Rajendra Joshi

Centre for Development of Advanced Computing, Poona, Mahārāshtra, India

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Publications (31)119.37 Total impact

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    ABSTRACT: Bio-prospecting of natural molecules is essential to overcome serious environmental issues and pesticide resistance in insects. Here we are reporting insights into insecticidal activity of a plant natural phenol. In silico and in vitro screening of multiple molecules supported by in vivo validations suggested that caffeic acid (CA) is a potent inhibitor of Helicoverpa armigera gut proteases. Protease activity and gene expression were altered in CA-fed larvae. Structure-activity relationship of CA highlighted that all the functional groups are crucial for inhibition of protease activity. Biophysical studies and molecular dynamic simulations revealed that sequential binding of multiple CA molecules induces conformational changes in the protease(s) and thus lead to significant decline in their activity. CA treatment significantly inhibits the insect's detoxification enzymes, thus intensifying the insecticidal effect. Our findings suggest that CA can be implicated as a potent insecticidal molecule and explored for the development of effective dietary pesticides.
    Journal of agricultural and food chemistry. 10/2014;
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    ABSTRACT: Recent evidences suggest that a substantial amount of genome is transcribed more than that was anticipated, giving rise to a large number of unknown or novel transcripts. Identification of novel transcripts can provide key insights into understanding important cellular functions as well as molecular mechanisms underlying complex diseases like cancer. RNA-Seq has emerged as a powerful tool to detect novel transcripts, which previous profiling techniques failed to identify. A number of tools are available for enabling identification of novel transcripts at different levels. Read mappers such as TopHat, MapSplice, and SOAPsplice predict novel junctions, which are the indicators of novel transcripts. Cufflinks assembles novel transcripts based on alignment information and Oases performs de novo construction of transcripts. A common limitation of all these tools is prediction of sizable number of spurious or false positive (FP) novel transcripts. An approach that integrates information from all above sources and simultaneously scrutinizes FPs to correctly identify authentic novel transcripts of high confidence is proposed.
    Journal of Bioinformatics and Computational Biology 08/2014; · 0.93 Impact Factor
  • Vinod Jani, Uddhavesh B Sonavane, Rajendra Joshi
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    ABSTRACT: Proteins fold by diverse pathways which depend on the energy barriers involved in reaching different intermediates. There has been a lot of development in the theoretical aspects of protein folding, from force-field to simulation techniques. One such simulation approach is replica exchange molecular dynamics simulation (REMD), which provides an efficient conformational sampling method to understand the events involved in protein folding. In this study, an attempt is made to explore the folding funnel of engrailed homeodomain protein (EnHD) using REMD simulations. EnHD is a 54 residue long helix bundle protein which has a folding time of about 15 μs. The protein was represented using the Amber United atom model in order to reduce the system size which helped to speed up the simulation. Individual replicas were simulated for 1.4-2 μs making cumulative time of more than 100 μs of REMD simulations. Free energy analysis was carried out to understand the folding behavior of EnHD protein. Effects of temperature range and exchange frequency in REMD simulations have been explored. In addition to this, multiple umbrella sampling (US) simulations of a total of 320 ns were also carried out, followed by weighted histogram analysis method (WHAM) to investigate the energy barriers involved during the folding of various intermediates. US studies were also carried on mutational variants of EnHD protein to see effect of the mutations on the folding pathway of the protein. The use of US technique may be helpful for predicting fast folding mutants or protein engineering. The combination of REMD with US may help in understanding the energetics between multiple pathways of fast folding proteins and their mutant counterparts.
