Structure prediction and molecular simulation of gases diffusion pathways in hydrogenase


Shanthy Sundaram1,*, Ashutosh Tripathi1, Vipul Gupta1



1Centre for Biotechnology, University of Allahabad, Nehru Science Centre, Allahabad, U.P, India.

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Article Type



Received July 20, 2010; accepted August 20, 2010; published October 06, 2010



Although hydrogen is considered to be one of the most promising future energy sources and the technical aspects involved in using it have advanced considerably, the future supply of hydrogen from renewable sources is still unsolved. The [Fe]- hydrogenase enzymes are highly efficient H2 catalysts found in ecologically and phylogenetically diverse microorganisms, including the photosynthetic green alga, Chlamydomonas reinhardtii. While these enzymes can occur in several forms, H2 catalysis takes place at a unique [FeS] prosthetic group or H-cluster, located at the active site. 3D structure of the protein hydA1 hydrogenase from Chlamydomonas reinhardtti was predicted using the MODELER 8v2 software. Conserved region was depicted from the NCBI CDD Search. Template selection was done on the basis NCBI BLAST results. For single template 1FEH was used and for multiple templates 1FEH and 1HFE were used. The result of the Homology modeling was verified by uploading the file to SAVS server. On the basis of the SAVS result 3D structure predicted using single template was chosen for performing molecular simulation. For performing molecular simulation three strategies were used. First the molecular simulation of the protein was performed in solvated box containing bulk water. Then 100 H2 molecules were randomly inserted in the solvated box and two simulations of 50 and 100 ps were performed. Similarly 100 O2 molecules were randomly placed in the solvated box and again 50 and 100 ps simulation were performed. Energy minimization was performed before each simulation was performed. Conformations were saved after each simulation. Analysis of the gas diffusion was done on the basis of RMSD, Radius of Gyration and no. of gas molecule/ps plot.




Molecular simulation, Hydrogenase, Modeler, Root mean square deviation


Sundaram et al. Bioinformation 5(4): 177-183(2010)

Edited by

P. Kangueane






Biomedical Informatics



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