Planarity and out-of-plane vibrational modes of tryptophan and tyrosine in biomolecular modeling

摘要: Tryptophan and tyrosine are amino acids that play significant roles in the folding processes of proteins at water–membrane interfaces because their amphipathic heteroaromatic rings. Employing appropriate molecular structures is essential for obtaining accurate dynamics predictive capabilities simulations these acids. In this study, applied most recent version CHARMM36 force field were conducted on aqueous solutions tryptophan tyrosine. Geometric analysis quantified how aromatic rings deviated from planar exhibited out-of-plane fluctuations. Radial distribution functions showed possible biological significance extent ring planarity slightly affected local water concentrations near Instantaneous all-atom normal mode (NMA) Fourier transformation time autocorrelation displacements to study vibrations atoms The NMA started with minimum energy configurations then averaged over fluctuations solution. frequencies frequency patterns obtained differed literature reports Raman spectra, infrared calculated using quantum mechanics, some modes found higher frequencies. Effects imposing improper torsion potentials changing angle constants investigated all Results show coarse variations only affect within rings, not other vibrations. Although increasing reduced deviations significantly, it increased Reducing (with without torsions) shifted lower A combination decreasing both including forces attained more similar spectra. These decreased extents tryptophan, especially around nitrogen atom ring, but Conclusions unaffected by peptide endgroup, water, or simulation ensemble.