Effect of 1-methyl-3-octyleimmidazolium chloride on the stability and activity of lysozyme: a spectroscopic and molecular dynamics studies

<p>Herein, the binding of 1-methyl-3-octylimidazolium chloride [OMIM][Cl] ionic liquid with hen egg white lysozyme (HEWL) has been studied using fluorescence, time resolved fluorescence, UV–visible and circular dichroism (CD) spectroscopy, in combination with computational study. The fluorescence results revealed that [OMIM][Cl] quenches the fluorophore of HEWL through static quenching mechanism. The calculated thermodynamic parameters show that [OMIM][Cl] bind with HEWL through hydrophobic interactions. In addition, the negative value of Gibbs energy change (∆<i>G</i>) indicates that the binding process was spontaneous. Furthermore, UV–vis and CD results indicate that [OMIM][Cl] induce the conformational change in HEWL and increase its enzymatic activity. Additionally, molecular docking results showed that [OMIM][Cl] binds at the active site of HEWL where both the fluorophore residues (Trp108 and Trp62) and the catalytic residues (Glu35 and Asp52) reside. Molecular dynamic simulation results show the reduction of intra-molecular hydrogen bond of HEWL when it binds with [OMIM][Cl].</p

Bayesian skyline plots of Indian Cosmopolitan DENV-2 strains.

<p>X axis: Time, Y axis: Relative genetic diversity (Neτ). Black solid line is the median estimate of Neτ. Blue shaded area shows 95% HPD.</p

Correlation of mutations in the envelope protein of the study strains with the predicted T and B cell epitopes.

<p>Correlation of mutations in the envelope protein of the study strains with the predicted T and B cell epitopes.</p

Maximum Clade Credibility tree of Dengue 2 virus.

<p>Tree derived with the best fit model (relaxed uncorrelated lognormal clock & Bayesian skyline tree prior) showing node ages. Strains sequenced in the present study are coloured. Lineages showing Valine or Isoleucine at position 322 have been marked.</p

Modelled structure of Envelope Protein (289–440) showing position of I322V & T404I mutations.

<p>Modelled structure of Envelope Protein (289–440) showing position of I322V & T404I mutations.</p

Maximum Likelihood Phylogenetic tree of DENV-2 strains.

<p>Strains sequenced in the study are marked by shapes (2014 strains: diamonds; 2013 strains: circles; 2012 strains: rectangles; 2014 strains: triangles). Numbers on nodes indicate bootstrap support generated by 1000 replicates. Bootstrap values of >70 are shown.</p

Structural insights into Rab21 GTPase activation mechanism by molecular dynamics simulations

<p>Rab proteins belong to the family of monomeric GTPases which are involved in the cellular membrane trafficking. Rab21 protein exists in interchangeable GTP- and GDP-bound states. Rabs switch between two active and inactive conformations like other GTPases. The inactive form of Rab is bound to GDP while its active form is bounded with the GTP. Interexchange between active and inactive form is mediated by the GDP/GTP exchange factor (GEF) which catalyses the conversion from GDP-bound to GTP-bound form, thereby activating the Rab. While the GTP hydrolysis of Rabs is regulated by a GTPase-activating protein (GAP) which causes Rab inactivation. Here, we report the structural flexibility of the Rab21-GTP and Rab21-GDP complexes by docking and molecular dynamics (MD) simulations. Structural analysis of exchange mechanisms of the co-factors complexed with Rab21 reveals that Cys29, Thr33, His48, Gln78 and Lys133 are essentially important in the activation of proteins. Furthermore, a significant change in the orientation of the interacting co-factors, with slight variation in the free energy of binding was observed. Complexation of GEF with Rab21-GTP and Rab21-GDP reveal a flipping of the switchable residues. Finally, 50 ns MD simulations confirm that the GTP-bound Rab21 complex is thermodynamically more favoured than the corresponding GDP-bound complex. This study provides a detailed understanding of the structural elements involved in the conformational changes of Rab21.</p

Global amino acid variability of the 2^nd HVR of G gene of BA9 lineage is represented by Shannon entropy plot.

<p>BioEdit software was used for calculation of entropy values of every amino acid at a particular position. Entropy values <0.2 were considered conserved whereas amino acids with >0.2 values are considered variable. High entropy value showed maximum variability at that particular position.</p

Positively selected amino acid positions of the BA9 lineage.

<p>Positively selected amino acid positions of the BA9 lineage.</p

BA9 lineage of respiratory syncytial virus from across the globe and its evolutionary dynamics

<div><p>Respiratory syncytial virus (RSV) is an important pathogen of global significance. The BA9 is one of the most predominant lineages of the BA genotype of group B RSV that has acquired a 60bp duplication in its G protein gene. We describe the local and global evolutionary dynamics of the second hyper variable region in the C- terminal of the G protein gene of the BA9 lineage. A total of 418 sequences (including 31 study and 387 GenBank strains) from 29 different countries were used for phylogenetic analysis. This analysis showed that the study strains clustered with BA (BA9 and BA8) and SAB4 genotype of group B RSV. We performed time-scaled evolutionary clock analyses using Bayesian Markov chain Monte Carlo methods. We also carried out glycosylation, selection pressure, mutational, entropy and Network analyses of the BA9 lineage. The time to the most recent common ancestor (tMRCA) of the BA genotype and BA9 lineage were estimated to be the years 1995 (95% HPD; 1987–1997) and 2000 (95% HPD; 1998–2001), respectively. The nucleotide substitution rate of the BA genotype [(4.58×10⁻³ (95% HPD; 3.89–5.29×10⁻³) substitution/site/year] was slightly faster than the BA9 lineage [4.03×10⁻³ (95% HPD; 4.65–5.2492×10⁻³)]. The BA9 lineage was categorized into 3 sub lineages (I, II and III) based on the Bayesian and Network analyses. The local transmission pattern suggested that BA9 is the predominant lineage of BA viruses that has been circulating in India since 2002 though showing fluctuations in its effective population size. The BA9 lineage established its global distribution with report from 23 different countries over the past 16 years. The present study augments our understanding of RSV infection, its epidemiological dynamics warranting steps towards its overall global surveillance.</p></div