    Journal of Molecular Modeling 06/2014; 20(6):2283. · 1.98 Impact Factor
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    ABSTRACT: (+)-(1S,5R)-7,10-Dimethoxy-3-((S)-1-phenylethyl)-1,2,3,4,5,6-hexahydro-1,5-epoxybenzo[d]azocineC21H25NO3[α]D26.7=+27.8 (c 1, CHCl3)Source of chirality: (S)-ProlineAbsolute configuration: (1S,5R) (3S)
    Tetrahedron Asymmetry 04/2014; · 2.12 Impact Factor
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    ABSTRACT: Two ruthenium(II) polypyridyl complexes [Ru(phen)3](2+) (1) and [Ru(phen)2(bxbg)](2+) (2) (where phen = 1,10 phenanthroline, bxbg = bis(o-xylene)bipyridine glycoluril) have been evaluated for acetylcholinesterase (AChE) and Amyloid-β peptide (Aβ) aggregation inhibition. Complex 2 exhibits higher potency of AChE inhibition and kinetics and molecular modeling studies indicate that ancillary ligand plays significant role in inhibitory potency exhibited by complex 2. The inhibitory effect of these complexes on Aβ (1-40) aggregation is investigated using Thioflavin T fluorescence and Transmission Electron Microscopy. Both complexes efficiently inhibit Aβ (1-40) aggregation and are negligibly toxic to human neuroblastoma cells. This is the first demonstration that ruthenium(II) polypyridyl complexes simultaneously inhibit AChE and Aβ aggregation.
    European Journal of Medicinal Chemistry 01/2014; 75C:375-381. · 3.43 Impact Factor
  • Neeru Sharma, Uddhavesh Sonavane, Rajendra Joshi
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    ABSTRACT: Ras is one of the most common oncogenes in human cancers. It belongs to a family of GTPases that functions as binary conformational switches by timely switching of their conformations from GDP to GTP and vice versa. It attains the final active state structure via an intermediate GTP-bound state. The transition between these states is a millisecond-time-scale event. This makes studying this mechanism beyond the scope of classical molecular dynamics. In the present study, we describe the activation pathway of the HRas protein complex along the distance-based reaction coordinate using steered molecular dynamics. Approximately ~720 ns of MD simulations using CMD and SMD was performed. We demonstrated the change in orientation and arrangement of the two switch regions and the role of various hydrogen bonds during the activation process. The weighted histogram analysis method was also performed, and the potential of mean force was calculated between the inactive and active via the intermediate state (state 1) of HRas. The study indicates that water seems to play a crucial role in the activation process and to transfer the HRas protein from its intermediate state to the fully active state. The implications of our study hereby suggest that the HRas activation mechanism is a multistep process. It starts from the inactive state to an intermediate state 1 followed by trapping of water molecules and flipping of the Thr35 residue to form a fully active state (state 2). This state 2 also comprises Gly60, Thr35, GTP, Mg(2+) and water-forming stable interactions.
    Biophysics of Structure and Mechanism 01/2014; · 2.44 Impact Factor
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    ABSTRACT: Ligand recognition in purine riboswitches is a complex process requiring different levels of conformational changes. Recent efforts in the area of purine riboswitch research have focused on ligand analogue binding studies. In the case of the guanine xanthine phosphoribosyl transferase (xpt) riboswitch, synthetic analogues that resemble guanine have the potential to tightly bind and subsequently influence the genetic expression of xpt mRNA in prokaryotes. We have carried out 25 ns Molecular Dynamics (MD) simulation studies of the aptamer domain of the xpt G-riboswitch in four different states: guanine riboswitch in free form, riboswitch bound with its cognate ligand guanine, and with two guanine analogues SJ1 and SJ2. Our work reveals novel interactions of SJ1 and SJ2 ligands with the binding core residues of the riboswitch. The ligands proposed in this work bind to the riboswitch with greater overall stability and lower root mean square deviations and fluctuations compared to guanine ligand. Reporter gene assay data demonstrate that the ligand analogues, upon binding to the RNA, lower the genetic expression of the guanine riboswitch. Our work has important implications for future ligand design and binding studies in the exciting field of riboswitches.
    Journal of biomolecular Structure & Dynamics 01/2014; · 2.98 Impact Factor
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    ABSTRACT: p53 is a transcription factor involved in the expression of a number of downstream genes in response to genotoxic stress. It is activated through post translation modifications in normal as well as cancerous cells. However, due to mutations occurring in p53 in cancer cells it is not able to perform its function of DNA binding which leads to cell proliferation. It is found to be mutated in 50 % of the cancers. These mutations occur at a high frequency in the DNA binding region of the p53. Among the known seven hot spot cancer mutations G245S, R249S, and R273C have been studied here using quantum mechanics and molecular mechanics (QM-MM) simulations. These mutations along with their experimentally proven rescue mutations have also been included in the present work. A comparative study of these cancer mutations along with wild type and their rescue mutations has been performed. A computational measure based on the free energy changes occurring in the binding of the p53 to the DNA has been presented. A correlation between the DNA binding property and important interaction between p53 and DNA has been observed for all the mutants. The keys residues which contribute to the binding of p53 to DNA by forming crucial hydrogen bonds have also been discussed in detail. A 30 ns simulation study was analyzed to observe the local structural changes and DNA binding property of p53 in case of wild type, cancer and rescue mutants.
