| Title: | Water reveals non-Arrhenius kinetics in protein folding experiments |
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| Authors: | ID Badasyan, Artem (Copyright holder)
ID Badasyan, Artem (Author) |
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| Files: |  Abstract-Book_IOCFN_July2020.pdf (2,35 MB)
MD5: 3B3C6F96270A1BBEFAC1DE6CF9586EE5
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| Language: | English |
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| Work type: | Not categorized |
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| Typology: | 1.10 - Published Scientific Conference Contribution Abstract (invited lecture) |
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| Organization: | UNG - University of Nova Gorica
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| Abstract: | Statistical theories describe systems in equilibrium, and cannot be used to study kinetics. However, the theo-
ries are based on coarse-grained parameters, that include assumptions regarding the underlying kinetics. If
such assumptions are incorrect, the theoretical expressions, used to process the experimental data, will not
fit. I report on one such case we have met within the application of Zimm-Bragg [1] theory to process folding
experiments, and discuss the reasons and consequences.
Studies of relaxation phenomena in glass-forming liquids by default account for the shift in temperature by
some value, corresponding to the glass formation temperature, .In particular, temperature
shift
appears in hydrated proteins because of the presence of partially glassy states giving rise to
non-
Arrhenius relaxation times log τ ~ [2].
A phenomenological approach was suggested
by Adam and Gibbs as early as in 1965 to describe
the sudden increase of viscosity and the slowing down of the collective modes in super-cooled liquids as the
temperature is approaching[3]. The key idea of Adam-Gibbs theory was to consider the supercooled liquid
as a set of clusters (cooperatively rearranging regions) of different sizes that change with temperature,
giving rise to the shift in re-
laxation time. The temperature shift factor is present in many theories
describing properties of water.
Thus, Truskett and Dill had to include the Adamm-Gibbs temperature
shift into their simple analytical model of water to achieve the agreement with experimental data on the tem-
perature dependence of self-diffusion coefficient [4]. Later, Schiro and Weik have summarised recent in vitro
and in silico experimental results regarding the role of hydration water in the onset of protein structural dy-
namics, and have reported the presence of super-Arrhenius relaxation region above the ”protein dynamic
transition” temperature [4]. Recently, Mallamace et al have used the Adam-Gibbs theory in their NMR meas-
urements of protein folding-unfolding in water [4] and to rationalise the complicated pressure-temperature
diagrams in these glass-forming systems.
Motivated by the considerations above, and taking into account the
relationship between the
unimolecular rate of folding in water and the relaxation time 45 , we
introduce the
tem-
perature shift into the formulas used to fit experimental data on hydrated polypeptides.
By doing so we resolve the paradox and complete the new method of processing the Circular Dichroism ex-
perimental data on protein folding |
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| Keywords: | water, protein folding, non-Arrhenius kinetics |
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| Year of publishing: | 2020 |
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| Number of pages: | 1 |
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| PID: | 20.500.12556/RUNG-5659  |
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| COBISS.SI-ID: | 23055107 |
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| NUK URN: | URN:SI:UNG:REP:RVBL17HE |
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| Publication date in RUNG: | 20.07.2020 |
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| Views: | 3529 |
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| Downloads: | 117 |
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| Metadata: |    |
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