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Malik VK, Sangwan P, Singh M, Kumari P, Sheoran N, Ahalawat N, Kumar M, Deep H, Malik K, Verma P, Yadav P, Dhariwal S, Aakash, Dhal S. Erratum: Stem Rot of Pearl Millet Prevalence, Symptomatology, Disease Cycle, Disease Rating Scale and Pathogen Characterization in Pearl Millet-Klebsiella Pathosystem. Plant Pathol J 2024; 40:233. [PMID: 38606452 PMCID: PMC11016557 DOI: 10.5423/ppj.er.09.2023.0126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Affiliation(s)
- Vinod Kumar Malik
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Pooja Sangwan
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Manjeet Singh
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Pavitra Kumari
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Niharika Sheoran
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Navjeet Ahalawat
- Department of Bioinformatics and Computational Biology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Mukesh Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Harsh Deep
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Kamla Malik
- Department of Microbiology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Preety Verma
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Pankaj Yadav
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Sheetal Dhariwal
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Aakash
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Sambandh Dhal
- Department of Microbiology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
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Malik VK, Sangwan P, Singh M, Kumari P, Shoeran N, Ahalawat N, Kumar M, Deep H, Malik K, Verma P, Yadav P, Kumari S, Aakash, Dhal S. Stem Rot of Pearl Millet Prevalence, Symptomatology, Disease Cycle, Disease Rating Scale and Pathogen Characterization in Pearl Millet-Klebsiella Pathosystem. Plant Pathol J 2024; 40:48-58. [PMID: 38326958 PMCID: PMC10850534 DOI: 10.5423/ppj.oa.09.2023.0126] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/14/2023] [Accepted: 12/29/2023] [Indexed: 02/09/2024]
Abstract
The oldest and most extensively cultivated form of millet, known as pearl millet (Pennisetum glaucum (L.) R. Br. Syn. Pennisetum americanum (L.) Leeke), is raised over 312.00 lakh hectares in Asian and African countries. India is regarded as the significant hotspot for pearl millet diversity. In the Indian state of Haryana, where pearl millet is grown, a new and catastrophic bacterial disease known as stem rot of pearl millet spurred by the bacterium Klebsiella aerogenes (formerly Enterobacter) was first observed during fall 2018. The disease appears in form of small to long streaks on leaves, lesions on stem, and slimy rot appearance of stem. The associated bacterium showed close resemblance to Klebsiella aerogenes that was confirmed by a molecular evaluation based on 16S rDNA and gyrA gene nucleotide sequences. The isolates were also identified to be Klebsiella aerogenes based on biochemical assays, where Klebsiella isolates differed in D-trehalose and succinate alkalisation tests. During fall 2021-2023, the disease has spread all the pearl millet-growing districts of the state, extending up to 70% disease incidence in the affected fields. The disease is causing considering grain as well as fodder losses. The proposed scale, consisting of six levels (0-5), is developed where scores 0, 1, 2, 3, 4, and 5 have been categorized as highly resistant, resistant, moderately resistant, moderately susceptible, susceptible, and highly susceptible disease reaction, respectively. The disease cycle, survival of pathogen, and possible losses have also been studied to understand other features of the disease.
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Affiliation(s)
- Vinod Kumar Malik
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Pooja Sangwan
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Manjeet Singh
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Pavitra Kumari
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Niharika Shoeran
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Navjeet Ahalawat
- Department of Bioinformatics and Computational Biology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Mukesh Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Harsh Deep
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Kamla Malik
- Department of Microbiology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Preety Verma
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Pankaj Yadav
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Sheetal Kumari
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Aakash
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Sambandh Dhal
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77840, USA
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Rani N, Boora N, Rani R, Kumar V, Ahalawat N. Molecular dynamics simulation of RAC1 protein and its de novo variants related to developmental disorders. J Biomol Struct Dyn 2023:1-10. [PMID: 37897175 DOI: 10.1080/07391102.2023.2275188] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023]
Abstract
Neurodevelopmental disorders (NDDs) are conceptualized as childhood disability, but it has increasingly been recognized as lifelong neurological conditions that could notably impact adult functioning and quality of life. About 1%-3% of the general population suffers from NDDs including ADHD, ASD, IDD, communication disorders, motor disorders, etc. Studies suggest that Rho GTPases are key in neuronal development, highlighting the importance of altered GTPase signaling in NDDs. RAC1, a member of the Rho GTPase family, plays a critical role in neurogenesis, migration, synapse formation, axon growth, and regulation of actin cytoskeleton dynamics. We performed 6µs all-atom molecular dynamics simulation of native RAC1 (PDB: 3TH5) and three-point mutations (C18Y, N39S, and Y64D) related to developmental disorders to understand the impact of mutations on protein stability and functional dynamics. Our analysis, which included root mean square deviation (RMSD), root mean square fluctuation (RMSF), solvent accessible surface area (SASA), radius of gyration (Rg), free energy landscape (FEL), and principal component analysis (PCA), revealed that the N39S and Y64D mutations induced significant structural changes in RAC1. These alterations primarily occurred in the functional region adjacent to switch II, a region crucial for complex conformational rearrangements during the GDP and GTP exchange cycle.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nigam Rani
