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Maharana J, Hwang SK, Singha DL, Panda D, Singh S, Okita TW, Modi MK. Exploring the structural assembly of rice ADP-glucose pyrophosphorylase subunits using MD simulation. J Mol Graph Model 2024; 129:108761. [PMID: 38552302 DOI: 10.1016/j.jmgm.2024.108761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/15/2024]
Abstract
ADP-glucose pyrophosphorylase plays a pivotal role as an allosteric enzyme, essential for starch biosynthesis in plants. The higher plant AGPase comparises of a pair of large and a pair of small subunits to form a heterotetrameric complex. Growing evidence indicates that each subunit plays a distinct role in regulating the underlying mechanism of starch biosynthesis. In the rice genome, there are four large subunit genes (OsL1-L4) and three small subunit genes (OsS1, OsS2a, and OsS2b). While the structural assembly of cytosolic rice AGPase subunits (OsL2:OsS2b) has been elucidated, there is currently no such documented research available for plastidial rice AGPases (OsL1:OsS1). In this study, we employed protein modeling and MD simulation approaches to gain insights into the structural association of plastidial rice AGPase subunits. Our results demonstrate that the heterotetrameric association of OsL1:OsS1 is very similar to that of cytosolic OsL2:OsS2b and potato AGPase heterotetramer (StLS:StSS). Moreover, the yeast-two-hybrid results on OsL1:OsS1, which resemble StLS:StSS, suggest a differential protein assembly for OsL2:OsS2b. Thus, the regulatory and catalytic mechanisms for plastidial AGPases (OsL1:OsS1) could be different in rice culm and developing endosperm compared to those of OsL2:OsS2b, which are predominantly found in rice endosperm.
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Affiliation(s)
- Jitendra Maharana
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India.
| | - Seon-Kap Hwang
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Dhanawantari L Singha
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India; Department of Botany, Rabindranath Tagore University, Hojai, Assam, 782435, India
| | - Debashis Panda
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Salvinder Singh
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Thomas W Okita
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Mahendra Kumar Modi
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India.
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Mohanty S, Mishra SS, Kuldeep, Maharana J, Subuddhi U. Insight into the Effect of Submicellar Concentrations of Sodium Deoxycholate on the Structure, Stability, and Activity of Bovine and Human Serum Albumin: An Interesting Comparison between Single and Double Tryptophan Proteins. Langmuir 2024; 40:5228-5244. [PMID: 38413419 DOI: 10.1021/acs.langmuir.3c03541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
The progressive escalation in the applications of bile salts in diverse fields has triggered research on their interaction with various biological macromolecules, especially with proteins. A proper understanding of the interaction process of bile salts, particularly in the lower concentrations range, with the serum albumin seems important since the normal serum concentration of bile salts is approximately in the micromolar range. The current study deals with a comprehensive and comparative analysis of the interaction of submicellar concentrations of sodium deoxycholate (NaDC) with two homologous transport proteins: bovine serum albumin (BSA) and human serum albumin (HSA). HSA and BSA with one and two tryptophans, respectively, provide the opportunity for an interesting comparison of tryptophan fluorescence behavior on interaction with NaDC. The study suggests a sequential interaction of NaDC in three discrete stages with the two proteins. A detailed study using warfarin and ibuprofen as site markers provides information about the sites of interaction, which is further confirmed by inclusive molecular dynamics simulation analysis. Moreover, the comparison of the thermodynamics and stability of the NaDC-serum albumin complexes confirms the stronger interaction of NaDC with BSA as compared to that with HSA. The differential interaction between the bile salt and the two serum albumins is further established from the difference in the extent of decrease in the esterase-like activity assay of the proteins in the presence of NaDC. Therefore, the present study provides important insight into the effect of submicellar concentrations of NaDC on the structure, stability, and activity of the two homologous serum albumins and thus can contribute not only to the general understanding of the complex nature of serum albumin-bile salt interactions but also to the design of more effective pharmaceutical formulations in the field of drug delivery and biomedical research.
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Affiliation(s)
- Subhrajit Mohanty
- Department of Chemistry, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Smruti Snigdha Mishra
- Department of Chemistry, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Kuldeep
- Department of Chemistry, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Jitendra Maharana
- Distributed Information Centre, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, Assam, India
| | - Usharani Subuddhi
- Department of Chemistry, National Institute of Technology, Rourkela 769008, Odisha, India
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Saikia B, S R, Debbarma J, Maharana J, Sastry GN, Chikkaputtaiah C. CRISPR/Cas9-based genome editing and functional analysis of SlHyPRP1 and SlDEA1 genes of Solanum lycopersicum L. in imparting genetic tolerance to multiple stress factors. Front Plant Sci 2024; 15:1304381. [PMID: 38371406 PMCID: PMC10869523 DOI: 10.3389/fpls.2024.1304381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/15/2024] [Indexed: 02/20/2024]
Abstract
CRISPR/Cas is a breakthrough genome editing system because of its precision, target specificity, and efficiency. As a speed breeding system, it is more robust than the conventional breeding and biotechnological approaches for qualitative and quantitative trait improvement. Tomato (Solanum lycopersicum L.) is an economically important crop, but its yield and productivity have been severely impacted due to different abiotic and biotic stresses. The recently identified SlHyPRP1 and SlDEA1 are two potential negative regulatory genes in response to different abiotic (drought and salinity) and biotic stress (bacterial leaf spot and bacterial wilt) conditions in S. lycopersicum L. The present study aimed to evaluate the drought, salinity, bacterial leaf spot, and bacterial wilt tolerance response in S. lycopersicum L. crop through CRISPR/Cas9 genome editing of SlHyPRP1 and SlDEA1 and their functional analysis. The transient single- and dual-gene SlHyPRP1 and SlDEA1 CRISPR-edited plants were phenotypically better responsive to multiple stress factors taken under the study. The CRISPR-edited SlHyPRP1 and SlDEA1 plants showed a higher level of chlorophyll and proline content compared to wild-type (WT) plants under abiotic stress conditions. Reactive oxygen species accumulation and the cell death count per total area of leaves and roots under biotic stress were less in CRISPR-edited SlHyPRP1 and SlDEA1 plants compared to WT plants. The study reveals that the combined loss-of-function of SlHyPRP1 along with SlDEA1 is essential for imparting significant multi-stress tolerance (drought, salinity, bacterial leaf spot, and bacterial wilt) in S. lycopersicum L. The main feature of the study is the detailed genetic characterization of SlDEA1, a poorly studied 8CM family gene in multi-stress tolerance, through the CRISPR/Cas9 gene editing system. The study revealed the key negative regulatory role of SlDEA1 that function together as an anchor gene with SlHyPRP1 in imparting multi-stress tolerance in S. lycopersicum L. It was interesting that the present study also showed that transient CRISPR/Cas9 editing events of SlHyPRP1 and SlDEA1 genes were successfully replicated in stably generated parent-genome-edited line (GEd0) and genome-edited first-generation lines (GEd1) of S. lycopersicum L. With these upshots, the study's key findings demonstrate outstanding value in developing sustainable multi-stress tolerance in S. lycopersicum L. and other crops to cope with climate change.
