Abstract
The effect of polarization in biomolecular force field is investigated by performing Molecular Dynamics (MD) simulation of HIV-protease by using two AMBER force fields, namely ff99 (non-polarizable) and ff02 (polarizable). The results of simulation show that the overall structural fluctuation of HIV-protease is reduced in the polarizable simulation. Comparison with the NMR order parameters with the calculated values shows that although some residues are less flexible in the ff02 simulation, the dynamics of two β-hairpins (flaps), the most flexible part of the protein, is relatively insensitive to the effect of polarization. The flap-active site distance, a measure of flap opening, is distinctly more in the non-polarizable simulation. The water count and radial distribution functions are investigated near a representative residue of three types — charged, polar and hydrophobic. Both water count and radial distribution function differ significantly near the charged residue (catalytic Asp25) between the force fields. However, the water movement is similar near the polar (Ser37) and hydrophobic (Ile85) residues. The preliminary results of this investigation show that polarization is likely to influence both global and specific local motions of protein and solvent.
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Meher, B.R., Satish Kumar, M.V. & Bandyopadhyay, P. Molecular dynamics simulation of HIV-protease with polarizable and non-polarizable force fields. Indian J Phys 83, 81–90 (2009). https://doi.org/10.1007/s12648-009-0005-3
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DOI: https://doi.org/10.1007/s12648-009-0005-3