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In the biomedical industry, nanoparticles (NPs-exclusively small particles with size ranging from 1-100 nanometres) are recently employed as powerful tools due to their huge potential in sophisticated and enhanced cancer theragnostic (i.e. therapeutics and diagnostics). Cancer is a life-threatening disease caused by carcinogenic agents and mutation in cells, leading to uncontrolled cell growth and harming the body's normal functioning while affecting several factors like low levels of reactive oxygen species, hyperactive antiapoptotic mRNA expression, reduced proapoptotic mRNA expression, damaged DNA repair, and so on. NPs are extensively used in early cancer diagnosis and are functionalized to target receptors overexpressing cancer cells for effective cancer treatment. This review focuses explicitly on how NPs alone and combined with imaging techniques and advanced treatment techniques have been researched against 'women's cancer' such as breast, ovarian, and cervical cancer which are substantially occurring in women. NPs, in combination with numerous imaging techniques (like PET, SPECT, MRI, etc) have been widely explored for cancer imaging and understanding tumor characteristics. Moreover, NPs in combination with various advanced cancer therapeutics (like magnetic hyperthermia, pH responsiveness, photothermal therapy, etc), have been stated to be more targeted and effective therapeutic strategies with negligible side effects. Furthermore, this review will further help to improve treatment outcomes and patient quality of life based on the theragnostic application-based studies of NPs in women's cancer treatment.
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Nanopartículas , Feminino , Humanos , Antineoplásicos/química , Antineoplásicos/farmacologia , Neoplasias da Mama/tratamento farmacológico , Nanopartículas/química , Neoplasias/terapia , Neoplasias/tratamento farmacológico , Neoplasias Ovarianas/tratamento farmacológico , Neoplasias Ovarianas/diagnóstico por imagem , Nanomedicina Teranóstica , Neoplasias do Colo do Útero/tratamento farmacológicoRESUMO
Rice (Oryza sativa) being among the most important food crops in the world is also susceptible to various bacterial and fungal diseases that are the major stumbling blocks in the way of increased production and productivity. The bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae and the sheath blight disease caused by Rhizoctonia solani are among the most devastating diseases of the rice crop. In spite of the availability of array of chemical control, there are chances of development of resistance. Thus, there is a need for the nanotechnological intervention for management of disease in the form of copper and silver nano-composites. The copper (CuNPs) and silver nanoparticles (AgNPs) were synthesized using green route and characterized using different high throughput techniques, i.e., UV-Vis, FT-IR, DLS, XRD, FE-SEM, TEM. The particle size and zeta potential of synthesized CuNPs and AgNPs were found 273 nm and - 24.2 mV; 95.19 nm and - 25.5 mV respectively. The nanocomposite of CuNPs and AgNPs were prepared having particle size in the range of 375-306 nm with improved stability (zeta potential - 54.7 to - 39.4 mV). The copper and silver nanoparticle composites evaluated against Xanthomonas oryzae pv. oryzae and Rhizoctonia solani were found to have higher antibacterial (inhibition zone 13 mm) and antifungal activities (77%) compared to only the copper nanoparticle (8 mm; 62% respectively). Net house trials of nano-composite formulations against the bacterial blight of rice also corroborated the potential of nanocomposite formulation. In silico studies were carried out selecting two disease-causing proteins, peptide deformylase (Xanthomonas oryzae) and pectate lyase (Rhizoctonia solani) to perform the molecular docking. Interaction studies indicatedthat both of these proteins generated better complex with CuNPs than AgNPs. The study suggested that the copper and silver nano-composites could be used for developing formulations to control these devastating rice diseases.
