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101.
Narayanaperumal Pravin Rakesh Kumar Shalini Tripathi Pardeep Kumar Ganesh M Mohite Ambuja Navalkar Rajlaxmi Panigrahi Namrata Singh Laxmikant G. Gadhe Shaffi Manchanda Makoto Shimozawa Per Nilsson Jan Johansson Ashutosh Kumar Samir K. Maji Maheswaran Shanmugam 《Journal of neurochemistry》2021,156(6):1003-1019
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V.S. Avinash Priyabrata Panigrahi C.G. Suresh Archana V. PundleSureshkumar Ramasamy 《Biochemical and biophysical research communications》2013
Penicillin V acylases (PVAs) and bile salt hydrolases (BSHs) have considerable sequence and structural similarity; however, they vary significantly in their substrate specificity. We have identified a PVA from a Gram-negative organism, Pectobacterium atrosepticum (PaPVA) that turned out to be a remote homolog of the PVAs and BSHs reported earlier. Even though the active site residues were conserved in PaPVA it showed high specificity towards penV and interestingly the penV acylase activity was inhibited by bile salts. Comparative modelling and docking studies were carried out to understand the structural differences of the binding site that confer this characteristic property. We show that PaPVA exhibits significant differences in structure, which are in contrast to those of known PVAs and such enzymes from Gram-negative bacteria require further investigation. 相似文献
105.
Venkateshwar Rao Gummadi Sujatha Rajagopalan Chung-Yeng Looi Mohammadjavad Paydar Girish Aggunda Renukappa Bharathi Raja Ainan Narasimha Rao Krishnamurthy Sunil Kumar Panigrahi Kumari Mahasweta Sangeetha Raghuramachandran Manoj Rajappa Anuradha Ramanathan Anirudha Lakshminarasimhan Murali Ramachandra Pooi-Fong Wong Mohammad Rais Mustafa Srinivas Nanduri Subramanya Hosahalli 《Bioorganic & medicinal chemistry letters》2013,23(17):4911-4918
We have identified a novel 7-azaindole series of anaplastic lymphoma kinase (ALK) inhibitors. Compounds 7b, 7m and 7n demonstrate excellent potencies in biochemical and cellular assays. X-ray crystal structure of one of the compounds (7k) revealed a unique binding mode with the benzyl group occupying the back pocket, explaining its potency towards ALK and selectivity over tested kinases particularly Aurora-A. This binding mode is in contrast to that of known ALK inhibitors such as Crizotinib and NVP-TAE684 which occupy the ribose binding pocket, close to DFG motif. 相似文献
106.
The specific targeting of protein to organelles is achieved by targeting signals being recognised by their cognate receptors. Cytosolic chaperones, bound to precursor proteins, are recognized by specific receptors of the import machinery enabling transport into the specific organelle. The aim of this study was to gain greater insight into the mode of recognition of the C-termini of Hsp70 and Hsp90 chaperones by the Tetratricopeptide Repeat (TPR) domain of the chloroplast import receptor Toc64 from Arabidopsis thaliana (At). The monomeric TPR domain binds with 1∶1 stoichiometry in similar micromolar affinity to both Hsp70 and Hsp90 as determined by isothermal titration calorimetry (ITC). Mutations of the terminal EEVD motif caused a profound decrease in affinity. Additionally, this study considered the contributions of residues upstream as alanine scanning experiments of these residues showed reduced binding affinity. Molecular dynamics simulations of the TPR domain helices upon peptide binding predicted that two helices within the TPR domain move backwards, exposing the cradle surface for interaction with the peptide. Our findings from ITC and molecular dynamics studies suggest that AtToc64_TPR does not discriminate between C-termini peptides of Hsp70 and Hsp90. 相似文献
107.
