@article { ISI:000241085200021, title = {Synthesis, characterization, and molecular modeling studies of novel polyurethanes based on 2,2 {\textquoteright}-[ethane-1,2-diylbis(nitrilomethylylidene)]diphenol and 2,2 {\textquoteright}-[hexane-1,6-diylbis(nitrilomethylylidene)]diphenol hard segments}, journal = {Journal of Polymer Science Part A-Polymer Chemistry}, volume = {44}, number = {20}, year = {2006}, month = {OCT}, pages = {6032-6046}, publisher = {JOHN WILEY \& SONS INC}, type = {Article}, address = {111 RIVER ST, HOBOKEN, NJ 07030 USA}, abstract = {

Novel polyurethanes (PUS) based on 2,2 {\textquoteleft}-[ethane-1,2-diylbis(nitrilomethylylidene)]diphenol and 2,2 {\textquoteleft}-[hexane-1,6-diylbis(nitrilomethylylidene)]diphenol as hard segments containing four aromatic diisocyanates (4,4 {\textquoteleft}-diphenylmethane diisocyanate, toluene 2,4-diisocyanate, isophorone diisocyanate, and hexamethylene diisocyanate) have been prepared. Fourier transform infrared, UV spectrophotometry, fluorescence spectroscopy, H-1 NMR and C-13 NMR spectroscopy, thermogravimetric analysis, and differential thermal analysis have been used to determine the structural characterization and thermal properties of the segmented PUS. All the PUS contain domains of both semicrystalline and amorphous structures, as indicated by X-ray diffraction. The acoustic properties have been calculated with the group contribution method. Molecular dynamics simulations have been performed on all the PUS to estimate the cohesive energy density and solubility parameter values, which compare well with the values calculated with the group contribution method. Furthermore, the simulation protocols have been applied to the PUS to produce X-ray diffraction plots to determine the phase morphology of the PUS. The surface properties of the PUS have been estimated from the simulation protocols. (c) 2006 Wiley Periodicals, Inc.

}, keywords = {amorphous, hard segments, molecular dynamics, Morphology, polyurethanes, Schiff base containing polymers, Thermal properties}, issn = {0887-624X}, doi = {10.1002/pola.21686}, author = {Raghu, A. V. and Gadaginamath, G. S. and Jawalkar, S. S. and Halligudi, Shivaraj B. and Aminabhavi, T. A.} } @article { ISI:000308300700010, title = {Prediction of structure and energy of trans-1,4-polybutadiene glassy surface by atomistic simulations of free-standing ultrathin films}, journal = {Journal of Macromolecular Science Part B-Physics}, volume = {51}, number = {11}, year = {2012}, month = {MAR}, pages = {2201-2221}, publisher = {TAYLOR \& FRANCIS INC}, type = {Article}, address = {325 CHESTNUT ST, SUITE 800, PHILADELPHIA, PA 19106 USA}, abstract = {

Atomistic modeling of amorphous trans-1,4-polybutadiene (TPBD), using molecular mechanics and molecular dynamics (MD) simulations, is performed to generate three-dimensionally periodic bulk and two-dimensionally periodic thin film condensed phases. The condensed structures are constructed using multiple polymer chains. Structural and energetic relaxations and sampling of properties are performed using MD in the canonical ensemble (NVT) by a procedure that relieves local high-energy spots and brings the system to realistic thermodynamic states. The calculated surface energy for TPBD, 30.72 erg/cm(2), is in excellent agreement with the reported experimental value of 31 erg/cm(2). The structure of the surface layers is probed in terms of the atomic mass density variations, bond-bond orientation function profiles, and the distribution of the dihedral angles about the rotatable backbone bonds. The thickness of the surface layer over which the density varies smoothly but rapidly is found to be approximately 15 angstrom. The level of agreement of the calculated surface energy with the experimental value is superior in comparison to previous investigations in the literature using the atomistic approach for flexible polymers.

}, keywords = {4-polybutadiene, atomistic simulation, bond-orientation, Conformation, molecular dynamics, polymer glass, surface energy, trans-1}, issn = {0022-2348}, doi = {10.1080/00222348.2012.669683}, author = {Ijantkar, Ashwini S. and Natarajan, Upendra} } @article { ISI:000301712600016, title = {Rapid self-healing hydrogels}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {12}, year = {2012}, month = {MAR}, pages = {4383-4388}, publisher = {NATL ACAD SCIENCES}, address = {2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA}, abstract = {

