Temperature Dependence of Looping Rates in a Short Peptide
2007-03-15T00:00:00Z (GMT) by
Knowledge of the influence of chain length and amino acid sequence on the structural and dynamic properties of small peptides in solution provides essential information on protein folding pathways. The combination of time-resolved optical spectroscopy and molecular dynamics (MD) simulation methods has become a powerful tool to investigate the kinetics of end-to-end collisions (looping rates) in short peptides, which are relevant in early protein folding events. We applied the combination of both techniques to study temperature-dependent (280−340 K) looping rates of the Dbo-AlaGlyGln-Trp-NH<sub>2</sub> peptide, where Dbo represents a 2,3-diazabicyclo[2.2.2]oct-2-ene-labeled asparagine, which served as a fluorescent probe in the time-resolved spectroscopic experiments. The experimental looping rates increased from 4.8 × 10<sup>7</sup> s<sup>-1</sup> at 283 K to 2.0 × 10<sup>8</sup> s<sup>-1</sup> at 338 K in H<sub>2</sub>O. The corresponding Arrhenius plot provided as activation parameters <i>E</i><sub>a</sub> = 21.5 ± 1.0 kJ mol<sup>-1</sup> and ln(<i>A</i>/s<sup>-1</sup>) = 26.8 ± 0.2 in H<sub>2</sub>O. The results in D<sub>2</sub>O were consistent with a slight solvent viscosity effect, i.e., the looping rates were 10−20% slower. MD simulations were performed with the GROMOS96 force field in a water solvent model, which required first a parametrization of the synthetic amino acid Dbo. After corrections for solvent viscosity effects, the calculated looping rates varied from 1.5 × 10<sup>8</sup> s<sup>-1</sup> at 280 K to 8.2 × 10<sup>8</sup> s<sup>-1</sup> at 340 K in H<sub>2</sub>O, which was about four times larger than the experimental data. The calculated activation parameters were <i>E</i><sub>a</sub> = 24.7 ± 1.5 kJ mol<sup>-1</sup> and ln(<i>A</i>/s<sup>-1</sup>) = 29.4 ± 0.1 in H<sub>2</sub>O.