Repozitorij Univerze v Novi Gorici

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Naslov:New method to process Circular Dichroism experimental data on heat and cold denaturation of polypeptides in water
Avtorji:Badasyan, Artem V. (Avtor)
Valant, Matjaž (Avtor)
Datoteke:Gradivo nima datotek. Gradivo je morda fizično dosegljivo v knjižnici fakultete, zalogo lahko preverite v COBISS-u. Povezava se odpre v novem oknu
Jezik:Angleški jezik
Vrsta gradiva:Delo ni kategorizirano (r6)
Tipologija:1.12 - Objavljeni povzetek znanstvenega prispevka na konferenci
Organizacija:UNG - Univerza v Novi Gorici
Opis: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)
Ključne besede:Biopolymers, Circular Dichroism, Zimm-Bragg model, helix-coil transition.
Leto izida:2018
COBISS_ID:5252859 Povezava se odpre v novem oknu
URN:URN:SI:UNG:REP:TDM6SXLE
Število ogledov:1055
Število prenosov:0
Metapodatki:XML RDF-CHPDL DC-XML DC-RDF
Področja:Gradivo ni uvrščeno v področja.
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Skupna ocena:(0 glasov)
Vaša ocena:Ocenjevanje je dovoljeno samo prijavljenim uporabnikom.

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Gradivo je del monografije

Naslov:Zbornik povzetkov Slovenski kemijski dnevi 2018, 19.–21. september, Portorož
Prireditelj konference:Slovensko kemiško društvo
ISBN:978-961-93849-4-7
Kraj izida:Ljubljana, Slovenia
Leto izida:2018

Gradivo je financirano iz projekta

Financer:ARRS - Agencija za raziskovalno dejavnost Republike Slovenije (ARRS)
Program financ.:Cilnji raziskovalni programi
Številka projekta:P2-0379
Naslov:Modeliranje in simulacija materialov in procesov
Akronim:
ID projekta:info:eu-repo/grantAgreement/ARRS/Cilnji%20raziskovalni%20programi/P2-0379

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