    Journal of Molecular Modeling 11/2013; · 1.98 Impact Factor
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    ABSTRACT: The long perceived notion that G-Protein Coupled Receptors (GPCRs) function in monomeric form has recently been changed by the description of a number of GPCRs that are found in oligomeric states. The mechanism of GPCR oligomerization, and its effect on receptor function, is not well understood. In the present study, coarse grained molecular dynamics (CGMD) approach was adopted for studying the self-assembly process of the human GPCR, β2-adrenergic receptor (β2-AR), for which several experimental evidences of the dimerization process and its effect on cellular functions are available. Since the crystal structure of β2-AR lacks the third intracellular loop, initially it was modelled and simulated using restrained MD in order to get a stable starting conformation. This structure was then converted to CG representation and 16 copies of it, inserted into a hydrated lipid bilayer, were simulated for 10μs using the MARTINI force field. At the end of 10μs, oligomers of β2-AR were found to be formed through the self-assembly mechanism which were further validated through various analyses of the receptors. The lipid bilayer analysis also helped to quantify this assembly mechanism. In order to identify the domains which are responsible for this oligomerization, a reverse transformation of the CG system back to all-atom structure and simulated annealing run were carried out at the end of 10μs CGMD run. Analysis of the all-atom dimers thus obtained, revealed that TM1/TM1, H8/H8, TM1/TM5 and TM6/TM6 regions formed most of the dimerization surfaces, which is in accordance with some of the experimental observations and recent simulation results.
    Computational biology and chemistry 11/2013; 48C:29-39. · 1.37 Impact Factor
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    ABSTRACT: The present invention relates to a method for pest management using inhibitory repeat domain IRD 9 (Seq ID No.2) proteinase inhibitor showing enhanced inhibitory activity against the gut proteases of insects. More particularly, the present invention relates to a IRD 9 (Seq ID No.2) proteinase inhibitor from non-host plant Capsicum annuum, which possesses significantly high insect protease inhibition activity against the gut proteases of Helicoverpa armigera.
    Ref. No: WO2013102937, Year: 07/2013
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    ABSTRACT: The principle of antisense technologies is based on the specific inhibition of unwanted gene expression by blocking mRNA activity. A rapid increase in the number of antisense molecules in clinical trials was observed. The 2′-O-methoxyethyl modification (MOE) showed a good safety profile with limited binding affinity, whereas locked nucleic acid (LNA) showed high potency by exhibiting strong binding affinity and high toxicity. The novel 2′-4′ conformationally restricted nucleoside analogue has the structural features of both MOE (second generation) and LNA (third generation). It is possible to acquire the positive features of both MOE and LNA and show high potency without an increase in the hepatotoxicity. Structural insight at the monomer level can be useful in understanding the function of the modification and designing derivatives of these molecules. Therefore, the quantum chemical studies of the antisense nucleoside modifications like MOE, LNA, and two stereo isomers of constrained MOE (cMOE) were performed at the monomer level. The conformational preferences of these antisense monomers were studied using a multidimensional conformational search. The semiempirical method PM6 of the MOPAC software was used for the conformational search. Three structures were chosen based upon energy criteria after the conformational search for all the monomers. Full geometry optimization calculations were done on the three structures (most stable, alternate stable, start structures) of all the monomers using the Hartree–Fock method. This was followed by single-point density functional theory (DFT) calculations in gas phase and solvent phase using the B3LYP/6-311G** basis set. Quantum chemical descriptors were derived for the stable geometries of all these monomers. Structural properties and reactivity descriptors of all four antisense modifications in the gas phase and the solvent phase were also studied. The results suggest that LNA is more reactive, that is, highly toxic in nature and with a good binding affinity, while MOE is less reactive, that is, less toxic with weak binding affinity. These results agree with the experimental findings. Properties of 2′-4′ conformationally restricted modifications (ScMOE and RcMOE) showed better stability than MOE and less reactivity than LNA. Therefore, these cMOEs may show less toxicity with high binding affinity toward the target, as shown in the experiments. Study at the monomer level would help in understanding the conformational flexibility available with all modifications, along with various reactivity descriptors, which may help guide the design of new modifications. This study attempts to find an indirect relationship between the quantum chemical descriptors and the experimental data, which may be useful in designing new molecules or modifications tuned for specific requirements of antisense molecules
    International Journal of Quantum Chemistry 06/2013; · 1.17 Impact Factor
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    ABSTRACT: Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment. Fifty-four methods representing the state of the art for protein function prediction were evaluated on a target set of 866 proteins from 11 organisms. Two findings stand out: (i) today's best protein function prediction algorithms substantially outperform widely used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is considerable need for improvement of currently available tools.