Schwarzerová K Petrásek J Panigrahi KC Zelenková S Opatrný Z Nick P 《Protoplasma》2006,227(2-4):185-196
Summary. Concurrently with cold-induced disintegration of microtubular structures in the cytoplasm, gradual tubulin accumulation was
observed in a progressively growing proportion of interphase nuclei in tobacco BY-2 cells. This intranuclear tubulin disappeared
upon rewarming. Simultaneously, new microtubules rapidly emerged from the nuclear periphery and reconstituted new cortical
arrays, as was shown by immunofluorescence. A rapid exclusion of tubulin from the nucleus during rewarming was also observed
in vivo in cells expressing GFP-tubulin. Nuclei were purified from cells that expressed GFP fused to an endoplasmic-reticulum
retention signal (BY-2-mGFP5-ER), and green-fluorescent protein was used as a diagnostic marker to confirm that the nuclear
fraction was not contaminated by nuclear-envelope proteins. These purified, GFP-free nuclei contained tubulin when isolated
from cold-treated cells, whereas control nuclei were void of tubulin. Furthermore, highly conserved putative nuclear-export
sequences were identified in tubulin sequences. These results led us to interpret the accumulation of tubulin in interphasic
nuclei, as well as its rapid nuclear export, in the context of ancient intranuclear tubulin function during the cell cycle
progression.
Correspondence and reprints: Department of Plant Physiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague
2, Czech Republic. 相似文献
108.
Budheswar Dehury Mahesh Chandra Patra Jitendra Maharana Jagajjit Sahu Priyabrata Sen Mahendra Kumar Modi Manabendra Dutta Choudhury Madhumita Barooah 《PloS one》2014,9(5)
The NADPH-dependent HC-toxin reductases (HCTR1 and 2) encoded by enzymatic class of disease resistance homologous genes (Hm1 and Hm2) protect maize by detoxifying a cyclic tetrapeptide, HC-toxin, secreted by the fungus Cochliobolus carbonum race 1(CCR1). Unlike the other classes'' resistance (R) genes, HCTR-mediated disease resistance is an inimitable mechanism where the avirulence (Avr) component from CCR1 is not involved in toxin degradation. In this study, we attempted to decipher cofactor (NADPH) recognition and mode of HC-toxin binding to HCTRs through molecular docking, molecular dynamics (MD) simulations and binding free energy calculation methods. The rationality and the stability of docked complexes were validated by 30-ns MD simulation. The binding free energy decomposition of enzyme-cofactor complex was calculated to find the driving force behind cofactor recognition. The overall binding free energies of HCTR1-NADPH and HCTR2-NADPH were found to be −616.989 and −16.9749 kJ mol−1 respectively. The binding free energy decomposition revealed that the binding of NADPH to the HCTR1 is mainly governed by van der Waals and nonpolar interactions, whereas electrostatic terms play dominant role in stabilizing the binding mode between HCTR2 and NADPH. Further, docking analysis of HC-toxin with HCTR-NADPH complexes showed a distinct mode of binding and the complexes were stabilized by a strong network of hydrogen bond and hydrophobic interactions. This study is the first in silico attempt to unravel the biophysical and biochemical basis of cofactor recognition in enzymatic class of R genes in cereal crop maize. 相似文献
109.
Arvizo RR Miranda OR Moyano DF Walden CA Giri K Bhattacharya R Robertson JD Rotello VM Reid JM Mukherjee P 《PloS one》2011,6(9):e24374
BACKGROUND: Inorganic nanoparticles provide promising tools for biomedical applications including detection, diagnosis and therapy. While surface properties such as charge are expected to play an important role in their in vivo behavior, very little is known how the surface chemistry of nanoparticles influences their pharmacokinetics, tumor uptake, and biodistribution. METHOD/PRINCIPAL FINDINGS: Using a family of structurally homologous nanoparticles we have investigated how pharmacological properties including tumor uptake and biodistribution are influenced by surface charge using neutral (TEGOH), zwitterionic (Tzwit), negative (TCOOH) and positive (TTMA) nanoparticles. Nanoparticles were injected into mice (normal and athymic) either in the tail vein or into the peritoneum. CONCLUSION: Neutral and zwitterionic nanoparticles demonstrated longer circulation time via both i.p. and i.v. administration, whereas negatively and positively charged nanoparticles possessed relatively short half-lives. These pharmacological characteristics were reflected on the tumor uptake and biodistribution of the respective nanoparticles, with enhanced tumor uptake by neutral and zwitterionic nanoparticles via passive targeting. 相似文献
110.