Synthetic materials that are capable of autonomous healing upon damage are being developed at a rapid pace because of their many potential applications. Despite these advancements, achieving self-healing in permanently cross-linked hydrogels has remained elusive because of the presence of water and irreversible cross-links. Here, we demonstrate that permanently cross-linked hydrogels can be engineered to exhibit self-healing in an aqueous environment. We achieve this feature by arming the hydrogel network with flexible-pendant side chains carrying an optimal balance of hydrophilic and hydrophobic moieties that allows the side chains to mediate hydrogen bonds across the hydrogel interfaces with minimal steric hindrance and hydrophobic collapse. The self-healing reported here is rapid, occurring within seconds of the insertion of a crack into the hydrogel or juxtaposition of two separate hydrogel pieces. The healing is reversible and can be switched on and off via changes in pH, allowing external control over the healing process. Moreover, the hydrogels can sustain multiple cycles of healing and separation without compromising their mechanical properties and healing kinetics. Beyond revealing how secondary interactions could be harnessed to introduce new functions to chemically crosslinked polymeric systems, we also demonstrate various potential applications of such easy-to-synthesize, smart, self-healing hydrogels.

}, keywords = {adhesives, biomimetic materials, Hydrophobicity, molecular dynamics, smart materials}, issn = {0027-8424}, doi = {10.1073/pnas.1201122109}, author = {Phadke, Ameya and Zhang, Chao and Arman, Bedri and Hsu, Cheng-Chih and Mashelkar, Raghunath Anant and Lele, Ashish K. and Tauber, Michael J. and Arya, Gaurav and Varghese, Shyni} } @article { ISI:000313077100009, title = {Characterization of the structures and dynamics of phosphoric acid doped benzimidazole mixtures: a molecular dynamics study}, journal = {Journal of Molecular Modeling}, volume = {19}, number = {1}, year = {2013}, month = {JAN}, pages = {109-118}, publisher = {SPRINGER}, address = {233 SPRING ST, NEW YORK, NY 10013 USA}, abstract = {

Benzimidazole-based polymer membranes like poly(2,5-benzimidazole) (ABPBI) doped with phosphoric acid (PA) are electrolytes that exhibit high proton conductivity in fuel cells at elevated temperatures. The benzimidazole (BI) moiety is an important constituent of these membranes, so the present work was performed in order to achieve a molecular understanding of the BI-PA interactions in the presence of varying levels of the PA dopant, using classical molecular dynamics (MD) simulations. The various hydrogen-bonding interactions, as characterized based on structural properties and hydrogen-bond lifetime calculations, show that both BI and PA molecules exhibit dual proton-acceptor/donor functionality. An examination of diffusion coefficients showed that the diffusion of BI decreases with increasing PA uptake, whereas the diffusion of PA slightly increases. The hydrogen-bond lifetime calculations pointed to the existence of competitive hydrogen bonding between various sites in BI and PA.

}, keywords = {Diffusion coefficient, Hydrogen bond, molecular dynamics, Radial distribution functions}, issn = {1610-2940}, doi = {10.1007/s00894-012-1519-8}, author = {More, Minal and Pahari, Swagata and Roy, Sudip and Venkatnathan, Arun} } @article { ISI:000368702300006, title = {Molecular interaction of selected phytochemicals under the charged environment of Plasmodium falciparum chloroquine resistance transporter (PfCRT) model}, journal = {Journal of Biomolecular Structure \& Dynamics}, volume = {34}, number = {2}, year = {2016}, month = {FEB}, pages = {290-303}, publisher = {TAYLOR \& FRANCIS INC}, address = {530 WALNUT STREET, STE 850, PHILADELPHIA, PA 19106 USA}, abstract = {

Phytochemicals of Catharanthus roseus Linn. and Tylophora indica have been known for their inhibition of malarial parasite, Plasmodium falciparum in cell culture. Resistance to chloroquine (CQ), a widely used antimalarial drug, is due to the CQ resistance transporter (CRT) system. The present study deals with computational modeling of Plasmodium falciparum chloroquine resistance transporter (PfCRT) protein and development of charged environment to mimic a condition of resistance. The model of PfCRT was developed using Protein homology/analogy engine (PHYRE ver 0.2) and was validated based on the results obtained using PSI-PRED. Subsequently, molecular interactions of selected phytochemicals extracted from C. roseus Linn. and T. indica were studied using multiple-iterated genetic algorithm-based docking protocol in order to investigate the translocation of these legends across the PfCRT protein. Further, molecular dynamics studies exhibiting interaction energy estimates of these compounds within the active site of the protein showed that compounds are more selective toward PfCRT. Clusters of conformations with the free energy of binding were estimated which clearly demonstrated the potential channel and by this means the translocation across the PfCRT is anticipated.