    Nature Methods 01/2013; 10(3):221-227. · 23.57 Impact Factor
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    ABSTRACT: Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment. Fifty-four methods representing the state of the art for protein function prediction were evaluated on a target set of 866 proteins from 11 organisms. Two findings stand out: (i) today's best protein function prediction algorithms substantially outperform widely used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is considerable need for improvement of currently available tools.
    Nature Methods 01/2013; 10(3):221-227. · 23.57 Impact Factor
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    ABSTRACT: p53 is a transcription factor involved in expression of a number of downstream genes in response to genotoxic stress. In normal cells, it is present in the latent or inactive state, and the in case of cancer cells it is activated by various post translation modifications. It is found to be mutated in 50% of the cancers. These mutations occur at a high frequency in the DNA binding region of p53. All seven hot spot cancer mutations R175H, Y220C, G245S, R248Q, R249S, R273C, and R282 W have been studied here using quantum and molecular mechanics hybrid simulations. The experimentally proven rescue mutations of the above mentioned cancer mutants have also been included in the present work. Each of the p53 mutants has been simulated for 30 ns each. A comparative study of these cancer mutations along with wild-type and their rescue mutations have been studied. The key residues which contribute to the binding of the p53 to the DNA by forming crucial hydrogen bonds have been studied in detail. Free energy changes, principal component analysis, hydrogen bonding, and various other structural parameters have been calculated to quantify the loss and gain in DNA binding property and local structural alterations of all the p53 mutants.
    Journal of biomolecular Structure & Dynamics 01/2013; 31. · 2.98 Impact Factor
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    ABSTRACT: Capsicum annuum (L.) expresses diverse potato type II family proteinase inhibitors comprising of inhibitory repeat domain (IRD) as basic functional unit. Most IRDs contain eight conserved cysteines forming four disulfide bonds, which are indispensible for their stability and activity. We investigated the functional significance of evolutionary variations in IRDs and their role in mediating interaction between the inhibitor and cognate proteinase. Among the 18 IRDs encoded by C. annuum, IRD-7, -9, and -12 were selected for further characterization on the basis of variation in their reactive site loop, number of conserved cysteine residues, and higher theoretical ΔG (bind) for interaction with Helicoverpa armigera trypsin. Moreover, inhibition kinetics showed that IRD-9, despite loss of some of the disulfide bonds, was a more potent proteinase inhibitor among the three selected IRDs. Molecular dynamic simulations revealed that serine residues in the place of cysteines at seventh and eighth positions of IRD-9 resulted in an increase in the density of intramolecular hydrogen bonds and reactive site loop flexibility. Results of the serine residues chemical modification also supported this observation and provided a possible explanation for the remarkable inhibitory potential of IRD-9. Furthermore, this natural variant among IRDs showed special attributes like stability to proteolysis and synergistic inhibitory effect on other IRDs. It is likely that IRDs have coevolved selective specialization of their structure and function as a response towards specific insect proteases they encountered. Understanding the molecular mechanism of pest protease-plant proteinaceous inhibitor interaction will help in developing effective pest control strategies. An animated interactive 3D complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:39.
