Articles you may be interested inOptimizing conical intersections of solvated molecules: The combined spin-flip density functional theory/effective fragment potential method J. Chem. Phys. 137, 034116 (2012); 10.1063/1.4734314 Solvent effect on the folding dynamics and structure of E6-associated protein characterized from ab initio protein folding simulations J. Chem. Phys. 136, 135102 (2012); 10.1063/1.3698164 Communication: Free-energy analysis of hydration effect on protein with explicit solvent: Equilibrium fluctuation of cytochrome cThe spectral diffusion dynamics of free base cytochrome c ͑H2-Cc͒ in a dry trehalose film is tremendously enhanced as compared to a glycerol/water glass. We show that relaxation as well as fluctuation processes contribute to the spectral diffusion dynamics. Relaxation shows up in aging phenomena which can be measured in a separate fashion. In both solvents, the spectral diffusion as well as the aging dynamics follow power laws in time. The respective exponents are quite different, yet the influence of the solvent on them is only marginal. The large difference in the magnitude of the spectral diffusion dynamics in the two solvents can be traced back to a correspondingly large difference in the inhomogeneous width which itself seems to come from the much higher glass transition temperature in trehalose, which is close to the unfolding temperature of cytochrome c.

We present results of a hole burning study with thermal cycling and waiting time spectral diffusion experiments on a modified cytochrome - c protein in its native as well as in its denatured state. The experiments show features which seem to be characteristic for the protein state of matter and its associated dynamics at low temperature. The properties responsible for the observed patterns are organisation paired with randomness and, in addition, the finite size which gives rise to surface and solvent effects. We discuss some general model approaches which might serve as guide lines for understanding these features.Comment: To Appear in the Journal of Low Temperature Physics, 200

Spectral diffusion broadening of cytochrome c carrying the free-base analogue of heme is investigated in its unfolded state and compared with the corresponding broadening in the native state. Spectral diffusion is much larger in the unfolded state, in comparison to the native state. Interestingly, the time law that governs spectral diffusion changes as the aging time increases, from a power-law behavior in the native state to an apparent logarithmic behavior in the unfolded state.

Frozen proteins are nonergodic systems and are subject to two types of structural motions, namely relaxation and fluctuation. Relaxation manifests itself in aging processes which slow the fluctuations. Within certain approximations we are able to experimentally separate the aging dynamics from the fluctuation dynamics by introducing two time parameters, namely an aging time t a and a waiting time t w . Both processes follow power laws in time. The fluctuation dynamics shows features of universality characterized by a rather uniform exponent of 1 4/ . This universality features were shown to be possible due to a random walk on a 1D random trajectory in conformational phase space. A very interesting aspect of protein dynamics concerns the influence of the host solvent on structural motions of the protein cores. We present results for sugar solvents and discuss possible mechanisms.

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