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Bhushan D Pandey A Chattopadhyay A Choudhary MK Chakraborty S Datta A Chakraborty N 《Journal of proteome research》2006,5(7):1711-1720
The extracellular matrix (ECM) or cell wall is a dynamic system and serves as the first line mediator in cell signaling to perceive and transmit extra- and intercellular signals in many pathways. Although ECM is a conserved compartment ubiquitously present throughout evolution, a compositional variation does exist among different organisms. ECM proteins account for 10% of the ECM mass, however, comprise several hundreds of different molecules with diverse functions. To understand the function of ECM proteins, we have developed the cell wall proteome of a crop legume, chickpea (Cicer arietinum). This comprehensive overview of the proteome would provide a basis for future comparative proteomic efforts for this important crop. Proteomic analyses revealed new ECM proteins of unknown functions vis-à-vis the presence of many known cell wall proteins. In addition, we report here evidence for the presence of unexpected proteins with known biochemical activities, which have never been associated with ECM. 相似文献
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Ahmed Kamal E. Vijaya Bharathi M. Janaki Ramaiah D. Dastagiri J. Surendranadha Reddy A. Viswanath Farheen Sultana S.N.C.V.L. Pushpavalli Manika Pal-Bhadra Hemant Kumar Srivastava G. Narahari Sastry Aarti Juvekar Subrata Sen Surekha Zingde 《Bioorganic & medicinal chemistry》2010,18(2):526-542
A series of novel quinazolinone linked pyrrolobenzodiazepine (PBD) conjugates were synthesized. These compounds 4a–f and 5a–f were prepared in good yields by linking C-8 of DC-81 with quinazolinone moiety through different alkane spacers. These conjugates were tested for anticancer activity against 11 human cancer cell lines and found to be very potent anticancer agents with GI50 values in the range of <0.1–26.2 μM. Among all the PBD conjugates, one of the conjugate 5c was tested against a panel of 60 human cancer cells. This compound showed activity for individual cancer cell lines with GI50 values of <0.1 μM. The thermal denaturation studies exhibited effective DNA binding ability compared to DC-81 and these results are further supported by molecular modeling studies. The detailed biological aspects of these conjugates on A375 cell line were studied. It was observed that compounds 4b and 5c induced the release of cytochrome c, activation of caspase-3, cleavage of PARP and subsequent cell death. Further, these compounds when treated with A375 cells showed the characteristic features of apoptosis like enhancement in the levels of p53, p21 and p27 inhibition of cyclin dependent kinase-2 (CDK2) and suppression of NF-κB. Moreover, these two compounds 4b and 5c control the cell proliferation by regulating anti-apoptotic genes like (B-cell lymphoma 2) Bcl-2. Therefore, the data generated suggests that these PBD conjugates activate p53 and inhibit NF-κB and thereby these compounds could be promising anticancer agents with better therapeutic potential for the suppression of tumours. 相似文献
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The association of structurally disordered proteins with a number of diseases has engendered enormous interest and therefore
demands a prediction method that would facilitate their expeditious study at molecular level. The present study describes
the development of a computational method for predicting disordered proteins using sequence and profile compositions as input
features for the training of SVM models. First, we developed the amino acid and dipeptide compositions based SVM modules which
yielded sensitivities of 75.6 and 73.2% along with Matthew’s Correlation Coefficient (MCC) values of 0.75 and 0.60, respectively.
