02479nas a2200241 4500008004100000022001400041245010300055210006900158260005700227300000800284490000700292520161300299653002101912653001501933653002201948653003301970653002002003100001902023700001802042700002702060700002202087856012802109 2015 eng d a1610-294000aIn silico ligand binding studies of cyanogenic beta-glucosidase, dhurrinase-2 from Sorghum bicolor0 aIn silico ligand binding studies of cyanogenic betaglucosidase d a233 SPRING ST, NEW YORK, NY 10013 USAbSPRINGERcJUL a1840 v213 a

Dhurrinase, a cyanogenic beta-glucosidase from Sorghum bicolor is the key enzyme responsible for the hydrolysis of dhurrin to produce toxic hydrogen cyanide, as a part of plant defence mechanism. Dhurrinase 1 (SbDhr1) and dhurrinase 2 (SbDhr2), two isozymes have been isolated and characterized from S. bicolor. However, there is no information in the literature about the three dimensional (3D) structure of SbDhr2 and molecular interactions involved between the protein and ligand. In this study, the three dimensional structure of SbDhr2 was built based on homology modeling by using the X-ray crystallographic structure of its close homologue SbDhr1 as the template. The generated 3D model was energy minimized and the quality was validated by Ramachndran plot, various bioinformatic tools and their relevant parameters. Stability, folding-unfolding and flexibility of the modeled SbDhr2 was evaluated on the basis of RMSD, radius of gyration (R-g) and RMSF values respectively, obtained through molecular dynamic (MD) simulation. Further, molecular docking was performed with its natural substrate dhurrin, one substrate analogue, three un-natural substrates, and one inhibitor. Analysis of molecular interactions in the SbDhr2-ligand complexes revealed the key amino acid residues responsible to stabilize the ligands within the binding pocket through non-bonded interactions and some of them were found to be conserved (Glu239, Tyr381, Trp426, Glu454, Trp511). Reasonably broader substrate specificity of SbDhr2 was explained through the wider entrance passage observed in comparison to SbDhr1.

10abeta-Glucosidase10aDhurrinase10aMolecular docking10aMolecular dynamic simulation10aSorghum bicolor1 aMahajan, Chavi1 aPatel, Krunal1 aKhan, Bashir, Mohammad1 aRawal, Shuban, S. uhttps://library.ncl.res.in/content/silico-ligand-binding-studies-cyanogenic-beta-glucosidase-dhurrinase-2-sorghum-bicolor-102099nas a2200253 4500008004100000022001400041245007600055210006900131260000800200300001400208490000700222520131000229653001501539653001901554653001601573653001301589653003301602100002601635700002201661700001901683700002301702700001901725856010101744 2016 eng d a1875-510000aEffect of the amino acid L-histidine on methane hydrate growth kinetics0 aEffect of the amino acid Lhistidine on methane hydrate growth ki cSEP a1453-14620 v353 a

In the present study, the effect of a polar amino acid, L-histidine on methane hydrate growth kinetics has been investigated. Methane hydrate formation experiments were carried out in a stirred tank reactor setup at pressure and temperature conditions of 274.15 K and 5.0 MPa respectively. Two different concentrations (0.1 and 1 wt %) of L-histidine were studied. Hydrate growth through molecular dynamic (MD) simulation was also studied; pressure and temperature conditions for the simulations were set at 10.0 MPa and 270.0 K, while the concentration of L-histidine was kept fixed at 0.94 wt %. Hydrate formation runs using MD simulation were carried out with optimal concentration of methane in water. The presence of L-histidine in the system was found to significantly enhance methane hydrate growth kinetics as compared to pure water for both experimental and MD simulation runs. Final gas consumption with 1 wt % L-histidine was found to be comparable to that with 1 wt % SDS, the most commonly used additive for hydrate promotion studies. L-histidine is a benign additive which offers considerable enhancement in methane hydrate formation kinetics and can be utilized for various hydrate based technologies such as methane storage and transport. (C) 2016 Elsevier B.V. All rights reserved.