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Affiliation(s)
- Banashree Saikia
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Remya S
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
| | - Johni Debbarma
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Jitendra Maharana
- Distributed Information Centre (DIC), Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - G. Narahari Sastry
- Advanced Computational and Data Science Division, CSIR-NEIST, Jorhat, Assam, India
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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4
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Debbarma J, Saikia B, Singha DL, Das D, Keot AK, Maharana J, Velmurugan N, Arunkumar KP, Reddy PS, Chikkaputtaiah C. CRISPR/Cas9-Mediated Mutation in XSP10 and SlSAMT Genes Impart Genetic Tolerance to Fusarium Wilt Disease of Tomato ( Solanum lycopersicum L.). Genes (Basel) 2023; 14:488. [PMID: 36833415 PMCID: PMC9956927 DOI: 10.3390/genes14020488] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/29/2023] [Accepted: 02/11/2023] [Indexed: 02/17/2023] Open
Abstract
Fusarium wilt is a major devastating fungal disease of tomato (Solanum lycopersicum L.) caused by Fusarium oxysporum f. sp. lycopersici (Fol) which reduces the yield and production. Xylem sap protein 10 (XSP10) and Salicylic acid methyl transferase (SlSAMT) are two putative negative regulatory genes associated with Fusarium wilt of tomato. Fusarium wilt tolerance in tomato can be developed by targeting these susceptible (S) genes. Due to its efficiency, high target specificity, and versatility, CRISPR/Cas9 has emerged as one of the most promising techniques for knocking out disease susceptibility genes in a variety of model and agricultural plants to increase tolerance/resistance to various plant diseases in recent years. Though alternative methods, like RNAi, have been attempted to knock down these two S genes in order to confer resistance in tomato against Fusarium wilt, there has been no report of employing the CRISPR/Cas9 system for this specific intent. In this study, we provide a comprehensive downstream analysis of the two S genes via CRISPR/Cas9-mediated editing of single (XSP10 and SlSAMT individually) and dual-gene (XSP10 and SlSAMT simultaneously). Prior to directly advancing on to the generation of stable lines, the editing efficacy of the sgRNA-Cas9 complex was first validated using single cell (protoplast) transformation. In the transient leaf disc assay, the dual-gene editing showed strong phenotypic tolerance to Fusarium wilt disease with INDEL mutations than single-gene editing. In stable genetic transformation of tomato at the GE1 generation, dual-gene CRISPR transformants of XSP10 and SlSAMT primarily exhibited INDEL mutations than single-gene-edited lines. The dual-gene CRISPR-edited lines (CRELs) of XSP10 and SlSAMT at GE1 generation conferred a strong phenotypic tolerance to Fusarium wilt disease compared to single-gene-edited lines. Taken together, the reverse genetic studies in transient and stable lines of tomato revealed that, XSP10 and SlSAMT function together as negative regulators in conferring genetic tolerance to Fusarium wilt disease.
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Affiliation(s)
- Johni Debbarma
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Banashree Saikia
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Dhanawantari L. Singha
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, Assam, India
| | - Debajit Das
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, Assam, India
| | - Ajay Kumar Keot
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Jitendra Maharana
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, Assam, India
| | - Natarajan Velmurugan
- Branch Laboratory-Itanagar, Biological Sciences Division, CSIR-NEIST, Naharlagun 791110, Arunachal Pradesh, India
| | - Kallare P. Arunkumar
- Central Muga Eri Research and Training Institute (CMER&TI), Lahdoigarh, Jorhat 785700, Assam, India
| | - Palakolanu Sudhakar Reddy
- International Crop Research Institute for the Semi Arid Tropics (ICRISAT), Hyderabad 502324, Telangana, India
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
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Kode J, Maharana J, Dar AA, Mukherjee S, Gadewal N, Sigalapalli DK, Kumar S, Panda D, Ghosh S, Keshry SS, Mamidi P, Chattopadhyay S, Pradhan T, Kailaje V, Inamdar S, Gujjarwar V. 6-Shogaol Exhibits Anti-viral and Anti-inflammatory Activity in COVID-19-Associated Inflammation by Regulating NLRP3 Inflammasomes. ACS Omega 2023; 8:2618-2628. [PMID: 36687062 PMCID: PMC9850479 DOI: 10.1021/acsomega.2c07138] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Recent global health concern motivated the exploration of natural medicinal plant resources as an alternative target for treating COVID-19 infection and associated inflammation. In the current study, a phytochemical, 6-shogaol [1-(4-hydroxy-3-methoxyphenyl)dec-4-en-3-one; 6-SHO] was investigated as a potential anti-inflammatory and anti-COVID-19 agent. In virus release assay, 6-SHO efficiently (94.5%) inhibited SARS-CoV2 replication. When tested in the inflammasome activation model, 6-SHO displayed mechanistic action by regulating the expression of the inflammasome pathway molecules. In comparison to the existing drugs, remdesivir and hydroxy-chloroquine, 6-SHO was not only found to be as effective as the standard anti-viral drugs but also much superior and safe in terms of predicted physicochemical properties and clinical toxicity. Comparative molecular dynamics simulation demonstrated a stable interaction of 6-SHO with NLRP3 (the key inflammasome regulator) in the explicit water environment. Overall, this study provides important cues for further development of 6-SHO as potential anti-inflammatory and anti-viral therapeutic agents.
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Affiliation(s)
- Jyoti Kode
- Kode
Lab, Tumor Immunology & Immunotherapy Group, Advanced Centre for
Treatment, Research & Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India
- Homi
Bhabha National Institute (HBNI), Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Jitendra Maharana
- Department
of Bioinformatics, Odisha University of
Agriculture and Technology, Bhubaneswar, Odisha 751001, India
| | - Asif Amin Dar
- Division
of Protective Immunity, The Children’s
Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States
| | - Shayanti Mukherjee
- The
Ritchie Centre, Hudson Institute of Medical
Research, Clayton 3168, Victoria, Australia
- Department
of Obstetrics and Gynaecology, Monash Medical Centre, Monash University, Clayton 3168, Victoria, Australia
| | - Nikhil Gadewal
- Bioinformatics
Centre, Advanced Centre for Treatment, Research & Education in
Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India
| | - Dilep Kumar Sigalapalli
- Department
of Pharmaceutical Chemistry, Vignan Pharmacy College, Jawaharlal Nehru Technological University, Vadlamudi 522213, Andhra Pradesh, India
| | - Satyanshu Kumar
- ICAR-Directorate
of Medicinal and Aromatic Plants Research, Boriavi 387310, Anand, Gujarat, India
| | - Debashis Panda
- DBT-APSCS&T,
Centre of Excellence for Bioresources and Sustainable
Development, Kimin 791121, Arunachal Pradesh, India
| | - Soumyajit Ghosh
- Infectious Disease Biology, Institute of
Life Sciences, Nalco Square, Bhubaneswar 751023, Odisha, India
- Regional Centre for Biotechnology, Faridabad 121001, India
| | - Supriya Suman Keshry
- Infectious Disease Biology, Institute of
Life Sciences, Nalco Square, Bhubaneswar 751023, Odisha, India
- School of Biotechnology, Kalinga
Institute
of Industrial Technology (KIIT), Deemed-to-be-University, Bhubaneswar 751024, India
| | - Prabhudutta Mamidi
- Infectious Disease Biology, Institute of
Life Sciences, Nalco Square, Bhubaneswar 751023, Odisha, India
| | - Soma Chattopadhyay
- Infectious Disease Biology, Institute of
Life Sciences, Nalco Square, Bhubaneswar 751023, Odisha, India
| | - Trupti Pradhan
- Kode
Lab, Tumor Immunology & Immunotherapy Group, Advanced Centre for
Treatment, Research & Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India
| | - Vaishali Kailaje
- Digital Imaging Facility, Advanced Centre for Treatment,
Research
& Education in Cancer, Tata Memorial
Centre, Kharghar, Navi Mumbai 410210, India
| | - Sunil Inamdar
- Department of Rasashastra and B.K., Late
Kedari Redekar Ayurvedic Mahavidyalaya, P-2, MIDC Area, Shendri Mal, Gadhinglaj, Kolhapur, Maharashtra 416502, India
- Sukhayu
Ayurved and Panchkarma Centre, Ayodhya Park, Kawala Naka, Kolhapur 416002, India
| | - Vidula Gujjarwar
- Ch.
