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Sudip Kundu Dhananjay Bhattacharya Ashoke Ranjan Thakur Rabi Majumdar 《Journal of biomolecular structure & dynamics》2013,31(4):527-533
Abstract Based on worm like chain model, DNA structural parameters—tilt, roll and rise, derived from crystallographic database have been used to determine the flexibility of DNA that regulates the nucleosomal translational positioning. Theoretically derived data has been compared to the experimental values available in Ioshikhes and Trifonov's database. The methodology has been extended to determine the flexibility of 18S rRNA genome in eukarya, where yeast shows a distinct difference when compared with mammals like human, mouse and rabbit. 相似文献
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Vigdis Aas Siril S. Bakke Yuan Z. Feng Eili Tranheim Kase Jørgen Jensen Sudip Bajpeyi G. Hege Thoresen Arild C. Rustan 《Cell and tissue research》2013,354(3):671-682
Satellite cells can be isolated from skeletal muscle biopsies, activated to proliferating myoblasts and differentiated into multinuclear myotubes in culture. These cell cultures represent a model system for intact human skeletal muscle and can be modulated ex vivo. The advantages of this system are that the most relevant genetic background is available for the investigation of human disease (as opposed to rodent cell cultures), the extracellular environment can be precisely controlled and the cells are not immortalized, thereby offering the possibility of studying innate characteristics of the donor. Limitations in differentiation status (fiber type) of the cells and energy metabolism can be improved by proper treatment, such as electrical pulse stimulation to mimic exercise. This review focuses on the way that human myotubes can be employed as a tool for studying metabolism in skeletal muscles, with special attention to changes in muscle energy metabolism in obesity and type 2 diabetes. 相似文献
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Kanika Narula Pooja Choudhary Sudip Ghosh Eman Elagamey Niranjan Chakraborty Subhra Chakraborty 《Proteomics》2019,19(3)
Modulation of plant immune system by extrinsic/intrinsic factors and host‐specific determinants fine‐tunes cellular components involving multiple organelles, particularly nucleus to mount resistance against pathogen attack. Rice blast, caused by hemibiotrophic fungus Magnaporthe oryzae, is one of the most devastating diseases that adversely affect rice productivity. However, the role of nuclear proteins and their regulation in response to M. oryzae remains unknown. Here, the nucleus‐associated immune pathways in blast‐resistant rice genotype are elucidated. Temporal analysis of nuclear proteome is carried out using 2‐DE coupled MS/MS analysis. A total of 140 immune responsive proteins are identified associated with nuclear reorganization, cell division, energy production/deprivation, signaling, and gene regulation. The proteome data are interrogated using correlation network analysis that identified significant functional modules pointing toward immune‐related coinciding processes through a common mechanism of remodeling and homeostasis. Novel clues regarding blast resistance include nucleus‐associated redox homeostasis and glycolytic enzyme–mediated chromatin organization which manipulates cell division and immunity. Taken together, the study herein provides evidence that the coordination of nuclear function and reprogramming of host translational machinery regulate resistance mechanism against blast disease. 相似文献
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Amritlal Mandal Sudip DasTapati Chakraborti Pulak KarBiswarup Ghosh Sajal Chakraborti 《Biochimica et Biophysica Acta (BBA)/General Subjects》2006
The properties of Ca2+-ATPase purified and reconstituted from bovine pulmonary artery smooth muscle microsomes {enriched with endoplasmic reticulum (ER)} were studied using the detergents 1,2-diheptanoyl-sn-phosphatidylcholine (DHPC), poly(oxy-ethylene)8-lauryl ether (C12E8) and Triton X-100 as the solubilizing agents. Solubilization with DHPC consistently gave higher yields of purified Ca2+-ATPase with a greater specific activity than solubilization with C12E8 or Triton X-100. DHPC was determined to be superior to C12E8; while that the C12E8 was determined to be better than Triton X-100 in active enzyme yields and specific activity. DHPC solubilized and purified Ca2+-ATPase retained the E1Ca−E1*Ca conformational transition as that observed for native microsomes; whereas the C12E8 and Triton X-100 solubilized preparations did not fully retain this transition. The coupling of Ca2+ transported to ATP hydrolyzed in the DHPC purified enzyme reconstituted in liposomes was similar to that of the native micosomes, whereas that the coupling was much lower for the C12E8 and Triton X-100 purified enzyme reconstituted