were significantly upregulated after challenge with a bacterial pathogen (Aeromonas hydrophila) and MDP in a time-dependent manner. Additionally, the JNK pathway was found to be involved in regulating the MDP-induced expression levels of inflammatory cytokines (IL-6, IL-8, and TNF-α) in the intestine of grass carp. Moreover, the nutritional dipeptide carnosine and Ala–Gln could effectively alleviate MDP-induced intestinal inflammation by regulating the intestinal expression of JNK pathway genes and inflammatory cytokines in grass carp. Finally, fluorescence microscopy and dual-reporter assays indicated that CiJNK could associate with CiMKK4 and CiMKK7 involved in the regulation of the AP-1 signaling pathway. Overall, these results provide the first experimental demonstration that the JNK signaling pathway is involved in the intestinal immune response to MDP challenge in C. idella, which may provide new insight into the pathogenesis of inflammatory bowel disease.
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Affiliation(s)
- Fufa Qu
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Wenqian Xu
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Zhangren Deng
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Yifang Xie
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Jianzhou Tang
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Zhiguo Chen
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Wenjie Luo
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Ding Xiong
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Dafang Zhao
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Jiamei Fang
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Zhigang Zhou
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhen Liu
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, China.,Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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Sen N, Kanitkar TR, Roy AA, Soni N, Amritkar K, Supekar S, Nair S, Singh G, Madhusudhan MS. Predicting and designing therapeutics against the Nipah virus. PLoS Negl Trop Dis 2019; 13:e0007419. [PMID: 31830030 PMCID: PMC6907750 DOI: 10.1371/journal.pntd.0007419] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 11/04/2019] [Indexed: 11/28/2022] Open
Abstract
Despite Nipah virus outbreaks having high mortality rates (>70% in Southeast Asia), there are no licensed drugs against it. In this study, we have considered all 9 Nipah proteins as potential therapeutic targets and computationally identified 4 putative peptide inhibitors (against G, F and M proteins) and 146 small molecule inhibitors (against F, G, M, N, and P proteins). The computations include extensive homology/ab initio modeling, peptide design and small molecule docking. An important contribution of this study is the increased structural characterization of Nipah proteins by approximately 90% of what is deposited in the PDB. In addition, we have carried out molecular dynamics simulations on all the designed protein-peptide complexes and on 13 of the top shortlisted small molecule ligands to check for stability and to estimate binding strengths. Details, including atomic coordinates of all the proteins and their ligand bound complexes, can be accessed at http://cospi.iiserpune.ac.in/Nipah. Our strategy was to tackle the development of therapeutics on a proteome wide scale and the lead compounds identified could be attractive starting points for drug development. To counter the threat of drug resistance, we have analysed the sequences of the viral strains from different outbreaks, to check whether they would be sensitive to the binding of the proposed inhibitors.
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Affiliation(s)
- Neeladri Sen
- Indian Institute of Science Education and Research, Pune, India
| | | | | | - Neelesh Soni
- Indian Institute of Science Education and Research, Pune, India
| | | | - Shreyas Supekar
- Indian Institute of Science Education and Research, Pune, India
| | - Sanjana Nair
- Indian Institute of Science Education and Research, Pune, India
| | - Gulzar Singh
- Indian Institute of Science Education and Research, Pune, India
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11
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Wang J, Yu S, Li J, Li H, Jiang H, Xiao P, Pan Y, Zheng J, Yu L, Jiang J. Protective role of N-acetyl-l-tryptophan against hepatic ischemia-reperfusion injury via the RIP2/caspase-1/IL-1β signaling pathway. PHARMACEUTICAL BIOLOGY 2019; 57:385-391. [PMID: 31184936 PMCID: PMC6566838 DOI: 10.1080/13880209.2019.1617750] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/29/2019] [Accepted: 05/01/2019] [Indexed: 06/09/2023]
Abstract
Context: Hepatic ischemia-reperfusion injury (HIRI) is a complex process observed during liver resection and transplantation. N-acetyl-l-tryptophan (l-NAT), an antagonist of neurokinin 1 receptor, has been used for the treatment of nausea and neurodegenerative diseases. Objective: This study investigates the protective effect of l-NAT against HIRI and explores the potential underlying mechanisms. Materials and methods: Adult male Sprague-Dawley (SD) rats were randomly divided into three groups: sham, I/R and I/R + l-NAT. HIRI model was generated by clamping the hepatic artery, portal vein and common bile duct with a microvascular bulldog clamp for 45 min, and then removing the clamp and allowing reperfusion for 6 h. BRL cells were exposed to 200 µM H2O2 with or without 10 µM l-NAT for 6 h. Results: After l-NAT intervention, the structure of hepatic lobules was intact, and no swelling was noted in the cells. Furthermore, cell viability was found to be significantly enhanced when compared with the controls (p < 0.05). The mRNA and protein expression levels of serine-threonine kinase 2 (RIP2) and interleukin-1β (IL-1β) were significantly increased in the I/R and H2O2 groups when compared with the controls; however, these levels were significantly decreased after l-NAT intervention. Similarly, IL-1β activity and caspase-1 activity were significantly decreased in the H2O2 group when compared with the controls, after l-NAT intervention. Conclusions: Our findings indicated that l-NAT may exert a hepatoprotective role in HIRI through inhibiting RIP2/caspase-1/IL-1β signaling pathway, which can provide evidence for l-NAT to be a potential effective drug against HIRI during clinical practice.