- Department of Human Development and Family Studies, CCS Haryana Agricultural University Hisar, Hisar, India
| | - Nisha Boora
- Department of Bioinformatics and Computational Biology, CCS Haryana Agricultural University Hisar, Hisar, India
| | - Reena Rani
- Department of Molecular Biology and Biotechnology, CCS Haryana Agricultural University Hisar, Hisar, India
| | - Vinay Kumar
- Department of Mathematics and Statistics, CCS Haryana Agricultural University Hisar, Hisar, India
| | - Navjeet Ahalawat
- Department of Bioinformatics and Computational Biology, CCS Haryana Agricultural University Hisar, Hisar, India
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Dandekar B, Ahalawat N, Sinha S, Mondal J. Markov State Models Reconcile Conformational Plasticity of GTPase with Its Substrate Binding Event. JACS Au 2023; 3:1728-1741. [PMID: 37388689 PMCID: PMC10302740 DOI: 10.1021/jacsau.3c00151] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 07/01/2023]
Abstract
Ras GTPase is an enzyme that catalyzes the hydrolysis of guanosine triphosphate (GTP) and plays an important role in controlling crucial cellular signaling pathways. However, this enzyme has always been believed to be undruggable due to its strong binding affinity with its native substrate GTP. To understand the potential origin of high GTPase/GTP recognition, here we reconstruct the complete process of GTP binding to Ras GTPase via building Markov state models (MSMs) using a 0.1 ms long all-atom molecular dynamics (MD) simulation. The kinetic network model, derived from the MSM, identifies multiple pathways of GTP en route to its binding pocket. While the substrate stalls onto a set of non-native metastable GTPase/GTP encounter complexes, the MSM accurately discovers the native pose of GTP at its designated catalytic site in crystallographic precision. However, the series of events exhibit signatures of conformational plasticity in which the protein remains trapped in multiple non-native conformations even when GTP has already located itself in its native binding site. The investigation demonstrates mechanistic relays pertaining to simultaneous fluctuations of switch 1 and switch 2 residues which remain most instrumental in maneuvering the GTP-binding process. Scanning of the crystallographic database reveals close resemblance between observed non-native GTP binding poses and precedent crystal structures of substrate-bound GTPase, suggesting potential roles of these binding-competent intermediates in allosteric regulation of the recognition process.
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Affiliation(s)
| | - Navjeet Ahalawat
- Department
of Bioinformatics and Computational Biology, College of Biotechnology, CCS Haryana Agricultural University, Hisar, 125004 Haryana, India
| | - Suman Sinha
- Institute
of Pharmaceutical Research, GLA University, Mathura, 281406 Uttar Pradesh, India
| | - Jagannath Mondal
- Tata
Institute of Fundamental Research, Hyderabad, Telangana 500046, India
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Ahalawat N, Sahil M, Mondal J. Resolving Protein Conformational Plasticity and Substrate Binding via Machine Learning. J Chem Theory Comput 2023; 19:2644-2657. [PMID: 37068044 DOI: 10.1021/acs.jctc.2c00932] [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: 04/18/2023]
Abstract
A long-standing target in elucidating the biomolecular recognition process is the identification of binding-competent conformations of the receptor protein. However, protein conformational plasticity and the stochastic nature of the recognition processes often preclude the assignment of a specific protein conformation to an individual ligand-bound pose. Here, we demonstrate that a computational framework coined as RF-TICA-MD, which integrates an ensemble decision-tree-based Random Forest (RF) machine learning (ML) technique with an unsupervised dimension reduction approach time-structured independent component analysis (TICA), provides an efficient and unambiguous solution toward resolving protein conformational plasticity and the substrate binding process. In particular, we consider multimicrosecond-long molecular dynamics (MD) simulation trajectories of a ligand recognition process in solvent-inaccessible cavities of archetypal proteins T4 lysozyme and cytochrome P450cam. We show that in a scenario in which clear correspondence between protein conformation and binding-competent macrostates could not be obtained via an unsupervised dimension reduction approach, an a priori decision-tree-based supervised classification of the simulated recognition trajectories via RF would help characterize key amino acid residue pairs of the protein that are deemed sensitive for ligand binding. A subsequent unsupervised dimensional reduction of the selected residue pairs via TICA would then delineate a conformational landscape of protein which is able to demarcate ligand-bound poses from unbound ones. The proposed RF-TICA-MD approach is shown to be data agnostic and found to be robust when using other ML-based classification methods such as XGBoost. As a promising spinoff of the protocol, the framework is found to be capable of identifying distal protein locations which would be allosterically important for ligand binding and would characterize their roles in recognition pathways. A Python implementation of a proposed ML workflow is available in GitHub https://github.com/navjeet0211/rf-tica-md.
