Escherichia coli HypC plays an important role in the maturation process of the large subunit of (Ni-Fe) hydrogenase. It is a metal-free enzyme and consists of 90 amino acid residues. To determine the motional properties and mode of action of HypC, molecular dynamics simulation of E. coli HypC in aqueous environment was carried out with GROMACS software. By analyzing the time evolution of Root Mean Square Deviation (RMSD), Radius of Gyration (Rg), Root Mean Square Fluctuation (RMSF), it is clear that the protein is not much flexible. Among the secondary structures, two helices, H1 & H2 and b2 & b4 strands are very much flexible. So they can be used in the protein-protein interaction. A loop L34 (Leu30 to Gln46) is also quite flexible in nature. Principal Component Analysis (PCA) was also performed for a better understanding of the motional properties in reduced dimension. It also suggests that the protein HypC, as a whole, is of rigid nature.

Molecular hydrogen, H2, is evolved and used by certain organisms in many biochemical metabolic processes. The enzyme responsible for both evolution and uptake of hydrogen is hydrogenase. This enzyme is used mainly by the prokaryotes, but examples are also known from eukaryotes.

On the basis of metal composition of the active site, hydrogenase can be categorized primarily into three classes: NiFe, Fe and metal-free hydrogenases (Tamaghini et al., 2002). The main difference among the three types of hydrogenases is based on their structure, active site metal center and the sequence of the constituent of the structural polypeptides, but they all have a common structural feature, CN and/or CO ligands at the active site Fe.

Among the three classes of hydrogenase enzyme (Ni-Fe), hydrogenase enzyme is available in almost all bacteria and archea classes and catalyzes the reversible formation of molecular hydrogen (Vignais et al., 2001). Maturation of this enzyme goes through a very complex pattern of biochemical reactions using several accessory proteins (such as hyp operons) (Blokesch and Bock, 2002).

Usually Hyp genes are consisting of a set of hypABCDEF genes (E.coli) (Vignais et al., 2001). Each member of this set has its own individual functions in the maturation of (Ni-Fe) hydrogenase enzyme. HypA and HypB deliver the nickel atom by forming complex into the precursor of the large subunit (Olson et al., 2001). Synthesis of the CN ligand, which is coordinated to the active site iron atom of the enzyme, is performed by the hypE and hypF (Blokesch et al., 2004). HypC and HypD are required for insertion of Fe atom through complex formation (Watanable et al., 2007).

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