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Affiliation(s)
- Jianxin Wang
- Department of Anatomy, Weifang Medical University, Weifang, China
| | - Shuna Yu
- Department of Anatomy, Weifang Medical University, Weifang, China
| | - Jianguo Li
- Department of Anatomy, Weifang Medical University, Weifang, China
| | - Huiting Li
- Department of Anatomy, Weifang Medical University, Weifang, China
| | - Hongxin Jiang
- Morphology Laboratory of Weifang Medical University, Weifang, China
| | - Peilun Xiao
- Department of Anatomy, Weifang Medical University, Weifang, China
| | - Yitong Pan
- Department of Anatomy, Weifang Medical University, Weifang, China
| | - Jie Zheng
- Department of Pathology, Weifang Medical University, Weifang, China
| | - Li Yu
- Departments of Histology and Embryology, Weifang Medical University, Weifang, China
| | - Jiying Jiang
- Department of Anatomy, Weifang Medical University, Weifang, China
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Verma A, Nayek A, Kumar A, Singh R, Salotra P. Elucidation of role of an acetyltransferase like protein in paromomycin resistance in Leishmania donovani using in silico and in vitro approaches. J Biomol Struct Dyn 2019; 38:4449-4460. [PMID: 31625467 DOI: 10.1080/07391102.2019.1682674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Paromomycin, an aminoglycoside antibiotic, is an effective treatment for VL (visceral leishmaniasis) in India. The modification of aminoglycoside antibiotics by enzymes such as aminoglycoside acetyltransferases is the predominant mechanism of resistance to antibiotics in bacterial system. In the present study, we identified and characterized LdATLP (an acetyltransferase-like protein) and elucidated its role in paromomycin resistance in Leishmania donovani. Gene encoding LdATLP was consistently up-regulated (>2fold) in three distinct paromomycin resistant in comparison with sensitive parasites, although the gene sequence was identical in the two. In silico analysis revealed that LdATLP consisted of conserved GNAT (GCN5-related N-Acetyltransferase) domain which is characteristic of aminoglycoside N-acetyltransferases. Evolutionary relationship among LdATLP of Leishmania and aminoglycoside acetyltransferases of bacteria was established by phylogenetic analysis. The 3D structure of LdATLP, predicted by ab-initio modeling, constituted 6 α-helices and 6 β-sheets. A few residues, such as R175, R177, E196, R197, V198, V200, K202, R205, C206, D208, G210, R211, R215, A234, S237, S238, K239, D240, F241 and Y242 of GNAT domain were predicted to be present at active site. Molecular docking of LdATLP with paromomycin or indolicidin (broad spectrum inhibitor of aminoglycoside modifying enzymes), followed by molecular dynamics simulation of docked complex suggested that both paromomycin and indolicidin bind to LdATLP with comparable free energy of binding. In vitro studies revealed that in the presence of indolicidin, paromomycin resistant parasites exhibited reversion of phenotype into sensitive parasites with marked increase in paromomycin susceptibility, suggesting the role of LdATLP in paromomycin resistance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aditya Verma
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India.,Faculty of Health and Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - Arnab Nayek
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
| | - Amit Kumar
- ICMR Computational Genomics Center, Division of ISRM, ICMR, New Delhi, India
| | - Ruchi Singh
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
| | - Poonam Salotra
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
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Muramyl Dipeptide Enhances Thermal Injury-Induced Autophagy and Inflammatory Cytokine Response of Lungs via Activation of NOD2/Rick Signaling Pathway in Rats. Shock 2019; 50:606-612. [PMID: 29215417 DOI: 10.1097/shk.0000000000001077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE Nucleotide-binding oligomerization domain 2 (NOD2) is the innate receptor of muramyl dipeptide (MDP). Our previous study revealed that MDP could enhance thermal injury-induced inflammatory cytokine production and organ function injury in rats. The present study was to determine the effect of MDP on autophagy and NOD2/receptor-interacting serine/threonine protein kinases (RICK) signaling pathway of lung injury after thermal injury. METHODS Forty male Sprague-Dawlay rats were randomly divided into four groups: normal control (NC) group, MDP group, Scald group, and MDP + Scald group. Scald group only suffered 20% total body surface area third-degree (TBSA) thermal injury. MDP group was only administered 5.0 mg/kg MDP through the left femoral vein; 5.0 mg/kg MDP was administered through the left femoral vein at 24 h after thermal injury in the MDP + Scald group. RESULTS TBSA thermal injury (20%) not only significantly increased the plasma inflammatory cytokines production, but also elevated the expression of LC3-I/II, the accumulation of autophagosome in the lung tissue. Compared with the Scald group, MDP + Scald double hit led to more serious inflammatory responses and higher expression of NOD2 mRNA, RICK, NF-κB p65, LC3-I/II, and the accumulation of more autophagosome in the lung tissue. CONCLUSIONS MDP enhances thermal injury-induced autophagy and proinflammatory cytokine response of lung injury, which could be achieved via activating the NOD2/RICK signaling pathway in rats.
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Heim VJ, Stafford CA, Nachbur U. NOD Signaling and Cell Death. Front Cell Dev Biol 2019; 7:208. [PMID: 31632962 PMCID: PMC6783575 DOI: 10.3389/fcell.2019.00208] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 09/11/2019] [Indexed: 01/18/2023] Open
Abstract
Innate immune signaling and programmed cell death are intimately linked, and many signaling pathways can regulate and induce both, transcription of inflammatory mediators or autonomous cell death. The best-characterized examples for these dual outcomes are members of the TNF superfamily, the inflammasome receptors, and the toll-like receptors. Signaling via the intracellular peptidoglycan receptors NOD1 and NOD2, however, does not appear to follow this trend, despite involving signaling proteins, or proteins with domains that are linked to programmed cell death, such as RIP kinases, inhibitors of apoptosis (IAP) proteins or the CARD domains on NOD1/2. To better understand the connections between NOD signaling and cell death induction, we here review the latest findings on the molecular regulation of signaling downstream of the NOD receptors and explore the links between this immune signaling pathway and the regulation of cell death.
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Affiliation(s)
- Valentin J Heim
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Che A Stafford
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ueli Nachbur
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
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15
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Rout AK, Paramanik S, Dehury B, Acharya V, Swain HS, Pradhan SK, Behera B, Pati SK, Behera BK, Das BK. Elucidating the molecular interaction of Zebrafish (Danio rerio) peptidoglycan recognition protein 2 with diaminopimelic acid and lysine type peptidoglycans using in silico approaches. J Biomol Struct Dyn 2019; 38:3687-3699. [DOI: 10.1080/07391102.2019.1666742] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Ajaya Kumar Rout
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Sunanda Paramanik
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, India
| | - Budheswar Dehury
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Varsha Acharya
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Himanshu Sekhar Swain
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Sukanta Kumar Pradhan
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, India
| | - Bhaskar Behera
- Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore, India
| | - Soumen Kumar Pati
- Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, Haringhata, India
| | - Bijay Kumar Behera
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Basanta Kumar Das
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
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16
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Qu F, Tang J, Peng X, Zhang H, Shi L, Huang Z, Xu W, Chen H, Shen Y, Yan J, Li J, Lu S, Liu Z. Two novel MKKs (MKK4 and MKK7) from Ctenopharyngodon idella are involved in the intestinal immune response to bacterial muramyl dipeptide challenge. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 93:103-114. [PMID: 30633955 DOI: 10.1016/j.dci.2019.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/03/2019] [Accepted: 01/03/2019] [Indexed: 06/09/2023]
Abstract
Mitogen-activated protein kinase kinases (MKKs) are a class of evolutionarily conserved signalling intermediates of the MAPK signalling pathway that can be activated by a diverse range of pathogenic stimuli and are crucial for the regulation of host immune defence. In this study, two fish MKK genes (CiMKK4 and CiMKK7) were first identified and characterized from grass carp (Ctenopharyngodon idella). Similar to other reported MKKs, the present CiMKK4 and CiMKK7 contained a conserved serine/threonine protein kinase (S_TKc) domain and a canonical dual phosphorylation motif. Quantitative real-time PCR results showed that CiMKK4 and CiMKK7 were broadly transcribed in all selected tissues and developmental stages of grass carp. The mRNA expression levels of CiMKK4 and CiMKK7 in the intestine were significantly induced by bacterial muramyl dipeptide (MDP) challenge in a time-dependent manner (P < 0.01). Additionally, the stimulatory effects of bacterial MDP on CiMKK4 and CiMKK7 expression in the intestine were inhibited by the bioactive dipeptide β-alanyl-l-histidine (carnosine) and alanyl-glutamine (Ala-Gln) (P < 0.05). Moreover, overexpression analysis revealed that CiMKK4 and CiMKK7 were localized throughout the entire cell and could significantly enhance AP-1 reporter gene activation in HEK293T cells. Taken together, these results provide the first experimental demonstration that CiMKK4 and CiMKK7 are involved in the intestinal immune response to MDP challenge in C. idella, which may provide new insight into the bacterial-induced intestinal inflammation of bony fishes.