in liposomes. The specific activity of Ca2+-ATPase reconstituted into dioleoyl-phosphatidylcholine (DOPC) vesicles with DHPC was 2.5-fold and 3-fold greater than that achieved with C12E8 and Triton X-100, respectively. Addition of the protonophore, FCCP caused a marked increase in Ca2+ uptake in the reconstituted proteoliposomes compared with the untreated liposomes. Circular dichroism analysis of the three detergents solubilized and purified enzyme preparations showed that the increased negative ellipticity at 223 nm is well correlated with decreased specific activity. It, therefore, appears that the DHPC purified Ca2+-ATPase retained more organized and native secondary conformation compared to C12E8 and Triton X-100 solubilized and purified preparations. The size distribution of the reconstituted liposomes measured by quasi-elastic light scattering indicated that DHPC preparation has nearly similar size to that of the native microsomal vesicles whereas C12E8 and Triton X-100 preparations have to some extent smaller size. These studies suggest that the Ca2+-ATPase solubilized, purified and reconstituted with DHPC is superior to that obtained with C12E8 and Triton X-100 in many ways, which is suitable for detailed studies on the mechanism of ion transport and the role of protein–lipid interactions in the function of the membrane-bound enzyme. 相似文献
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Sudip?Biswas Samsad?Razzaque Sabrina?M.?Elias U.?S.?Mahzabin?Amin Taslima?Haque S.?M.?Touhidul?Islam Laisa?A.?Lisa Farhana?Naznin Noorain?M.?Rasul Zeba?I.?SerajEmail author 《Acta Physiologiae Plantarum》2015,37(1):1730
The vacuolar Na+/H+ antiporter is known to alleviate saline stress by sequestering Na+ in both wild-type Arabidopsis and rice and when over-expressed in many transgenic plants. Here we report on the effect of the NHX1 transgene on the salt tolerance properties it confers to a rice landrace and a commercial cultivar suitable for the dry winter season, but which suffers loss due to seasonal stresses, particularly in the coastal areas. The Nipponbare Na+/H+ antiporter 1.9 kb cDNA was cloned into pCAMBIA1305.1 under the control of the CaMV35S promoter and transformed into tissue-culture-responsive rice landrace Binnatoa (BA). The best-expressing transgenic line at T2 was found to be significantly tolerant at the seedling stage and was advanced to T3. The transgene was then transferred to the tissue-culture recalcitrant farmer-popular commercial rice genotype, BRRIdhan 28 (BR28) by crossing. The data generated both from semi-quantitative RT-PCR and western blot hybridization revealed that the transgene showed similar expression in the crossbred BR28 plants and BA transgenic line. Comparative stress tolerance tests, however, revealed that the BR28 crossbred lines were significantly less tolerant than its transgenic parent BA at both seedling and reproductive stages. A single successful transgenic event may therefore not show the same performance in the recipient genetic background, if introgressed by crossing. 相似文献
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Coevolutionary constraints in the sequence‐space of macromolecular complexes reflect their self‐assembly pathways 下载免费PDF全文
Is the order in which biomolecular subunits self‐assemble into functional macromolecular complexes imprinted in their sequence‐space? Here, we demonstrate that the temporal order of macromolecular complex self‐assembly can be efficiently captured using the landscape of residue‐level coevolutionary constraints. This predictive power of coevolutionary constraints is irrespective of the structural, functional, and phylogenetic classification of the complex and of the stoichiometry and quaternary arrangement of the constituent monomers. Combining this result with a number of structural attributes estimated from the crystal structure data, we find indications that stronger coevolutionary constraints at interfaces formed early in the assembly hierarchy probably promotes coordinated fixation of mutations that leads to high‐affinity binding with higher surface area, increased surface complementarity and elevated number of molecular contacts, compared to those that form late in the assembly. Proteins 2017; 85:1183–1189. © 2017 Wiley Periodicals, Inc. 相似文献
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Basab Roy Arindam Chakraborty Sudip K. Ghosh Amit Basak 《Bioorganic & medicinal chemistry letters》2009,19(24):7007-7010
A new class of chimeric molecules have been developed. These are based on polyphenols like catechin and epicatechin and monocyclic β-lactams. The two units are joined via a triazole linker using the ‘Click Chemistry’ conditions. The compounds showed good to weak antibacterial activity against Escherichia coli as well as moderate inhibition of RNase A. 相似文献
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