(222f) Investigating the Planarity of Aromatic Rings in Bimolecular Modeling
The accuracy of biomolecular modeling results is based in part on Force field (FF) parameters. Charmm FF is one of the best FFs in describing the intermolecular interactions of biological systems. In this work, Monte Carlo (MC) simulations were conducted of a novel antibacterial peptide on the basis of Charmm27 FF. Implementation of Charmm FF led to some structural deficiencies in aromatic rings from their expected physical structure. As the simulations progressed to equilibrium, nonplanarity was seen for the aromatic rings of Tryptophan (TRP) and Tyrosine (TYR). It was found that Charmm27 does not provide any improper torsion for carbon atoms in aromatic rings of these two units. These atoms have an SP2 hybridization and thus are typically planar. In addition, certain minimum angle parameters in Charmm27 induce these rings in both units to deviate from being in a plane.Considering improper torsion and amending the minimum angle parameters in MC simulation brings the aromatic rings in TYR and TRP closer to planar; however, the aromatic ring of TRP still has unacceptable deficiencies from planarity. Nevertheless, it cannot be stated that current Charmm FF (without improper torsion parameters) induces nonplanar structures of planar rings over simulation in TYR and TRP. Natural vibration of atoms in molecule might be the reason of this nonplanarity. All atom Normal Mode Analysis (NMA) provides the vibrational frequencies of atoms in those rings. Comparing the results of this calculation to vibrational spectra data can clarify to a certain extent the effect of Charmm FF in the deficiencies of aromatic ring from planarity. To that end, molecular dynamics (MD) simulations of TYR and TRP in the water are carried out on the basis of either the last version of Charmm(36) or modified Charmm by considering some improper torsion parameters and amending minimum angles parameters for atoms in the aromatic rings of TYR and TRP. Analytical and numerical NMA is applied on the configuration results of MD simulation to calculate the average vibrational frequency and normal mode of each atom in the system. The results of NMA are compared to infrared spectra of TRP and TYR. This comparison of simulation and experimental data can show how considering improper torsion or adding amending minimum angle parameters can change the calculated vibrational spectra of short peptides.