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Affiliation(s)
- Fufa Qu
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China; State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
| | - Jianzhou Tang
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China
| | - Xiangyu Peng
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China
| | - Hui Zhang
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China
| | - Liping Shi
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China
| | - Zhenzhen Huang
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China
| | - Wenqian Xu
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China
| | - Huiqing Chen
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China
| | - Ying Shen
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China
| | - Jinpeng Yan
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410017, China
| | - Jianzhong Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
| | - Shuangqing Lu
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China
| | - Zhen Liu
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China; State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China.
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17
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Qu F, Tang J, Liao J, Chen B, Song P, Luo W, Xiong D, Liu T, Gao Q, Lu S, Liu Z. Mitogen-activated protein kinase kinase 6 is involved in the immune response to bacterial di-/tripeptide challenge in grass carp Ctenopharyngodon idella. FISH & SHELLFISH IMMUNOLOGY 2019; 84:795-801. [PMID: 30393177 DOI: 10.1016/j.fsi.2018.10.073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/19/2018] [Accepted: 10/26/2018] [Indexed: 06/08/2023]
Abstract
Mitogen-activated protein kinase kinase 6 (MKK6) is an essential component of the p38MAPK signaling pathway, which is involved in the modulation of inflammation, cell apoptosis and survival responses in mammals. However, the function of MKK6s in teleosts is still unclear. In this study, a fish MKK6 homolog (CiMKK6) was first identified from the grass carp (Ctenopharyngodon idella), a freshwater fish. CiMKK6 cDNA encodes a putative protein of 357 amino acids that contains conserved structural characteristics of the MKK6 family, including the S_TKc domain, SVAKT motif and DVD site. The deduced CiMKK6 protein exhibits high sequence homology with other reported fish MKK6s and shares the closest relationship with MKK6 from Danio rerio. Quantitative real-time PCR (qRT-PCR) analysis revealed that CiMKK6 mRNA was widely expressed in all tested tissues and stages of embryonic development. Additionally, the transcript levels of CiMKK6 in the intestine were significantly upregulated in response to bacterial muramyl dipeptide (MDP) and L-Ala-γ-D-Glu-meso-diaminopimelic acid (Tri-DAP) stimulation. Moreover, subcellular localization analysis indicated that CiMKK6 was distributed in both the cytoplasm and the nucleus of HEK293T cells. Finally, overexpression of CiMKK6 significantly enhanced the transcriptional activity of the AP-1 reporter gene in HEK293T cells. Overall, these findings may help better clarify the immune function of teleost MKK6s and provide new insight into the immune defense mechanisms of grass carp.
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Affiliation(s)
- Fufa Qu
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China; State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
| | - Jianzhou Tang
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China
| | - Jinting Liao
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China
| | - Bei Chen
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China
| | - Peng Song
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China
| | - Wenjie Luo
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China; State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
| | - Ding Xiong
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China
| | - Tianting Liu
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China
| | - Qianting Gao
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China
| | - Shuangqing Lu
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China
| | - Zhen Liu
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China; State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China.
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Maharana J, Panda D, De S. Deciphering the ATP-binding mechanism(s) in NLRP-NACHT 3D models using structural bioinformatics approaches. PLoS One 2018; 13:e0209420. [PMID: 30571723 PMCID: PMC6301626 DOI: 10.1371/journal.pone.0209420] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 12/05/2018] [Indexed: 01/04/2023] Open
Abstract
Nucleotide-binding and oligomerization domain (NOD)-like receptors (NLRs), the first line of defense, are the cytosolic pattern recognition receptors (PRRs) that regulate the inflammatory activity in response to invading pathogens. NLRs are the members of AAA+ ATPase superfamily that comprises of N-terminal EBD(s), a centrally positioned NOD/NACHT and varying range of LRRs towards the C-terminal end. Due to the lack of structural data, the functional aspects of NLRP-signaling mechanism, which includes pathogen recognition, nucleotide-binding, and sensor-adaptor-effector interactions, are not fully understood. In this study, we implemented structural bioinformatics approaches including protein modeling, docking, and molecular dynamics simulations to explore the structural-dynamic features of ADP-/ATP-Mg2+ binding in NLRPNACHT models. Our results indicate a similar mode of ATP-Mg2+ binding in all NLRPNACHT models and the interacting residues are found consistent with reported mutagenesis data. Accompanied by the key amino acids (proposed to be crucial for ATP-Mg2+ coordination), we further have noticed that some additional conserved residues (including 'Trp' of the PhhCW motif, and 'Phe' and 'Tyr' of the GFxxxxRxxYF motif) are potentially interacting with ATP during dynamics; which require further experimentation for legitimacy. Overall, this study will help in understanding the ADP-/ATP-Mg2+ binding mechanisms in NLRPs in a broader perspective and the proposed ATP-binding pocket will aid in designing novel inhibitors for the regulation of inflammasome activity.