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Nanopartículas Metálicas , Oryza , Rhizoctonia , Xanthomonas , Prata/farmacologia , Prata/metabolismo , Nanopartículas Metálicas/química , Cobre/farmacologia , Cobre/metabolismo , Simulação de Acoplamento Molecular , Espectroscopia de Infravermelho com Transformada de Fourier , Doenças das Plantas/prevenção & controle , Doenças das Plantas/microbiologiaRESUMO
BACKGROUND: The Ag-NPs by green synthesis has a notable interest because of their eco-friendliness, economic views, feasibility, and applications in a wide range. Herein, native plants of Jharkhand (Polygonum plebeium, Litsea glutinosa, and Vangueria spinosus) were selected for the current work of Ag-NP synthesis and further antibacterial activity. Green synthesis was performed for Ag-NPs using Silver nitrate solution as precursor and the dried leaf extract performs as a reductant and stabilizer here. RESULT: Visually Ag-NP formation was observed along with a colour change and confirmed by UV-visible spectrophotometry on which an absorbance peak occurs at around 400-450nm. Further characterization was done on DLS, FTIR, FESEM, and XRD. Size around 45-86 nm of synthesized Ag-NPs was predicted through DLS. The synthesized Ag-NPs exhibited significant antibacterial activity against Bacillus subtilis (Gram-positive bacteria) and Salmonella typhi (Gram-negative bacteria). The finest antibacterial activity was disclosed by the Ag-NPs synthesized by Polygonum plebeium extract. The diameter of the zone of inhibition in the bacterial plate measured was 0-1.8 mm in Bacillus and 0-2.2 mm in Salmonella typhi. Protein-Protein interaction study was performed to study the effect of Ag-NPs towards different antioxidant enzyme system of bacterial cell. CONCLUSION: Present work suggest the Ag-NPs synthesized from P. plebeium were more stable for long term and might have prolonged antibacterial activity. In the future, these Ag-NPs can be applied in various fields like antimicrobial research, wound healing, drug delivery, bio-sensing, tumour/cancer cell treatment, and detector (detect solar energy). Schematic representation of Ag-NPs green synthesis, characterization, antibacterial activity and at the end, in silico study to analyse the mechanism of antibacterial activity.
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Cancer is recognized as one of the world's deadliest diseases, with more than 10 million new cases each year. Over the past 2 decades, several studies have been performed on cancer to pursue solutions for effective treatment. One of the vital benefits of utilizing nanoparticles (NPs) in cancer treatment is their high adaptability for modification and amalgamation of different physicochemical properties to boost their anti-cancer activity. Various nanomaterials have been designed as nanocarriers attributing nontoxic and biocompatible drug delivery systems with improved bioactivity. The present review article briefly explained various types of nanocarriers, such as organic-inorganic-hybrid NPs, and their targeting mechanisms. Here a special focus is given to the synthesis, benefits, and applications of polymeric NPs (PNPs) involved in various anti-cancer therapeutics. It has also been discussed about the drug delivery approach by the functionalized/encapsulated PNPs (without/with targeting ability) that are being applied in the therapy and diagnostic (theranostics). Overall, this review can give a glimpse into every aspect of PNPs, from their synthesis to drug delivery application for cancer cells.
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Nanopartículas , Neoplasias , Humanos , Sistemas de Liberação de Fármacos por Nanopartículas , Sistemas de Liberação de Medicamentos/métodos , Polímeros/química , Neoplasias/tratamento farmacológico , Nanopartículas/químicaRESUMO
Plant nutrition is crucial in crop productivity and providing food security to the ever-expanding population. Application of chemical/biological fertilizers and pesticides are the mainstays for any agricultural economy. However, there are unintended consequences of using chemical fertilizers and pesticides. The environment and ecological balance are adversely affected by their usage. Biofertilizers and biopesticides counter some undesired environmental effects of chemical fertilizers/pesticides; despite some drawbacks associated with their use. The recent developments in nanotechnology offer promise toward sustainable agriculture. Sustainable agriculture involves addressing the concerns about agriculture as well as the environment. This review briefs about important nanomaterials used in agriculture as nanofertilizers, nanopesticides, and a combination called nanobiofertilizers. Both nanofertilizers and nanopesticides enable slow and sustained release besides their eco-friendly nature. They can be tailored to the specific needs of to crop. Nanofertilizers also offer greater stress tolerance and, therefore, are of considerable value in the era of climate change. Furthermore, nanofertilizers/nanopesticides are applied in minute amounts, reducing transportation costs associated and thus positively affecting the economy. Their uses extend beyond such as if nanoparticles (NPs) are used at high concentrations; they affect plant pathogens adversely. Polymer-based biodegradable nanofertilizers and nanopesticides offer various benefits. There is also a dark side to the use of nanomaterials in agriculture. Nanotechnology often involves the use of metal/metal oxide nanoparticles, which might get access to human bodies leading to their accumulation through bio-magnification. Although their effects on human health are not known, NPs may reach toxic concentrations in soil and runoff into rivers, and other water bodies with their removal to become a huge economic burden. Nevertheless, a risk-benefit analysis of nanoformulations must be ensured before their application in sustainable agriculture.
