Molecular dynamics of tryptophan in ribonuclease-T1. II. Correlations with fluorescence

Biophysical Journal
P H Axelsen, F G Prendergast

Abstract

The interactions of tryptophan-59 (TRP-59) and its protein environment in ribonuclease-T1 (RNAse-T1) were examined in a 50-ps molecular dynamics simulation. The simulation used was previously shown to demonstrate a fluorescence anisotropy decay that closely agreed with the experimentally determined limiting anisotropy for RNAse-T1 (Axelsen, P. H., C. Haydock, and F. G. Prendergast. 1988. Biophys. J. 54:249-258). Further characterization of TRP-59 side chain dynamics and its protein environment has now been completed and correlated to other photophysical properties of this protein. Angular fluctuations of the side chain occur at rates of 1-10 cycles/ps and are limited to +/- 0.3 radians in all directions. Side chain motions are primarily limited by nonpolar collisions, although most side chain atoms have some collisional contact with polar atoms in the adjacent protein matrix or water. The steric relationship between PRO-39 and TRP-59 changes abruptly at 16 ps into the simulation. Two types of interaction with water are observed. First, a structural water appears to H-bond with the greater than N-H group of TRP-59. Second, water frequently contacts the six-atom ring. The electrostatic field experienced by the TRP-59 rings appear...Continue Reading

Citations

Mar 1, 1997·Journal of Molecular Recognition : JMR·D LiP H Axelsen
Sep 1, 1992·Journal of Fluorescence·M GonnelliG B Strambini
Feb 13, 2003·European Journal of Biochemistry·Priyaranjan PattanaikHemalatha Balaram
Apr 28, 2001·Biophysical Journal·J T Vivian, P R Callis
Sep 12, 2007·Biochemistry·Maria StaianoKonstantin K Turoverov
Nov 20, 1991·Journal of Molecular Biology·J Martinez-OyanedelW Saenger
May 19, 2012·Journal of the American Chemical Society·Rasmus Lybech JensenPeter R Ogilby
Jul 22, 2014·The Journal of Physical Chemistry. B·Wei-Chih ChaoPi-Tai Chou

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