Brahm Prakash Ayurved Charak Sansthan, Khera Dabar, New Delhi 110073, India
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Kode J, Maharana J, Kumar KN, Pradhan T, Ingle A, Barkume M, Patkar M, Thampi N, Patil A, Vaibhaw A, Kovvuri J, Kamal A. Abstract 4222: Phenstatin based indole linked chalcone compound 9a exhibits anti-oral cancer activity through regulating NLRP3 inflammasome innate immune pathway. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-4222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Oral cancer is the sixth most prevalent malignancy in the world and oral squamous cell carcinoma accounts for majority of all oral malignancies. Upregulated NLRP3 inflammasome innate immune pathway is of importance to tumor development. Current efforts are being focused on identifying small molecules that exhibit anti-cancer activity as inflammasome pathway inhibitors. Our previously published work on phenstatin based indole linked chalcone scaffold 9a with 1-methyl, 2- and 3-methoxy substituents in the aromatic ring revealed 9a as an anti-oral cancer compound. 9a was found to act through inhibiting tubulin polymerization at protein level, using in vitro models oral cancer cell line/spheroid cells and in vivo animal oral cancer xenograft model. 9a had also shown significant reduction in radiolabeled-glucose uptake in xenograft mice model. Current study was undertaken to evaluate if small molecule inhibitor 9a acts through regulating the NLRP3 pathway. Using computation approach, we predicted the binding of 9a with NLRP3NACHT domain, which revealed stable interaction as similar to that exhibited by NLRP3 inhibitors MCC950 and ADP. Further, we checked immune mechanistic activity of 9a on NLRP3 pathway intermediates in oral cancer cells. AW13516 cell line which was human tongue squamous tumor-derived cell line; indigenously developed at our department previously, was activated for NLRP3 inflammasome pathway using LPS and activator Nigericin in presence of 9a. MCC950 treated cells and only LPS or LPS/Nigericin treated cells served as controls. NLRP3, caspase-1 and mitochondrial protein expression was analyzed in these cells by immunofluorescence (IF) and found to be increased upon LPS/NIG activation and reduced significantly upon MCC950 and 9a treatment. Activation led to puncta formation which was found diffused after MCC950/9a treatment. Similarly treated AW13516 cells were also validated using western blotting experiments. Expression of 118kDa NLRP3 protein was found increased upon inflammasome activation that was significantly reduced in 9a treated cells and reduction was dose dependent. 9a had shown significant reduction in oral cancer xenograft of AW13516 in NOD-SCID mice model. We tested formalin-fixed paraffin sections of these tumors by immunohistochemistry. Tumor areas were assessed for expression of NLRP3 pathway markers and there was significant reduction in NLRP3, Caspase-1, GSDMD and IL-1β in 9a treated tumors compared to control tumors. This reduction was at par with that shown by Adriamycin. Summarizingly, 9a has been found to be regulating inflammatory immune mechanisms and can be developed further as immunomodulatory anti-cancer agent. Since macrophages are major resource immune cells of NLRP3, further studies are underway to test 9a on macrophages from nlrp3-/- and caspase-/- mice in comparison with normal mice.
Citation Format: Jyoti Kode, Jitendra Maharana, K. Nirmal Kumar, Trupti Pradhan, Arvind Ingle, Madan Barkume, Meena Patkar, Namitha Thampi, Ankita Patil, Anand Vaibhaw, Jeshma Kovvuri, Ahmed Kamal. Phenstatin based indole linked chalcone compound 9a exhibits anti-oral cancer activity through regulating NLRP3 inflammasome innate immune pathway [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4222.
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Affiliation(s)
- Jyoti Kode
- 1Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India
| | - Jitendra Maharana
- 2Odisha University of Agriculture and Technology, Bhubaneswar-751003, India
| | - K. Nirmal Kumar
- 1Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India
| | - Trupti Pradhan
- 1Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India
| | - Arvind Ingle
- 1Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India
| | - Madan Barkume
- 1Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India
| | - Meena Patkar
- 1Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India
| | - Namitha Thampi
- 1Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India
| | - Ankita Patil
- 1Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India
| | - Anand Vaibhaw
- 1Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India
| | - Jeshma Kovvuri
- 3Vardhaman College of Engineering (Autonomous), Shamshabad, Hyderabad, Telangana, India
| | - Ahmed Kamal
- 4Birla Institute of Technology & Science, Pilani, Hyderabad Campus, Telangana, India
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Marwein R, Singh S, Maharana J, Kumar S, Arunkumar KP, Velmurugan N, Chikkaputtaiah C. Transcriptome-wide analysis of North-East Indian rice cultivars in response to Bipolaris oryzae infection revealed the importance of early response to the pathogen in suppressing the disease progression. Gene 2022; 809:146049. [PMID: 34743920 DOI: 10.1016/j.gene.2021.146049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 11/18/2022]
Abstract
Brown spot disease (BSD) of rice (Oryza sativa L.) caused by Bipolaris oryzae is one of the major and neglected fungal diseases worldwide affecting rice production. Despite its significance, very limited knowledge on genetics and genomics of rice in response to B. oryzae available. Our study firstly identified moderately resistant (Gitesh) and susceptible (Shahsarang) North-East Indian rice cultivars in response to a native Bipolaris oryzae isolate BO1. Secondly, a systematic comparative RNA seq was performed for both cultivars at four different time points viz. 12, 24, 48, and 72 hours post infestation (hpi). Differential gene expression analysis revealed the importance of early response to the pathogen in suppressing disease progression. The pathogen negatively regulates the expression of photosynthetic-related genes at early stages in both cultivars. Of the cell wall modification enzymes, cellulose synthase and callose synthase are important for signal transduction and defense. Cell wall receptors OsLYP6, OsWAK80 might positively and OsWAK25 negatively regulate disease resistance. Jasmonic acid and/or abscisic acid signaling pathways are presumably involved in disease resistance, whereas salicylic acid pathway, and an ethylene response gene OsEBP-89 in promoting disease. Surprisingly, pathogenesis-related proteins showed no antimicrobial impact on the pathogen. Additionally, transcription factors OsWRKY62 and OsWRKY45 together might negatively regulate resistance to the pathogen. Taken together, our study has identified and provide key regulatory genes involved in response to B. oryzae which serve as potential resources for functional genetic analysis to develop genetic tolerance to BSD of rice.
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Affiliation(s)
- Riwandahun Marwein
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, Assam, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Sanjay Singh
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, Assam, India
| | - Jitendra Maharana
- Distributed Information Centre (DIC), Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India; Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Sanjeev Kumar
- Department of Bioscience and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Kallare P Arunkumar
- Central Muga Eri Research and Training Institute (CMER&TI), Lahdoigarh, Jorhat 785700, Assam, India
| | - Natarajan Velmurugan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India; Biological Sciences Division, Branch Laboratory-Itanagar, CSIR-NEIST, Naharlagun 791110, Arunachal Pradesh, India
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, Assam, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India.
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8
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Singha DL, Das D, Sarki YN, Chowdhury N, Sharma M, Maharana J, Chikkaputtaiah C. Harnessing tissue-specific genome editing in plants through CRISPR/Cas system: current state and future prospects. Planta 2021; 255:28. [PMID: 34962611 DOI: 10.1007/s00425-021-03811-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
In a nutshell, tissue-specific CRISPR/Cas genome editing is the most promising approach for crop improvement which can bypass the hurdle associated with constitutive GE such as off target and pleotropic effects for targeted crop improvement. CRISPR/Cas is a powerful genome-editing tool with a wide range of applications for the genetic improvement of crops. However, the constitutive genome editing of vital genes is often associated with pleiotropic effects on other genes, needless metabolic burden, or interference in the cellular machinery. Tissue-specific genome editing (TSGE), on the other hand, enables researchers to study those genes in specific cells, tissues, or organs without disturbing neighboring groups of cells. Until recently, there was only limited proof of the TSGE concept, where the CRISPR-TSKO tool was successfully used in Arabidopsis, tomato, and cotton, laying a solid foundation for crop improvement. In this review, we have laid out valuable insights into the concept and application of TSGE on relatively unexplored areas such as grain trait improvement under favorable or unfavorable conditions. We also enlisted some of the prominent tissue-specific promoters and described the procedure of their isolation with several TSGE promoter expression systems in detail. Moreover, we highlighted potential negative regulatory genes that could be targeted through TSGE using tissue-specific promoters. In a nutshell, tissue-specific CRISPR/Cas genome editing is the most promising approach for crop improvement which can bypass the hurdle associated with constitutive GE such as off target and pleotropic effects for targeted crop improvement.