}, keywords = {homology modeling, molecular dynamics, Plasmodium falciparum chloroquine, resistance transporter model}, issn = {0739-1102}, doi = {10.1080/07391102.2015.1028449}, author = {Patel, Saumya K. and Khedkar, Vijay M. and Jha, Prakash C. and Jasrai, Yogesh T. and Pandya, Himanshu A. and George, Linz-Buoy and Highland, Hyacinth N. and Skelton, Adam A.} } @article { ISI:000368973000001, title = {Structural analysis of a penicillin V acylase from pectobacterium atrosepticum confirms the importance of two Trp residues for activity and specificity}, journal = {Journal of Structural Biology}, volume = {193}, number = {2}, year = {2016}, month = {FEB}, pages = {85-94}, publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE}, address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA}, abstract = {

Penicillin V acylases (PVA) catalyze the deacylation of the beta-lactam antibiotic phenoxymethylpenicillin (Pen V). They are members of the Ntn hydrolase family and possess an N-terminal cysteine as the main catalytic nucleophile residue. They form the evolutionarily related cholylglycine hydrolase (CGH) group which includes bile salt hydrolases (BSH) responsible for bile deconjugation. Even though a few PVA and BSH structures have been reported, no structure of a functional PVA from Gram-negative bacteria is available. Here, we report the crystal structure of a highly active PVA from Gram-negative Pectobacterium atrosepticum (PaPVA) at 2.5 angstrom resolution. Structural comparison with PVAs from Gram-positive bacteria revealed that PaPVA had a distinctive tetrameric structure and active site organization. In addition, mutagenesis of key active site residues and biochemical characterization of the resultant variants elucidated the role of these residues in substrate binding and catalysis. The importance of residue Trp23 and Trp87 side chains in binding and correct positioning of Pen V by PVAs was confirmed using mutagenesis and substrate docking with a 15 ns molecular dynamics simulation. These results establish the unique nature of Gram-negative CGHs and necessitate further research about their substrate spectrum. (C) 2015 Elsevier Inc. All rights reserved.

}, keywords = {Aromatic stacking, Cholylglycine hydrolase, molecular dynamics, Mutagenesis, Oligomeric interactions}, issn = {1047-8477}, doi = {10.1016/j.jsb.2015.12.008}, author = {Avinash, Vellore Sunder and Panigrahi, Priyabrata and Chand, Deepak and Pundle, Archana and Suresh, Cheravakattu Gopalan and Ramasamy, Sureshkumar} } @article {44551, title = {Structure and function of a highly active Bile Salt Hydrolase (BSH) from Enterococcus faecalis and post-translational processing of BSH enzymes}, journal = {Biochim Biophys Acta.}, volume = {1866}, year = {2018}, month = {JAN}, pages = {507-518}, type = {Journal Article}, abstract = {Bile Salt Hydrolase (BSH), a member of Cholylglycine hydrolase family, catalyzes the de-conjugation of bile acids and is evolutionarily related to penicillin V acylase (PVA) that hydrolyses a different substrate such as penicillin V. We report the three-dimensional structure of a BSH enzyme from the Gram-positive bacteria Enterococcus faecalis (EfBSH) which has manifold higher hydrolase activity compared to other known BSHs and displays unique allosteric catalytic property. The structural analysis revealed reduced secondary structure content compared to other known BSH structures, particularly devoid of an anti-parallel β-sheet in the assembly loop and part of a β-strand is converted to increase the length of a substrate binding loop 2. The analysis of the substrate binding pocket showed reduced volume owing to altered loop conformations and increased hydrophobicity contributed by a higher ratio of hydrophobic to hydrophilic groups present. The aromatic residues F18, Y20 and F65 participate in substrate binding. Thus, their mutation affects enzyme activity. Docking and Molecular Dynamics simulation studies showed effective polar complementarity present for the three hydroxyl (-OH) groups of GCA substrate in the binding site contributing to higher substrate specificity and efficient catalysis. These are unique features characteristics of this BSH enzyme and thought to contribute to its higher activity and specificity towards bile salts as well as allosteric effects. Further, mechanism of autocatalytic processing of Cholylglycine Hydrolases by the excision of an N-terminal Pre-peptide was examined by inserting different N-terminal pre-peptides in EfBSH sequence. The results suggest that two serine residues next to nucleophile cysteine are essential for autocalytic processing to remove precursor peptide. Since pre-peptide is absent in EfBSH the mutation of these serines is tolerated. This suggests that an evolution-mediated subordination of the pre-peptide excision site resulted in loss of pre-peptide in EfBSH and other related Cholylglycine hydrolases.}, keywords = {autocatalytic processing, Bile salt hydrolase, molecular dynamics, Mutagenesis, Polar complementarity, X-ray crystallography}, issn = {15709639}, doi = {0.1016/j.bbapap.2018.01.003.}, author = {Chand, D.}, editor = {Panigrahi, P.} } @article {46342, title = {Differential dynamics underlying the Gln27Glu population variant of the beta(2)-adrenergic receptor}, journal = {Journal of Membrane Biology}, volume = {252}, year = {2019}, month = {OCT}, pages = {499-507}, type = {Article}, abstract = {