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Fertilizantes , Praguicidas , Agricultura , Produção Agrícola , Fertilizantes/análise , Humanos , Nanotecnologia , PlantasRESUMO
Kheria Sabars are an indigenous community living in the rural areas of Purulia, West Bengal, India. This work aims to study dietary intake and its relation to nutritional status among adult Kheria Sabar males aged 18-60. The study entails the recording of anthropometric variables like height (cm) and weight (kg) as per the standard protocol and calculating body mass index (BMI). Dietary intake was recorded on the basis of the 24-h dietary recall method. The intake of different nutrients was computed and compared with the Recommended Dietary Allowances (RDA) for Indians by the Indian Council of Medical Research Expert Committee. Results revealed a paradox where undernutrition was prevalent (44.28%) despite balanced nutrient intake. This paradox creates scope for further exploratory research among other communities living in similar habitats.
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Desnutrição , Estado Nutricional , Adulto , Dieta , Ingestão de Alimentos , Ingestão de Energia , Humanos , Índia/epidemiologia , Masculino , Desnutrição/epidemiologiaRESUMO
BACKGROUND: Oral Squamous Cell Carcinoma (OSCC) results from a series of genetic alteration in squamous cells. This particular type of cancer considers one of the most aggressive malignancies to control because of its frequent local invasions to the regional lymph node. Although several biomarkers have been reported, the key marker used to predict the behavior of the disease is largely unknown. Here we report Long INterpersed Element-1 (LINE1 or L1) retrotransposon activity in post-operative oral cancer samples. L1 is the only active retrotransposon occupying around 17% of the human genome with an estimated 500,000 copies. An active L1 encodes two proteins (L1ORF1p and L1ORF2p); both of which are critical in the process of retrotransposition. Several studies report that the L1 retrotransposon is highly active in many cancers. L1 activity is generally determined by assaying L1ORF1p because of its high expression and availability of the antibody. However, due to its lower expression and unavailability of a robust antibody, detection of L1ORF2p has been limited. L1ORF2p is the crucial protein in the process of retrotransposition as it provides endonuclease and reverse transcriptase (RT) activity. METHODS: Immunohistochemistry and Western blotting were performed on the post-operative oral cancer samples and murine tissues. RESULTS: Using in house novel antibodies against both the L1 proteins (L1ORF1p and L1ORF2p), we found L1 retrotransposon is extremely active in post-operative oral cancer tissues. Here, we report a novel human L1ORF2p antibody generated using an 80-amino-acid stretch from the RT domain, which is highly conserved among different species. The antibody detects significant L1ORF2p expression in human oral squamous cell carcinoma (OSCC) samples and murine germ tissues. CONCLUSIONS: We report exceptionally high L1ORF1p and L1ORF2p expression in post-operative oral cancer samples. The novel L1ORF2p antibody reported in this study will serve as a useful tool to understand why L1 activity is deregulated in OSCC and how it contributes to the progression of this particular cancer. Cross-species reactivity of L1ORF2p antibody due to the conserved epitope will be useful to study the retrotransposon biology in mice and rat germ tissues.