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Affiliation(s)
- Dhanawantari L Singha
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India.
| | - Debajit Das
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Yogita N Sarki
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Naimisha Chowdhury
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Monica Sharma
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Jitendra Maharana
- Distributed Information Centre (DIC), Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Debbarma J, Saikia B, Singha DL, Maharana J, Velmuruagan N, Dekaboruah H, Arunkumar KP, Chikkaputtaiah C. XSP10 and SlSAMT, Fusarium wilt disease responsive genes of tomato ( Solanum lycopersicum L.) express tissue specifically and interact with each other at cytoplasm in vivo. Physiol Mol Biol Plants 2021; 27:1559-1575. [PMID: 34366597 PMCID: PMC8295444 DOI: 10.1007/s12298-021-01025-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
Fusarium wilt caused by Fusarium oxysporum f. sp. lycopersici (Fol) is a major fungal disease of tomato (Solanum lycopersicum L.). Xylem sap protein 10 (XSP10) and Salicylic acid methyl transferase (SlSAMT) have been identified as putative negative regulatory genes associated with Fusarium wilt of tomato. Despite their importance as potential genes for developing Fusarium wilt disease tolerance, very little knowledge is available about their expression, cell biology, and functional genomics. Semi-quantitative and quantitative real-time PCR expression analysis of XSP10 and SlSAMT, in this study, revealed higher expression in root and flower tissue respectively in different tomato cultivars viz. Micro-Tom (MT), Arka Vikas (AV), and Arka Abhed (AA). Therefore, the highly up-regulated expression of XSP10 and SlSAMT in biotic stress susceptible tomato cultivar (AV) than a multiple disease resistant cultivar (AA) suggested the disease susceptibility nature of these genes for Fusarium wilt. Sub-cellular localization analysis through the expression of gateway cloning constructs in tomato protoplasts and seedlings showed the predominant localization of XSP10 in the nucleus and SlSAMT at the cytoplasm. A strong in vivo protein-protein interaction of XSP10 with SlSAMT at cytoplasm from bi-molecular fluorescent complementation study suggested that these two proteins function together in regulating responses to Fusarium wilt tolerance in tomato. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01025-y.
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Affiliation(s)
- Johni Debbarma
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, 785006 Assam India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002 Uttar Pradesh India
| | - Banashree Saikia
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, 785006 Assam India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002 Uttar Pradesh India
| | - Dhanawantari L. Singha
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, 785006 Assam India
| | - Jitendra Maharana
- Distributed Information Centre (DIC), Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam India
- Present Address: Institute of Biological Chemistry, Academia Sinica, Taipei, 11529 Taiwan
| | - Natarajan Velmuruagan
- Biological Sciences Division, Branch Laboratory-Itanagar, CSIR-NEIST, Naharlagun, 791110 Arunachal Pradesh India
| | - Hariprasanna Dekaboruah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, 785006 Assam India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002 Uttar Pradesh India
| | - Kallare P. Arunkumar
- Central Muga Eri Research and Training Institute (CMER&TI), Lahdoigarh, Jorhat, 785006 Assam India
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, 785006 Assam India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002 Uttar Pradesh India
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, 785006 Assam India
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11
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Saikia B, Debbarma J, Maharana J, Singha DL, Velmuruagan N, Dekaboruah H, Arunkumar KP, Chikkaputtaiah C. SlHyPRP1 and DEA1, the multiple stress responsive eight-cysteine motif family genes of tomato ( Solanum lycopersicum L.) are expressed tissue specifically, localize and interact at cytoplasm and plasma membrane in vivo. Physiol Mol Biol Plants 2020; 26:2553-2568. [PMID: 33424164 PMCID: PMC7772121 DOI: 10.1007/s12298-020-00913-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/22/2020] [Accepted: 11/17/2020] [Indexed: 05/09/2023]
Abstract
Owing to rapid global climate change, the occurrence of multiple abiotic stresses is known to influence the outburst of biotic stress factors which affects crop productivity. Therefore, it is essential to understand the molecular and cell biology of key genes associated with multiple stress responses in crop plants. SlHyPRP1 and DEA1, the members of eight-cysteine motif (8CM) family genes have been recently identified as putative regulators of multiple stress responses in tomato (Solanum lycopersicum L.). In order to gain deeper insight into cell and molecular biology of SlHyPRP1 and DEA1, we performed their expression analysis in three tomato cultivars and in vivo cell biological analysis. The semi-quantitative PCR and qRT-PCR results showed the higher expression of SlHyPRP1 and DEA1 in leaf, stem, flower and root tissues as compared to fruit and seed tissues in all three cultivars. The expression levels of SlHyPRP1 and DEA1 were found to be relatively higher in a wilt susceptible tomato cultivar (Arka Vikas) than a multiple disease resistant cultivar (Arka Abhed). In vivo cell biological analysis through Gateway cloning and Bi-FC assay revealed the predominant sub-cellular localization and strong protein-protein interaction of SlHyPRP1 and DEA1 at the cytoplasm and plasma membrane. Moreover, SlHyPRP1 showed in vivo interaction with stress responsive proteins WRKY3 and MST1. Our findings suggest that SlHyPRP1 with DEA1 are co-expressed with tissue specificity and might function together by association with WRKY3 and MST1 in plasma membrane for regulating multiple stress responses in the tomato plant.
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Affiliation(s)
- Banashree Saikia
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785 006 India
- Academy of Scientific and Innovative Research (AcSIR), Uttar Pradesh, Ghaziabad, 201 002 India
| | - Johni Debbarma
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785 006 India
- Academy of Scientific and Innovative Research (AcSIR), Uttar Pradesh, Ghaziabad, 201 002 India
| | - Jitendra Maharana
- Distributed Information Centre (DIC), Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam India
- Present Address: Institute of Biological Chemistry, Academia Sinica, Taipei, 11529 Taiwan
| | - Dhanawantari L. Singha
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785 006 India
| | - Natarajan Velmuruagan
- Biological Sciences Division, Branch Laboratory-Itanagar, CSIR-NEIST, Arunachal Pradesh, Naharlagun, 791 110 India
| | - Hariprasanna Dekaboruah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785 006 India
- Academy of Scientific and Innovative Research (AcSIR), Uttar Pradesh, Ghaziabad, 201 002 India
| | - Kallare P. Arunkumar
- Central Muga Eri Research and Training Institute (CMER&TI), Lahdoigarh, Jorhat, Assam, 785 700 India
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785 006 India
- Academy of Scientific and Innovative Research (AcSIR), Uttar Pradesh, Ghaziabad, 201 002 India
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12
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Das S, Mohanty S, Maharana J, Jena SR, Nayak J, Subuddhi U. Microwave-assisted β-cyclodextrin/chrysin inclusion complexation: An economical and green strategy for enhanced hemocompatibility and chemosensitivity in vitro. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113257] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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14
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Singha DL, Maharana J, Panda D, Dehury B, Modi MK, Singh S. Understanding the thermal response of rice eukaryotic transcription factor eIF4A1 towards dynamic temperature stress: insights from expression profiling and molecular dynamics simulation. J Biomol Struct Dyn 2020; 39:2575-2584. [PMID: 32367760 DOI: 10.1080/07391102.2020.1751295] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Eukaryotic translation initiation factors (eIFs) are the group of regulatory proteins that are involved in the initiation of translation events. Among them, eIF4A1, a member of the DEAD-box RNA helicase family, participates in a wide spectrum of activities which include, RNA splicing, ribosome biogenesis, and RNA degradation. It is well known that ATP-binding and subsequent hydrolysis activities are crucial for the functionality of such helicases. Although the stress-responsive upregulation of eIF4A1 has been reported in plants during stress, it is difficult to anticipate the functionality of the corresponding protein product. Therefore, to understand the activity of eIF4A1 in rice in response to temperature stress, we first conducted an expression analysis of the gene and further investigated the structural stability of the eIF4A1-ATP/Mg2+ complex through molecular dynamics (MD) simulations at different temperature conditions (277 K, 300 K, and 315 K). Our results demonstrated a three to fourfold increased expression of rice eIF4A1 both in root and shoot at 42 °C compared to control. Furthermore, the MD simulation portrayed strong ATP/Mg2+ binding at a higher temperature in comparison to control and cold temperature. Overall, the increased expression pattern of eIF4A1 and strong ATP/Mg2+ binding at higher temperature indicated the heat stress-tolerant capacity of the gene in rice. The results from our study will help in understanding the activity of gene and guide the researchers for screening of novel stress inducible candidate genes for the engineering of temperature stress tolerant plants.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dhanawantari L Singha