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Affiliation(s)
- Navjeet Ahalawat
- Department of Bioinformatics and Computational Biology, College of Biotechnology, CCS Haryana Agricultural University, Hisar 125 004, Haryana, India
| | - Mohammad Sahil
- Center for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad 500046, India
| | - Jagannath Mondal
- Center for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad 500046, India
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Malik VK, Singh M, Sangwan P, Kumari P, Sharma BL, Kumari P, Verma P, Yadav P, Sheoran N, Singh A, Singh DP, Arya SK, Ahalawat N, Malik J. First report of Klebsiella Leaf Streak on Sorghum Caused by Klebsiella variicola in Haryana, India. Plant Dis 2023; 107:2215. [PMID: 36593667 DOI: 10.1094/pdis-09-22-2200-pdn] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Sorghum (Sorghum bicolor [L.] Moench) is one of the top ten cereal crops in the world and is grown for fodder and seed purposes. During the fall of 2019 to 2022, a disease causing small to long streaks on leaves was observed in sorghum fields of Hisar (29° 9' 6.6996'' N, 75° 43' 16.0428'' E), Rohtak (28° 53' 43.8540'' N, 76° 36' 23.8068'' E) and Mohindergarh (28° 16' 6.0492'' N, 76° 9' 3.3552'' E) regions of Haryana between July and October. The reddish brown streaks were observed in the interveinal spaces of upper and lower leaves. The disease incidence reached 20-30% of plants in affected fields. The diseased leaf tissues were disinfected with 70% alcohol and placed in a tube with sterile water. After 30 minutes, 100 µl of the suspension was inoculated onto nutrient agar medium, incubated at 28 ± 2°C for three days, and a pure culture was obtained by restreaking on nutrient agar (Janse, 2005). The rod-shaped gram-negative bacterium with round, cream to white colonies was positive for methyl red, citrate utilization, urease activity, and glucose, lactose, sorbitol, rhamnose and sucrose fermentation tests. The genomic DNA of the bacterial suspension was extracted and 16S rDNA was amplified using universal 27F/1492R primers (Marchesi et al. 1998), resulting in tentative identification as Klebsiella sp. It was further confirmed with PCR amplification of Klebsiella specific primers (F:5'-CGCGTACTATACGCCATGAACGTA-3'; R:5'-ACCGTTGATCACTTCGGTCAGG-3') for gyrA gene (Brisse and Verhoef 2001). Discrete PCR amplicons of 1,500 (16S rDNA) and 300 bp (gyrA) were observed in a 1% (w/v) agarose gel. Forward and reverse DNA sequencing of both amplicons of the Hisar isolate (VMKV101) was carried out using a BDT v3.1 Cycle sequencing kit and consensus sequences were generated by using the program SeqMan Ultra (DNASTAR Lasergene). Sequences of the PCR products were deposited in GenBank with accession numbers MZ569433 (16S rDNA) and OP390080 (gyrA). The 16S rDNA sequence was 97.32% similar to K. variicola strain 13450 (CP026013; 1,450/1,490 bp) and the gyrA sequence had 99.66% similarity to K. variicola strain FH-1 (CP054254; 297/298 bp). A 16S RNA-based phylogenetic tree done by MEGA11 (Tamura et al. 2021) using the Maximum Likelihood method showed that strain VMKV101 clustered with K. variicola type strain F2R9. The complete bacterial genome (GCA025629215), sequenced by the Ion GeneStudio S5 system using Ion 530 chips (Thermo Fisher Scientific), was 99.03% identical by average nucleotide identity (ANI) to the type genome (CP045783) of Klebsiella variicola, with 87.8% genome coverage. For pathogenicity testing, a bacterial suspension (10 ml, 1×107 colony forming units/ml) was injected into the whole whorl after mechanical injury on 15-20 days old seedlings of the susceptible genotype HC-171, then plants were incubated at 35 ± 2°C, >80% relative humidity. Control plants were injected with sterile distilled water. Initial symptoms were observed on leaves of inoculated plants after 5 to 7 days as narrow, small longitudinal reddish brown streaks. As the disease progressed, the streaks on the leaf blade increased in number and size maintaining the reddish brown color. These streaks had slightly wavy margins and were surrounded by bright yellow halos. After 15 to 20 days, the streaks were 0.5 to 2.0 mm wide and 1.0 to 5.0 cm long, occasionally up to 10.0 cm long on both side of the leaves. Over time, neighboring streaks coalesced to form large necrotic areas. All inoculated plants exhibited identical symptoms. No symptoms were observed on control leaves. The reisolated bacterium from diseased sorghum leaves showed exactly the same morphological, biochemical and 16S RNA and gyrA molecular characteristics. To our knowledge, this is the first report of K. variicola causing a leaf streak disease on sorghum. Klebsiella species primarily cause diseases in humans and animals, but K. variicola has been found to incite banana soft rot (Fan et al. 2015) and K. aerogenes to cause stem rot in pearl millet (Malik et al. 2022). Differences of prevalence, spread and control between K. variicola and two other bacteria (Xanthomonas vasicola pv. holcicola causing Bacterial leaf streak; Paraburkholderia andropogonis causing Bacterial leaf stripe) causing leaf streak diseases on sorghum need to be determined. The identification of Klebsiella leaf streak disease lays the groundwork for future investigations into epidemiology and management of K. variicola on sorghum.
