Dynamics studies of tryptophan and single tryptophan containing peptides: simulations and an analytical model

Yi Hu; Jean M. MacInnis; Binny J. Cherayil; Graham R. Fleming; Karl F. Freed; Angelo Perico

doi:10.1117/12.17707

1 May 1990 Dynamics studies of tryptophan and single tryptophan containing peptides: simulations and an analytical model

Yi Hu, Jean M. MacInnis, Binny J. Cherayil, Graham R. Fleming, Karl F. Freed, Angelo Perico

Author Affiliations +

Proceedings Volume 1204, Time-Resolved Laser Spectroscopy in Biochemistry II; (1990) https://doi.org/10.1117/12.17707
Event: OE/LASE '90, 1990, Los Angeles, CA, United States

Abstract

The optimized Rouse-Zimm model is modified leading to a theory for long time random coil polypeptide dynamics [Perico etal., J. Chem. Phys., (1987), 87, 3677, Perico, J. Chem. Phys., (1988), 88, 3996, and Biopolymers, (1989), 28, 1527]. The description necessitates the knowledge of the rotational potential energy for specific amino acid residues and their friction coefficients. Static information, such as the amino acid sequence, the length of the polypeptide chain, and the location of the probe are found to affect the rotational correlation function P₂(t) and the local persistence length markedly. Compared with the fluorescence anisotropy measurements of tryptophan containing polypeptides (of the order of nanoseconds), the theory gives a reasonable prediction for the fluorescence depolarization correlation times of random coil polypeptides, but the calculated rotational correlation function predicts a much faster initial decay and a slower final decay than is observed. Possible theoretical improvements are discussed. Molecular dynamics simulations of tryptophan reorientation are also briefly described.

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Yi Hu, Jean M. MacInnis, Binny J. Cherayil, Graham R. Fleming, Karl F. Freed, and Angelo Perico "Dynamics studies of tryptophan and single tryptophan containing peptides: simulations and an analytical model", Proc. SPIE 1204, Time-Resolved Laser Spectroscopy in Biochemistry II, (1 May 1990); https://doi.org/10.1117/12.17707

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