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Jitendra Maharana
- Distributed Information Centre (DIC), Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Debashis Panda
- Distributed Information Centre (DIC), Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Budheswar Dehury
- Department of Biochemistry, University of Cambridge, Cambridge, UK.,Department of Chemistry, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Mahendra Kumar Modi
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India.,Distributed Information Centre (DIC), Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Salvinder Singh
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
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Vats A, Gautam D, Maharana J, Singh Chera J, Kumar S, Rout PK, Werling D, De S. Poly I:C stimulation in-vitro as a marker for an antiviral response in different cell types generated from Buffalo (Bubalus bubalis). Mol Immunol 2020; 121:136-143. [PMID: 32200171 DOI: 10.1016/j.molimm.2020.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 02/06/2020] [Accepted: 03/09/2020] [Indexed: 01/17/2023]
Abstract
The innate immune system is activated upon virus invasion of a host cell by recognizing viral component, such as dsRNA through specific receptors, resulting in the production of type- I IFNs, which confer an antiviral state within the invaded as well as surrounding cells. In the present study, fibroblast, monocyte and macrophage cells derived from water Buffalo (Bubalus bubalis) were exposed to a synthetic dsRNA analogue, poly I:C to mimic viral invasion in each cell type. Recognition of poly I:C through cytosolic helicase receptors RIG-I and MDA5 molecule lead to the activation of the RLR pathway, subsequently activating the MAVS-IRF3/7 cascade and the production of antiviral effector molecule like IFNβ and ISGs. Within the different cell types, we identified variability in RLR receptor and IFNβ expression after poly I:C administration. Fibroblasts responded quickly and strongly with IFNβ production, followed by macrophages and monocytes. Despite absolute expression variability among different cell types the expression trend of RLRs pathway genes were similar. Length of poly I:C molecule also influence IFNβ expression in response of RLR pathway. Short (LMW) poly I:C induce stronger IFN-β expression in myeloid (macrophage and monocyte) cells. In contrast long (HMW) poly I:C preferably elicit higher IFNβ expression in non-myeloid (fibroblast) cell. Therefore, MDA5 and RIG-1 plays an indispensable role in eliciting antiviral response in non- immune (fibroblast) host cell. Thus, stimulation of RLR pathway with suitable and potentially cell-type specific agonist molecules successfully elicit antiviral state in the host animal, with fibroblasts conferring a stronger antiviral state compared with the monocytes and macrophages.
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Affiliation(s)
- Ashutosh Vats
- Animal Genomics Lab., Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Devika Gautam
- Animal Genomics Lab., Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Jitendra Maharana
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Jatinder Singh Chera
- Animal Genomics Lab., Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Sushil Kumar
- Animal Genomics Lab., Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Pramod K Rout
- ICAR-Central Institute for Research on Goats, Mathura, Uttar Pradesh, India
| | - Dirk Werling
- The Royal Veterinary College, University of London, Hawkshead Lane, North Mymms, Hatfield, AL9 7TA, UK
| | - Sachinandan De
- Animal Genomics Lab., Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, Haryana, India.
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Roy P, Rout AK, Maharana J, Sahoo DR, Panda SP, Pal A, Nayak KK, Behera BK, Das BK. Molecular characterization, constitutive expression and GTP binding mechanism of Cirrhinus mrigala (Hamilton, 1822) Myxovirus resistance (Mx) protein. Int J Biol Macromol 2019; 136:1258-1272. [PMID: 31242450 DOI: 10.1016/j.ijbiomac.2019.06.161] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/11/2019] [Accepted: 06/21/2019] [Indexed: 12/30/2022]
Abstract
Myxovirus resistance (Mx) proteins represents the subclass of the dynamin superfamily of large Guanosine triphosphates (GTPases), play esential role in intracellular vesicle trafficking, endocytosis, organelle homeostasis and mitochondria distribution. These proteins are key players of the vertebrate immune system, induced by type-I and type-III interferons (IFN) of infected host and inhibit viral replication by sequestering its nucleoprotein. In the present study, we report the sequencing and characterization of Cirrhinus mrigala Mx protein (CmMx) for the first time and observed its constitutive expression in different tissues for a period of fourteen days. The synthetic peptide, LSGVALPRGTGI, was dissolved in PBS and injected into a rabbit and the antibody raised against CmMx was used to study the level of its expression. The full length of the CmMx cDNA is 2244 bp with a molecular mass of 70.9 kDa and a predicted isoelectric point of 8.25. The 627 amino acids polypeptide formed of three main functional domains: N-terminal GTPase domain (GD), a middle domain (MD) and GTPase effector domain (GED) with carboxy terminal leucine zipper motif. The 3D models of CmMx protein was modeled based on available close structural homologs and further validated through molecular dynamics (MD) simulations. MD study revealed the importance of G-domain responsible for recognition of GTP, which perfectly corroborate with earlier studies. MM/PBSA binding free energy analysis displayed that van der Waals and electrostatic energy were the key driving force behind molecular recognition of GTP by CmMx protein. The results from this study will illuminate more lights into the ongoing research on myxovirus resistance protein and its role in inhibition of viral replication in other eukaryotic system as well.
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Affiliation(s)
- Pragyan Roy
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751012, Odisha, India
| | - Ajaya Kumar Rout
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700120, West Bengal, India
| | - Jitendra Maharana
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar 751003, Odisha, India
| | - Deepak Ranjan Sahoo
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751012, Odisha, India
| | - Soumya Prasad Panda
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751012, Odisha, India
| | - Arttatrana Pal
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751012, Odisha, India
| | | | - Bijay Kumar Behera
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700120, West Bengal, India
| | - Basanta Kumar Das
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751012, Odisha, India; Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700120, West Bengal, India.
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17
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Das S, Maharana J, Mohanty S, Subuddhi U. Spectroscopic and computational insights into theophylline/β-cyclodextrin complexation: inclusion accomplished by diverse methods. J Microencapsul 2019; 35:667-679. [PMID: 30669907 DOI: 10.1080/02652048.2019.1572239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Current scenario in asthmatic prevalence worldwide calls for a facile, cost-effective, and energy efficient methodology to formulate the potent bronchodilator, theophylline (THP), into an effective dosage forms. Since the uses of THP are severely impeded by its poor aqueous solubility and low bioavailability, solid inclusion complexes (ICs) of THP in β-cyclodextrin (β-CD) were prepared to overcome the limitations. The ICs were developed by conventional methods and also by microwave irradiation method, which is environmentally more benign and requires lesser reaction time. The complexation phenomenon was effectual by the co-precipitation, freeze-drying, and microwave methods as affirmed from various spectroscopic analyses. 1H NMR and molecular docking studies illustrated the total inclusion of THP into β-CD cavity. Better efficacy of the microwaved product was witnessed in terms of drug content, dissolution, and anti-biofilm activities. Thus microwave irradiation can be utilised as a naive and economical methodology to design β-CD-THP dosage formulations.
