Klaus Schulten, Hui Lu, and Linsen Bai.
Probing protein motion through temperature echoes.
In Henrik Flyvbjerg, John Hertz, Mogens H. Jensen, Ole G. Mouritsen,
and Kim Sneppen, editors, Physics of Biological Systems: From Molecules
to Species, Lecture Notes in Physics, pp. 117-152. Springer, 1997.
SCHU97
In this tutorial lecture we demonstrate the existence of protein normal modes which maintain phase coherence for about one picosecond. We also study the dissipation of energy in proteins. The analysis is based on numerical experiments in which motional coherence, generated through two reassignments of Cartesian atomic velocities, induces echoes in the kinetic energy (temperature) and potential energy of proteins. Various echoes are produced in the case of the membrane protein bacteriorhodopsin. The echo phenomenon is then explained through a description of protein motion as an ensemble of harmonic oscillators. This description reveals that the echo can be expressed in terms of the temperature-temperature correlation function. A description in terms of Langevin oscillators allows one to account for decoherence effects. Finally, we consider echoes arising in an analytically tractable linear harmonic chain.
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