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Affiliation(s)
- Vinod Kumar Malik
- CCS HAU, 29052, Plant Pathology, Dr V K Malik, Deptt. of Plant Pathology, College of Agriculture, CCSHAU, Hisar, Hisar, Haryana, India, 125004;
| | - Manjeet Singh
- CCS HAU, 29052, Genetics and Plant Breeding, Hisar, Haryana, India;
| | - Pooja Sangwan
- CCS HAU, 29052, Plant Pathology, Hisar, Haryana, India;
| | - Pummy Kumari
- CCS HAU, 29052, Genetics and Plant Breeding, Hisar, Haryana, India;
| | | | | | - Preety Verma
- CCS HAU, 29052, Plant Pathology, Hisar, Haryana, India;
| | - Pankaj Yadav
- CCS HAU, 29052, Plant Pathology, Hisar, Haryana, India;
| | | | - Ajit Singh
- CCS HAU, 29052, Plant Patholgy, Hisar, Haryana, India;
| | | | | | - Navjeet Ahalawat
- CCS HAU, 29052, Bioinformatics and Computational Biology, Hisar, Haryana, India;
| | - Janvi Malik
- CCS HAU, 29052, Plant Pathology, Hisar, Haryana, India;
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Mehla S, Kumar U, Kapoor P, Singh Y, Sihag P, Sagwal V, Balyan P, Kumar A, Ahalawat N, Lakra N, Singh KP, Pesic V, Djalovic I, Mir RR, Dhankher OP. Structural and functional insights into the candidate genes associated with different developmental stages of flag leaf in bread wheat ( Triticum aestivum L.). Front Genet 2022; 13:933560. [PMID: 36092892 PMCID: PMC9449350 DOI: 10.3389/fgene.2022.933560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 07/04/2022] [Indexed: 02/05/2023] Open
Abstract
Grain yield is one of the most important aims for combating the needs of the growing world population. The role of development and nutrient transfer in flag leaf for higher yields at the grain level is well known. It is a great challenge to properly exploit this knowledge because all the processes, starting from the emergence of the flag leaf to the grain filling stages of wheat (Triticum aestivum L.), are very complex biochemical and physiological processes to address. This study was conducted with the primary goal of functionally and structurally annotating the candidate genes associated with different developmental stages of flag leaf in a comprehensive manner using a plethora of in silico tools. Flag leaf-associated genes were analyzed for their structural and functional impacts using a set of bioinformatics tools and algorithms. The results revealed the association of 17 candidate genes with different stages of flag leaf development in wheat crop. Of these 17 candidate genes, the expression analysis results revealed the upregulation of genes such as TaSRT1-5D, TaPNH1-7B, and TaNfl1-2B and the downregulation of genes such as TaNAP1-7B, TaNOL-4D, and TaOsl2-2B can be utilized for the generation of high-yielding wheat varieties. Through MD simulation and other in silico analyses, all these proteins were found to be stable. Based on the outcome of bioinformatics and molecular analysis, the identified candidate genes were found to play principal roles in the flag leaf development process and can be utilized for higher-yield wheat production.