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Affiliation(s)
- Subhraseema Das
- a Department of Chemistry , National Institute of Technology Rourkela , Rourkela , India
| | - Jitendra Maharana
- b Department of Agricultural Biotechnology, Distributed Information Centre , Assam Agricultural University , Jorhat , India
| | - Subhrajit Mohanty
- a Department of Chemistry , National Institute of Technology Rourkela , Rourkela , India
| | - Usharani Subuddhi
- a Department of Chemistry , National Institute of Technology Rourkela , Rourkela , India
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Hwang SK, Singh S, Maharana J, Kalita S, Tuncel A, Rath T, Panda D, Modi MK, Okita TW. Mechanism Underlying Heat Stability of the Rice Endosperm Cytosolic ADP-Glucose Pyrophosphorylase. Front Plant Sci 2019; 10:70. [PMID: 30804963 PMCID: PMC6378277 DOI: 10.3389/fpls.2019.00070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 01/17/2019] [Indexed: 05/22/2023]
Abstract
Rice grains accumulate starch as their major storage reserve whose biosynthesis is sensitive to heat. ADP-glucose pyrophosphorylase (AGPase) is among the starch biosynthetic enzymes severely affected by heat stress during seed maturation. To increase the heat tolerance of the rice enzyme, we engineered two dominant AGPase subunits expressed in developing endosperm, the large (L2) and small (S2b) subunits of the cytosol-specific AGPase. Bacterial expression of the rice S2b with the rice L2, potato tuber LS (pLS), or with the mosaic rice-potato large subunits, L2-pLS and pLS-L2, produced heat-sensitive recombinant enzymes, which retained less than 10% of their enzyme activities after 5 min incubation at 55°C. However, assembly of the rice L2 with the potato tuber SS (pSS) showed significantly increased heat stability comparable to the heat-stable potato pLS/pSS. The S2b assembled with the mosaic L2-pLS subunit showed 3-fold higher sensitivity to 3-PGA than L2/S2b, whereas the counterpart mosaic pLS-L2/S2b showed 225-fold lower sensitivity. Introduction of a QTC motif into S2b created an N-terminal disulfide linkage that was cleaved by dithiothreitol reduction. The QTC enzyme showed moderate heat stability but was not as stable as the potato AGPase. While the QTC AGPase exhibited approximately fourfold increase in 3-PGA sensitivity, its substrate affinities were largely unchanged. Random mutagenesis of S2bQTC produced six mutant lines with elevated production of glycogen in bacteria. All six lines contained a L379F substitution, which conferred enhanced glycogen production in bacteria and increased heat stability. Modeled structure of this mutant enzyme revealed that this highly conserved leucine residue is located in the enzyme's regulatory pocket that provides interaction sites for activators and inhibitors. Our molecular dynamic simulation analysis suggests that introduction of the QTC motif and the L379F mutation improves enzyme heat stability by stabilizing their backbone structures possibly due to the increased number of H-bonds between the small subunits and increased intermolecular interactions between the two SSs and two LSs at elevated temperature.
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Affiliation(s)
- Seon-Kap Hwang
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Salvinder Singh
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
| | - Jitendra Maharana
- Distributed Information Centre (DIC), Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
| | - Samhita Kalita
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
| | - Aytug Tuncel
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Tanmayee Rath
- Distributed Information Centre (DIC), Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
| | - Debashish Panda
- Distributed Information Centre (DIC), Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
| | - Mahendra Kumar Modi
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
| | - Thomas W. Okita
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
- *Correspondence: Thomas W. Okita,
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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: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Rout AK, Mishra J, Dehury B, Maharana J, Acharya V, Karna SK, Parida PK, Behera BK, Das BK. Structural bioinformatics insights into ATP binding mechanism in zebrafish (Danio rerio) cyclin-dependent kinase-like 5 (zCDKL5) protein. J Cell Biochem 2018; 120:9437-9447. [PMID: 30569538 DOI: 10.1002/jcb.28219] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 11/15/2018] [Indexed: 11/06/2022]
Abstract
In mammalian systems, the conserved cyclin-dependent protein kinases (CDKs) control the process of cell division and curb the transcription mechanism in response to diverse signaling events that are essential for the catalytic activity. In zebrafish, zCDKL5 portrays differential expression profiling in several tissues and presumed to play a vital role in the neuronal development. In this present study, the sequence-structure relationship and mode of ATP binding in zCDKL5 was unveiled through theoretical modeling, molecular docking, and MD simulations. Like human CDKs, the modeled zCDKL5 was found to be bipartite in nature, where, ATP binds to the central cavity of the catalytic domain through a strong network of H-bonding, electrostatic, and hydrophobic interactions. MD simulation portrayed that conserved residues, viz, Ile10, Gly11, Glu12, Val18, Val64, Glu81, Cys143, and Asp144 were indispensable for tight anchoring of ATP and contribute to the stability of the zCDKL5-ATP complex. MM/PBSA binding free energy analysis displayed that van der Waal energy (ΔG vwd ) and Electrostatic energy (ΔG ele ) were the major contributors towards the overall binding free energy. Thus, the comparative structural bioinformatics approach has shed new insights into the dynamics and ATP binding mechanism of zCDKL5. The results from the study will help to undertake further research on the role of phosphorylated CDKL5 in the onset of neurodevelopmental disorders caused by mutations in higher eukaryotic systems.
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Affiliation(s)
- Ajaya Kumar Rout
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
| | - Jagruti Mishra
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - Budheswar Dehury
- Biomedical Informatics Centre, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India.,Department of Chemistry, Technical University of Denmark, Denmark
| | - Jitendra Maharana
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - Varsha Acharya
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - Subodha Kumar Karna
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
| | - Pranaya Kumar Parida
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
| | - Bijay Kumar Behera
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
| | - Basanta Kumar Das
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
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Rout AK, Dehury B, Maharana J, Nayak C, Baisvar VS, Behera BK, Das BK. Deep insights into the mode of ATP-binding mechanism in Zebrafish cyclin-dependent protein kinase-like 1 (zCDKL1): A molecular dynamics approach. J Mol Graph Model 2018; 81:175-183. [PMID: 29574323 DOI: 10.1016/j.jmgm.2018.02.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 01/28/2018] [Accepted: 02/02/2018] [Indexed: 12/21/2022]
Abstract
In eukaryotes, the serine/threonine kinases (STKs) belonging to cyclin-dependent protein kinases (CDKs) play significant role in control of cell division and curb transcription in response to several extra and intra-cellular signals indispensable for enzymatic activity. The zebrafish cyclin-dependent protein kinase-like 1 protein (zCDKL1) shares a high degree of sequence and structural similarity with mammalian orthologs and express in brain, ovary, testis, and low levels in other tissues. Regardless of its importance in the developmental process, the structure, function and mode of ATP recognition have not been investigated yet due to lack of experimental data. Henceforth, to gain atomistic insights in to the structural dynamics and mode of ATP binding, a series of computational techniques involving theoretical modeling, docking, molecular dynamics (MD) simulations and MM/PBSA binding free energies were employed. The modeled bi-lobed zCDKL1 shares a high degree of secondary structure topology with human orthologs where ATP prefers to lie in the central cavity of the bi-lobed catalytic domain enclosed by strong hydrogen bonding, electrostatic and hydrophobic contacts. Long range MD simulation portrayed that catalytic domain of zCDKL1 to be highly rigid in nature as compared to the complex (zCDKL1-ATP) form. Comparative analysis with its orthologs revealed that conserved amino acids i.e., Ile10, Gly11, Glu12, Val18, Arg31, Phe80, Glu 130, Cys143 and Asp144 were crucial for ATP binding mechanism, which needs further investigation for legitimacy. MM/PBSA method revealed that van der Waals, electrostatic and polar solvation energy mostly contributes towards negative free energy. The implications of ATP binding mechanism inferred through these structural bioinformatics approaches will help in understanding the catalytic mechanisms of important STKs in eukaryotic system.