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Antígenos de Neoplasias/imunologia , Elementos Nucleotídeos Longos e Dispersos/genética , Neoplasias Bucais/genética , Fases de Leitura Aberta/imunologia , Carcinoma de Células Escamosas de Cabeça e Pescoço/genética , Sequência de Aminoácidos/genética , Animais , Antígenos de Neoplasias/genética , Células HEK293 , Humanos , Camundongos , Mucosa Bucal/imunologia , Mucosa Bucal/patologia , Mucosa Bucal/cirurgia , Neoplasias Bucais/imunologia , Neoplasias Bucais/patologia , Neoplasias Bucais/cirurgia , Fases de Leitura Aberta/genética , Ratos , Alinhamento de Sequência , Carcinoma de Células Escamosas de Cabeça e Pescoço/patologia , Carcinoma de Células Escamosas de Cabeça e Pescoço/cirurgiaRESUMO
Systems biology is one of the integrated ways to study biological systems and is more favourable than the earlier used approaches. It includes metabolic pathway analysis, modelling, and regulatory as well as signal transduction for getting insights into cellular behaviour. Among the various techniques of modelling, simulation, analysis of networks and pathways, flux-based analysis (FBA) has been recognised because of its extensibility as well as simplicity. It is widely accepted because it is not like a mechanistic simulation which depends on accurate kinetic data. The study of fluxes through the network is informative and can give insights even in the absence of kinetic data. FBA is one of the widely used tools to study biochemical networks and needs information of reaction stoichiometry, growth requirements, specific measurement parameters of the biological system, in particular the reconstruction of the metabolic network for the genome-scale, many of which have already been built previously. It defines the boundaries of flux distributions which are possible and achievable with a defined set of genes. This review article gives an insight into FBA, from the extension of flux balancing to mathematical representation followed by a discussion about the formulation of flux-balance analysis problems, defining constraints for the stoichiometry of the pathways and the tools that can be used in FBA such as FASIMA, COBRA toolbox, and OptFlux. It also includes broader areas in terms of applications which can be covered by FBA as well as the queries which can be addressed through FBA.
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Biologia Computacional/tendências , Modelos Biológicos , Fenômenos Físicos , Biologia de Sistemas/tendências , Algoritmos , Simulação por Computador , Redes Reguladoras de Genes/genética , Cinética , Redes e Vias Metabólicas/genética , Transdução de Sinais/genéticaRESUMO
Oral squamous cell carcinoma (OSCC) is highly predominant in India due to excessive use of tobacco. Here we investigated Long INterpersed Element 1 (LINE or L1) retrotransposon activity in OSCC samples in the same population. There are almost 500,000 copies of L1 occupied around 30% of the human genome. Although most of them are inactive, around 150-200 copies are actively jumping in a human genome. L1 encodes two proteins designated as ORF1p and ORF2p and expression of both proteins are critical for the process of retrotransposition. Here we have analyzed L1 ORF1p expression in a small cohort (n = 15) of paired cancer-normal tissues obtained from operated oral cancer patients. Immunohistochemistry (IHC) with the human ORF1 antibody showed the presence of ORF1p in almost 60% cancer samples, and few of them also showed aberrant p53 expression. Investigating L1 promoter methylation status, showed certain trends towards hypomethylation of the L1 promoter in cancer tissues compared to its normal counterpart. Our data raise the possibility that L1ORF1p expression might have some role in the onset and progression of this particular type of cancer.
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Biomarcadores Tumorais/genética , Carcinoma de Células Escamosas/patologia , Metilação de DNA , Elementos Nucleotídeos Longos e Dispersos , Neoplasias Bucais/patologia , Regiões Promotoras Genéticas , Proteínas/genética , Carcinoma de Células Escamosas/genética , Humanos , Neoplasias Bucais/genética , Projetos Piloto , PrognósticoRESUMO
MicroRNAs (miRNAs) are one of the major cytoplasmic tools employed by the eukaryotes for post-transcriptional gene regulation. These Ë21â¯nt small non-coding RNA molecules are highly conserved among species which forms a base for identification of new miRNAs. In this study, we used previously known mature miRNAs to search their homologs in Arachis hypogaea ESTs. A total of 50 non-protein coding sequences showing homology with no more than 3 mismatches were folded back to hairpin stem-loop structures using mfold. These predicted structures were passed through strict filtration criteria to obtain 18 miRNAs, all of which were other than those reported in miRBase. Out of 18 miRNAs, 7 were found to be new. These miRNAs belonged to miR156, miR166, miR167, miR319, miR398, miR399, miR482 and miR1507 family. These miRNAs were found to target a total of 118 genes in Arabidopsis. These targets included disease resistant proteins, auxin responsive proteins, squamosa promoter binding like proteins, co-transporter protein, transposable element genes, NAD(P) binding protein and topoisomerase II. KEGG pathway analysis showed potential involvement of these miRNAs in regulating different pathways. Apart from miRNA and their targets, microRNA encoded peptides (miPEPs) for 14 miRNAs were also identified. These findings can be used in the appropriate manipulation of miRNAs and corresponding miPEPs that will be helpful towards the peanut crop improvement.
