Study on the Docking Analysis of Homocitrate Synthase Responsible for Hydrogen Production in &lt;i&gt;Nostoc &lt;/i&gt;&lt;i&gt;p&lt;/i&gt;&lt;i&gt;un&lt;/i&gt;&lt;i&gt;ctiforme ATCC29133&lt;/i&gt;

Lakshmi P T V,A Annamalai,Devi Priyanka

doi:10.5923/j.bioinformatics.20120206.02

Abstract

<b> </b>In the case of Nitrogenase-based Hydrogen production, inactivation of the uptake hydrogenase (Hup) leads to significant increase in hydrogen production activity but it lasts only for few hours under the combined nitrogen atmosphere supplied by active hydrogenase. The catalytic FeMo cofactor of nitrogenase binds homocitrate, which is required for efficient nitrogen fixation. Hence blocking of Homocitrate synthase will be an efficient strategy for the significant hydrogen production. <i>Nostoc punctiforme</i> ATCC29133, a nitrogen fixing cyanobacterium that has the genes encoding only for the homocitrate synthase and not for uptake hydrogenase. Since the structure of homocitrate synthase is not yet elucidated, it was taken for modeling using Modeler9v5. The inhibitors for homocitrate synthase were identified from literature and were retrieved from Pubchem. The inhibitors identified were 1,10-phenanthroline, 2,2â-Dipyridyl, Hydroxylysine, Iodoacetic acid, Oxalylglycine, Pipecolic acid, Thialysine, and oxalate were docked with the homocitrate synthase using Argus lab to compare their activities. However, among these eight inhibitors screened, 1,10-phenanthroline and Oxalylglycine were found to have best docking score and proved efficient in terms of both binding affinity and strong hydrogen bond interactions.

Highlights

While the uptake hydrogenase is present in all nitrogen fixing strains tested so far, the distribution of bid irect ional enzy me is not universal
The mo lecular masses indicated for the uptake hydrogenase subunits are mean values calculated fro m the deduced amino acid sequences of Anabaena strain PCC 7120, Nostoc strain PCC 73102, and A. variabilis ATCC 29413, wh ile the values for the subunits of the bidirectional enzy me are based on data exclusively fro m A. variabilis ATCC 29413 (Tamagnini et al, 2002)
The present study demonstrates the presence of genes for Ho mocitrate synthase and absence of genes for uptake hydrogenase in Nostoc punctiforme ATCC29133

Summary

Introduction

Quite uniform in nutritional and metabolic respects, cyanobacteria are a mo rphologically d iverse group with unicellular, filamentous, and colonial forms[2]. It p ossess several en zy mes th at are invo lved in h yd ro ge n. While the uptake hydrogenase is present in all nitrogen fixing strains tested so far, the distribution of bid irect ional enzy me is not universal (may be present in both nitrogen-fixing and non-nitrogen-fixing cyanobacteria). The mo lecular masses indicated for the uptake hydrogenase subunits are mean values calculated fro m the deduced amino acid sequences of Anabaena strain PCC 7120 , Nostoc strain PCC 73102 , and A. variabilis ATCC 29413 , wh ile the values for the subunits of the bidirectional enzy me are based on data exclusively fro m A. variabilis ATCC 29413 (Tamagnini et al, 2002)

Methods

Results

Conclusion