@article { ISI:000335773800005, title = {Vesicle structures from bolaamphiphilic biosurfactants: experimental and molecular dynamics simulation studies on the effect of unsaturation on sophorolipid self-assemblies}, journal = {Chemistry-A European Journal}, volume = {20}, number = {21}, year = {2014}, month = {MAY}, pages = {6246-6250}, publisher = {WILEY-V C H VERLAG GMBH}, address = {BOSCHSTRASSE 12, D-69469 WEINHEIM, GERMANY}, abstract = {

The formation of giant-vesicle-like structures by self-assembling linolenic acid sophorolipid (LNSL) molecules is revealed. Sophorolipids belong to the class of bolaamphiphilic glycolipid biosurfactants. Interestingly, the number of double bonds present in the hydrophobic core of sophorolipids is seen to have a great influence on the type of self-assembled structures formed. Dye encapsulation results establish the presence of an aqueous compartment inside the LNSL vesicles. Molecular dynamics simulation (MD) studies suggest the existence of two possible conformations of LNSLs inside the self-assembled structures and that LNSL molecules arrange in layered structures.

}, keywords = {bolaamphiphiles, MD simulations, Self-assembly, sophorolipids, vesicles}, issn = {0947-6539}, doi = {10.1002/chem.201304719}, author = {Dhasaiyan, Prabhu and Pandey, Prithvi Raj and Visaveliya, Nikunjkumar and Roy, Sudip and Bhagavatula L. V. Prasad} } @article {46291, title = {In vitro and in silico studies on membrane interactions of diverse Capsicum annuum flower gamma-thionin peptides}, journal = {Proteins-Structure Function and Bioinformatics}, year = {2019}, month = {AUG}, type = {Article; Early Access}, abstract = {

Thionins are small, cysteine-rich peptides that play an important role in plant defense, primarily through their interactions with membranes. Eight novel gamma-thionin peptides (CanThio1-8) were isolated from the flower of Capsicum annuum. Sequence analysis revealed that the peptides cluster into three groups. A representative peptide from each group (CanThio1, 2, and 3) was used for experimental characterization. Interestingly, peptides were found to possess some cytotoxic activity against normal human embryonic kidney cell line but higher cytotoxicity against cancer cell line MCF-7. CanThio3 peptide was chosen as a representative peptide to study the molecular mechanism of action on membranes. Microsecond timescale atomistic simulations of CanThio3 were performed in the presence of a POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) lipid bilayer. Simulations revealed that CanThio3 interacts with the bilayer and causes lipid thinning in the vicinity. Nonpolar amino acids specific to the alpha-core region of CanThio3 along with nonpolar residues in the gamma-core region are seen to interact with the lipid tails. The differences in the amino acid sequence of CanThio peptides in these regions explain the variability in cytotoxic activities. In summary, our results demonstrate the membrane-mediated activity of a novel series of gamma-thionin peptides from C. annuum.

}, keywords = {Capsicum annuum, Cytotoxicity, gamma-thionin, MD simulations, Membrane}, issn = {0887-3585}, doi = {10.1002/prot.25791}, author = {Nikte, Siddhanta and Gahankari, Apurva and Mulla, Javed and Sengupta, Durba and Joshi, Manali and Tamhane, Vaijayanti} } @article {46747, title = {Elucidating the effect of CaF 2 on structure, biocompatibility and antibacterial properties of S53P4 glass}, journal = {Journal of Alloys and Compounds}, volume = {831}, year = {2020}, month = {AUG }, pages = {154704}, type = {Article}, abstract = {

The present work focuses on the synthesis and structural elucidation of fluoride containing bioactive glasses in the system (in mol\%) given by (53.86) SiO2\ {\textendash} (22.65) Na2O {\textendash} (21.77-x) CaO {\textendash} (1.72) P2O5\ {\textendash} x CaF2, where, x\ =\ 0, 5.44, 10.885 and 16.33. The role of the incorporated fluoride and its distribution within the glass were interpreted and analyzed using Molecular dynamics (MD) simulations and the results were compared with the modified random network (MRN) model. The interpretations from the model have been verified using the MAS-NMR spectroscopy technique. According to this model, fluoride containing bioactive glasses have been proposed to consist of silicate rich network regions and modifier cation {\textendash} fluoride rich inter-network regions. The interface region was found to consist of non-bridging oxygen species (NBO) and phosphate cations which are either isolated orthophosphates (Q0P) or bridged with silicates in the form of pyrophosphate (Q1P) units forming Si{\textendash}O{\textendash}P bonds. The gradual substitution of CaF2\ for CaO in the base glass resulted in an increase in the silicate network connectivity with a reduction in the NBOs and lead to an increase in the association of modifier cations with fluoride ions. However, fluoride ions were found to show a marginal preference to associate with Na+\ cations leading to a decrease in the association of Na+\ ions with orthophosphate and silicate units. These overall structural findings were correlated with the\ in\ vitro\ ion dissolution behaviour of the bioactive glasses as well as with the thermal properties. The glasses were tested for their\ in\ vitro\ cell viability towards mouse osteoblast type (MC3T3) cells in which fluoride containing bioactive glasses did not show any toxicity and exhibited better cell proliferation. The antibacterial efficacy of the fluoride containing glasses was tested at various concentrations (5, 10 and 20\ mg/ml) in\ E.coli\ bacterial inoculum in which bactericidal action was evidenced.