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Arachis/química , Biologia Computacional , MicroRNAs/genética , Peptídeos/química , Bases de Dados de Ácidos Nucleicos , Regulação da Expressão Gênica de Plantas/genética , Análise de Sequência de RNARESUMO
This work is the first report on the isolation and structural elucidation of xylan from bambara and cowpea biomass. The xylans, isolated using acidic delignification followed by NaOH extraction method gave 12.3% and 13.6% yield, respectively. 1H NMR analyses revealed that both the xylans were glucuronoxylan. The presence of xylose and glucuronic acid was confirmed by monosaccharide analysis and uronic acid assay. Further, xylooligosaccharide production from bambara and cowpea xylans was carried out using xylanase from three different glycoside hydrolase families, and the products were analyzed by TLC and MALDI-ToF MS. The hydrolysis products of both xylans resembled hardwood glucuronoxylan fragments, generated under similar conditions. The most common oligosaccharides observed in the hydrolysates were Xyl2, Xyl3, MeGlcA3Xyl3, MeGlcAXyl4 and MeGlcAXyl5. A series of computational approaches were also used to study the interactions of the three different xylanases with xylan. Thus, untapped biomass such as bambara and cowpea could serve as a potential source for xylan which could further be converted to xylooligosaccharides and many other value-added chemicals.
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Biomassa , Vigna/química , Xilanos/química , Simulação por Computador , Endo-1,4-beta-Xilanases/química , Endo-1,4-beta-Xilanases/metabolismo , Simulação de Acoplamento Molecular , Conformação Proteica , Xilanos/metabolismoRESUMO
With the enhancement of commercial manifestation of silver nanoparticles, concerned has risen on their accumulation in aquatic system and consequent effects on fish development and metabolism. In this study, experiments were conducted to assess the impacts of silver nanoparticles on early life cycles of fish considering Zebrafish (Danio rerio) as experimental model. Silver nanoparticles were synthesized through chemical reduction method and characterized through UV-visible spectroscopy, dynamic light scattering (DLS), and HR-TEM. Different sub lethal doses of nanosilver were applied (13.6, 21.6, 42.4, 64, and 128⯵gL-1) to post-fertilization phases of Zebrafish embryos and their interaction effects were monitored up to six days period. No significant morphological variations were observed at 13.6, 21.6, 42.4⯵gL-1 dose of silver nanoparticles, whereas 64 and 128⯵gL-1 exposure dose exhibited bending in myotome, deformity in tail region, somites, notochord and swelling in anterior and posterior region of embryos and larva. Hatching performances analysis elicited highest hatching success in 13.6 and 21.6⯵gL-1 doses of silver nanoparticles followed by positive and negative control, whereas exposure dose of 64 and 128⯵gL-1 exhibited comparatively lower success. Western blot analysis were conducted on developing hatchlings with Oct4 antibody and at 13.6 and 21.6⯵gL-1dose,it showed over expression elucidating stimulatory role of nanosilver in these mentioned doses. In silico analysis depicted a firm interaction of nanosilver with Oct4 revealing their key role in growth stimulation of developing embryos. The study demonstrates the function of nanosilver as a growth promoter rather only as a toxicant in fish metabolic system.