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Affiliation(s)
- Sheetal Mehla
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Biotechnology, CCS Haryana Agricultural University, Hisar, India
| | - Upendra Kumar
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Biotechnology, CCS Haryana Agricultural University, Hisar, India
| | - Prexha Kapoor
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Biotechnology, CCS Haryana Agricultural University, Hisar, India
| | - Yogita Singh
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Biotechnology, CCS Haryana Agricultural University, Hisar, India
| | - Pooja Sihag
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Biotechnology, CCS Haryana Agricultural University, Hisar, India
| | - Vijeta Sagwal
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Biotechnology, CCS Haryana Agricultural University, Hisar, India
| | - Priyanka Balyan
- Department of Botany, Deva Nagri P. G. College, CCS University, Meerut, India
| | - Anuj Kumar
- Shantou University Medical College, Shantou, China
- Dalhousie University, Halifax, NS, Canada
| | - Navjeet Ahalawat
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Biotechnology, CCS Haryana Agricultural University, Hisar, India
| | - Nita Lakra
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Biotechnology, CCS Haryana Agricultural University, Hisar, India
| | - Krishna Pal Singh
- Biophysics Unit, College of Basic Sciences and Humanities, GB Pant University of Agriculture and Technology, Pantnagar, India
- Vice-Chancellor’s Secretariat, Mahatma Jyotiba Phule Rohilkhand University, Bareilly, India
| | - Vladan Pesic
- Department of Genetics and Plant Breeding, Faculty of Agriculture, University of Belgrade, Belgrade, Serbia
| | - Ivica Djalovic
- Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Maxim Gorki 30, Novi Sad, Serbia
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-Kashmir), Srinagar, India
| | - Om Parkash Dhankher
- Stockbridge School of Agriculture, University of Massachusetts Amherst, Amherst, MA, United States
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Dandekar BR, Ahalawat N, Mondal J. Reconciling conformational heterogeneity and substrate recognition in cytochrome P450. Biophys J 2021; 120:1732-1745. [PMID: 33675756 PMCID: PMC8204291 DOI: 10.1016/j.bpj.2021.02.040] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 02/20/2021] [Accepted: 02/24/2021] [Indexed: 01/08/2023] Open
Abstract
Cytochrome P450, the ubiquitous metalloenzyme involved in detoxification of foreign components, has remained one of the most popular systems for substrate-recognition process. However, despite being known for its high substrate specificity, the mechanistic basis of substrate-binding by archetypal system cytochrome P450cam has remained at odds with the contrasting reports of multiple diverse crystallographic structures of its substrate-free form. Here, we address this issue by elucidating the probability of mutual dynamical transition to the other crystallographic pose of cytochrome P450cam and vice versa via unbiased all-atom computer simulation. A robust Markov state model, constructed using adaptively sampled 84-μs-long molecular dynamics simulation trajectories, maps the broad and heterogenous P450cam conformational landscape into five key substates. In particular, the Markov state model identifies an intermediate-assisted dynamic equilibrium between a pair of conformations of P450cam, in which the substrate-recognition sites remain "closed" and "open," respectively. However, the estimate of a significantly higher stationary population of closed conformation, coupled with faster rate of open → closed transition than its reverse process, dictates that the net conformational equilibrium would be swayed in favor of "closed" conformation. Together, the investigation quantitatively infers that although a potential substrate of cytochrome P450cam would, in principle, explore a diverse array of conformations of substrate-free protein, it would mostly encounter a "closed" or solvent-occluded conformation and hence would follow an induced-fit-based recognition process. Overall, the work reconciles multiple precedent crystallographic, spectroscopic investigations and establishes how a statistical elucidation of conformational heterogeneity in protein would provide crucial insights in the mechanism of potential substrate-recognition process.
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Affiliation(s)
- Bhupendra R Dandekar
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad, India
| | - Navjeet Ahalawat
- Department of Molecular Biology, Biotechnology and Bioinformatics, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad, India.
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Abstract
Computer simulation approaches in biomolecular recognition processes have come a long way. In this Perspective, we highlight a series of recent success stories in which computer simulations have played a remarkable role in elucidating the atomic resolution mechanism of kinetic processes of protein-ligand binding in a quantitative fashion. In particular, we show that a robust combination of unbiased simulation, harnessed by a high-fidelity computing environment, and Markov state modeling approaches has been instrumental in revealing novel protein-ligand recognition pathways in multiple systems. We also elucidate the role of recent developments in enhanced sampling approaches in providing the much-needed impetus in accelerating simulation of the ligand recognition process. We identify multiple key issues, including force fields and the sampling bottleneck, which are currently preventing the field from achieving quantitative reconstruction of experimental measurements. Finally, we suggest a possible way forward via adoption of multiscale approaches and coarse-grained simulations as next steps toward efficient elucidation of ligand binding kinetics.
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Affiliation(s)
- Navjeet Ahalawat
- Department of Molecular Biology, Biotechnology and Bioinformatics, Chaudhary Charan Singh, Haryana Agricultural University, Hisar 125004, India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad 500046, India
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Sharma N, Ahalawat N, Sandhu P, Strauss E, Mondal J, Anand R. Role of allosteric switches and adaptor domains in long-distance cross-talk and transient tunnel formation. Sci Adv 2020; 6:eaay7919. [PMID: 32284973 PMCID: PMC7124931 DOI: 10.1126/sciadv.aay7919] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 01/08/2020] [Indexed: 06/11/2023]
Abstract
Transient tunnels that assemble and disassemble to facilitate passage of unstable intermediates in enzymes containing multiple reaction centers are controlled by allosteric cues. Using the 140-kDa purine biosynthetic enzyme PurL as a model system and a combination of biochemical and x-ray crystallographic studies, we show that long-distance communication between ~25-Å distal active sites is initiated by an allosteric switch, residing in a conserved catalytic loop, adjacent to the synthetase active site. Further, combinatory experiments seeded from molecular dynamics simulations help to delineate transient states that bring out the central role of nonfunctional adaptor domains. We show that carefully orchestrated conformational changes, facilitated by interplay of dynamic interactions at the allosteric switch and adaptor-domain interface, control reactivity and concomitant formation of the ammonia tunnel. This study asserts that substrate channeling is modulated by allosteric hotspots that alter protein energy landscape, thereby allowing the protein to adopt transient conformations paramount to function.