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Affiliation(s)
- Jitendra Maharana
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, Odisha, India
- * E-mail: (JM); (SD)
| | - Debashis Panda
- Distributed Information Centre (DIC), Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Sachinandan De
- Animal Genomics Lab., Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, Haryana, India
- * E-mail: (JM); (SD)
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Avishek K, Ahuja K, Pradhan D, Gannavaram S, Selvapandiyan A, Nakhasi HL, Salotra P. A Leishmania-specific gene upregulated at the amastigote stage is crucial for parasite survival. Parasitol Res 2018; 117:3215-3228. [DOI: 10.1007/s00436-018-6020-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 07/17/2018] [Indexed: 01/03/2023]
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20
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Gobec M, Tomašič T, Štimac A, Frkanec R, Trontelj J, Anderluh M, Mlinarič-Raščan I, Jakopin Ž. Discovery of Nanomolar Desmuramylpeptide Agonists of the Innate Immune Receptor Nucleotide-Binding Oligomerization Domain-Containing Protein 2 (NOD2) Possessing Immunostimulatory Properties. J Med Chem 2018. [PMID: 29543461 DOI: 10.1021/acs.jmedchem.7b01052] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Muramyl dipeptide (MDP), a fragment of bacterial peptidoglycan, has long been known as the smallest fragment possessing adjuvant activity, on the basis of its agonistic action on the nucleotide-binding oligomerization domain-containing protein 2 (NOD2). There is a pressing need for novel adjuvants, and NOD2 agonists provide an untapped source of potential candidates. Here, we report the design, synthesis, and characterization of a series of novel acyl tripeptides. A pivotal structural element for molecular recognition by NOD2 has been identified, culminating in the discovery of compound 9, the most potent desmuramylpeptide NOD2 agonist to date. Compound 9 augmented pro-inflammatory cytokine release from human peripheral blood mononuclear cells in synergy with lipopolysaccharide. Furthermore, it was able to induce ovalbumin-specific IgG titers in a mouse model of adjuvancy. These findings provide deeper insights into the structural requirements of desmuramylpeptides for NOD2-activation and highlight the potential use of NOD2 agonists as adjuvants for vaccines.
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Affiliation(s)
- Martina Gobec
- Faculty of Pharmacy , University of Ljubljana , Aškerčeva 7 , SI-1000 Ljubljana , Slovenia
| | - Tihomir Tomašič
- Faculty of Pharmacy , University of Ljubljana , Aškerčeva 7 , SI-1000 Ljubljana , Slovenia
| | - Adela Štimac
- Centre for Research and Knowledge Transfer in Biotechnology , University of Zagreb , Rockefellerova 10 , 10000 Zagreb , Croatia
| | - Ruža Frkanec
- Centre for Research and Knowledge Transfer in Biotechnology , University of Zagreb , Rockefellerova 10 , 10000 Zagreb , Croatia
| | - Jurij Trontelj
- Faculty of Pharmacy , University of Ljubljana , Aškerčeva 7 , SI-1000 Ljubljana , Slovenia
| | - Marko Anderluh
- Faculty of Pharmacy , University of Ljubljana , Aškerčeva 7 , SI-1000 Ljubljana , Slovenia
| | - Irena Mlinarič-Raščan
- Faculty of Pharmacy , University of Ljubljana , Aškerčeva 7 , SI-1000 Ljubljana , Slovenia
| | - Žiga Jakopin
- Faculty of Pharmacy , University of Ljubljana , Aškerčeva 7 , SI-1000 Ljubljana , Slovenia
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Gao FY, Pang JC, Lu MX, Yang XL, Zhu HP, Ke XL, Liu ZG, Cao JM, Wang M. Molecular characterization, expression and functional analysis of NOD1, NOD2 and NLRC3 in Nile tilapia (Oreochromis niloticus). FISH & SHELLFISH IMMUNOLOGY 2018; 73:207-219. [PMID: 29242132 DOI: 10.1016/j.fsi.2017.12.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 12/08/2017] [Accepted: 12/10/2017] [Indexed: 06/07/2023]
Abstract
The nucleotide-binding oligomerization domain proteins NOD1, NOD2 and NLRC3 are cytoplasmic pattern recognition receptors (PRRs) of the Nod-like receptor (NLR) family. In the present study, the Nile tilapia (Oreochromis niloticus) NOD1 (ntNOD1), NOD2 (ntNOD2) and NLRC3 (ntNLRC3) genes were cloned and characterized. The full-length ntNOD1, ntNOD2 and ntNLRC3 genes were 3924, 3886 and 4574 bp, encoding 941, 986 and 1130 amino acids, respectively. The three Nod-like receptors have a NACHT domain and a C-terminal leucine-rich repeat (LRR) domain. In addition, ntNOD1 and ntNOD2 have a N-terminal CARD domain (ntNOD2 has two). Phylogenetic analysis showed that the three NLRs are highly conserved. Tissue expression analysis of the three receptors revealed that the highest mRNA and protein levels of ntNOD1, ntNOD2 and ntNLRC3 were in the spleen. The expression patterns of NLRs during embryonic development showed that the expression levels of ntNOD2 and ntNLRC3 significantly increased from 2 to 8 days post-fertilization (dpf). The expression levels of ntNOD1 significantly increased from 2 to 6 dpf, decreased at 7 dpf and then increased at 8 dpf. Upon stimulation with an intraperitoneal injection of Streptococcus agalactiae, expression levels of the ntNOD1, ntNOD2 and ntNLRC3 mRNA and protein were clearly altered in the blood, spleen, kidney, intestine and gill. Furthermore, after cotransfection with an NF-κB reporter plasmid, NF-κB activation in ntNOD1-overexpressing 293T cells significantly increased compared with that in control cells, before or after i-EDPA-stimulation. By contrast, compared with control, ntNOD2 and ntNLRC3 had no effect on NF-κB activation in 293T cells, when their potential ligands were not stimulated. However, after MDP-stimulation, ntNOD2 and ntNLRC3 overexpression increased NF-κB activation in 293T cells. NOD1 and NLRC3 were uniformly distributed throughout the cytoplasm in 293T cells, whereas NOD2 was distributed throughout the cytoplasm and nucleus. Our results indicate that the three Nod-like receptors are functionally conserved and may play pivotal roles in defense against pathogens such as Streptococcus agalactiae.
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Affiliation(s)
- Feng-Ying Gao
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China; Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510380, China; Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, PR China
| | - Ji-Cai Pang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510380, China; Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, PR China
| | - Mai-Xin Lu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510380, China; Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, PR China.
| | - Xian-le Yang
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China.
