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Time-Dependent Spectral Shifts in Tryptophan Fluorescence: Bridging Experiments with Molecular Dynamics Simulations

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Reviews in Fluorescence 2015

Part of the book series: Reviews in Fluorescence ((RFLU,volume 8))

Abstract

Molecular dynamics (MD) simulations are widely used to model protein motions. Although the time resolution of MD simulations is virtually unlimited, simulated MD is seldom compared with experimental data on the picosecond time scale because few experimental techniques can probe molecular vibrations in the frequency range between 300 MHz and 300 GHz. Time-dependent spectral shift (TDSS, also known as dynamic Stokes shift) in fluorescence emission from solvatochromic dyes has long been used to study relaxation dynamics of polar solvents on the picosecond time scale. This chapter reviews the use of TDSS in connection with protein dynamics. Different methods of calculating TDSS from the non-equilibrium and equilibrium MD are compared and the limits of their applicability are defined. Methods for separating the contributions of water and protein to TDSS are considered. Two relaxation modes of bulk water are described and their effects on the TDSS in proteins are examined. The rates of water relaxation near interfaces and inside protein pockets are evaluated. A method for identifying conformational changes responsible for the TDSS on different time scales is introduced.

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Acknowledgments

This research was supported by the National Science Foundation awards MCB-0719248 and MCB-1051996.

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  1. Department of Biology, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD, 21218, USA

    Dmitri Toptygin

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Correspondence to Dmitri Toptygin .

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  1. Institute of Fluorescence, University of Maryland Baltimore County Institute of Fluorescence, BALTIMORE, Maryland, USA

    Chris D. Geddes

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Toptygin, D. (2016). Time-Dependent Spectral Shifts in Tryptophan Fluorescence: Bridging Experiments with Molecular Dynamics Simulations. In: Geddes, C. (eds) Reviews in Fluorescence 2015. Reviews in Fluorescence, vol 8. Springer, Cham. https://doi.org/10.1007/978-3-319-24609-3_2

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