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35. Nitrate as a probe of cytochrome c surface : crystallographic identification of crucial "hot spots" for protein-protein recognitionMatteo De March, Nicola Demitri, Rita De Zorzi, Angela Casini, Chiara Gabbiani, Annalisa Guerri, Luigi Messori, Silvano Geremia, 2014, original scientific article Keywords: cytochrome c, electron transfer complexes, electrostatic surface, redox protein Published in RUNG: 03.03.2021; Views: 2189; Downloads: 0 This document has many files! More... |
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37. The finite size effects and two-state paradigm of protein foldingArtem Badasyan, Matjaž Valant, Jože Grdadolnik, Vladimir N. Uversky, 2021, original scientific article Abstract: The coil to globule transition of the polypeptide chain is the physical phenomenon behind the folding of globular proteins. Globular proteins with a single domain usually consist of about 30 to 100 amino acid residues, and this finite size extends the transition interval of the coil-globule phase transition. Based on the pedantic derivation of the two-state model, we introduce the number of amino acid residues of a polypeptide chain as a parameter in the expressions for two cooperativity measures and reveal their physical significance. We conclude that the k2 measure, defined as the ratio of van ’t Hoff and calorimetric enthalpy is related to the degeneracy of the denatured state and describes the number of cooperative units involved in the transition; additionally, it is found that the widely discussed k2=1 is just the necessary condition to classify the protein as the two-state folder. We also find that Ωc, a quantity not limited from above and growing with system size, is simply proportional to the square of the transition interval. This fact allows us to perform the classical size scaling analysis of the coil-globule phase transition. Moreover, these two measures are shown to describe different characteristics of protein folding Keywords: protein folding, two-state model, size scaling, thermodynamic cooperativity Published in RUNG: 24.02.2021; Views: 2150; Downloads: 66 Link to full text This document has many files! More... |
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39. Water reveals non-Arrhenius kinetics in protein folding experimentsArtem Badasyan, 2020, published scientific conference contribution abstract (invited lecture) 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 Keywords: water, protein folding, non-Arrhenius kinetics Published in RUNG: 20.07.2020; Views: 2682; Downloads: 112 Full text (2,35 MB) |
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