| | - Hua-Ping Zhu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510380, China; Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, PR China
| | - Xiao-Li Ke
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510380, China; Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, PR China
| | - Zhi-Gang Liu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510380, China; Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, PR China
| | - Jian-Meng Cao
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510380, China; Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, PR China
| | - Miao Wang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510380, China; Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, PR China
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Characterization of the ligand binding of PGRP-L in half-smooth tongue sole ( Cynoglossus semilaevis ) by molecular dynamics and free energy calculation. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2017.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Maharana J. Elucidating the interfaces involved in CARD-CARD interactions mediated by NLRP1 and Caspase-1 using molecular dynamics simulation. J Mol Graph Model 2017; 80:7-14. [PMID: 29324327 DOI: 10.1016/j.jmgm.2017.12.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/21/2017] [Accepted: 12/22/2017] [Indexed: 12/23/2022]
Abstract
Inflammasomes are the multi-protein caspase-activating complexes mainly assembled by the sensor proteins (NLRs/ALRs), adaptor molecule (ASC) and effector molecule pro-caspase-1 for the production and release of proinflammatory cytokines, IL-1β and IL-18. NLRP1 is the first NLR known to assemble the multi-protein complex. Unlike NLRP3, NLRP1 has an additional effector binding domain (CARD) at the carboxyl-terminal, which is reported to interact with pro-caspase-1 (precluding the recruitment of ASC) for the transmission of danger signals. So far no direct interaction has been observed between the NLRP1 and CASP1 at the structural level. In this study, an attempt has been made to elucidate the possible mode of interaction(s) between CASP1 and NLRP1 CARDs using structural bioinformatics approaches. The results revealed that the type-Ia patch of CASP1CARD (R10, K11, and R55) is probably the favorable interface for 1:1 interaction. Moreover, the interactions mediated in the type-II and/(or) type-III interfaces of counter CARDs can also be not ruled out altogether. Overall, the findings of this study can be beneficial in understanding the underlying molecular mechanism(s) associated with NLRP1-mediated inflammasome.
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Affiliation(s)
- Jitendra Maharana
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar-751003, Odisha, India.
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Lauro ML, D’Ambrosio EA, Bahnson BJ, Grimes CL. Molecular Recognition of Muramyl Dipeptide Occurs in the Leucine-rich Repeat Domain of Nod2. ACS Infect Dis 2017; 3:264-270. [PMID: 27748583 DOI: 10.1021/acsinfecdis.6b00154] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Genetic mutations in the innate immune receptor nucleotide-binding oligomerization domain-containing 2 (Nod2) have demonstrated increased susceptibility to Crohn's disease, an inflammatory bowel disease that is hypothesized to be accompanied by changes in the gut microbiota. Nod2 responds to the presence of bacteria, specifically a fragment of the bacterial cell wall, muramyl dipeptide (MDP). The proposed site of this interaction is the leucine-rich repeat (LRR) domain. Surface plasmon resonance and molecular modeling were used to investigate the interaction of the LRR domain with MDP. A functional and pure LRR domain was obtained from Escherichia coli expression in high yield. The LRR domain binds to MDP with high affinity, with a KD of 212 ± 24 nM. Critical portions of the receptor were determined by mutagenesis of putative binding residues. Fragment analysis of MDP revealed that both the peptide and carbohydrate portion contribute to the binding interaction.
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Affiliation(s)
- Mackenzie L. Lauro
- Department of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Elizabeth A. D’Ambrosio
- Department of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Brian J. Bahnson
- Department of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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Maharana J, Vats A, Gautam S, Nayak BP, Kumar S, Sendha J, De S. POP1 might be recruiting its type-Ia interface for NLRP3-mediated PYD-PYD interaction: Insights from MD simulation. J Mol Recognit 2017; 30. [PMID: 28370480 DOI: 10.1002/jmr.2632] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 02/14/2017] [Accepted: 02/23/2017] [Indexed: 11/12/2022]
Abstract
Inflammasomes are multiprotein caspase-activating complexes that enhance the maturation and release of proinflammatory cytokines (IL-1β and IL-18) in response to the invading pathogen and/or host-derived cellular stress. These are assembled by the sensory proteins (viz NLRC4, NLRP1, NLRP3, and AIM-2), adaptor protein (ASC), and effector molecule procaspase-1. In NLRP3-mediated inflammasome activation, ASC acts as a mediator between NLRP3 and procaspase-1 for the transmission of signals. A series of homotypic protein-protein interactions (NLRP3PYD :ASCPYD and ASCCARD :CASP1CARD ) propagates the downstream signaling for the production of proinflammatory cytokines. Pyrin-only protein 1 (POP1) is known to act as the regulator of inflammasome. It modulates the ASC-mediated inflammasome assembly by interacting with pyrin domain (PYD) of ASC. However, despite similar electrostatic surface potential, the interaction of POP1 with NLRP3PYD is obscured till date. Herein, to explore the possible PYD-PYD interactions between NLRP3PYD and POP1, a combined approach of protein-protein docking and molecular dynamics simulation was adapted. The current study revealed that POP1's type-Ia interface and type-Ib interface of NLRP3PYD might be crucial for 1:1 PYD-PYD interaction. In addition to type-I mode of interaction, we also observed type-II and type-III interaction modes in two different dynamically stable heterotrimeric complexes (POP1-NLRP3-NLRP3 and POP1-NLRP3-POP1). The inter-residual/atomic distance calculation exposed several critical residues that possibly govern the said interaction, which need further investigation. Overall, the findings of this study will shed new light on hitherto concealed molecular mechanisms underlying NLRP3-mediated inflammasome, which will have strong future therapeutic implications.
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Affiliation(s)
- Jitendra Maharana
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, -751003, Odisha, India
| | - Ashutosh Vats
- Animal Genomics Lab, Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, 751003, Haryana, India
| | - Santwana Gautam
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, -751003, Odisha, India
| | - Bibhu Prasad Nayak
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, -751003, Odisha, India
| | - Sushil Kumar
- Animal Genomics Lab, Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, 751003, Haryana, India
| | - Jasobanta Sendha
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, -751003, Odisha, India
| | - Sachinandan De
- Animal Genomics Lab, Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, 751003, Haryana, India
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Maharana J, Pradhan SK, De S. NOD1CARD Might Be Using Multiple Interfaces for RIP2-Mediated CARD-CARD Interaction: Insights from Molecular Dynamics Simulation. PLoS One 2017; 12:e0170232. [PMID: 28114344 PMCID: PMC5256935 DOI: 10.1371/journal.pone.0170232] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 01/02/2017] [Indexed: 12/20/2022] Open
Abstract
The nucleotide-binding and oligomerization domain (NOD)-containing protein 1 (NOD1) plays the pivotal role in host-pathogen interface of innate immunity and triggers immune signalling pathways for the maturation and release of pro-inflammatory cytokines. Upon the recognition of iE-DAP, NOD1 self-oligomerizes in an ATP-dependent fashion and interacts with adaptor molecule receptor-interacting protein 2 (RIP2) for the propagation of innate immune signalling and initiation of pro-inflammatory immune responses. This interaction (mediated by NOD1 and RIP2) helps in transmitting the downstream signals for the activation of NF-κB signalling pathway, and has been arbitrated by respective caspase-recruitment domains (CARDs). The so-called CARD-CARD interaction still remained contradictory due to inconsistent results. Henceforth, to understand the mode and the nature of the interaction, structural bioinformatics approaches were employed. MD simulation of modelled 1:1 heterodimeric complexes revealed that the type-Ia interface of NOD1CARD and the type-Ib interface of RIP2CARD might be the suitable interfaces for the said interaction. Moreover, we perceived three dynamically stable heterotrimeric complexes with an NOD1:RIP2 ratio of 1:2 (two numbers) and 2:1. Out of which, in the first trimeric complex, a type-I NOD1-RIP2 heterodimer was found interacting with an RIP2CARD using their type-IIa and IIIa interfaces. However, in the second and third heterotrimer, we observed type-I homodimers of NOD1 and RIP2 CARDs were interacting individually with RIP2CARD and NOD1CARD (in type-II and type-III interface), respectively. Overall, this study provides structural and dynamic insights into the NOD1-RIP2 oligomer formation, which will be crucial in understanding the molecular basis of NOD1-mediated CARD-CARD interaction in higher and lower eukaryotes.