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Affiliation(s)
- Nandini Sharma
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Navjeet Ahalawat
- Center for Interdisciplinary Science, Tata Institute of Fundamental Research, Hyderabad 500107, India
| | - Padmani Sandhu
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Erick Strauss
- Department of Biochemistry, Stellenbosch University, Stellenbosch 7602, South Africa
| | - Jagannath Mondal
- Center for Interdisciplinary Science, Tata Institute of Fundamental Research, Hyderabad 500107, India
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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11
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Prakashchand DD, Ahalawat N, Bandyopadhyay S, Sengupta S, Mondal J. Nonaffine Displacements Encode Collective Conformational Fluctuations in Proteins. J Chem Theory Comput 2020; 16:2508-2516. [DOI: 10.1021/acs.jctc.9b01100] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Dube Dheeraj Prakashchand
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad 500107, India
| | - Navjeet Ahalawat
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad 500107, India
- Department of Molecular Biology, Biotechnology and Bioinformatics, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Satyabrata Bandyopadhyay
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad 500107, India
| | - Surajit Sengupta
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad 500107, India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad 500107, India
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12
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Affiliation(s)
- Navjeet Ahalawat
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad 500107, India
- Department of Molecular Biology, Biotechnology and Bioinformatics, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Satyabrata Bandyopadhyay
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad 500107, India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad 500107, India
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13
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Abstract
Cytochrome P450s are ubiquitous metalloenzymes involved in the metabolism and detoxification of foreign components via catalysis of the hydroxylation reactions of a vast array of organic substrates. However, the mechanism underlying the pharmaceutically critical process of substrate access to the catalytic center of cytochrome P450 is a long-standing puzzle, further complicated by the crystallographic evidence of a closed catalytic center in both substrate-free and substrate-bound cytochrome P450. Here, we address a crucial question whether the conformational heterogeneity prevalent in cytochrome P450 translates to heterogeneous pathways for substrate access to the catalytic center of these metalloenzymes. By atomistically capturing the full process of spontaneous substrate association from bulk solvent to the occluded catalytic center of an archetypal system P450cam in multi-microsecond-long continuous unbiased molecular dynamics simulations, we here demonstrate that the substrate recognition in P450cam always occurs through a single well-defined dominant pathway. The simulated final bound pose resulting from these unguided simulations is in striking resemblance with the crystallographic bound pose. Each individual binding trajectory reveals that the substrate, initially placed at random locations in bulk solvent, spontaneously lands on a single key channel on the protein-surface of P450cam and resides there for an uncharacteristically long period, before correctly identifying the occluded target-binding cavity. Surprisingly, the passage of substrate to the closed catalytic center is not accompanied by any large-scale opening in protein. Rather, the unbiased simulated trajectories (∼57 μs) and underlying Markov state model, in combination with free-energy analysis, unequivocally show that the substrate recognition process in P450cam needs a substrate-induced side-chain displacement coupled with a complex array of dynamical interconversions of multiple metastable substrate conformations. Further, the work reconciles multiple precedent experimental and theoretical observations on P450cam and establishes a comprehensive view of substrate-recognition in cytochrome P450 that only occurs via substrate-induced structural rearrangements.
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Affiliation(s)
- Navjeet Ahalawat
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences , Hyderabad 500107 , India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences , Hyderabad 500107 , India
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14
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Ahalawat N, Mondal J. Assessment and optimization of collective variables for protein conformational landscape: GB1 β-hairpin as a case study. J Chem Phys 2018; 149:094101. [PMID: 30195312 DOI: 10.1063/1.5041073] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Collective variables (CVs), when chosen judiciously, can play an important role in recognizing rate-limiting processes and rare events in any biomolecular systems. However, high dimensionality and inherent complexities associated with such biochemical systems render the identification of an optimal CV a challenging task, which in turn precludes the elucidation of an underlying conformational landscape in sufficient details. In this context, a relevant model system is presented by a 16-residue β-hairpin of GB1 protein. Despite being the target of numerous theoretical and computational studies for understanding the protein folding, the set of CVs optimally characterizing the conformational landscape of the β-hairpin of GB1 protein has remained elusive, resulting in a lack of consensus on its folding mechanism. Here we address this by proposing a pair of optimal CVs which can resolve the underlying free energy landscape of the GB1 hairpin quite efficiently. Expressed as a linear combination of a number of traditional CVs, the optimal CV for this system is derived by employing the recently introduced time-structured independent component analysis approach on a large number of independent unbiased simulations. By projecting the replica-exchange simulated trajectories along these pair of optimized CVs, the resulting free energy landscape of this system is able to resolve four distinct well-separated metastable states encompassing the extensive ensembles of folded, unfolded, and molten globule states. Importantly, the optimized CVs were found to be capable of automatically recovering a novel partial helical state of this protein, without needing to explicitly invoke helicity as a constituent CV. Furthermore, a quantitative sensitivity analysis of each constituent in the optimized CV provided key insights on the relative contributions of the constituent CVs in the overall free energy landscapes. Finally, the kinetic pathways connecting these metastable states, constructed using a Markov state model, provide an optimum description of the underlying folding mechanism of the peptide. Taken together, this work offers a quantitatively robust approach toward comprehensive mapping of the underlying folding landscape of a quintessential model system along its optimized CV.