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Affiliation(s)
- Ajaya Kumar Rout
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, West Bengal, India
| | - Budheswar Dehury
- Biomedical Informatics Centre, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India
| | - Jitendra Maharana
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, 751003, Odisha, India
| | - Chirasmita Nayak
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, 751003, Odisha, India
| | - Vishwamitra Singh Baisvar
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, West Bengal, India
| | - Bijay Kumar Behera
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, West Bengal, India.
| | - Basanta Kumar Das
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, West Bengal, India.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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] [What about the content of this article? (0)] [Affiliation(s)] [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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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. Mol Biosyst 2016; 11:2324-36. [PMID: 26079944 DOI: 10.1039/c5mb00212e] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Dehury B, Maharana J, Sahoo BR, Sahu J, Sen P, Modi MK, Barooah M. Molecular recognition of avirulence protein (avrxa5) by eukaryotic transcription factor xa5 of rice (Oryza sativa L.): insights from molecular dynamics simulations. J Mol Graph Model 2015; 57:49-61. [PMID: 25655560 DOI: 10.1016/j.jmgm.2015.01.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 11/06/2014] [Accepted: 01/09/2015] [Indexed: 11/17/2022]
Abstract
The avirulence gene avrxa5 of bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) recognized by the resistant rice lines having corresponding resistance (xa5) gene in a gene-for-gene manner. We used a combinatorial approach involving protein-protein docking, molecular dynamics (MD) simulations and binding free energy calculations to gain novel insights into the gene-for-gene mechanism that governs the direct interaction of R-Avr protein. From the best three binding poses predicted by molecular docking, MD simulations were performed to explore the dynamic binding mechanism of xa5 and avrxa5. Molecular Mechanics/Poisson Boltzmann Surface Area (MM/PBSA) techniques were employed to calculate the binding free energy and to uncover the thriving force behind the molecular recognition of avrxa5 by eukaryotic transcription factor xa5. Binding free energy analysis revealed van der Waals term as the most constructive component that favors the xa5 and avrxa5 interaction. In addition, hydrogen bonds (H-bonds) and essential electrostatic interactions analysis highlighted amino acid residues Lys54/Asp870, Lys56/Ala868, Lys56/Ala866, Lys56/Glu871, Ile59/His862, Gly61/Phe858, His62/Arg841, His62/Leu856, Ser101/Ala872 and Ser105/Asp870 plays pivotal role for the energetically stability of the R-Avr complex. Insights gained from the present study are expected to unveil the molecular mechanisms that define the transcriptional activator mediated transcriptome modification in host plants.
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Affiliation(s)
- Budheswar Dehury
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat -785013, Assam, India; Department of Life Science and Bioinformatics, Assam University, Silchar -788011, Assam, India.
| | - Jitendra Maharana
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar -751003, Odisha, India
| | - Bikash Ranjan Sahoo
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar -751003, Odisha, India
| | - Jagajjit Sahu
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat -785013, Assam, India
| | - Priyabrata Sen
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat -785013, Assam, India
| | - Mahendra Kumar Modi
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat -785013, Assam, India
| | - Madhumita Barooah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat -785013, Assam, India.
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Sahoo BR, Maharana J, Bhoi GK, Lenka SK, Patra MC, Dikhit MR, Dubey PK, Pradhan SK, Behera BK. A conformational analysis of mouse Nalp3 domain structures by molecular dynamics simulations, and binding site analysis. Mol Biosyst 2014; 10:1104-16. [PMID: 24595807 DOI: 10.1039/c3mb70600a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Scrutinizing various nucleotide-binding oligomerization domain (NOD)-like receptor (NLR) genes in higher eukaryotes is very important for understanding the intriguing mechanism of the host defense against pathogens. The nucleotide-binding domain (NACHT), leucine-rich repeat (LRR), and pyrin domains (PYD)-containing protein 3 (Nalp3), is an intracellular innate immune receptor and is associated with several immune system related disorders. Despite Nalp3's protective role during a pathogenic invasion, the molecular features and structural organization of this crucial protein is poorly understood. Using comparative modeling and molecular dynamics simulations, we have studied the structural architecture of Nalp3 domains, and characterized the dynamic and energetic parameters of adenosine triphosphate (ATP) binding in NACHT, and pathogen-derived ligands muramyl dipeptide (MDP) and imidazoquinoline with LRR domains. The results suggested that walker A, B and extended walker B motifs were the key ATP binding regions in NACHT that mediate self-oligomerization. The analysis of the binding sites of MDP and imidazoquinoline revealed LRR 7-9 to be the most energetically favored site for imidazoquinoline interaction. However, the binding free energy calculations using the Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) method indicated that MDP is incompatible for activating the Nalp3 molecule in its monomeric form, and suggest its complex interaction with NOD2 or other NLRs accounts for MDP recognition. The high binding affinity of ATP with NACHT was correlated to the experimental data for human NLRs. Our binding site prediction for imidazoquinoline in LRR warrants further investigation via in vivo models. This is the first study that provides ligand recognition in mouse Nalp3 and its spatial structural arrangements.
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Affiliation(s)
- Bikash R Sahoo
- Department of Bioinformatics, Centre for Post-Graduate Studies, Orissa University of Agriculture & Technology, Bhubaneswar-751003, Odisha, 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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Sahoo BR, Maharana J, Patra MC, Bhoi GK, Lenka SK, Dubey PK, Goyal S, Dehury B, Pradhan SK. Structural and dynamic investigation of bovine folate receptor alpha (FOLR1), and role of ultra-high temperature processing on conformational and thermodynamic characteristics of FOLR1-folate complex. Colloids Surf B Biointerfaces 2014; 121:307-18. [PMID: 25023142 DOI: 10.1016/j.colsurfb.2014.05.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 04/12/2014] [Accepted: 05/17/2014] [Indexed: 01/12/2023]
Abstract
The folate receptor alpha (FOLR1) present in milk has widely been studied to investigate the effects of pasteurization, ultra-high temperature (UHT) processing and fermentation on net folate concentration. However, the folate binding mechanism with FOLR1, and effect of temperature on FOLR1-folate complex is poorly explored till now in bovine milk which is a chief resource of folate. Despite of enormous importance of folic acid and the routine intake of bovine milk, folic acid deficiency diseases are common in human race. To understand the folate deficiency in milk after processing, in absence of experimental structure, 3D model of bovine FOLR1 (bvFOLR1) was built followed by 40ns molecular dynamics (MD) simulation. The folate and its derivatives binding sites in bvFOLR1 were anticipated by molecular docking using AutoDock 4.2. Essential MD studies suggested the presence of a longer signal peptide (22 residues) and a short propeptide (7 residues) at the C-terminus that may cleaved during post-translational modification. MD analysis of bvFOLR1-folate complex at 298, 323, 353, 373 and 408K followed by binding energy (BE) calculation showed maximum binding affinity at ∼353K. However, at 373K and UHT (408K), the folate BE is significantly decreased with substantial conformational alteration. Heating at UHT followed by cooling within 298-408K range demoed no structural reformation with temperature reduction, and the folate was displaced from the active site. This study presented the disintegration of folate from bvFOLR1 during high temperature processing and revealed a lower folate concentration in UHT milk and dairy products.
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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.