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Affiliation(s)
- Jitendra Maharana
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, Odisha, India
- * E-mail: (JM); (SD)
| | - Sukanta Kumar Pradhan
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - Sachinandan De
- Animal Genomics Lab., Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, Haryana, India
- * E-mail: (JM); (SD)
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Raghuraman P, Jesu Jaya Sudan R, Lesitha Jeeva Kumari J, Sudandiradoss C. Casting the critical regions in nucleotide binding oligomerization domain 2 protein: a signature mediated structural dynamics approach. J Biomol Struct Dyn 2016; 35:3297-3315. [PMID: 27790943 DOI: 10.1080/07391102.2016.1254116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nucleotide binding oligomerization domain 2 (NOD2), a protein involved in the first line defence mechanism has a pivotal role in innate immunity. Impaired function of this protein is implicated in disorders such as Blau syndrome and Crohn's disease. Since an altered function is linked to protein's structure, we framed a systematic strategy to interpret the structure-function relationship of the protein. Initiated with mutation-based pattern prediction and identified a distant ortholog (DO) of NOD2 from which the intra-residue interaction network was elucidated. The network was used to identify hotspots that serve as critical points to maintain the stable architecture of the protein. Structural comparison of NOD2 domains with a DO revealed the minimal number of intra-protein interactions required by the protein to maintain the structural fold. In addition, the conventional molecular dynamics simulation emphasized the conformational transitions at hot spot residues between native NOD2 domains and its respective mutants (G116R, R42W and R54A) structures. The analysis of intra-protein interactions globally and the displacement of residues locally around the mutational site revealed loss of several critical bonds and residues vital for the protein's function. Conclusively we report, about 10 residues in leucine-rich repeat, 13 residues in NOD and 6 residues in CARD domain are required by the NOD2 to maintain its function. This protocol will help the researchers to achieve for more prospective studies to attest druggable site utility in discovering novel drug candidates.
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Affiliation(s)
- P Raghuraman
- a Department of Biotechnology , School of Bioscience and Technology, VIT University , Vellore 632301 , India
| | - R Jesu Jaya Sudan
- a Department of Biotechnology , School of Bioscience and Technology, VIT University , Vellore 632301 , India
| | - J Lesitha Jeeva Kumari
- a Department of Biotechnology , School of Bioscience and Technology, VIT University , Vellore 632301 , India
| | - C Sudandiradoss
- a Department of Biotechnology , School of Bioscience and Technology, VIT University , Vellore 632301 , India
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28
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Maharana J, Dehury B, Sahoo JR, Jena I, Bej A, Panda D, Sahoo BR, Patra MC, Pradhan SK. Structural and functional insights into CARDs of zebrafish (Danio rerio) NOD1 and NOD2, and their interaction with adaptor protein RIP2. MOLECULAR BIOSYSTEMS 2016; 11:2324-36. [PMID: 26079944 DOI: 10.1039/c5mb00212e] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nucleotide-binding and oligomerization domain-containing protein 1 (NOD1) and NOD2 are cytosolic pattern-recognition receptors (PRRs) composed of an N-terminal caspase activation and recruitment domain (CARD), a central NACHT domain and C-terminal leucine-rich repeats (LRRs). They play a vital role in innate immune signaling by activating the NF-κB pathway via recognition of peptidoglycans by LRRs, and ATP-dependent self-oligomerization of NACHT followed by downstream signaling. After oligomerization, CARD/s play a crucial role in activating downstream signaling via the adaptor molecule, RIP2. Due to the inadequacy of experimental 3D structures of CARD/s of NOD2 and RIP2, and results from differential experimental setups, the RIP2-mediated CARD-CARD interaction has remained as a contradictory statement. We employed a combinatorial approach involving protein modeling, docking, molecular dynamics simulation, and binding free energy calculation to illuminate the molecular mechanism that shows the possible involvement of either the acidic or basic patch of zebrafish NOD1/2-CARD/a and RIP2-CARD in CARD-CARD interaction. Herein, we have hypothesized 'type-I' mode of CARD-CARD interaction in NOD1 and NOD2, where NOD1/2-CARD/a involve their acidic surfaces to interact with RIP2. Asp37 and Glu51 (of NOD1) and Arg477, Arg521 and Arg529 (of RIP2) were identified to be crucial for NOD1-RIP2 interaction. However, in NOD2-RIP2, Asp32 (of NOD2) and Arg477 and Arg521 (of RIP2) were anticipated to be significant for downstream signaling. Furthermore, we found that strong electrostatic contacts and salt bridges are crucial for protein-protein interactions. Altogether, our study has provided novel insights into the RIP2-mediated CARD-CARD interaction in zebrafish NOD1 and NOD2, which will be helpful to understand the molecular basis of the NOD1/2 signaling mechanism.
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Affiliation(s)
- Jitendra Maharana
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar-751003, Odisha, India.