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Affiliation(s)
- Navjeet Ahalawat
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad 500107, India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad 500107, India
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15
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Ray A, Ahalawat N, Mondal J. Atomistic Insights into Structural Differences between E3 and E4 Isoforms of Apolipoprotein E. Biophys J 2018; 113:2682-2694. [PMID: 29262361 DOI: 10.1016/j.bpj.2017.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 10/04/2017] [Accepted: 10/05/2017] [Indexed: 12/23/2022] Open
Abstract
Among various isoforms of Apolipoprotein E (ApoE), the E4 isoform (ApoE4) is considered to be the strongest risk factor for Alzheimer's disease, whereas the E3 isoform (ApoE3) is neutral to the disease. Interestingly, the sequence of ApoE4 differs from its wild-type ApoE3 by a single amino acid C112R in the 299-amino-acid-long sequence. Hence, the puzzle remains: how a single-amino-acid difference between the ApoE3 and ApoE4 sequences can give rise to structural dissimilarities between the two isoforms, which can potentially lead to functional differences with significant pathological consequences. The major obstacle in addressing this question has been the lack of a 3D atomistic structure of ApoE4 to date. In this work, we resolve the issue by computationally modeling a plausible atomistic 3D structure of ApoE4. Our microsecond-long atomistic simulations elucidate key structural differences between monomeric ApoE3 and ApoE4, which renders ApoE4 thermodynamically less stable, less structured, and topologically less rigid compared to ApoE3. Consistent with an experimental report of the molten globule state of ApoE4, simulations identify multiple partially folded intermediates for ApoE4, which are implicated in the stronger aggregation propensity of ApoE4.
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Affiliation(s)
- Angana Ray
- Tata Institute of Fundamental Research, Hyderabad, Telangana, India
| | - Navjeet Ahalawat
- Tata Institute of Fundamental Research, Hyderabad, Telangana, India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research, Hyderabad, Telangana, India.
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16
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Ahalawat N, Murarka RK. Molecular Mechanism of Nucleotide-Dependent Allosteric Regulation in AMP-Activated Protein Kinase. J Phys Chem B 2017; 121:2919-2930. [PMID: 28345916 DOI: 10.1021/acs.jpcb.6b11223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The AMP-activated protein kinase (AMPK), a central enzyme in the regulation of energy homeostasis, is an important drug target for type 2 diabetes, obesity, and cancer. Binding of adenosine nucleotides to the regulatory γ-subunit tightly regulates the activity of this enzyme. Though recent crystal structures of AMPK have provided important insights into the allosteric activation of AMPK, molecular details of the regulatory mechanism of AMPK activation is still elusive. Here, we have performed extensive all-atom molecular dynamics (MD) simulations and shown that the kinase domain (KD) and γ-subunit come closer resulting in a more compact heterotrimeric AMPK complex in AMP-bound state compared to the ATP-bound state. The binding of ATP at site 3 of regulatory γ-subunit allosterically inhibits AMPK by destabilizing different regulatory regions of α-subunit: the autoinhibitory domain, the linker region, and the activation loop of the kinase core. The catalytically important residues experience a change in mechanical stress, and major rearrangements in community structure derived from residue-residue interaction energy-based network are observed in KD and α-linker region upon binding of different nucleotides. Our results also highlight the role of conserved charged residues forming an ionic network near the site 3 of γ-subunit in allosteric communications.