    Journal of biomolecular Structure & Dynamics 12/2012; · 2.98 Impact Factor
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    ABSTRACT: Human immunodeficiency virus type 1 (HIV-1) requires the human tRNA(3) (Lys) as a reverse transcriptase (RT) primer. The annealing of 3' terminal 18 nucleotides of tRNA(3) (Lys) with the primer binding site (PBS) of viral RNA (vRNA) is crucial for reverse transcription. Additional contacts between the A rich (A-loop) region of vRNA and the anticodon domain of tRNA(3) (Lys) are necessary, which show the specific requirement of tRNA(3) (Lys). The importance of modified nucleosides, present in tRNA(3) (Lys), in giving stability to the primer-template complex has been determined in earlier experiments. It has been observed that the PNA oligomer targeted to PBS of vRNA destabilized the crucial interactions between primer and template due to which the reverse transcription is inhibited. Molecular dynamics simulations have been carried out to study the effect of modified nucleosides on the vRNA-tRNA(3) (Lys) complex stability and the destabilization effect of PNA oligomer on the vRNA-tRNA(3) (Lys)-PNA complex. The root-mean-square deviation, hydrogen bonding, tertiary interactions, and free energy calculations of the simulation data support the experimental results. The analyses have revealed the structural changes in PBS region of vRNA which might be another strong reason for the inability of RT binding to 7F helix for its normal functioning of reverse transcription.
    Journal of biomolecular Structure & Dynamics 08/2012; · 2.98 Impact Factor
  • International Journal of Computer Science Issues. 01/2012; 9(6).
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    ABSTRACT: Human ocular albinism type 1 protein (OA1)-a member of the G-protein coupled receptor (GPCR) superfamily-is an integral membrane glycoprotein expressed exclusively by intracellular organelles known as melanocytes, and is responsible for the proper biogenesis of melanosomes. Mutations in the Oa1 gene are responsible for the disease ocular albinism. Despite its clinical importance, there is a lack of in-depth understanding of its structure and mechanism of activation due to the absence of a crystal structure. In the present study, homology modeling was applied to predicting OA1 structure following thorough sequence analysis and secondary structure predictions. The predicted model had the signature residues and motifs expected of GPCRs, and was used for carrying out molecular docking studies with an endogenous ligand, L-DOPA and an antagonist, dopamine; the results agreed quite well with the available experimental data. Finally, three sets of explicit molecular dynamics simulations were carried out in lipid bilayer, the results of which not only confirmed the stability of the predicted model, but also helped witness some differences in structural features such as rotamer toggle switch, helical tilts and hydrogen bonding pattern that helped distinguish between the agonist- and antagonist-bound receptor forms. In place of the typical "D/ERY"-motif-mediated "ionic lock", a hydrogen bond mediated by the "DAY" motif was observed that could be used to distinguish the agonist and antagonist bound forms of OA1. In the absence of a crystal structure, this study helped to shed some light on the structural features of OA1, and its behavior in the presence of an agonist and an antagonist, which might be helpful in the future drug discovery process for ocular albinism.
    Journal of Molecular Modeling 09/2011; 18(5):2117-33. · 1.98 Impact Factor
  • Vinod Jani, Uddhavesh B Sonavane, Rajendra Joshi
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    ABSTRACT: Reaching the experimental time scale of millisecond is a grand challenge for protein folding simulations. The development of advanced Molecular Dynamics techniques like Replica Exchange Molecular Dynamics (REMD) makes it possible to reach these experimental timescales. In this study, an attempt has been made to reach the multi microsecond simulation time scale by carrying out folding simulations on a three helix bundle protein, Villin, by combining REMD and Amber United Atom model. Twenty replicas having different temperatures ranging from 295 K to 390 K were simulated for 1.5 µs each. The lowest Root Mean Square Deviation (RMSD) structure of 2.5 Å was obtained with respect to native structure (PDB code 1VII), with all the helices formed. The folding population landscapes were built using segment-wise RMSD and Principal Components as reaction coordinates. These analyses suggest the two-stage folding for Villin. The combination of REMD and Amber United Atom model may be useful to understand the folding mechanism of various fast folding proteins.
    Journal of biomolecular Structure & Dynamics 06/2011; 28(6):845-60. · 2.98 Impact Factor
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    Rajendra Joshi
    Journal of biomolecular Structure & Dynamics 02/2011; 28(4):667-8; discussion 669-674. · 2.98 Impact Factor