Dynamics protein-glass transition

Toumier, A.L., Xu, J., and Smith, J.C. Translational hydration water dynamics drives the protein glass transition, Biophys.., 85,1871, 2003. 

Compared to natively folded proteins, compact denatured states ( MGs ) experience a modest increase in the number of water molecules in the hydration layer, and a slightly smaller perturbation of hydration water dynamics. Soluble protein-water dynamical coupling has been elucidated by simultaneous examination of transitions in protein and water dynamics as a function of temperature. Hydrated proteins at room temperature exhibit liquid-like motion on the subnanosecond timescale and behave like glasses at low temperature. The dynamical (or glass) transition between the low-temperature glassy state and room-temperature liquid-like state plays an important role in energy flow processes in proteins (see Ref [86] and Chapters 7 and 11). 

Protein-glass transition and hydration-layer dynamics... 

Protein-glass transition at 200 K role of water dynamics... 

The proximity of this liquid-liquid transition to the protein-glass transition temperature is suggestive. Clearly, at temperatures below 220 K or so, the dynamics of water and protein are highly coupled. A recent computer simulation study has shown that the stmctural relaxation of protein requires relaxation of the water HB network and translational displacement of interfacial water molecules. It is, therefore, clear that the dynamics of water at the interface can play an important role. This is an interesting problem that deserves further investigation. 

A low-tcmpcraturc, dynamically driven structural transition observed in a polypeptide by solid-state NMR spectroscopy has been reported by Bajaj et At low temperatures, proteins and other biomolecules are generally found to exhibit dynamic as well as structural transitions. This includes a so-called protein glass transition that is universally observed in systems cooled between 200 and 230 K, and which is generally attributed to interactions between hydrating solvent molecules and protein side chains. However, there is also experimental and theoretical evidence for a low-temperature transition in the intrinsic dynamics of the protein itself, absent any solvent. In the study by Bajaj et al., low-temperature solid-state NMR was used to examine site-specific fluctuations in atomic structure and dynamics in the absence of solvents. In particular, they employed MAS NMR to examine a structural phase transition associated with dynamic processes in a solvent-free polypeptide lattice at temperatures as low as 90 K. Several quantitative solid-state NMR experiments were employed to provide site-specific measurements of structural and motional features of the observed transition. 

Molecular dynamics simulations have also been used to interpret phase behavior of DNA as a function of temperature. From a series of simulations on a fully solvated DNA hex-amer duplex at temperatures ranging from 20 to 340 K, a glass transition was observed at 220-230 K in the dynamics of the DNA, as reflected in the RMS positional fluctuations of all the DNA atoms [88]. The effect was correlated with the number of hydrogen bonds between DNA and solvent, which had its maximum at the glass transition. Similar transitions have also been found in proteins. 

In order to understand the effect of temperature on the water dynamics and how it leads to the glass transition of the protein, we have performed a study of a model protein-water system. The model is quite similar to the DEM, which deals with the collective dynamics within and outside the hydration layer. However, since we want to calculate the mean square displacement and diffusion coefficients, we are primarily interested in the single particle properties. The single particle dynamics is essentially the motion of a particle in an effective potential described by its neighbors and thus coupled to the collective dynamics. A schematic representation of the d)mamics of a water molecule within the hydration layer can be given by ... 

In order to understand the role of water in the glass transition of the protein and its subsequent loss of functionality, we have performed a temperature dependent study of the hydration layer dynamics. The study shows that at low temperatures the bound to free conversion rates reduce drastically and this leads to a non-diffusive motion of the bound water. The mean square displacement obtained after 10 ps and the diffusion coefficient... 

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