Quanta of local conformational change: conformons in alpha-helical proteins
Quanta of local conformational change: conformons in alpha-helical proteins, Proc Workshop on Quantum Effects in Biological Systems - QuEBS, Cambridge, MA, United States, Vol. 1, pp. 1 - 1, June, 2010.
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We propose the conformon as a quantum of local conformational
change for energy transfer in alpha-helical proteins. The underlying mechanism of
interaction between the quantum of excitation and the conformational degrees
of freedom is nonlinear and leads to solitary wave packets of conformational
energy. The phenomenon is specific to alpha-helices and not to beta-sheets in proteins
due to the three strands of hydrogen bonds constituting the alpha-helical backbone.
Pumpprobe experiments revealed that low-frequency nonlinear
modes are essential for functionally important conformational transitions in proteins containing
alpha-helices (Xie A, van der Meer L and Austin R H, Phys. Rev. Lett. 88, 018102, 2002).
The characteristic lifetime of these states is 15 ps (although for the vision-relevant
bacteriorhodopsin it can go over 500 ps). The same experiments also revealed that
amino acids and predominantly beta-sheet proteins do not have such long-lived states. The
proposed quanta of conformation already make the qualitative distinction between sections of the secondary
structure of proteins due to the full use of the geometry of the hydrogen bonds’ network
in alpha-helices. Quantitatively, we estimate the relevant physical constants, but their
experimental determination remains an open problem. Other nonlinear mechanisms of
energy transport in alpha-helical proteins fail to exhibit such a long lifetime. Thus the
conformons proposed here might have the answer for the mechanism of direct coherent flow
of conformational energy for a variety of vital biological processes ranging from electron
transfer to enzyme action.