@article {46401, title = {Allostery mapping in enterococcus faecalis Bile Salt Hydrolase (BSH)}, journal = {Acta Crystallographica A-Foundation and Advances}, volume = {70}, year = {2014}, month = {MAY}, pages = {C274}, type = {Meeting Abstract}, keywords = {Allostery, Bile salt hydrolase, MD Simulation}, issn = {2053-2733}, author = {Yadav, Yashpal and Ramasamy, Sureshkumar} } @article { ISI:000375723900014, title = {Structural insight into self assembly of sophorolipids: a molecular dynamics simulation study}, journal = {Zeitschrift Fur Physikalische Chemie-International Journal of Research in Physical Chemistry \& Chemical Physics}, volume = {230}, number = {5-7, SI}, year = {2016}, month = {MAY}, pages = {819-836}, publisher = {WALTER DE GRUYTER GMBH}, address = {GENTHINER STRASSE 13, D-10785 BERLIN, GERMANY}, abstract = {

Sophorolipids contain hydrophilic head groups at the ends of a long hydrophobic tail. As a result, sophorolipids can self assemble into variety of structures in water. Atomistic self assembly simulations of sophorolipids are performed in water. Two sophorolipids, oleic acid sophorolipid and linolenic acid sophorolipid, differing in number of double bonds in the hydrophobic tail are considered for this study. Long time self assembly simulations are performed considering 1 :3 lipid to water ratio by weight for both oleic and linolenic acid sophorolipids. In addition to 1 : 3 ratio, long time self assembly simulations are also performed with 1 : 1 and 1 : 2 ratios for linolenic acid sophorolipids. Distinctions in structural arrangements of sophorolipid molecules in the self assembled configuration for all the systems are investigated. The present study aims to provide structural insight into the different self assembled configurations of sophorolipids in water.

}, keywords = {MD Simulation, self assembly, sophorolipids, United Atom Force Field}, issn = {0942-9352}, doi = {10.1515/zpch-2015-0719}, author = {Pandey, Prithvi Raj and Dhasaiyan, Prabhu and Bhagavatula L. V. Prasad and Roy, Sudip} } @article {45736, title = {Functional stability and structural transitions of kallikrein: spectroscopic and molecular dynamics studies}, journal = {Journal of Biomolecular Structure \& Dynamics}, volume = {35}, year = {2017}, month = {MAR}, pages = {330-342}, type = {Article}, abstract = {

Kallikrein, a physiologically vital serine protease, was investigated for its functional and conformational transitions during chemical (organic solvents, Gdn-HCl), thermal, and pH induced denaturation using biochemical and biophysical techniques and molecular dynamics (MD) simulations approach. The enzyme was exceptionally stable in isopropanol and ethanol showing 110\% and 75\% activity, respectively, after 96h, showed moderate tolerance in acetonitrile (45\% activity after 72h) and much lower stability in methanol (40\% activity after 24h) (all the solvents [90\% v/v]). Far UV CD and fluorescence spectra indicated apparent reduction in compactness of KLKp structure in isopropanol system. MD simulation studies of the enzyme in isopropanol revealed (1) minimal deviation of the structure from native state (2) marginal increase in radius of gyration and solvent accessible surface area (SASA) of the protein and the active site, and (3) loss of density barrier at the active site possibly leading to increased accessibility of substrate to catalytic triad as compared to methanol and acetonitrile. Although kallikrein was structurally stable up to 90 degrees C as indicated by secondary structure monitoring, it was functionally stable only up to 45 degrees C, implicating thermolabile active site geometry. In GdnHCl [1.0M], 75\% of the activity of KLKp was retained after incubation for 4h, indicating its denaturant tolerance. A molten globule-like structure of KLKp formed at pH 1.0 was more thermostable and exhibited interesting structural transitions in organic solvents. The above results provide deeper understanding of functional and structural stability of the serine proteases at molecular level.

}, keywords = {isopropanol tolerance, Kallikrein, MD Simulation, Molten globule, Serine protease, Thermostability}, issn = {0739-1102}, doi = {10.1080/07391102.2016.1138884}, author = {Dalal, Sayli and Mhashal, Anil and Kadoo, Narendra and Gaikwad, Sushama M.} } @article {46068, title = {Impact of plasticizer addition on molecular properties of polybutadiene rubber and its manifestations to glass transition temperature}, journal = {Macromolecular Theory and Simulations}, volume = {28}, year = {2019}, month = {JUL}, pages = {1900003}, type = {Article}, abstract = {

Effect of blending low and high T-g polymer on the structural, spatial, and temporal properties of the polybutadiene rubber are investigated using molecular dynamics simulations. It is elucidated that smaller chain length counterpart of polybutadiene (5mer-OB) acts as plasticizer for the polybutadiene rubber matrix (32mer-PB). Observed flexibility at macroscopic level by plasticizer addition is corroborated at the molecular level in the form of lower conformational rigidity and faster diffusion of polybutadiene chains in the mixtures. It is inferred that plasticizers decreases T-g of the matrix, due to cooperative influence of decreased chain packing and rigidity. Opposite effect is observed in mixtures with high T-g polymer, polystyrene. T-g of the mixtures showed substantial dependence on the type, concentration, chain length as well as miscibility of plasticizers in the matrix. However, the effect of increasing chain length is more pronounced but counter-controlled by the spatially heterogeneous distribution of the plasticizer. Clustering of polystyrene chains induced significant dynamic heterogeneity in the homogeneous polybutadiene matrix, which apparently lead to reduced plasticization effect. Addition of plasticizers in rubber induce discernible changes in the structural and dynamic properties of the rubber matrix, which manifest as the variation in glass transition and explains the real-life activity of plasticizers.

}, keywords = {Glass transition temperature, MD Simulation, plasticizer action, polybutadiene rubber, Polystyrene, spatial and dynamic heterogeneity}, issn = {1022-1344}, doi = {10.1002/mats.201900003}, author = {Sharma, Pragati and Roy, Sudip and Karimi-Varzaneh, Hossein Ali} }