}, keywords = {Fluoride bioactive glasses, In~vitro apatite formation and bactericidal action, MAS-NMR spectroscopy, MD simulations}, issn = {0925-8388}, doi = {10.1016/j.jallcom.2020.154704}, author = {Prasad, Sakthi and Ganisetti, Sudheer and Jana, Anuradha and Kant, Shashi and Sinha, P. K. and Tripathy, Sucheta and Illath, Kavya and Ajithkumar, T. G. and Annapurna, K. and Allu, Amarnath R. and Biswas, Kaushik} } @article {48229, title = {Elucidating the influence of structure and Ag+ -Na+ ion-exchange on crack-resistance and ionic conductivity of Na3Al1.8Si1.65 P-1.8 O-12 glass electrolyte}, journal = {Acta Materialia}, volume = {227}, year = {2022}, month = {APR }, pages = {117745}, type = {Article}, abstract = {

Glasses are emerging as promising and efficient solid electrolytes for all-solid-state sodium-ion batteries. However, they still suffer from poor ionic conductivity and crack-resistance, which need to be improved for better battery performance, reliability, and service life. The current study shows a significant enhancement in crack resistance (from 11.3 N to 32.9 N) for Na3Al (1.8) Si-1.65 P1.8O12 glass (Ag-0 glass) upon Na+ -Ag+ ion-exchange (IE) due to compressive stresses generated in the glass surface while the ionic conductivity values (similar to 10(-5) S/cm at 473 K) were retained. In this study, magic angle spinning-nuclear magnetic resonance (MAS-NMR), molecular dynamics (MD) simulations, Vickers micro hardness, and impedance spectroscopic techniques were used to evaluate the intermediate-range structure, atomic structure, crack resistance and conductivity of the glass. MAS-NMR and MD simulations confirm the presence of Si-OAl-O-P groups in the glass, thus enabling formation of Na percolated channel regions. AC-conductivity analysis for Ag-0 and ion-exchanged Ag-0 glass suggests that the mobility of Na+ ion increases with increasing temperature. It is observed that the measured mean square displacement (root \< R-2(t(p))\>) for sodium cations using AC-conductivity isotherms is nearly constant up to 448 K and then increases with increasing temperature up to 523 K. From the impedance spectra for ion-exchanged Ag-0 glass, it is identified that the increase in root \< R-2 (t(nu))\> and thereby, the mobility of sodium-ions for Ag-0 glass is due to the structural variations in the Ag-0 glass with increasing the temperature. Overall, the mechanisms presented in this article helps in formulating better glass based electrolyte materials for room temperature or high temperature sodium-ion batteries. (C) 2022 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

}, keywords = {amorphous, Ion-exchange, Ionic-conductivity, MD simulations, Mechanical property}, issn = {1359-6454}, doi = {10.1016/j.actamat.2022.117745}, author = {Keshri, Shweta R. and Mandal, Indrajeet and Ganisetti, Sudheer and Kasimuthumaniyan, S. and Kumar, Rajesh and Gaddam, Anuraag and Shelke, Ankita and Ajithkumar, Thalasseril G. and Gosvami, Nitya Nand and Krishnan, N. M. Anoop and Allu, Amarnath R.} } @article {47062, title = {First synthesis of podocarflavone A and its analogs and evaluation of their antimycobacterial potential against mycobacterium tuberculosis with the support of virtual screening}, journal = {Natural Product Research}, volume = {36}, year = {2022}, month = {AUG}, pages = {3879-3886}, type = {Article}, abstract = {

The first synthetic route developed for Podocarflavone A reported from Podocarpus macrophyllus and its analogs in 7 steps. Computational analysis for binding with the pantothenate kinase (3AVO) of Mycobacterium tuberculosis showed their docking score (ds) in the range of -8.9 to -9.3 Kcal/mol. MD simulations delineated the stability of the protein-ligand complexes in the TIP3P model. MMGBSA and MMPBSA values of 8d were -42.46 Kcal/mol and -14.58 Kcal/mol, respectively. Further in-vitro antitubercular screening of compounds 8a, 8d, and 8e against M. tuberculosis H37Ra using XRMA protocol exhibited promising antimycobacterial activity with IC50 values 21.82 mu g/mL, 15.55 mu g/mL, and 16.56 mu g/mL, respectively. Compounds 8a, 8d, and 8e showed antibacterial activity with IC50 values 41.56 mu g/mL, 24.72 mu g/mL, and 72.45 mu g/mL respectively against the Staphylococcus aureus. 8a and 8d showed inhibition with IC50 values 39.6 mu g/mL and 27.64 mu g/mL, respectively, against Bacillus subtilis. The present study could help in the further development of lead molecules against tuberculosis.

}, keywords = {and MMGBSA, antimycobacterial activity, docking, MD simulations, MMPBSA, Podocarflavone A synthesis}, issn = {1478-6419}, doi = {10.1080/14786419.2021.1893317}, author = {Puranik, Ninad V. and Swami, Sagar and Misar, Ashwini V. and Mamgain, Ritu and Gulawani, Swapnaja S. and Dhiman, Sarkar and Srivastava, Pratibha} }