NOPR Collection:

Comparative modelling of tetramanganese cluster of Chaetosphaeridium globosum

Fri, 01 Oct 2004 00:00:00 GMT

Title: Comparative modelling of tetramanganese cluster of Chaetosphaeridium globosum Authors: Rath, L S; Raval, M K Abstract: The D1 protein of photosystem II (PS II) complex of a micro-alga Chaetosphaeridium globosum has been theoretically modelled from its sequence using comparative modeling with known backbone structure of D1 protein from bacterium Thermosynechococcus vulcanus as template. The model is built with missing loops and all side chains, which are not resolved in the structure of the template. The structure of the tetramanganese cluster (TMC) and the ligand forming side chains have been subjected to modeling studies in order to gather more information useful to understanding of the water splitting reactions. Earlier models of TMC have been scrutinized and an insight into the manganese coordination sphere has been provided. Page(s): 258-262

Characterization of non-planar peptide groups in protein crystal structures

Fri, 01 Oct 2004 00:00:00 GMT

Title: Characterization of non-planar peptide groups in protein crystal structures Authors: Dasgupta, Anjan Kumar; Majumdar, Rabi; Bhattacharyya, Dhananjay Abstract: Peptide groups are generally assumed to be planar in protein structure, due to 'rigid' partial double bond character of peptide bonds, thus the value of peptide torsion angle ω should be restricted to 180° for the usual/rans form of peptide unit. However, on analyzing the ultra-high resolution protein crystal database, we find that in some cases, ω deviates> 10° from its usual value of 180°, indicating significant non-planarity of peptide groups. Moreover, the non-planarity for most of the amino acids is found to be 'biased' towards values of ω smaller than 180°. Similar trend for ω is confirmed by the neutron diffraction data for proteins. The neutron diffraction database also reveals that non-planar peptide groups are generally correlated to 'pyramidal' structure of the peptide-nitrogen bonds. Consequently, the hydrogen atom of peptide group deviates from its planar position, as measured by the 'improper' torsion angle θ. Thus, we find that both the angles ω and θ point towards a significant amount of non-planarity of peptide groups, which cannot be ignored. The role of peptide non-planarity in protein function is, however, not yet clear. Page(s): 233-240

Numerical solution of unsteady blood flow through an indented tube with atherosclerosis

Fri, 01 Oct 2004 00:00:00 GMT

Title: Numerical solution of unsteady blood flow through an indented tube with atherosclerosis Authors: Venkateswarlu, K; Rao, J Anand Abstract: The unsteady blood flow through an indented tube with atherosclerosis in the presence of mild stenosis has been studied numerically by finite difference method. The effects of hematocrit, frequency parameter, height of stenosis, parameter determining the shape of the constriction on velocity field, volumetric flow rate, pressure gradient of the fluid in stenotic region and wall shear stress at the surface of stenosis are obtained and shown graphically. Page(s): 241-245

Iron dependence and zinc inhibition of duodenal cytosolic aconitase of rat

Fri, 01 Oct 2004 00:00:00 GMT

Title: Iron dependence and zinc inhibition of duodenal cytosolic aconitase of rat Authors: Sreedhar, Bodiga; Nair, K Madhavan Abstract: The response of duodenal cytosolic aconitase (c-aconitase) to oral repletion of graded doses of iron (Fe) during Fe-deficiency was studied in rats (WNIN strain). In addition, in vitro effect of zinc (Zn) on the enzyme activity was studied using duodenal cytosol. Iron-depleted male rats were orally repleted with either 100 or 190 or 370 μg of Fe/day (n=6, each) for 2 weeks. Fe repletion was found to increase linearly the activity of duodenal c-aconitase along with the indicators of iron status. The correlation coefficient (r) between c-aconitase and haemoglobin and mucosal ferritin was 0.6453 and 0.8441, respectively. The effects of zinc (0-40 μM) in vitro on the kinetics of c-aconitase from iron-replete stock diet fed rats (n=4) showed that Zn competitively inhibited the enzyme with a Ki (app.) of 28 μM. These observations suggest that c-aconitase is a critical target involved in the assimilation of Fe and excess dietary Zn can result in negative interactions. Page(s): 250-253