<span style="font-size:15.0pt;font-family: "Times New Roman";mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: Mangal;mso-ansi-language:EN-GB;mso-fareast-language:EN-US;mso-bidi-language: HI;mso-bidi-font-weight:bold" lang="EN-GB">Molecular dynamics simulation of homology modeled<span style="font-size:15.0pt;font-family:"Times New Roman";mso-fareast-font-family: "Times New Roman";mso-bidi-font-family:Mangal;mso-ansi-language:EN-GB; mso-fareast-language:EN-US;mso-bidi-language:HI" lang="EN-GB"> <span style="mso-bidi-font-weight: bold">2-nitropropane dioxygenase from <i>Mycobacterium tuberculosis</i></span></span></span>

Abstract

<span style="font-size:9.0pt;mso-bidi-font-weight: bold" lang="EN-GB">3D model of 2NPD domain of FAS protein from <i>Mycobacterium tuberculosis </i>was refined using MD simulations for a time period of 10ns. Fluctuation in energy parameter which was noticed during heating stage remained fairly stable once the temperature was maintained at 300 K. The 2NPD structure attained global energy minimum at 1147^thps which in fact is the lowest energy state of the protein. RMSD of the trajectory structures showed that the intermediary stage remained fairly stable. Hydrogen bonding patterns revealed interaction of water molecules with hydrophilic amino acids of 2NPD. While the length of H-bond was 1.87 Å to 2.83 Å, bond angle varied from 33.6° to 50.2°. Residue numbers from 50 to 87 were involved in forming hydrogen bonds with water. Among these, his⁸³ was an active site residue which interacted with 3 water molecules (WAT¹³⁶⁷, WAT³⁷²⁹ and WAT⁶⁰⁹¹). Short occupancy period (5-20 %) on the lowest energy structure of 2NPD was, however, suggestive of a weak bond with water, which could easily be broken to facilitate ligand binding. MD simulation thus provides considerable insight into the protein folding pattern and offers refinement over the static 2NPD structure, which is more suitable for docking studies.<b style="mso-bidi-font-weight:normal"></b>

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