The beta (2)-adrenergic receptor (beta (2)AR) is a membrane-bound G-protein-coupled receptor and an important drug target for asthma. Clinical studies report that the population variant Gln27Glu is associated with a differential response to common asthma drugs, such as albuterol, isoproterenol and terbutaline. Interestingly, the 27th amino acid is positioned on the N-terminal region that is the most flexible and consequently the least studied part of the receptor. In this study, we probe the molecular origin of the differential drug binding by performing structural modeling and simulations of the wild-type (Gln) and variant (Glu) receptors followed by ensemble docking with the ligands, albuterol, isoproterenol and terbutaline. In line with clinical studies, the ligands were observed to interact preferentially with the Glu variant. Our results indicate that the Glu residue at the 27th position perturbs the network of electrostatic interactions that connects the N-terminal region to the binding site in the wild-type receptor. As a result, the Glu variant is observed to bind better to the three ligands tested in this study. Our study provides a structural basis to explain the variable drug response associated with the 27th position polymorphism in the beta (2)AR and is a starting step to identify genotype-specific therapeutics.

}, keywords = {beta(2)-Adrenergic receptor, G-protein-coupled receptor, GPCR, molecular dynamics, Pharmacogenetics, SNP}, issn = {0022-2631}, doi = {10.1007/s00232-019-00093-2}, author = {Bhosale, Sumedha and Nikte, V. Siddhanta and Sengupta, Durba and Joshi, Manali} } @article {47106, title = {Dynamic coupling analysis on plant sesquiterpene synthases provides leads for the identification of product specificity determinants}, journal = {Biochemical and Biophysical Research Communications}, volume = {536}, year = {2021}, month = {JAN }, pages = {107-114}, type = {Article}, abstract = {

Sesquiterpene synthases catalyse cyclisation of farnesyl pyrophosphate to produce diverse sesquiterpenes. Despite utilising the same substrate and exhibiting significant sequence and structural homology, these enzymes form different products. Previous efforts were based on identifying the effect of divergent residues present at the catalytic binding pocket on the product specificity of these enzymes. However, the rationales deduced for the product specificity from these studies were not generic enough to be applicable to other phylogenetically distant members of this family. To address this problem, we have developed a novel approach combining sequence, structural and dynamical information of plant sesquiterpene synthases (SSQs) to predict product modulating residues (PMRs). We tested this approach on the SSQs with known PMRs and also on sesquisabinene synthase 1 (SaSQS1), a SSQ from Indian sandalwood. Our results show that the dynamical sectors of SSQs obtained from molecular dynamics simulation and their hydrophobicity and vicinity indices together provide leads for the identification of PMRs. The efficacy of the technique was tested on SaSQS1 using mutagenesis. To the best of our knowledge, this is a first technique of this kind which provides cues on PMRs of SSQs, with divergent phylogenetic relationship. (C) 2020 Elsevier Inc. All rights reserved.

}, keywords = {molecular dynamics, Product specificity, Sesquiterpene synthases, Statistical coupling analysis, X-ray crystallography}, issn = {0006-291X}, doi = {10.1016/j.bbrc.2020.12.041}, author = {Singh, Sneha and Thulasiram, V, Hirekodathakallu and Sengupta, Durba and Kulkarni, Kiran} } @article {47034, title = {Loss of a water-mediated network results in reduced agonist affinity in a beta(2)-adrenergic receptor clinical variant}, journal = {Biochimica ET Biophysica Acta-Proteins and Proteomics}, volume = {1869}, year = {2021}, month = {APR}, pages = {140605}, type = {Article}, abstract = {

The beta(2)-adrenergic receptor (beta(2)AR) is a member of the G protein-coupled receptor (GPCR) family that is an important drug target for asthma and COPD. Clinical studies coupled with biochemical data have identified a critical receptor variant, Thr164Ile, to have a reduced response to agonist-based therapy, although the molecular mechanism underlying this seemingly {\textquoteleft}{\textquoteleft}non-deleterious{\textquoteright}{\textquoteright} substitution is not clear. Here, we couple molecular dynamics simulations with network analysis and free-energy calculations to identify the molecular determinants underlying the differential drug response. We are able to identify hydration sites in the transmembrane domain that are essential to maintain the integrity of the binding site but are absent in the variant. The loss of these hydration sites in the variant correlates with perturbations in the intra-protein interaction network and rearrangements in the orthosteric ligand binding site. In conjunction, we observe an altered binding and reduced free energy of a series of agonists, in line with experimental trends. Our work identifies a functional allosteric pathway connected by specific hydration sites in beta(2)AR that has not been reported before and provides insight into water-mediated networks in GPCRs in general. Overall, the work is one of the first step towards developing variant-specific potent and selective agonists.

