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Spin model of water and post-processing of protein folding experiments
Artem Badasyan, Knarik Yeritsyan, 2023, published scientific conference contribution abstract

Abstract: The presence of several distinct minima in nearest-neighbor potentials in polymers makes it possible to describe polymer conformations in terms of discrete isomeric states, naturally leading to spin language. Using this general approach, a decade ago we have suggested the Hamiltonian formulation for the Zimm and Bragg model of protein conformations [1,2]. Later we have augmented the model by an oversimplified spin model for water, resulting in both cold and hot denaturations [3]. We construct the Statistical Mechanics for the model and get access to its Thermodynamics. Resulting order parameter and specific heat expressions are successfully fit to available experimental data [4]. Thanks to solid and traceable theoretical foundations, the procedure provides better quality fits as compared to the state-of-the-art two-state model, routinely used to process protein folding experiments.
Keywords: spin model, water, protein folding
Published in RUNG: 04.09.2023; Views: 1180; Downloads: 7
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Potts spins, protein conformations and implicit water model
Artem Badasyan, 2023, published scientific conference contribution abstract (invited lecture)

Abstract: I will summarize past and current achievements in the field of spin model applications to protein conformations. Using classical Statistical Mechanics scheme and 1D many-body Hamiltonian, exact partition function can be estimated, giving access to the free energy, order parameter and specific heat. I will introduce a simplified water model as an additive term at the level of Hamiltonian, and will show how the solvent degrees of freedom can be summed out. The suggested procedure results in the effective Hamiltonian with the temperature dependent hydrogen bonding energy. If the many-body range is reduced to the nearest neighbour, the approach reduces to the Zimm-Bragg model. Obtained expressions for the order parameter and the specific heat nicely fit to the corresponding experiments for protein folding, providing an alternative or complementary scheme for the processing of experimental data.
Keywords: protein folding, Zimm-Bragg, protein-water interactions
Published in RUNG: 19.06.2023; Views: 1491; Downloads: 7
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16.
Spin Model of Protein Conformations in water: Theory vs Experiment.
Artem Badasyan, Knarik Yeritsyan, published scientific conference contribution abstract (invited lecture)

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
Published in RUNG: 15.05.2023; Views: 1659; Downloads: 0
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Protein quality control for improved data reproducibility and reliability
Kim Remans, Ario De Marco, Nick Berrow, Mario Lebendiker, Maria Garcia-Alai, Stefan Knauer, Andre Matagne, Anne Perret, Stephan Uebel, Bertrand Raynal, 2022, published scientific conference contribution abstract

Keywords: protein quality, evaluation assays, biophysical methods
Published in RUNG: 13.04.2023; Views: 1112; Downloads: 0
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Recombinant proteins as intermediate reagents : final applications will require alternative protocol design and quality controls
Ario De Marco, 2022, published scientific conference contribution abstract

Keywords: protein quality, protocol optimization, purification protocols
Published in RUNG: 18.11.2022; Views: 1338; Downloads: 6
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Identification of nanobodies targeting the BTB domain of the PATZ1 transcription factor
Sarah Barakat, Mustafa Tunçay, Alp Ertunga Eyupoglu, Emre Vatandaşlar, Ario De Marco, Batu Erman, 2022, published scientific conference contribution abstract

Keywords: PATZ1 protein, nanobodies, competitive binding
Published in RUNG: 20.06.2022; Views: 1710; Downloads: 0
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