10aAmino acid10aCrystal growth10aGas hydrate10akinetics10aMolecular dynamic simulation1 aBhattacharjee, Gaurav1 aChoudhary, Nilesh1 aKumar, Asheesh1 aChakrabarty, Suman1 aKumar, Rajnish uhttps://library.ncl.res.in/content/effect-amino-acid-l-histidine-methane-hydrate-growth-kinetics02629nas a2200253 4500008004100000022001400041245013500055210006900190260000800259490000700267520172200274653001401996653002202010653002202032653003302054653002202087100002602109700001902135700001802154700002602172700003002198700001802228856012902246 2022 eng d a0739-110200aMolecular phylogeny, structure modeling and in silico screening of putative inhibitors of aerolysin of Aeromonas hydrophila EUS1120 aMolecular phylogeny structure modeling and in silico screening o cJUN0 v403 a

Aeromonas hydrophila, a Gram-negative bacterium, causes diseases in fish, resulting in excessive loss to the aquaculture industry. Aeromonas is a highly heterogeneous group of bacteria, and the heterogeneity of the genus is attributed to variation and diversity in the virulence factors and toxins among various Aeromonas strains. One of the major toxins aerolysin, secreted by the bacterium, causes hemorrhagic-septicemia and diarrhea and can serve as a drug target. Here, we describe characterization, molecular phylogeny, and homology modeling of the aerolysin of A. hydrophila strain EUS112 (Ah(EUS112)) cloned in our lab. The encoded aerolysin is 485 amino acids long with an N-terminal signal sequence of 23 amino acids. Phylogenetic analysis of the aerolysin of Ah(EUS112) revealed that it belongs to a diverse group of toxins, showing maximum similarity with aerolysins of other Aeromonas strains followed by Vibrio toxin. The homology model of the mature aerolysin of Ah(EUS112) was generated using the crystal structure of a mutant aerolysin (PDB\#3g4n) as the template, which showed that the encoded aerolysin exists as a channel protein. Validation of the generated model using bioinformatics tool confirmed it to be a good quality model that can be used for drug design. Molecular dock analysis revealed that drugs, aralia-saponin I, cyclamin, ardisiacrispin B, and aralia-saponin II bind to aerolysin with a higher affinity as compared to other drugs and at functionally important amino acids of aerolysin. Hence, these molecules can act as an effective therapeutics for inhibiting the aerolysin pore formation and curtail the severity of Aeromonas infection. Communicated by Ramaswamy H. Sarma

10aAerolysin10ahomology modeling10aMolecular docking10aMolecular dynamic simulation10aphylogenetic tree1 aYadav, Sunita, Kumari1 aPanwar, Deepak1 aSingh, Ankita1 aTellis, Meenakshi, B.1 aJoshi, Rakesh, Shamsunder1 aDixit, Aparna uhttps://library.ncl.res.in/content/molecular-phylogeny-structure-modeling-and-silico-screening-putative-inhibitors-aerolysin02333nas a2200289 4500008004100000022001400041245007800055210006900133260000800202300001100210490000800221520142300229653001401652653002401666653002401690653002201714653003301736653002201769100001801791700001601809700002401825700002201849700002001871700002501891700002001916856010701936 2024 eng d a0141-813000aMulti-dimensional impact of captopril modification on human serum albumin0 aMultidimensional impact of captopril modification on human serum cAUG a1332890 v2743 a

Captopril is a thiol drug, widely used for the management of hypertension and cardiovascular diseases. Reactive thiols are found to covalently modify the cysteines of plasma proteins and affect their structure and function. Human serum albumin (HSA) is prone to undergo modification by various low molecular weight compounds, including drugs. Cysteine34 (Cys34) in HSA has a free thiol group with antioxidant properties, considered to be the most redox-sensitive amino acid in plasma. Through mass-spectrometric analysis, we demonstrate for the first time that captopril forms a disulfide adduct at Cys34 residue and increases the protease susceptibility of HSA to trypsin. As evidenced by our biophysical and electron microscopy studies, HSA undergoes structural alteration, aggregation and morphological changes when treated with different captopril concentrations. Molecular dynamics studies further revealed the regions of secondary structural changes in HSA due to disulfide adduct formation by captopril at Cys34. It also elucidated the residues involved in the noncovalent interactions with captopril. It is envisaged that structural change in HSA may influence the efficacy of drug delivery as well as its own biological function. These findings may thus provide significant insights into the field of pharmacology intriguing further investigation into the effects of long-term captopril treatment.

10aCaptopril10aElectron microscopy10aHuman serum albumin10aMass spectrometry10aMolecular dynamic simulation10aSpectrophotometry1 aGhosh, Amrita1 aJani, Vinod1 aSonavane, Uddhavesh1 aNaphade, Anvi, N.1 aJoshi, Rajendra1 aKulkarni, Mahesh, J.1 aGiri, Ashok, P. uhttps://library.ncl.res.in/content/multi-dimensional-impact-captopril-modification-human-serum-albumin