<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Shahane, Ganesh</style></author><author><style face="normal" font="default" size="100%">Parsania, Chirag</style></author><author><style face="normal" font="default" size="100%">Sengupta, Durba</style></author><author><style face="normal" font="default" size="100%">Joshi, Manali</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Molecular Insights into the dynamics of pharmacogenetically important N-terminal variants of the human beta(2)-adrenergic receptor</style></title><secondary-title><style face="normal" font="default" size="100%">Plos Computational Biology</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2014</style></year><pub-dates><date><style  face="normal" font="default" size="100%">DEC</style></date></pub-dates></dates><number><style face="normal" font="default" size="100%">12</style></number><publisher><style face="normal" font="default" size="100%">PUBLIC LIBRARY SCIENCE</style></publisher><pub-location><style face="normal" font="default" size="100%">1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA</style></pub-location><volume><style face="normal" font="default" size="100%">10</style></volume><pages><style face="normal" font="default" size="100%">e1004006</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The human beta(2)-adrenergic receptor (beta(2)AR), a member of the G-protein coupled receptor (GPCR) family, is expressed in bronchial smooth muscle cells. Upon activation by agonists, beta(2)AR causes bronchodilation and relief in asthma patients. The N-terminal polymorphism of beta(2)AR at the 16th position, Arg16Gly, has warranted a lot of attention since it is linked to variations in response to albuterol (agonist) treatment. Although the beta(2)AR is one of the well-studied GPCRs, the N-terminus which harbors this mutation, is absent in all available experimental structures. The goal of this work was to study the molecular level differences between the N-terminal variants using structural modeling and atomistic molecular dynamics simulations. Our simulations reveal that the N-terminal region of the Arg variant shows greater dynamics than the Gly variant, leading to differential placement. Further, the position and dynamics of the N-terminal region, further, affects the ligand binding-site accessibility. Interestingly, long-range effects are also seen at the ligand binding site, which is marginally larger in the Gly as compared to the Arg variant resulting in the preferential docking of albuterol to the Gly variant. This study thus reveals key differences between the variants providing a molecular framework towards understanding the variable drug response in asthma patients.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">12</style></issue><custom3><style face="normal" font="default" size="100%">Foreign</style></custom3><custom4><style face="normal" font="default" size="100%">3.46
</style></custom4></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Patra, Swarna M.</style></author><author><style face="normal" font="default" size="100%">Chakraborty, Sudip</style></author><author><style face="normal" font="default" size="100%">Shahane, Ganesh</style></author><author><style face="normal" font="default" size="100%">Prasanna, Xavier</style></author><author><style face="normal" font="default" size="100%">Sengupta, Durba</style></author><author><style face="normal" font="default" size="100%">Maiti, Prabal K.</style></author><author><style face="normal" font="default" size="100%">Chattopadhyay, Amitabha</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Differential dynamics of the serotonin(1A) receptor in membrane bilayers of varying cholesterol content revealed by all atom molecular dynamics simulation</style></title><secondary-title><style face="normal" font="default" size="100%">Molecular Membrane Biology</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">GPCR</style></keyword><keyword><style  face="normal" font="default" size="100%">Membrane cholesterol</style></keyword><keyword><style  face="normal" font="default" size="100%">molecular dynamics simulation</style></keyword><keyword><style  face="normal" font="default" size="100%">serotonin(1A) receptor</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2015</style></year><pub-dates><date><style  face="normal" font="default" size="100%">MAY</style></date></pub-dates></dates><number><style face="normal" font="default" size="100%">4</style></number><publisher><style face="normal" font="default" size="100%">TAYLOR &amp; FRANCIS LTD</style></publisher><pub-location><style face="normal" font="default" size="100%">4 PARK SQUARE, MILTON PARK, ABINGDON OX14 4RN, OXON, ENGLAND</style></pub-location><volume><style face="normal" font="default" size="100%">32</style></volume><pages><style face="normal" font="default" size="100%">127-137</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The serotonin(1A) receptor belongs to the superfamily of G protein-coupled receptors (GPCRs) and is a potential drug target in neuropsychiatric disorders. The receptor has been shown to require membrane cholesterol for its organization, dynamics and function. Although recent work suggests a close interaction of cholesterol with the receptor, the structural integrity of the serotonin(1A) receptor in the presence of cholesterol has not been explored. In this work, we have carried out all atom molecular dynamics simulations, totaling to 3s, to analyze the effect of cholesterol on the structure and dynamics of the serotonin(1A) receptor. Our results show that the presence of physiologically relevant concentration of membrane cholesterol alters conformational dynamics of the serotonin(1A) receptor and, on an average lowers conformational fluctuations. Our results show that, in general, transmembrane helix VII is most affected by the absence of membrane cholesterol. These results are in overall agreement with experimental data showing enhancement of GPCR stability in the presence of membrane cholesterol. Our results constitute a molecular level understanding of GPCR-cholesterol interaction, and represent an important step in our overall understanding of GPCR function in health and disease.