| Title: | New method to process Circular Dichroism experimental data on heat and cold denaturation of polypeptides in water |
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| Authors: | ID Badasyan, Artem (Author)
ID Valant, Matjaž (Author) |
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| Files: |
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| Language: | English |
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| Work type: | Not categorized |
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| Typology: | 1.12 - Published Scientific Conference Contribution Abstract |
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| Organization: | UNG - University of Nova Gorica
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| Abstract: | During the past decade the experimental studies of biopolymer conformations have reached an
unprecedented level of detailization and allow to study single molecules in vivo [1]. Processing of
experimental data essentially relies on theoretical approaches to conformational transitions in
biopolymers [2]. However, the models that are currently used, originate from the early 1960's and
contain several unjustified assumptions, widely accepted at that time. Thus, the view on the
conformational transitions in the polypeptides as a two-state process has very limited applicability
because the all-or-none transition mechanism takes place only in short polypeptides with sizes
comparable to the spatial correlation length; the original formulation of Zimm-Bragg model is
phenomenological and does not allow for a microscopic model for water; the implicit consideration of
the water-polypeptide interactions through the ansatz about the quadratic dependence of free energy
difference on temperature can only be justified through the assumption of an ideal gas with a constant
heat capacity. To get rid of these deficiencies, we augment the Hamiltonian formulation [3] of the
Zimm-Bragg model [4] with the term describing the water-polypeptide interactions [5]. The analytical
solution of the model results in a formula, ready to be fit to Circular Dichroism (CD) data for both heat
and cold denaturation. On the example of several sets of experimental data we show, that our formula
results in a significantly better fit, as compared to the existing approaches. Moreover, the application
of our procedure allows to compare the strengths of inter- and intra-molecular H-bonds, an
information, inaccessible before.
References
[1] I. König, A. Zarrine-Afsar, M. Aznauryan, A. Soranno, B. Wunderlich, F. Dingfelder, J. C. Stüber, A. Plückthun, D.
Nettels, B. Schuler, (2015), Single-molecule spectroscopy of protein conformational dynamics in live eukaryotic
cells/Nature Methods, 12, 773-779.
[2] J. Seelig, H.-J. Schönfeld, (2016), Thermal protein unfolding by differential scanning calorimetry and circular
dichroism spectroscopy. Two-state model versus sequential unfolding/Quarterly Reviews of Biophysics, 49, e9, 1-24.
[3] A.V. Badasyan, A. Giacometti, Y. Sh. Mamasakhlisov, V. F. Morozov, A. S. Benight, (2010), Microscopic formulation
of the Zimm-Bragg model for the helix-coil transition/Physical Review E, 81, 021921.
[4] B. H. Zimm, J. K. Bragg, (1959), Theory of the Phase Transition between Helix and Random Coil in Polypeptide
Chains/Journal of Chemical Physics, 31, 526.
[5] A. Badasyan, Sh.A. Tonoyan, A. Giacometti, R. Podgornik, V.A. Parsegian, Y.Sh. Mamasakhlisov, V.F. Morozov,
(2014), Unified description of solvent effects in the helix-coil transition/Physical Review E, 89, 022723.
Corresponding author: Artem Badasyan (artem.badasyan@ung.si) |
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| Keywords: | Biopolymers, Circular Dichroism, Zimm-Bragg model, helix-coil transition. |
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| Publication status: | Published |
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| Year of publishing: | 2018 |
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| PID: | 20.500.12556/RUNG-4167-2d6ed426-b297-be79-7dd6-7fd5c487c1ff |
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| COBISS.SI-ID: | 5252859 |
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| NUK URN: | URN:SI:UNG:REP:TDM6SXLE |
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| Publication date in RUNG: | 22.10.2018 |
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| Views: | 4860 |
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| Downloads: | 0 |
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