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International Journal of Photoenergy
Volume 2006 (2006), Article ID 89638, 9 pages
http://dx.doi.org/10.1155/IJP/2006/89638

Temperature-dependent loop formation kinetics in flexible peptides studied by time-resolved fluorescence spectroscopy

School of Engineering and Science, International University Bremen, Campus Ring 1, Bremen 28759, Germany

Received 20 February 2006; Accepted 16 April 2006

Copyright © 2006 Harekrushna Sahoo et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Looping rates in short polypeptides can be determined by intramolecular fluorescence quenching of a 2,3-diazabicyclo[2.2.2]oct-2-ene-labeled asparagine (Dbo) by tryptophan. By this methodology, the looping rates in glycine-serine peptides with the structure Trp-(Gly-Ser)n-Dbo-NH2 of different lengths (n = 0–10) were determined in dependence on temperature in D2O and the activation parameters were derived. In general, the looping rate increases with decreasing peptide length, but the shortest peptide (n=0) shows exceptional behavior because its looping rate is slower than that for the next longer ones (n=1,2). The activation energies increase from 17.5 kJ mol1 for the longest peptide (n=10) to 20.5 kJ mol1 for the shortest one (n=0), while the pre-exponential factors (log(A/s1)) range from 10.20 to 11.38. The data are interpreted in terms of an interplay between internal friction (stiffness of the biopolymer backbone and steric hindrance effects) and solvent friction (viscosity-limited diffusion). For the longest peptides, the activation energies resemble more and more the value expected for solvent viscous flow. Internal friction is most important for the shortest peptides, causing a negative curvature and a smaller than ideal slope (ca. –1.1) of the double-logarithmic plots of the looping rates versus the number of peptide chain segments (N). Interestingly, the corresponding plot for the pre-exponential factors (logA versus logN) shows the ideal slope (–1.5). While the looping rates can be used to assess the flexibility of peptides in a global way, it is suggested that the activation energies provide a measure of the “thermodynamic” flexibility of a peptide, while the pre-exponential factors reflect the “dynamic” flexibility.