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom3><style face="normal" font="default" size="100%">&lt;p&gt;Foreign&lt;/p&gt;</style></custom3><custom4><style face="normal" font="default" size="100%">1.983</style></custom4></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Yadav, Priya</style></author><author><style face="normal" font="default" size="100%">Shahane, Ganesh</style></author><author><style face="normal" font="default" size="100%">Ramasamy, Sureshkumar</style></author><author><style face="normal" font="default" size="100%">Sengupta, Durba</style></author><author><style face="normal" font="default" size="100%">Gaikwad, Sushama</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Structural-functional insights and studies on saccharide binding of Sophora japonica seed lectin</style></title><secondary-title><style face="normal" font="default" size="100%">International Journal of Biological Macromolecules</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Dissociation</style></keyword><keyword><style  face="normal" font="default" size="100%">docking</style></keyword><keyword><style  face="normal" font="default" size="100%">Homology model</style></keyword><keyword><style  face="normal" font="default" size="100%">Ligand binding</style></keyword><keyword><style  face="normal" font="default" size="100%">Sophora japonica seed lectin</style></keyword><keyword><style  face="normal" font="default" size="100%">Thermal transitions</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2016</style></year><pub-dates><date><style  face="normal" font="default" size="100%">OCT</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">91</style></volume><pages><style face="normal" font="default" size="100%">75-84</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Functional and conformational transitions of the Sophora japonica seed lectin (SJL) were studied in detail using bioinformatics and biophysical tools. Homology model of the lectin displayed all the characteristics of the legume lectin monomer and the experimental observations correlated well with the structural information. In silico studies were performed by protein-ligand docking, calculating the respective binding energies and the residues involved in the interactions were derived from LigPlot(+) analysis. Fluorescence titrations showed three times higher affinity of T-antigen disaccharide than N-acetyl galactosamine (GaINAc) towards SJL indicating extended sugar binding site of the lectin. Thermodynamic parameters of T-antigen binding to SJL indicated the process to be endothermic and entropically driven while those of GaINAc showed biphasic process. SDS-PAGE showed post-translationally modified homotetrameric species of the lectin under native conditions. In presence of guanidine hydrochloride (0.5-5.0 M), the tetramer first dissociated into dimers followed by unfolding of the protein as indicated by size exclusion chromatography, fluorescence and CD spectroscopy. Different structural rearrangements were observed during thermal denaturation of SJL at physiological pH 7.2, native pH 8.5 and molten globule inducing pH 1.0. Topological information revealed by solute quenching studies at respective pH indicated differential hydrophobic environment and charge density around tryptophan residues. (C) 2016 Elsevier B.V. All rights reserved.&lt;/p&gt;</style></abstract><work-type><style face="normal" font="default" size="100%">Article</style></work-type><custom3><style face="normal" font="default" size="100%">Foreign</style></custom3><custom4><style face="normal" font="default" size="100%">3.138</style></custom4></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Yadav, Priya</style></author><author><style face="normal" font="default" size="100%">Shahane, Ganesh</style></author><author><style face="normal" font="default" size="100%">Gaikwad, Sushama M.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Amaranthus caudatus lectin with polyproline II fold: conformational and functional transitions and molecular dynamics</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of biomolecular Structure &amp; Dynamics</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2017</style></year><pub-dates><date><style  face="normal" font="default" size="100%">JUL</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">1</style></volume><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Polyproline II (PPII) fold, a peculiar structural element was detected in the Amaranthus caudatus seed lectin (ACL) based on far UV circular dichroism spectrum, conformational transitions of the lectin and a distinct isodichroic point in thermal denaturation. It was confirmed by using PolyprOnline database to estimate the percentage of amino acids contributing to PPII fold and showed the values as 13.5% and 13.9% for PROSS and XTLSSTR, respectively. Investigations of the functional and conformational transitions of ACL during thermal, pH and guanidine hydrochloride (GdnHCl) induced denaturation were carried out using biochemical and biophysical techniques and molecular dynamics (MD) simulations approach. The lectin got aggregated at 60 °C with instantaneous structural alterations. The aggregation-prone regions in ACL were predicted using online servers viz. AGGRESCAN, AmylPred, FoldAmyloid and Waltz that were represented by Visual Molecular Dynamics tools. Nine conserved regions were identified by these softwares as being ‘hot-spots’ for aggregation. MD simulation studies of the lectin at 60 °C revealed increase in radius of gyration. The loss of PPII fold in 2.0 M GdnHCl was reversible. The partially unfolded intermediate of ACL with diminished PPII fold formed at pH 1.0 was stable up to 90 °C. The polyproline II fold has been rarely detected in lectins, ACL being the second after the potato lectin.</style></abstract><issue><style face="normal" font="default" size="100%">13</style></issue><work-type><style face="normal" font="default" size="100%">Article</style></work-type><custom3><style face="normal" font="default" size="100%">Foreign</style></custom3><custom4><style face="normal" font="default" size="100%">2.3</style></custom4></record></records></xml>