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Embrião não Mamífero/efeitos dos fármacos , Nanopartículas Metálicas/química , Fator 3 de Transcrição de Octâmero/biossíntese , Prata/química , Proteínas de Peixe-Zebra/biossíntese , Peixe-Zebra/embriologia , Animais , Desenvolvimento Embrionário/efeitos dos fármacos , Feminino , Masculino , Prata/farmacologia , Peixe-Zebra/metabolismoRESUMO
Biogenic synthesis of silver nanoparticles using microorganisms has found interest recently since last decade because of their prospect to synthesize nanoparticles of various size, shape and morphology which are eco-friendly. Here, an eco-friendly method for production of silver nanoparticles from Bacillus clausii cultured from Enterogermina is explored. Along with the biosynthesis and conformity test, in silico studies was done on NADPH dependent nitrate reductase enzymes from the view point of designing a rational enzymatic strategy for the synthesis. The detailed characterization of the nanoparticles was carried out using UV-Vis spectroscopy, Dynamic Light Scattering (DLS) particle size analysis, Transmission Electron Microscopy (TEM), X-Ray Diffraction (XRD) analysis. Computational profiling and in silico characterization of NADH dependent enzymes was carried out based on literature and work done so far. Nitrate reductase sequence was retrieved from NCBI for characterization. Secondary structure was evaluated and verified by JPred as well as SOPMA Tool. Tertiary structure was also modeled by MODELLER and ITASSER parallel and the best structure was selected based on energy values. Structure validation was done by GROMACS and RMSD, RMSF, temperature variation plot were also plotted. Interactions graphs between nitrate reductase and ligand silver nitrate was done through molecular docking using Hex.
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Combating Type-2 diabetes mellitus is a pivotal challenge in front of the present world. Several lines of therapy are in practice for resisting this deadly disease which often culminates with cardiovascular complexities, neuropathy and retinopathy. Among various therapies, administration of alpha glucosidase inhibitors is common and widely practiced. Sulfonylurea category of anti diabetic drug often suffers from cross reactivity with sulfamethoxazole (SMX), a common drug in use to treat a handful of microbial infections. However the specific cellular target generating postprandial hypoglycemia on SMX administration is till date unraveled. The present work has been initiated to elucidate the effects of a group of sulfonamide drugs inclusive of SMX for their amylase inhibitory role. SMX inhibits porcine pancreatic amylase (PPA) in a noncompetitive mode with an average IC50 value 0.94 mM respectively. Interaction of SMX with PPA is manifested with gradual quenching of tryptophan fluorescence with concomitant shift in lambda max value (λmax). Binding is governed by entropy driven factor (24.8 cal mol(-1) K(-1)) with unfavorable contribution from enthalpy change. SMX interferes with the activity of acarbose in a synergistic mode to reduce the effective dose of acarbose as evident from the in vitro PPA inhibition study. In summary, loss of PPA activity in presence of SMX is indicative of structural changes of PPA which is further augmented in the presence of acarbose as explained in the schematic model and docking study.
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Anti-Infecciosos/farmacologia , Inibidores Enzimáticos/farmacologia , alfa-Amilases Pancreáticas/antagonistas & inibidores , Sulfametoxazol/farmacologia , Animais , Anti-Infecciosos/química , Inibidores Enzimáticos/química , Simulação de Acoplamento Molecular , alfa-Amilases Pancreáticas/química , alfa-Amilases Pancreáticas/metabolismo , Sulfametoxazol/química , SuínosRESUMO
Gaining access to sequence and structure information of telomere-binding proteins helps in understanding the essential biological processes involve in conserved sequence-specific interaction between DNA and the proteins. Rice telomere-binding protein (RTBP1) and Nicotiana glutinosa telomere repeat binding factor (NgTRF1) are helix-turn-helix motif type of proteins that plays role in telomeric DNA protection and length regulation. Both the proteins share same type of domain, but till now there is very less communication on the in silico studies of these complete proteins. Here we intend to do a comparative study between two proteins through modeling of the complete proteins, physiochemical characterization, MD simulation and DNA-protein docking. I-TASSER and CLC protein work bench was performed to find out the protein 3D structure as well as the different parameters to characterize the proteins. MD simulation was completed by GROMOS forcefield of GROMACS for 10 ns of time stretch. The simulated 3D structures were docked with template DNA (3D DNA modeled through 3D-DART) of TTTAGGG conserved sequence motif using HADDOCK Web server. By digging up all the facts about the proteins, it was revealed that around 120 amino acids in the tail part were showing a good sequence similarity between the proteins. Molecular modeling, sequence characterization and secondary structure prediction also indicate the similarity between the protein's structure and sequence. The result of MD simulation highlights on the RMSD, RMSF, Rg, PCA and energy plots which also conveys the similar type of motional behavior between them. The best complex formation for both the proteins in docking result also indicates for the first interaction site which is mainly the helix3 region of the DNA-binding domain. The overall computational analysis reveals that RTBP1 and NgTRF1 proteins display good amount of similarity in their physicochemical properties, structure, dynamics and binding mode.