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29
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Brahma B, Patra MC, Mishra P, De BC, Kumar S, Maharana J, Vats A, Ahlawat S, Datta TK, De S. Computational studies on receptor-ligand interactions between novel buffalo (Bubalus bubalis) nucleotide-binding oligomerization domain-containing protein 2 (NOD2) variants and muramyl dipeptide (MDP). J Mol Graph Model 2016; 65:15-26. [PMID: 26897084 DOI: 10.1016/j.jmgm.2016.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 01/25/2016] [Accepted: 02/08/2016] [Indexed: 11/19/2022]
Abstract
Nucleotide binding and oligomerization domain 2 (NOD2), a member of intracellular NOD-like receptors (NLRs) family, recognizes the bacterial peptidoglycan, muramyl dipeptide (MDP) and initiates host immune response. The precise ligand recognition mechanism of NOD2 has remained elusive, although studies have suggested leucine rich repeat (LRR) region of NOD2 as the possible binding site of MDP. In this study, we identified multiple transcripts of NOD2 gene in buffalo (buNOD2) and at least five LRR variants (buNOD2-LRRW (wild type), buNOD2-LRRV1-V4) were found to be expressed in buffalo peripheral blood mononuclear cells. The newly identified buNOD2 transcripts were shorter in lengths as a result of exon-skipping and frame-shift mutations. Among the variants, buNOD2-LRRW, V1, and V3 were expressed more frequently in the animals studied. A comparative receptor-ligand interaction study through modeling of variants, docking, and molecular dynamics simulation revealed that the binding affinity of buNOD2-LRRW towards MDP was greater than that of the shorter variants. The absence of a LRR segment in the buNOD2 variants had probably affected their affinity toward MDP. Notwithstanding a high homology among the variants, the amino acid residues that interact with MDP were located on different LRR motifs. The binding free energy calculation revealed that the amino acids Arg850(LRR4) and Glu932(LRR7) of buNOD2-LRRW, Lys810(LRR3) of buNOD2-LRRV1, and Lys830(LRR3) of buNOD2-LRRV3 largely contributed towards MDP recognition. The knowledge of MDP recognition and binding modes on buNOD2 variants could be useful to understand the regulation of NOD-mediated immune response as well as to develop next generation anti-inflammatory compounds.
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Affiliation(s)
- Biswajit Brahma
- Animal Genomics Lab., Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Mahesh Chandra Patra
- Animal Genomics Lab., Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Purusottam Mishra
- Animal Genomics Lab., Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Bidhan Chandra De
- Animal Genomics Lab., Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Sushil Kumar
- Animal Genomics Lab., Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Jitendra Maharana
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar 751003, Odisha, India
| | - Ashutosh Vats
- Animal Genomics Lab., Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Sonika Ahlawat
- Animal Genomics Lab., Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Tirtha Kumar Datta
- Animal Genomics Lab., Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Sachinandan De
- Animal Genomics Lab., Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India.
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Structural models of zebrafish (Danio rerio) NOD1 and NOD2 NACHT domains suggest differential ATP binding orientations: insights from computational modeling, docking and molecular dynamics simulations. PLoS One 2015; 10:e0121415. [PMID: 25811192 PMCID: PMC4374677 DOI: 10.1371/journal.pone.0121415] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 02/01/2015] [Indexed: 11/25/2022] Open
Abstract
Nucleotide-binding oligomerization domain-containing protein 1 (NOD1) and NOD2 are cytosolic pattern recognition receptors playing pivotal roles in innate immune signaling. NOD1 and NOD2 recognize bacterial peptidoglycan derivatives iE-DAP and MDP, respectively and undergoes conformational alternation and ATP-dependent self-oligomerization of NACHT domain followed by downstream signaling. Lack of structural adequacy of NACHT domain confines our understanding about the NOD-mediated signaling mechanism. Here, we predicted the structure of NACHT domain of both NOD1 and NOD2 from model organism zebrafish (Danio rerio) using computational methods. Our study highlighted the differential ATP binding modes in NOD1 and NOD2. In NOD1, γ-phosphate of ATP faced toward the central nucleotide binding cavity like NLRC4, whereas in NOD2 the cavity was occupied by adenine moiety. The conserved ‘Lysine’ at Walker A formed hydrogen bonds (H-bonds) and Aspartic acid (Walker B) formed electrostatic interaction with ATP. At Sensor 1, Arg328 of NOD1 exhibited an H-bond with ATP, whereas corresponding Arg404 of NOD2 did not. ‘Proline’ of GxP motif (Pro386 of NOD1 and Pro464 of NOD2) interacted with adenine moiety and His511 at Sensor 2 of NOD1 interacted with γ-phosphate group of ATP. In contrast, His579 of NOD2 interacted with the adenine moiety having a relatively inverted orientation. Our findings are well supplemented with the molecular interaction of ATP with NLRC4, and consistent with mutagenesis data reported for human, which indicates evolutionary shared NOD signaling mechanism. Together, this study provides novel insights into ATP binding mechanism, and highlights the differential ATP binding modes in zebrafish NOD1 and NOD2.
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Xu J, Yuan H, Ran T, Zhang Y, Liu H, Lu S, Xiong X, Xu A, Jiang Y, Lu T, Chen Y. A selectivity study of sodium-dependent glucose cotransporter 2/sodium-dependent glucose cotransporter 1 inhibitors by molecular modeling. J Mol Recognit 2015; 28:467-79. [DOI: 10.1002/jmr.2464] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/15/2015] [Accepted: 01/15/2015] [Indexed: 01/01/2023]
Affiliation(s)
- Jinxing Xu
- Laboratory of Molecular Design and Drug Discovery, School of Science; China Pharmaceutical University; 639 Longmian Avenue Nanjing 211198 China
| | - Haoliang Yuan
- Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine; Jiangsu Institute of Nuclear Medicine; Wuxi 214063 China
| | - Ting Ran
- Laboratory of Molecular Design and Drug Discovery, School of Science; China Pharmaceutical University; 639 Longmian Avenue Nanjing 211198 China
| | - Yanmin Zhang
- Laboratory of Molecular Design and Drug Discovery, School of Science; China Pharmaceutical University; 639 Longmian Avenue Nanjing 211198 China
| | - Haichun Liu
- Laboratory of Molecular Design and Drug Discovery, School of Science; China Pharmaceutical University; 639 Longmian Avenue Nanjing 211198 China
| | - Shuai Lu
- Laboratory of Molecular Design and Drug Discovery, School of Science; China Pharmaceutical University; 639 Longmian Avenue Nanjing 211198 China
| | - Xiao Xiong
- Laboratory of Molecular Design and Drug Discovery, School of Science; China Pharmaceutical University; 639 Longmian Avenue Nanjing 211198 China
| | - Anyang Xu
- Laboratory of Molecular Design and Drug Discovery, School of Science; China Pharmaceutical University; 639 Longmian Avenue Nanjing 211198 China
| | - Yulei Jiang
- Laboratory of Molecular Design and Drug Discovery, School of Science; China Pharmaceutical University; 639 Longmian Avenue Nanjing 211198 China
| | - Tao Lu
- Laboratory of Molecular Design and Drug Discovery, School of Science; China Pharmaceutical University; 639 Longmian Avenue Nanjing 211198 China
- State Key Laboratory of Natural Medicines, School of Science; China Pharmaceutical University; 639 Longmian Avenue Nanjing 211198 China
| | - Yadong Chen
- Laboratory of Molecular Design and Drug Discovery, School of Science; China Pharmaceutical University; 639 Longmian Avenue Nanjing 211198 China
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32
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Understanding the distinguishable structural and functional features in zebrafish TLR3 and TLR22, and their binding modes with fish dsRNA viruses: an exploratory structural model analysis. Amino Acids 2014; 47:381-400. [DOI: 10.1007/s00726-014-1872-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 11/05/2014] [Indexed: 11/26/2022]
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Bej A, Sahoo BR, Swain B, Basu M, Jayasankar P, Samanta M. LRRsearch: An asynchronous server-based application for the prediction of leucine-rich repeat motifs and an integrative database of NOD-like receptors. Comput Biol Med 2014; 53:164-70. [PMID: 25150822 DOI: 10.1016/j.compbiomed.2014.07.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 07/18/2014] [Accepted: 07/22/2014] [Indexed: 01/01/2023]
Abstract
The leucine-rich repeat (LRR) motifs of the nucleotide-binding oligomerization domain like receptors (NLRs) play key roles in recognizing and binding various pathogen associated molecular patterns (PAMPs) resulting in the activation of downstream signaling and innate immunity. Therefore, identification of LRR motifs is very important to study ligand-receptor interaction. To date, available resources pose restrictions including both false negative and false positive prediction of LRR motifs from the primary protein sequence as their algorithms are relied either only on sequence based comparison or alignment techniques or are over biased for a particular LRR containing protein family. Therefore, to minimize the error (≤5%) and to identify a maximum number of LRR motifs in the wide range of proteins, we have developed "LRRsearch" web-server using position specific scoring matrix (PSSM) of 11 residue LRR-HCS (highly conserved segment) which are frequently observed motifs in the most divergent classes of LRR containing proteins. A data library of 421 proteins, distributed among five known NLR families has also been integrated with the "LRRsearch" for the rich user experience. The access to the "LRRsearch" program is freely available at http://www.lrrsearch.com/.