}, keywords = {beta(2)-Adrenergic receptor, G protein coupled receptor, GPCR, molecular dynamics, Pharmacogenetics, SNP}, issn = {1570-9639}, doi = {10.1016/j.bbapap.2021.140605}, author = {Nikte, V. Siddhanta and Sonar, Krushna and Tandale, Aditi and Joshi, Manali and Sengupta, Durba} } @article {47070, title = {Molecular characterization of the beta(2)-like octopamine receptor of helicoverpa armigera}, journal = {Journal of Membrane Biology}, volume = {254}, year = {2021}, month = {JUN}, type = {Article}, abstract = {

Helicoverpa armigera is a devastating polyphagous and cosmopolitan crop pest. There are reports of this insect being resistant to a variety of pesticides raising concern worldwide. The Octopamine (OA) binding beta(2)-like receptor (OAR), a GPCR, is widely distributed in the nervous system of the insect and plays essential roles in the physiology and development and thus is an important target for insecticides. Yet, the molecular characterization of the H. armigera OAR (HarmOAR) and rational design of compounds based on this receptor is lacking. As a first step, we performed multiple sequence alignment of all insect OARs, which revealed that the sequences contained all conserved class A GPCR motifs. Phylogenetic studies showed clade-specific variations in the protein sequences primarily arising owing to differences in the ICL3 loop region. Further, a structural model of HarmOAR was built using the inactive human beta(2)AR as a template. 0.9 mu s atomistic simulations revealed conserved inter helical contacts and water molecules of HarmOAR. The detailed binding of octopamine was studied using molecular docking and 0.3 mu s atomistic simulations. Twenty-two insecticides active against octopamine receptors of other insects were compiled and docked to HarmOAR followed by rescoring with binding free energies to prioritize them for H. armigera. Our study suggests alpha-terpineol to be a good candidate as an insecticide or insect repellent for Helicoverpa armigera.

}, keywords = {docking, Helicoverpa armigera, Insecticides, molecular dynamics, Octopamine receptor, Phylogeny}, issn = {0022-2631}, doi = {10.1007/s00232-021-00172-3, Early Access Date = FEB 2021}, author = {Gujar, Nidhi and Nikte, V, Siddhanta and Joshi, Rakesh S. and Joshi, Manali} } @article {48463, title = {Surface-induced demixing of self-assembled isomeric mixtures of citral}, journal = {Journal of Molecular Liquids}, volume = {381}, year = {2023}, month = {JUL }, pages = {121803}, type = {Article}, abstract = {

The self-assembly of organic molecules and their interactions with metal surfaces have been of considerable interest, both for developing novel functional materials and for understanding fundamental design principles of nanostructures. In this study, we investigate the solution and surface-induced self-assembly of two stereoisomers of citral molecules (geranial and neral) using atomistic molecular dynamics simulations. We demonstrate that the morphology of the aggregates in water is concentration dependent (ranging from distorted spherical to slab-like aggregates) but independent of isomer effects. The isomeric mixtures of citral indicate homogeneous mixing based on differential density maps and high values of Shannon entropy. Interestingly, surface-confinement of citral aggregates on a Cu(111) surface leads to phase segregation and demixing of the two isomers that is more apparent in the surface-bound monolayer in comparison to the adjacent layers. Positional ordering and formation of domains are observed over a series of isomeric citral mixtures with varying compositions, as indicated by high differential density and low values of Shannon entropy. Our work provides new insights into molecular self-assembly of organic molecules in nanostructures and metal-organic overlayers.(c) 2023 Elsevier B.V. All rights reserved.

}, keywords = {Citral, Isomers, Metal-organic interactions, molecular dynamics, Self-assembly, Shannon entropy}, issn = {0167-7322}, doi = {10.1016/j.molliq.2023.121803}, author = {Saraf, Deepashri and Prakash, Shikha and Pinjari, Aadil and Pujari, Bhalchandra and Sengupta, Durba} }