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961.
Arora Sakshi Singh Amarjeet Kumar Chaudhary Bhupendra 《Plant Cell, Tissue and Organ Culture》2020,141(3):511-531
Plant Cell, Tissue and Organ Culture (PCTOC) - In vitro regeneration of cotton seems to be highly genotype dependent and typically ensues through the extraordinarily complex mechanism of somatic... 相似文献
962.
Ruhar Singh Naveen Kumar Meena Trishala Das Ravi Datta Sharma 《Journal of biomolecular structure & dynamics》2020,38(17):5027-5036
AbstractThe funnel shaped energy landscape model of the protein folding suggests that progression of folding proceeds through multiple pathways, having the multiple intermediates which leads to multidimensional free-energy surface. Herein, we applied all-atom MD simulation to conduct a comparative study on the structure of β-lactoglobulin (β-LgA) in aqueous mixture of 8?M urea and 8?M dimethyl sulfoxide (DMSO), at different temperatures. The cumulative results of multiple simulations suggest a common unfolding pathway of β-LgA, occurred through the stable and meta-stable intermediates (I), in both urea and DMSO. However, the free-energy landscape (FEL) analyses show that the structural transitions of I-states are energetically different. In urea, FEL shows distinct ensemble of intermediates, I1 and I2, separated by the energy barrier of ~3.0?kcal mol?1. Similarly, we find the population of two distinct I1 and I2 states in DMSO, however, the I1 appeared transiently around ~30–35?ns and is short-lived. But, the I2 ensemble is observed structurally compact and long-lived (~50–150?ns) as compared to unfolding in urea. Furthermore, the I1 and I2 are separated through a high energy barrier of ~6.0?kcal mol?1. Thus, our results provide the structural insights of intermediates which essentially bear the signature of a different unfolding pathway of β-LgA in urea and DMSO. Abbreviations β-LgA β-lactoglobulin DMSO dimethyl sulfoxide FEL free-energy landscape GdmCl guanidinium chloride I intermediate state MG molten globule state PME particle mesh Ewald Q fraction of native contacts RMSD root mean square deviation RMSF root mean square fluctuation Rg radius of gyration SASA solvent Accessible Surface Area scSASA the side chain SASA Trp tryptophan Communicated by Ramaswamy H. Sarma 相似文献
963.
Jayashree Biswal Prajisha Jayaprakash Rayala Suresh Kumar Ganesh Venkatraman Saritha Poopandi Raghu Rangasamy 《Journal of biomolecular structure & dynamics》2020,38(1):13-31
Abstractp21-activated kinases (Paks) play an integral component in various cellular diverse processes. The full activation of Pak is dependent upon several serine residues present in the N-terminal region, a threonine present at the activation loop, and finally the phosphorylation of these residues ensure the complete activation of Pak1. The present study deals with the identification of novel potent candidates of Pak1 using computational methods as anti-cancer compounds. A diverse energy based pharmacophore (e-pharmacophore) was developed using four co-crystal inhibitors of Pak1 having pharmacophore features of 5 (DRDRR), 6 (DRHADR), and 7 (RRARDRP and DRRDADH) hypotheses. These models were used for rigorous screening against e-molecule database. The obtained hits were filtered using ADME/T and molecular docking to identify the high affinity binders. These hits were subjected to hierarchical clustering using dendritic fingerprint inorder to identify structurally diverse molecules. The diverse hits were scored against generated water maps to obtain WM/MM ΔG binding energy. Furthermore, molecular dynamics simulation and density functional theory calculations were performed on the final hits to understand the stability of the complexes. Five structurally diverse novel Pak1 inhibitors (4835785, 32198676, 32407813, 76038049, and 32945545) were obtained from virtual screening, water thermodynamics and WM/MM ΔG binding energy. All hits revealed similar mode of binding pattern with the hinge region residues replacing the unstable water molecules in the binding site. The obtained novel hits could be used as a platform to design potent drugs that could be experimentally tested against cancer patients having increased Pak1 expression. 相似文献
964.
Mohd Amir Taj Mohammad Kartikay Prasad Gulam Mustafa Hasan Vijay Kumar Ravins Dohare 《Journal of biomolecular structure & dynamics》2020,38(15):4625-4634
Communicated by Ramaswamy H. Sarma 相似文献
965.
Kumar Alok Singh Pradyumn Pandey Anshuman Gosipatala Sunil Babu 《Molecular biology reports》2020,47(9):6919-6927
Molecular Biology Reports - Promoter methylation mediated silencing of tumor suppressor genes plays an important role in the tumorigenesis of colorectal carcinoma (CRC). Tumor suppressor gene,... 相似文献
966.
Sharma Himanshu Bhandawat Abhishek Rahim Mohammed Saba Kumar Pankaj Choudhoury Mohini Pal Roy Joy 《Molecular biology reports》2020,47(5):3485-3500
Molecular Biology Reports - Introns experience lesser selection pressure, thus are liable for higher polymorphism. Intron Length Polymorphic (ILP) markers designed from exon-flanking introns... 相似文献
967.
Kumar Vikas Singh Jaswinder Bala Kiran Singh Jasbir 《Molecular biology reports》2020,47(12):9489-9497
Molecular Biology Reports - Insulin resistance may become the most powerful predictor of future development of type 2 diabetes mellitus (T2DM) and a therapeutic target for the treatment of the... 相似文献
968.
Kaur Jasmeet Akhatar Javed Goyal Anna Kaur Navneet Kaur Snehdeep Mittal Meenakshi Kumar Nitin Sharma Heena Banga Shashi Banga S. S. 《Molecular biology reports》2020,47(4):2963-2974
Molecular Biology Reports - We investigated phenotypic variations for pod shattering, pod length and number of seeds per pod in large germplasm collections of Brassica juncea (2n?=?36;... 相似文献
969.
Sharma Himanshu Kumar Pankaj Singh Abhishek Aggarwal Kanika Roy Joy Sharma Vikas Rawat Sandeep 《Molecular biology reports》2020,47(4):2447-2457
Molecular Biology Reports - The genus Rhododendron, known for large impressive flowers is widely distributed throughout the world. Rhododendrons have limited genetic information, despite of... 相似文献
970.
Kumar Alok Kalita J. Sinha Rohit A. Singh Gajendra B Anjum Shukla Mukti Tiwari Swasti Dhole T. N. Misra U. K. 《Neurochemical research》2020,45(9):2184-2195
Neurochemical Research - Role of autophagy in Japanese encephalitis viral (JEV) infection is not well known. In the present study, we reported the role of autophagy flux in microglia activation,... 相似文献