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Affiliation(s)
- Navjeet Ahalawat
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal , Bhopal By-pass Road, Bhauri, Bhopal 462 066, MP, India
| | - Rajesh K Murarka
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal , Bhopal By-pass Road, Bhauri, Bhopal 462 066, MP, India
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17
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Ahalawat N, Arora S, Murarka RK. Structural Ensemble of CD4 Cytoplasmic Tail (402–419) Reveals a Nearly Flat Free-Energy Landscape with Local α-Helical Order in Aqueous Solution. J Phys Chem B 2015; 119:11229-42. [DOI: 10.1021/acs.jpcb.5b03092] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Navjeet Ahalawat
- Department
of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal By-pass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Simran Arora
- Department
of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal By-pass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Rajesh K. Murarka
- Department
of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal By-pass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
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18
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Singh R, Ahalawat N, Murarka RK. Activation of corticotropin-releasing factor 1 receptor: insights from molecular dynamics simulations. J Phys Chem B 2015; 119:2806-17. [PMID: 25607803 DOI: 10.1021/jp509814n] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
G-protein-coupled receptors (GPCRs) constitute the largest family of membrane-bound proteins involved in translation of extracellular signals into intracellular responses. They regulate diverse physiological and pathophysiological processes, and hence, they are prime drug targets for therapeutic intervention. In spite of the recent advancements in membrane protein crystallography, limited information is available on the molecular signatures of activation of GPCRs. Although few studies have been reported for class A GPCRs, the activation mechanism of class B GPCRs remains unexplored. Corticotropin-releasing factor 1 receptor (CRF1R), a class B GPCR, is associated with various disease conditions including stress, anxiety, and irritable bowel syndrome. Here, we report the activation of CRF1R using accelerated molecular dynamics simulations of the apo receptor. The breakage of His155(2.50)-Glu209(3.50) and Glu209(3.50)-Thr316(6.42) interactions is found to be crucial in transition of the receptor to its active conformation. Compared to the inactive crystal structure, major structural rearrangements occurred in the intracellular region of the transmembrane (TM) domain upon activation: TM3 twisted away from TM2, and an opening of the G-protein binding site occurred as a result of the outward movements of TM5 and TM6 from the helical bundle. Further, an inward tilt of TM7 toward the helical core is observed at the extracellular side, in agreement with recent findings (Coin et al. Cell 2013, 155, 1258-1269), where it is proposed that this movement helps in establishing favorable interactions with peptide agonist. Moreover, different allosteric pathways in the inactive and active states are identified using the correlations in torsion angle space. The inactive state is found to be less dynamic as compared to the putative active state of the receptor. Results from the current study could present a model for class B GPCRs activation and aid in the design of CRF1R modulators against brain and metabolic disorders.
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Affiliation(s)
- Rajesh Singh
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal , Indore By-pass Road, Bhauri, Bhopal 462066, MP, India
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19
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Affiliation(s)
- Navjeet Ahalawat
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal , Bhauri, Bhopal, Madhya Pradesh 462066, India
| | - Rajesh K. Murarka
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal , Bhauri, Bhopal, Madhya Pradesh 462066, India
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20
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Balkrishna SJ, Kumar S, Azad GK, Bhakuni BS, Panini P, Ahalawat N, Tomar RS, Detty MR, Kumar S. An ebselen like catalyst with enhanced GPx activity via a selenol intermediate. Org Biomol Chem 2014; 12:1215-9. [DOI: 10.1039/c4ob00027g] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Benzamide ring-substituted, quinine-derived ebselen analogue is synthesized which exists in selenol form upon addition of PhSH. It catalyses oxidation of PhSH with H2O2 faster (103-fold) than ebselen.
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Affiliation(s)
- Shah Jaimin Balkrishna
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal (IISER)
- Bhopal, India
| | - Shailesh Kumar
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal (IISER)
- Bhopal, India
| | - Gajendra Kumar Azad
- Department of Biological Sciences
- Indian Institute of Science Education and Research Bhopal (IISER)
- Bhopal, India
| | - Bhagat Singh Bhakuni
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal (IISER)
- Bhopal, India
| | - Piyush Panini
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal (IISER)
- Bhopal, India
| | - Navjeet Ahalawat
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal (IISER)
- Bhopal, India
| | - Raghuvir Singh Tomar
- Department of Biological Sciences
- Indian Institute of Science Education and Research Bhopal (IISER)
- Bhopal, India
| | - Michael R. Detty
- Department of Chemistry
- University at Buffalo
- The State University of New York
- , USA
| | - Sangit Kumar
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal (IISER)
- Bhopal, India
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21
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Sudhamalla B, Gokara M, Ahalawat N, Amooru DG, Subramanyam R. Molecular Dynamics Simulation and Binding Studies of β-Sitosterol with Human Serum Albumin and Its Biological Relevance. J Phys Chem B 2010; 114:9054-62. [DOI: 10.1021/jp102730p] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Babu Sudhamalla
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, 500046, India, Department of Biotechnology, School of Life Sciences, University of Hyderabad, 500046, India, and Department of Chemistry, Yogi Vemana University, Kadapa, Andhrapradesh, 516003, India
| | - Mahesh Gokara
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, 500046, India, Department of Biotechnology, School of Life Sciences, University of Hyderabad, 500046, India, and Department of Chemistry, Yogi Vemana University, Kadapa, Andhrapradesh, 516003, India
| | - Navjeet Ahalawat
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, 500046, India, Department of Biotechnology, School of Life Sciences, University of Hyderabad, 500046, India, and Department of Chemistry, Yogi Vemana University, Kadapa, Andhrapradesh, 516003, India
| | - Damu G. Amooru
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, 500046, India, Department of Biotechnology, School of Life Sciences, University of Hyderabad, 500046, India, and Department of Chemistry, Yogi Vemana University, Kadapa, Andhrapradesh, 516003, India
| | - Rajagopal Subramanyam
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, 500046, India, Department of Biotechnology, School of Life Sciences, University of Hyderabad, 500046, India, and Department of Chemistry, Yogi Vemana University, Kadapa, Andhrapradesh, 516003, India
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