18 research outputs found
Evolutionary analysis of a novel zinc ribbon in the N-terminal region of threonine synthase
<p>Threonine synthase (TS) catalyzes the terminal reaction in the biosynthetic pathway of threonine and requires pyridoxal phosphate as a cofactor. TSs share a common catalytic domain with other fold type II PALP dependent enzymes. TSs are broadly grouped into two classes based on their sequence, quaternary structure, and enzyme regulation. We report the presence of a novel zinc ribbon domain in the N-terminal region preceding the catalytic core in TS. The zinc ribbon domain is present in TSs belonging to both classes. Our sequence analysis reveals that archaeal TSs possess all zinc chelating residues to bind a metal ion that are lacking in the structurally characterized homologs. Phylogenetic analysis suggests that TSs with an N-terminal zinc ribbon likely represents the ancestral state of the enzyme while TSs without a zinc ribbon must have diverged later in specific lineages. The zinc ribbon and its N- and C-terminal extensions are important for enzyme stability, activity and regulation. It is likely that the zinc ribbon domain is involved in higher order oligomerization or mediating interactions with other biomolecules leading to formation of larger metabolic complexes.</p
Additional file 1: of A novel RING finger in the C-terminal domain of the coatomer protein ÃŽÄ…-COP
Methods. Methods employed in this study (DOCX 32 kb
Additional file 3: of Evolutionary relationships between heme-binding ferredoxin α + β barrels
Ferredoxin α + β barrel structures in PDB (current till 30-12-15). (DOC 57 kb
Additional file 2: Figure S2. of Evolutionary relationships between heme-binding ferredoxin α + β barrels
Flowchart of the methodology followed in this study. (TIF 40368Â kb
Additional file 1: Figure S1. of Evolutionary relationships between heme-binding ferredoxin α + β barrels
Residue conservation between the heme-binding region of IsdG-like, OxdA, and Cld/Dyp/EfeB/HemQ. Ribbon diagrams of IsdG-like ferredoxin-like monomer (PDB identifier 2ZDP_A; colored purple), IsdG homolog without heme (PDB identifier 1TZ0_B; colored cyan), C-terminal heme-binding domain of OxdA-like (PDB identifier 3A16_A; colored red) and C-terminal heme-binding domain of Cld/DyP/EfeB/HemQ-like (PDB identifier 3NN1_A; colored green). Protein structures are shown as a trace of backbone Cα atoms and side chains of conserved residues around the heme moiety are as sticks. His299 (axial histidine residue) of 3A16_A is at an equivalent spatial position to Phe72 of 2ZDP_A, His75 of 1TZ0_B and His160 of 3NN1_A. Apart from the conserved axial histidine, Trp283, Trp292, His320 and Val322 of 3A16_A are also at the similar spatial position as Trp60, Trp69, His96 and Val98 of 1TZ0_A. Trp66 and Phe11 of 1TZ0_B structurally align with the Trp145 and Phe190 of 3NN1_A. The disordered region in the IsdG homolog without heme is shown as a dashed-connector. (TIF 54245 kb
Analytical approach for solving population balances: a homotopy perturbation method
.In the present work, a new approach is proposed for finding the analytical solution of population balances for aggregation and fragmentation process. This approach is relying on the idea of the homotopy perturbation method (HPM). The HPM solves both linear and nonlinear initial and boundary value problems without nonphysical restrictive assumptions such as linearization and discretization. It gives the solution in the form of series with easily computable solution components. The outcome of this study reveals that the proposed method can avoid numerical stability problems which often characterize in general numerical techniques related to this area. Several examples including Austin's kernel, available in literature, are examined to demonstrate the accuracy and applicability of the proposed method. In addition, the analytical solution to two new kernels (the power-law kernel in fragmentation and the Ruckenstein/Pulvermacher kernel in aggregation) are also introduced
Mathematical modelling and simulation of a spray fluidized bed granulator
In this present work, a study of the modelling and simulation for a top-sprayed fluidized
bed granulator (SFBG) is presented, which is substantially used by the pharmaceutical industry
to prepare granules. The idea is to build a number-based mathematical model using the notion of
population balances by dividing a top SFBG into two different zones, namely the wet zone and dry
zone. To solve a two-compartment model, an existing accurate and efficient finite volume scheme is
implemented. In order to validate the compartmental model, a new class of analytical moments is
derived corresponding to various combinations of aggregation and breakage kernels. To verify the
accuracy of a modified finite volume scheme, the zeroth and first order moments computed using the
finite volume scheme are compared with the newly-derived analytical results. Moreover, the stability
of the compartmental model and the numerical scheme is tested by varying the size of the wet zone.
It is also shown that the relative errors in both order moments increase with the increase in the size of
the wet zo
Synthetic diet composition for delivery of dsRNA in cotton leafhopper through membrane feeding.
<p>Synthetic diet composition for delivery of dsRNA in cotton leafhopper through membrane feeding.</p
Annotation of different target genes of cotton leafhopper from RNA sequence data using BlastoGo software and primers used for expression analysis of housekeeping genes.
<p>Annotation of different target genes of cotton leafhopper from RNA sequence data using BlastoGo software and primers used for expression analysis of housekeeping genes.</p
Corrected percent mortality in the leafhopper nymphs at 48h after dsRNA feeding.
<p>Corrected percent mortality in the leafhopper nymphs at 48h after dsRNA feeding.</p