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Simulação de Acoplamento Molecular , Nicotiana/metabolismo , Oryza/metabolismo , Proteínas de Plantas/química , Sequência de Aminoácidos , DNA/metabolismo , Estrutura Terciária de Proteína , Alinhamento de Sequência , Termodinâmica , Fatores de TempoRESUMO
Gaining access to sequence and structure information of telomere binding proteins helps in understanding the essential biological processes involve in conserved sequence specific interaction between DNA and the proteins. Rice telomere binding protein (RTBP1) and Nicotiana glutinosa telomere repeat binding factor (NgTRF1) are helix turn helix motif type of proteins that plays role in telomeric DNA protection and length regulation. Both the proteins share same type of domain but till now there is very less communication on the in silico studies of these complete proteins.Here we intend to do a comparative study between two proteins through modeling of the complete proteins, physiochemical characterization, MD simulation and DNA-protein docking. I-TASSER and CLC protein work bench was performed to find out the protein 3D structure as well as the different parameters to characterize the proteins. MD simulation was completed by GROMOS forcefield of GROMACS for 10 ns of time stretch. The simulated 3D structures were docked with template DNA (3D DNA modeled through 3D-DART) of TTTAGGG conserved sequence motif using HADDOCK web server.Digging up all the facts about the proteins it was reveled that around 120 amino acids in the tail part was showing a good sequence similarity between the proteins. Molecular modeling, sequence characterization and secondary structure prediction also indicates the similarity between the protein's structure and sequence. The result of MD simulation highlights on the RMSD, RMSF, Rg, PCA and Energy plots which also conveys the similar type of motional behavior between them. The best complex formation for both the proteins in docking result also indicates for the first interaction site which is mainly the helix3 region of the DNA binding domain. The overall computational analysis reveals that RTBP1 and NgTRF1 proteins display good amount of similarity in their physicochemical properties, structure, dynamics and binding mode.
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Support vector machine is a class of machine learning algorithms which uses a set of related supervised learning methods for classification and regression. Nowadays this method is vividly applied to many detection problems related with secondary structure, tumor cell and binding residue prediction. In this work, support vector machines (SVMs) have been trained on 90 sequences of transcription factors with HTH motif. Four sequence features were used as attribute for the prediction of interaction site in HTH motif. A web page was also developed so that user can easily enter the protein sequence and receive the output as interaction site predicted or not predicted. The generated model shows a very high amount of accuracy, sensitivity and specificity which proves to be a good model for the selected case.
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Telomere is a nucleoprotein complex that plays important role in stability and their maintenance and consists of random repeats of species specific motifs. In budding Saccharomyces cerevisiae, Repressor Activator Protein 1 (Rap1) is a sequence specific protein that involved in transcriptional regulation. Rap1 consist of three active domains like N-terminal BRCT-domain, DNA-binding domain and C-terminal RCT-domain. In this study the unknown 3D structure of Myb-type domain (having 61 residues) within DNAbinding domain was modeled by Modeller7, and verified using different online bioinformatics tools (ProCheck, WhatIf, Verify3D). Dynamics of Myb-type domain of Rap1was carried out through simulation studies using GROMACS software. Time dependent interactions among the molecules were analyzed by Root Mean Square Deviation (RMSD), Radius of Gyration (Rg) and Root Mean Square Fluctuation (RMSF) plots. Motional properties in reduced dimension were also performed by Principal Component Analysis (PCA). Result indicated that Rap1 interacts with DNA major groove through its Helix Turn Helix motifs. Helix 3 was rigid, less amount of fluctuation was found as it interacts with DNA major groove. Helix2 and N-terminal having considerable fluctuation in the time scale.