01647nas a2200169   4500008004100000022001400041245015000055210006900205260007100274300001400345490000800359520092000367100001801287700002501305700001501330856013201345       2015                        eng d  a1520-610600aPropensity of self-assembled leucine-lysine diblock copolymeric alpha-helical peptides to remain in parallel and antiparallel alignments in water0 aPropensity of selfassembled leucinelysine diblock copolymeric al  a1155 16TH ST, NW, WASHINGTON, DC 20036 USAbAMER CHEMICAL SOCcJUL  a9520-95310 v1193 a<p>Molecular dynamics Simulation study of alpha-helical diblock copolypeptides: preassembled in parallel and antiparallel alignments in water are presented. The assembled peptide lamellar structures were not disrupted even: after performing three step simulation protocols. Primarily hydrogen bonds between peptide are responsible for the stability: The analysis of the trajectory also suggests that Water plays a significant role in favoring self assembly We have detected continuous hydrogen bonded network structure, which is further responsible for the stability Of the lamellar structures. We have performed a detailed analysis of the hydrogen bonded network structure and its length. Further, free energy calculations revealed that the degree of stability for both lamellae are similar. The present study provides structural insight into the stability of self-assembled structures of block copolypeptides.</p>1 aSarkar, Sujit1 aPandey, Prithvi, Raj1 aRoy, Sudip  uhttps://library.ncl.res.in/content/propensity-self-assembled-leucine-lysine-diblock-copolymeric-alpha-helical-peptides-remain-002220nas a2200181   4500008004100000022001400041245013800055210006900193260011000262300001400372490000700386520144300393100001801836700001801854700002501872700001501897856012601912       2016                        eng d  a1463-907600aTransferability of different classical force fields for right and left handed alpha-helices constructed from enantiomeric amino acids0 aTransferability of different classical force fields for right an  aTHOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLANDbROYAL SOC CHEMISTRYcFEB  a5550-55630 v183 a<p>Amino acids can form D and L enantiomers, of which the L enantiomer is abundant in nature. The naturally occurring L enantiomer has a greater preference for a right handed helical conformation, and the D enantiomer for a left handed helical conformation. The other conformations, that is, left handed helical conformations of the L enantiomers and right handed helical conformations of the D enantiomers, are not common. The energetic differences between left and right handed alpha helical peptide chains constructed from enantiomeric amino acids are investigated using quantum chemical calculations (using the M06/6-311g(d,p) level of theory). Further, the performances of commonly used biomolecular force fields (OPLS/AA, CHARMM27/CMAP and AMBER) to represent the different helical conformations (left and right handed) constructed from enantiomeric (D and L) amino acids are evaluated. 5- and 10-mer chains from D and L enantiomers of alanine, leucine, lysine, and glutamic acid, in right and left handed helical conformations, are considered in the study. Thus, in total, 32 a-helical polypeptides (4 amino acids x 4 conformations of 5-mer and 10-mer) are studied. Conclusions, with regards to the performance of the force fields, are derived keeping the quantum optimized geometry as the benchmark, and on the basis of phi and psi angle calculations, hydrogen bond analysis, and different long range helical order parameters.</p>1 aBiswas, Santu1 aSarkar, Sujit1 aPandey, Prithvi, Raj1 aRoy, Sudip  uhttps://library.ncl.res.in/content/transferability-different-classical-force-fields-right-and-left-handed-alpha-helices-002323nas a2200217   4500008004100000022001400041245015600055210006900211260000800280300001400288490000600302520153700308100002001845700001701865700001801882700002001900700001501920700002101935700001801956856013101974       2017                        eng d  a2470-134300aDrug-triggered self-assembly of linear polymer into nanoparticles for simultaneous delivery of hydrophobic and hydrophilic drugs in breast cancer cells0 aDrugtriggered selfassembly of linear polymer into nanoparticles   cDEC  a8730-87400 v23 a<p>Breast cancer is the most devastating disease among females globally. Conventional chemotherapeutic regimen relies on the use of highly cytotoxic drugs as monotherapy and combination therapy leading to severe side effects to the patients as collateral damage. Moreover, combining hydrophobic and hydrophilic drugs create erratic biodistribution and suboptimal medicinal outcome. Hence, packaging multiple drugs of diverse mechanisms of action and biodistribution for safe delivery into tumor tissues with optimal dosages is indispensable for next-generation breast cancer therapy. To address these, in this report, we describe a unique cisplatin-triggered self-assembly of linear polymer into 3D-spherical sub 200 nm particles. These nano-particles comprise a hydrophobic (paclitaxel) and hydrophilic drug (cisplatin) simultaneously in a single particle. Molecular dynamics simulation revealed hydrophilic-hydrophilic interaction and interchain H-bonding as underlying mechanisms of self-assembly. Confocal microscopy studies evidently demonstrated that these novel nanoparticles can home into lysosomes in breast cancer cells, fragment subcellular nuclei, and prevent cell division, leading to improved breast cancer cell death compared to free drug combination. Moreover, 3D-breast tumor spheroids were reduced remarkably by the treatment of these nanoparticles within 24 h. These dual-drug-loaded self-assembled polymeric nanoparticles have prospective to be translated into a clinical strategy for breast cancer patients.</p>1 aPalvai, Sandeep1 aAnandi, Libi1 aSarkar, Sujit1 aAugustus, Meera1 aRoy, Sudip1 aLahiri, Mayurika1 aBasu, Sudipta  uhttps://library.ncl.res.in/content/drug-triggered-self-assembly-linear-polymer-nanoparticles-simultaneous-delivery-hydrophobic01992nas a2200229   4500008004100000022001400041245008900055210006900144260000900213300001200222490000800234520124000242653001901482653001901501653002501520653002601545653001801571100001801589700002401607700001501631856011601646       2018                        eng d  a0167-732200aPhase diagram of self-assembled sophorolipid morphologies from mesoscale simulations0 aPhase diagram of selfassembled sophorolipid morphologies from me  cMAR   a198-2070 v2543 a<p>We have constructed a phase diagram from the self-assembled morphologies of linolenic acid sophorolipid in water by performing mesoscale simulations in different concentrations. The dependence of morphologies and its properties of the self-assembled structure as a function of the concentration of bolaamphiphile in water are investigated. Two hydrophilic head groups and one hydrophobic tail group of bolaamphiphile have been mapped to beads for mesoscale simulation. The interaction parameters between different beads are calculated using Flory-Huggins solution theory. Flory-Huggins x-parameters have been calculated from atomistic simulation and experimental data of pure components constituting linolenic acid sophorolipid. We have obtained different self-assembled morphologies depending upon the concentrations of sophorolipid in water. We have explored the arrangements of hydrophobic and hydrophilic groups of the sophorolipid chains in the different morphologies. The sophorolipid chains found to be present in different structural arrangements. The residence time and flip frequency of these lipids in different orientations have been calculated and discussed in this work. (C) 2018 Elsevier B.V. All rights reserved.</p>10aBolaamphiphile10aFlip frequency10aMesoscale simulation10aOrientation of chains10aSelf-assembly1 aSarkar, Sujit1 aChakraborty, Souvik1 aRoy, Sudip  uhttps://library.ncl.res.in/content/phase-diagram-self-assembled-sophorolipid-morphologies-mesoscale-simulations