| | - Jitendra Maharana
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, 751001, India; Biotechnology Laboratory, Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, 700120, India
| | - Mahesh Chandra Patra
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, 751001, India; Animal Genomics Laboratory, Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, India
| | - 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
| | - Praveen Kumar Dubey
- Immunology Frontier Research Centre, Osaka University, Osaka Prefecture, 5650871, Japan
| | - Shubham Goyal
- RIKEN Center for Life Science Technologies, Yokohama, 2300045, Japan
| | - Budheswar Dehury
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, 785013, Assam, India
| | - Sukanta Kumar Pradhan
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, 751001, India
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Patra MC, Maharana J, Dehury B, De S. Computational insights into the binding mechanism of antagonists with neuropeptide B/W receptor 1. Mol BioSyst 2014; 10:2236-46. [DOI: 10.1039/c4mb00214h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Maharana J, Patra MC, De BC, Sahoo BR, Behera BK, De S, Pradhan SK. Structural insights into the MDP binding and CARD-CARD interaction in zebrafish (Danio rerio) NOD2: a molecular dynamics approach. J Mol Recognit 2014; 27:260-75. [DOI: 10.1002/jmr.2357] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Revised: 12/20/2013] [Accepted: 12/20/2013] [Indexed: 01/01/2023]
Affiliation(s)
- Jitendra Maharana
- Biotechnology Laboratory; Central Inland Fisheries Research Institute; Kolkata 700120 West Bengal India
| | - Mahesh Chandra Patra
- BIF-Centre, Department of Bioinformatics; Orissa University of Agriculture and Technology; Bhubaneswar 751003 Odisha India
- Animal Genomics Laboratory, Animal Biotechnology Centre; National Dairy Research Institute; Karnal 132001 Haryana India
| | - Bidhan Chandra De
- Biotechnology Laboratory; Central Inland Fisheries Research Institute; Kolkata 700120 West Bengal India
| | - Bikash Ranjan Sahoo
- BIF-Centre, Department of Bioinformatics; Orissa University of Agriculture and Technology; Bhubaneswar 751003 Odisha India
- Laboratory of Molecular Biophysics, Institute of Protein Research; Osaka University; Osaka Prefecture 5650871 Japan
| | - Bijay Kumar Behera
- Biotechnology Laboratory; Central Inland Fisheries Research Institute; Kolkata 700120 West Bengal India
| | - Sachinandan De
- Animal Genomics Laboratory, Animal Biotechnology Centre; National Dairy Research Institute; Karnal 132001 Haryana India
| | - Sukanta Kumar Pradhan
- BIF-Centre, Department of Bioinformatics; Orissa University of Agriculture and Technology; Bhubaneswar 751003 Odisha India
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Singh M, Brahma B, Maharana J, Patra MC, Kumar S, Mishra P, Saini M, De BC, Mahanty S, Datta TK, De S. Insight into buffalo (Bubalus bubalis) RIG1 and MDA5 receptors: a comparative study on dsRNA recognition and in-vitro antiviral response. PLoS One 2014; 9:e89788. [PMID: 24587036 PMCID: PMC3935933 DOI: 10.1371/journal.pone.0089788] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 01/24/2014] [Indexed: 12/24/2022] Open
Abstract
RIG1 and MDA5 have emerged as important intracellular innate pattern recognition receptors that recognize viral RNA and mediate cellular signals controlling Type I interferon (IFN-I) response. Buffalo RIG1 and MDA5 genes were investigated to understand the mechanism of receptor induced antiviral response. Sequence analysis revealed that RIG1 and MDA5 maintain a domain arrangement that is common in mammals. Critical binding site residues of the receptors are evolutionary conserved among mammals. Molecular dynamics simulations suggested that RIG1 and MDA5 follow a similar, if not identical, dsRNA binding pattern that has been previously reported in human. Moreover, binding free energy calculation revealed that MDA5 had a greater affinity towards dsRNA compared to RIG1. Constitutive expressions of RLR genes were ubiquitous in different tissues without being specific to immune organs. Poly I:C stimulation induced elevated expressions of IFN-β and IFN-stimulated genes (ISGs) through interferon regulatory factors (IRFs) mediated pathway in buffalo foetal fibroblast cells. The present study provides crucial insights into the structure and function of RIG1 and MDA5 receptors in buffalo.
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Affiliation(s)
- Manvender Singh
- Animal Genomics Lab, Animal Biotechnology Center, National Dairy Research Institute, Karnal, Haryana, India
| | - Biswajit Brahma
- Animal Genomics Lab, Animal Biotechnology Center, National Dairy Research Institute, Karnal, Haryana, India
| | - Jitendra Maharana
- Animal Genomics Lab, Animal Biotechnology Center, National Dairy Research Institute, Karnal, Haryana, India
| | - Mahesh Chandra Patra
- Animal Genomics Lab, Animal Biotechnology Center, National Dairy Research Institute, Karnal, Haryana, India
| | - Sushil Kumar
- Animal Genomics Lab, Animal Biotechnology Center, National Dairy Research Institute, Karnal, Haryana, India
| | - Purusottam Mishra
- Animal Genomics Lab, Animal Biotechnology Center, National Dairy Research Institute, Karnal, Haryana, India
| | - Megha Saini
- Animal Genomics Lab, Animal Biotechnology Center, National Dairy Research Institute, Karnal, Haryana, India
| | - Bidhan Chandra De
- Animal Genomics Lab, Animal Biotechnology Center, National Dairy Research Institute, Karnal, Haryana, India
| | - Sourav Mahanty
- Animal Genomics Lab, Animal Biotechnology Center, National Dairy Research Institute, Karnal, Haryana, India
| | - Tirtha Kumar Datta
- Animal Genomics Lab, Animal Biotechnology Center, National Dairy Research Institute, Karnal, Haryana, India
| | - Sachinandan De
- Animal Genomics Lab, Animal Biotechnology Center, National Dairy Research Institute, Karnal, Haryana, India
- * E-mail:
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Maharana J, Swain B, Sahoo BR, Dikhit MR, Basu M, Mahapatra AS, Jayasankar P, Samanta M. Identification of MDP (muramyl dipeptide)-binding key domains in NOD2 (nucleotide-binding and oligomerization domain-2) receptor of Labeo rohita. Fish Physiol Biochem 2013; 39:1007-1023. [PMID: 23255217 DOI: 10.1007/s10695-012-9758-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 12/06/2012] [Indexed: 06/01/2023]
Abstract
In lower eukaryotes-like fish, innate immunity contributed by various pattern recognition receptor (PRR) plays an essential role in protection against diseases. Nucleotide-binding and oligomerization domain (NOD)-2 is a cytoplasmic PRR that recognizes MDP (muramyl dipeptide) of the Gram positive and Gram negative bacteria as ligand and activates signalling to induce innate immunity. Hypothesizing a similar NOD2 signalling pathway of higher eukaryotes, the peripheral blood leucocytes (PBLs) of rohu (Labeo rohita) was stimulated with MDP. The data of quantitative real-time PCR (qRT-PCR) revealed MDP-mediated inductive expression of NOD2 and its down-stream molecule RICK/RIP2 (receptor-interacting serine-threonine protein kinase-2). This observation suggested the existence of MDP-binding sites in rohu NOD2 (rNOD2). To investigate it, 3D model of ligand-binding leucine-rich repeat (LRR) region of rNOD2 (rNOD2-LRR) was constructed following ab initio and threading approaches in I-TASSER web server. Structural refinement of the model was performed by energy minimization, and MD (molecular dynamics) simulation was performed in GROMACS (Groningen Machine for Chemical Simulations). The refined model of rNOD2-LRR was validated through SAVES, ProSA, ProQ, WHAT IF and MolProbity servers, and molecular docking with MDP was carried out in GOLD 4.1. The result of docking identified LRR3-7 comprising Lys820, Phe821, Asn822, Arg847, Gly849, Trp877, Trp901 and Trp931 as MDP-binding critical amino acids in rNOD2. This is the first study in fish to provide an insight into the 3D structure of NOD2-LRR region and its important motifs that are expected to be engaged in MDP binding and innate immunity.
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Affiliation(s)
- Jitendra Maharana
- Fish Health Management Division, Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751002, Odisha, India
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Patra MC, Maharana J, Pradhan SK, Rath SN. Molecular dynamics simulation of neuropeptide B and neuropeptide W in the dipalmitoylphosphatidylcholine membrane bilayer. J Biomol Struct Dyn 2013; 32:1118-31. [DOI: 10.1080/07391102.2013.811699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Sahoo BR, Basu M, Swain B, Maharana J, Dikhit MR, Jayasankar P, Samanta M. Structural insights of rohu TLR3, its binding site analysis with fish reovirus dsRNA, poly I:C and zebrafish TRIF. Int J Biol Macromol 2012; 51:531-43. [PMID: 22705475 DOI: 10.1016/j.ijbiomac.2012.06.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 06/01/2012] [Accepted: 06/06/2012] [Indexed: 11/30/2022]
Abstract
In response to double stranded RNA (dsRNA) viruses, toll-like receptor 3 (TLR3) in fish activates signaling like human, and induces innate immunity. This suggested the existence of dsRNA binding domains in fish TLR3 as reported in higher vertebrates. In in silico analysis, leucine rich repeat (LRR) regions (4-6, 13-14, 20-22), and LRR (8-15, 17-24) were identified as key domains in rohu TLR3 as poly I:C and dsRNA of fish reovirus (AGCRV,VHSV and IHNV) binding regions. 3D-models of rohu TLR3-TIR and zebrafish TRIF were generated by homology and ab initio modeling respectively, and their interacting domains were predicted. This is the first report of TLR3 modeling in fish.
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Affiliation(s)
- Bikash R Sahoo
- Fish Health Management Division, Central Institute of Freshwater Aquaculture-CIFA, Kausalyaganga, Bhubaneswar 751002, Orissa, India
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Maharana J, Singh LP. Path-integral formulation of the theory of loops and strings. Phys Rev D Part Fields 1985; 31:3162-3167. [PMID: 9955647 DOI: 10.1103/physrevd.31.3162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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