The correlation coefficient is found to be 0.89, 0.78, and 0.80, respectively, for polyalanine, 2I9M protein, and leucine zipper. Results show that the backbone hydrogen-bond strength is generally correlated with its specific local electrostatic environment, measured by the number of water molecules near the hydrogen bond in the first solvation shell. For comparison, the result from simulation using standard force field shows a much weaker correlation between hydrogen bond energy and local electrostatic environment due to the lack of polarization effect in the force field.ĪB - MD simulation study of several peptides including a polyalanine, a helix (pdb:2I9M), and a leucine zipper were carried out to investigate hydrogen bond energetics using dynamic polarized protein-specific charge (DPPC) to account for the polarization effect in protein dynamics. ![]() The current study helps demonstrate and support the understanding that hydrogen bonds are stronger in a hydrophobic surrounding than in a hydrophilic one. In the polyalanine, the energies of the backbone hydrogen bonds are very similar to each other due to their similar local electrostatic environment. N2 - MD simulation study of several peptides including a polyalanine, a helix (pdb:2I9M), and a leucine zipper were carried out to investigate hydrogen bond energetics using dynamic polarized protein-specific charge (DPPC) to account for the polarization effect in protein dynamics. We thank the Supercomputer Center of East China Normal University for CPU time support. T1 - Energetics of protein backbone hydrogen bonds and their local electrostatic environment For comparison, the result from simulation using standard force field shows a much weaker correlation between hydrogen bond energy and local electrostatic environment due to the lack of polarization effect in the force field.", ![]() For comparison, the result from simulation using standard force field shows a much weaker correlation between hydrogen bond energy and local electrostatic environment due to the lack of polarization effect in the force field.Ībstract = "MD simulation study of several peptides including a polyalanine, a helix (pdb:2I9M), and a leucine zipper were carried out to investigate hydrogen bond energetics using dynamic polarized protein-specific charge (DPPC) to account for the polarization effect in protein dynamics. ![]() ![]() MD simulation study of several peptides including a polyalanine, a helix (pdb:2I9M), and a leucine zipper were carried out to investigate hydrogen bond energetics using dynamic polarized protein-specific charge (DPPC) to account for the polarization effect in protein dynamics.
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