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Affiliation(s)
- Aritra Bej
- Fish Health Management Division, Central Institute of Freshwater Aquaculture (CIFA), Kausalyaganga, Bhubaneswar, Odisha 751002, India
| | - Bikash Ranjan Sahoo
- Fish Health Management Division, Central Institute of Freshwater Aquaculture (CIFA), Kausalyaganga, Bhubaneswar, Odisha 751002, India
| | - Banikalyan Swain
- Fish Health Management Division, Central Institute of Freshwater Aquaculture (CIFA), Kausalyaganga, Bhubaneswar, Odisha 751002, India
| | - Madhubanti Basu
- Fish Health Management Division, Central Institute of Freshwater Aquaculture (CIFA), Kausalyaganga, Bhubaneswar, Odisha 751002, India
| | - Pallipuram Jayasankar
- Central Institute of Freshwater Aquaculture (CIFA), Kausalyaganga, Bhubaneswar, Odisha 751002, India
| | - Mrinal Samanta
- Fish Health Management Division, Central Institute of Freshwater Aquaculture (CIFA), Kausalyaganga, Bhubaneswar, Odisha 751002, India.
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Maharana J, Sahoo BR, Bej A, Patra MC, Dehury B, Bhoi GK, Lenka SK, Sahoo JR, Rout AK, Behera BK. Structural and functional investigation of zebrafish (Danio rerio) NOD1 leucine rich repeat domain and its interaction with iE-DAP. ACTA ACUST UNITED AC 2014; 10:2942-53. [DOI: 10.1039/c4mb00212a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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35
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Sahoo BR, Dubey PK, Goyal S, Bhoi GK, Lenka SK, Maharana J, Pradhan SK, Kataria RS. Exploration of the binding modes of buffalo PGRP1 receptor complexed with meso-diaminopimelic acid and lysine-type peptidoglycans by molecular dynamics simulation and free energy calculation. Chem Biol Interact 2014; 220:255-68. [PMID: 25014416 DOI: 10.1016/j.cbi.2014.06.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Revised: 05/28/2014] [Accepted: 06/30/2014] [Indexed: 12/20/2022]
Abstract
The peptidoglycan recognition proteins (PGRPs) are the key components of innate-immunity, and are highly specific for the recognition of bacterial peptidoglycans (PGN). Among different mammalian PGRPs, the PGRP1 binds to murein PGN of Gram-positive bacteria (lysine-type) and also have bactericidal activity towards Gram-negative bacteria (diaminopimelic acid or Dap-type). Buffaloes are the major sources of milk and meat in Asian sub-continents and are highly exposed to bacterial infections. The PGRP activates the innate-immune signaling, but their studies has been confined to limited species due to lack of structural and functional information. So, to understand the structural constituents, 3D model of buffalo PGRP1 (bfPGRP1) was constructed and conformational and dynamics properties of bfPGRP1 was studied. The bfPGRP1 model highly resembled human and camel PGRP structure, and shared a highly flexible N-terminus and centrally placed L-shaped cleft. Docking simulation of muramyl-tripeptide, tetrapeptide, pentapeptide-Dap-(MTP-Dap, MTrP-Dap and MPP-Dap) and lysine-type (MTP-Lys, MTrP-Lys and MPP-Lys) in AutoDock 4.2 and ArgusLab 4.0.1 anticipated β1, α2, α4, β4, and loops connecting β1-α2, α2-β2, β3-β4 and α4-α5 as the key interacting domains. The bfPGRP1-ligand complex molecular dynamics simulation followed by free binding energy (BE) computation conceded BE values of -18.30, -35.53, -41.80, -25.03, -24.62 and -22.30 kJ mol(-1) for MTP-Dap, MTrP-Dap, MPP-Dap, MTP-Lys, MTrP-Lys and MPP-Lys, respectively. The groove-surface and key binding residues involved in PGN-Dap and Lys-type interaction intended by the molecular docking, and were also accompanied by significant BE values directed their importance in pharmacogenomics, and warrants further in vivo studies for drug targeting and immune signaling pathways exploration.
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Affiliation(s)
- Bikash Ranjan Sahoo
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar 751001, India; Laboratory of Molecular Biophysics, Institute for Protein Research, Osaka University, Osaka Prefecture 5650871, Japan.
| | - Praveen Kumar Dubey
- Immunology Frontier Research Centre, Osaka University, Osaka Prefecture 5650871, Japan.
| | - Shubham Goyal
- RIKEN Center for Life Science Technologies, Yokohama 2300045, Japan
| | - Gopal Krushna Bhoi
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar 751001, India
| | - Santosh Kumar Lenka
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar 751001, India
| | - Jitendra Maharana
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar 751001, India; Biotechnology Laboratory, Central Inland Fisheries Research Institute, Kolkata, West Bengal 700120, India
| | - Sukanta Kumar Pradhan
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar 751001, India
| | - Ranjit Singh Kataria
- Division of Animal Biotechnology, National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
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