Calculation of the circular dichroism spectrum of cyclo-(L-tyr-L-tyr) based on a molecular dynamics simulation.
Theoretical calculations of CD spectra have generally assumed a single conformation, or a small number of conformers with Boltzmann averaging. Solvent effects on both the conformation and the CD have been neglected. In this work, we have calculated the CD spectrum of cyclo(L-Tyr-L-Tyr) in aqueous solution, taking dynamics and solvation into account. Starting geometries with chi 1 approximately 300 degrees or 60 degrees for both Tyr side chains were derived from MNDO/MOPAC, followed by energy minimization using GROMOS. After addition of 368 water molecules, the system was simulated for 1000 ps at 300 K using GROMOS. In addition to the starting conformer, two other conformers were observed during each simulation. However, each trajectory gave a distinct set of conformers. Rotational strengths were calculated for the cyclic dipeptide at each ps along the trajectories, using the matrix method. The CD spectra calculated from these rotational strengths were averaged over the trajectories. Agreement is very good for the strong negative band near 200 nm, while for the lower energy bands (near 230 and 280 nm), the signs are correct, but the magnitudes are too low. The spectrum calculated from a Boltzmann-weighted average over the in vacuo MNDO/MOPAC conformers was in poor agreement with experiment. Although the solvent did not significantly affect the rotational strength calculated for a given conformer, it is essential to include the solvent in the MD simulations because it affects the relative energies of the conformers and promotes transitions among them.
Fleischhauer
J
J
Institute of Organic Chemistry, Rheinisch-Westfälische Technische Hochschule, Aachen, Germany.
Grötzinger
J
J
Kramer
B
B
Krüger
P
P
Wollmer
A
A
Woody
R W
RW
Zobel
E
E
D055598:Chemical Phenomena; D002627:Chemistry, Physical; D002942:Circular Dichroism; D004151:Dipeptides / Q000737:chemistry*; D010456:Peptides, Cyclic / Q000737:chemistry*; D011487:Protein Conformation; D012996:Solutions; D013696:Temperature
D004151:Dipeptides; D010456:Peptides, Cyclic; D012996:Solutions; C086820:cyclo(tyrosyl-tyrosyl)