Repository of University of Nova Gorica

Show document
A+ | A- | Help | SLO | ENG

Title:Spin Model of Protein Conformations in water: Theory vs Experiment.
Authors:ID Badasyan, Artem, UNG (Author)
ID Yeritsyan, Knarik (Author), et al.
Files:This document has no files that are freely available to the public. This document may have a physical copy in the library of the organization, check the status via COBISS. Link is opened in a new window
Work type:Not categorized
Typology:1.10 - Published Scientific Conference Contribution Abstract (invited lecture)
Organization:UNG - University of Nova Gorica
Abstract: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).
Keywords:Protein folding, CD, DSC, Zimm-Bragg
Publication status in journal:Pending publication
Number of pages:2 str
PID:20.500.12556/RUNG-8202 New window
COBISS.SI-ID:152137731 New window
Publication date in RUNG:15.05.2023
Copy citation
Average score:(0 votes)
Your score:Voting is allowed only for logged in users.
Share:Bookmark and Share

Hover the mouse pointer over a document title to show the abstract or click on the title to get all document metadata.

Record is a part of a monograph

Title:International Conference on Materials & Processes for Sustainable Development 2023 : May 10 & 11, 2023, Chenini, Gabes - Tunisia
Year of publishing:2023
COBISS.SI-ID:152136707 New window