In addition, the use of predicted secondary structure content (coil, sheet and helices) in the form of composition values
attained a sensitivity of 76.8% and MCC value of 0.77. Finally, the training of SVM models using evolutionary information
hidden in the multiple sequence alignment profile improved the prediction performance by achieving a sensitivity value of
78% and MCC of 0.78. Furthermore, when evaluated on an independent dataset of partially disordered proteins, the same SVM
module provided a correct prediction rate of 86.6%. Based on the above study, a web server (“DPROT”) was developed for the
prediction of disordered proteins, which is available at . 相似文献
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Aarti Paliwal Narpat S. Shekhawat Harchand R. Dagla 《In vitro cellular & developmental biology. Plant》2018,54(6):637-641
In the present study, an in vitro regeneration protocol for Glossonema varians (Stocks) Benth. ex Hook.f. of family Asclepiadaceae was optimized. Cotyledonary nodes of in vitro cultured seedlings were used as explants for activation of axillary shoot buds. Axillary shoot buds were initially activated on 0.1 mg L?1 6-benzylaminopurine (BAP) and then multiplied on 0.05 mg L?1 BAP. Shoots were rooted in vitro on 1/4 strength Murashige and Skoog medium containing 0.1 mg L?1 2-naphthoxyacetic acid and 100 mg L?1 activated charcoal. The cultures were maintained in a 12 h photoperiod at 40–50 μmol m?2 s?1 spectral flux photon, 25–30?±?2°C, and 60% relative humidity (RH). Up to 80% of in vitro regenerated plantlets were acclimatized on soilrite in cotton-plugged culture tubes in the greenhouse. This protocol can be a useful method to mass propagate and conserve this rare plant to balance biodiversity in the desert ecosystem. 相似文献
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Comparative proteome analysis reveals pathogen specific outer membrane proteins of Leptospira 下载免费PDF全文
Aarti Rana Rahul Brahma Yusuf Akhter Madathiparambil Gopalakrishnan Madanan 《Proteins》2018,86(7):712-722
Proteomes of pathogenic Leptospira interrogans and L. borgpetersenii and the saprophytic L. biflexa were filtered through computational tools to identify Outer Membrane Proteins (OMPs) that satisfy the required biophysical parameters for their presence on the outer membrane. A total of 133, 130, and 144 OMPs were identified in L. interrogans, L. borgpetersenii, and L. biflexa, respectively, which forms approximately 4% of proteomes. A holistic analysis of transporting and pathogenic characteristics of OMPs together with Clusters of Orthologous Groups (COGs) among the OMPs and their distribution across 3 species was made and put forward a set of 21 candidate OMPs specific to pathogenic leptospires. It is also found that proteins homologous to the candidate OMPs were also present in other pathogenic species of leptospires. Six OMPs from L. interrogans and 2 from L. borgpetersenii observed to have similar COGs while those were not found in any intermediate or saprophytic forms. These OMPs appears to have role in infection and pathogenesis and useful for anti‐leptospiral strategies. 相似文献
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Aarti Yadav Rajnish Kumar Aditya Sunkaria Nitin Singhal 《Journal of biomolecular structure & dynamics》2016,34(5):993-1007
Glyoxalase-I (GLO-I) is a component of the ubiquitous detoxification system involved in the conversion of methylglyoxal (MG) to d-lactate in the glycolytic pathway. MG toxicity arises from its ability to form advanced glycation end products. GLO-I has been reported to be frequently overexpressed in various types of cancer cells. In this study, we performed structure-based virtual screening of focused flavonoids commercial library to identify potential and specific inhibitors of GLO-I. The compounds were ranked based on Glide extra precision docking score and five hits (curcumin, quercetin, morin, naringin and silibinin) were selected on the basis of their interaction with active site amino acid residues of GLO-I. Mixed mode QM/MM calculation was performed on the top-scoring hit to ascertain the role of zinc ion in ligand binding. In addition, the identified hits were subjected to MM/GBSA binding energy prediction, ADME prediction and similarity studies. The hits were tested in vitro for cell viability, and GLO-I inhibition. Naringin (ST072162) was found to be most potent inhibitor of GLO-I among the identified hits with highest glide XP dock score of ?14.906. These findings suggest that naringin could be a new scaffold for designing inhibitors against GLO-I with potential application as anticancer agents. 相似文献
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S. Muthukrishnan Aarti Garg G.P.S. Raghava 《基因组蛋白质组与生物信息学报(英文版)》2007,(4):250-252
This study describes a method for predicting and classifying oxygen-binding pro- teins. Firstly, support vector machine (SVM) modules were developed using amino acid composition and dipeptide composition for predicting oxygen-binding pro- teins, and achieved maximum accuracy of 85.5% and 87.8%, respectively. Sec- ondly, an SVM module was developed based on amino acid composition, classify- ing the predicted oxygen-binding proteins into six classes with accuracy of 95.8%, 97.5%, 97.5%, 96.9%, 99.4%, and 96.0% for erythrocruorin, hemerythrin, hemo- cyanin, hemoglobin, leghemoglobin, and myoglobin proteins, respectively. Finally, an SVM module was developed using dipeptide composition for classifying the oxygen-binding proteins, and achieved maximum accuracy of 96.1%, 98.7%, 98.7%, 85.6%, 99.6%, and 93.3% for the above six classes, respectively. All modules were trained and tested by five-fold cross validation. Based on the above approach, a web server Oxypred was developed for predicting and classifying oxygen-binding proteins(available from http://www.imtech.res.in/raghava/oxypred/). 相似文献
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Kamal A Shankaraiah N Devaiah V Laxma Reddy K Juvekar A Sen S Kurian N Zingde S 《Bioorganic & medicinal chemistry letters》2008,18(4):1468-1473
1,2,3-Triazole based molecules are useful pharmacophores for several DNA-alkylating and cross-linking agents. A series of A/C8, C/C2 and A/C8-C/C2-linked 1,2,3-triazole-PBD conjugates have been synthesized by employing 'click' chemistry. These molecules have exhibited promising DNA-binding affinity and anticancer activity in selected human cancer cell lines. 相似文献