Repozitorij Univerze v Novi Gorici

Iskanje po repozitoriju
A+ | A- | Pomoč | SLO | ENG

Iskalni niz: išči po
išči po
išči po
išči po
* po starem in bolonjskem študiju

Opcije:
  Ponastavi


11 - 20 / 57
Na začetekNa prejšnjo stran123456Na naslednjo stranNa konec
11.
Spin Model of Protein Conformations in water: Theory vs Experiment.
Artem Badasyan, Knarik Yeritsyan, objavljeni povzetek znanstvenega prispevka na konferenci (vabljeno predavanje)

Opis: Background (approx. 70 words) I will overview the application of spin models of Statistical Mechanics to describe polypeptide conformations. Zimm and Bragg model is one of the most successful examples of such approach [1]. In 2010 we have suggested the microscopic formulation of the model [2], which was later augmented by including the interactions with water [3]. Adding the solvent opened doors for the direct comparisons with UV-vis, Circular Dichroism (CD) and Differential Scanning Calorimetry (DSC) experiments. Aim (approx. 30 words) Based on a statistical Potts-like spin model of protein folding we provide formulas for experimentally measurable quantities and report a perfect fit. Our approach suggest a new method to process the results of protein folding experiments. Method (approx. 100 words) We start from the microscopic Hamiltonian formulation of the polypeptide model in water and use the usual Statistical Mechanics route from the model to partition function and the thermodynamics. Using Mayer expansion and summation over the solvent degrees of freedom, the problem is shown to be equivalent to in vacuo model with some effective, temperature dependent interaction energy. Estimated partition function leads to the expressions for the thermodynamic potentials and order parameter averages. The comparison (least-square fit) with the experimental data points from CD and DSC experiments on protein folding allows to extract the information on hydrogen bonding strengths, not available with the classical approach. Results & Discussion (approx 200 words, or less if you paste an image or insert a table ) Proposed model allows for the cold denaturation under certain well-defined conditions. The agreement between the theoretical curves and data points is excellent, and the values of fitted parameters are within the expected ranges. The limitations of the approach are naturally related to the limitations of the Zimm-Bragg original model, intended to describe the changes of the secondary structure elements only. Taking into account that the so-called “two-state” model widely used nowadays to process the experiment does not contain any info regarding the hydrogen bonding energies, the method we suggest provides a promising alternative. Conclusion (70 words approximately) The proposed approach does what it is intended to do: processing of the experimental data on protein folding. However the model contains the very same serious limitations, as the two-state model: it is oversimplified in many respects. Whether the currently available experimental methods need a better model than already suggested ones or not, is an open question. References: [1] Zimm, B.H.; Bragg, J.K.; J. Chem. Phys. 31:526–535 (1959). [2] Badasyan, A.V. et al., Phys. Rev. E 81:021921 (2010). [3] Badasyan, A.V. et al., Phys. Rev. E 89:022723 (2014). [4] Badasyan, A. et al.; Eur.Phys. J. E 36:1–9 (2013).
Ključne besede: Protein folding, CD, DSC, Zimm-Bragg
Objavljeno v RUNG: 15.05.2023; Ogledov: 1628; Prenosov: 0
Gradivo ima več datotek! Več...

12.
13.
Analysis of CD and DSC protein folding data
Knarik Yeritsyan, predavanje na tuji univerzi

Ključne besede: helix-coil, chain length, helicity degree, heat capacity
Objavljeno v RUNG: 21.12.2022; Ogledov: 2457; Prenosov: 0
Gradivo ima več datotek! Več...

14.
15.
Helix-coil theory to process experimental data for short polypeptides in solvent
Knarik Yeritsyan, Matjaž Valant, Artem Badasyan, 2022, objavljeni povzetek znanstvenega prispevka na konferenci

Ključne besede: Zimm-Bragg model, helix-coil transition, thermal unfolding, chain length
Objavljeno v RUNG: 10.10.2022; Ogledov: 1426; Prenosov: 1
Gradivo ima več datotek! Več...

16.
Analysis of gambling slot machines : written report
Marko Žagar, 2022, raz. nal. na višji ali visoki šoli

Ključne besede: probability theory, statistics, combinatorics, slot machine games
Objavljeno v RUNG: 16.09.2022; Ogledov: 1256; Prenosov: 0

17.
Probing the folding of hen lyzozyme through molecular dynamics simulations
Bariş Kalfa, 2022, raz. nal. na višji ali visoki šoli

Ključne besede: molecular dynamics simulations, proteins, folding process, unfolding process, hen egg-white lysozyme
Objavljeno v RUNG: 25.08.2022; Ogledov: 1351; Prenosov: 0
Gradivo ima več datotek! Več...

18.
Solutions of the Ising model : written report
Jaka Strajn, 2022, raz. nal. na višji ali visoki šoli

Ključne besede: Ising model, transfer matrix method, mean-field model, variational principle, ferromagnetic phase transition
Objavljeno v RUNG: 15.06.2022; Ogledov: 3458; Prenosov: 0
Gradivo ima več datotek! Več...

19.
Finite size effects at protein folding from the two-state perspective
Artem Badasyan, Matjaž Valant, Jože Grdadolnik, Vladimir N. Uversky, 2021, objavljeni povzetek znanstvenega prispevka na konferenci

Ključne besede: protein folding, two-state model, finite size effects
Objavljeno v RUNG: 27.09.2021; Ogledov: 1975; Prenosov: 0
Gradivo ima več datotek! Več...

20.
System size dependence of the Zimm-Bragg model
Artem Badasyan, 2021, objavljeni povzetek znanstvenega prispevka na konferenci

Ključne besede: Zimm-Bragg model, final size effects
Objavljeno v RUNG: 27.09.2021; Ogledov: 1878; Prenosov: 0
Gradivo ima več datotek! Več...

Iskanje izvedeno v 0.05 sek.
Na vrh