1. Differential scanning calorimetry of proteins and the two-state model : comparison of two formulasKnarik Yeritsyan, Artem Badasyan, 2024, original scientific article Abstract: Differential Scanning Calorimetry (DSC) is a regular and powerful tool to measure the specific heat profile of various materials. In order to connect the measured profile to the properties of a particular protein, a model is required to fit. We discuss here the application of an exact two-state formula with its approximation and process the DSC experimental data on protein folding in water. The approximate formula relies on the smallness of the transition interval, which is different for each protein. With an example of the set of 33 different proteins, we show the practical validity of the approximation and the equivalence of exact and approximate two-state formulas for processing DSC data.
Keywords: protein folding, differential scanning calorimetry, heat capacity, two-state model, Hawley model
Published in RUNG: 21.05.2024; Views: 77; Downloads: 0
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2. A practical guide for the quality evaluation of fluobodies/chromobodiesUrša Štrancar, Claudia D'Ercole, Lucia Cikatricisová, Mirna Nakić, Matteo De March, Ario De Marco, 2024, original scientific article Keywords: fluorescent proteins, protein stability, protein degradation
Published in RUNG: 16.05.2024; Views: 138; Downloads: 2
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3. A concise guide to choosing suitable gene expression systems for recombinant protein productionAnja Schütz, Frank Bernhard, Nick Berrow, Johannes F. Buyel, Frederico Ferreira-da-Silva, Jurgen Haustraete, Joop Van den Heuvel, Jan-Erik Hoffmann, Ario De Marco, Yoav Peleg, 2023, original scientific article Keywords: recombinant protein, protein expression options, post-translational modifications
Published in RUNG: 06.11.2023; Views: 704; Downloads: 5
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5. Modelling water for calorimetry of proteinsKnarik Yeritsyan, Artem Badasyan, 2023, published scientific conference contribution abstract Abstract: Differential Scanning Calorimetry (DSC) is a powerful technique used to study the thermal stability and unfolding of proteins. DSC provides the excess heat capacity profile and is used to study the thermodynamics of a given protein. By fitting DSC data to the model, researchers can obtain valuable information about the thermodynamics of protein folding and unfolding, which can help them better understand protein structure, stability, and function.
Based on Hamiltonian representation of ZB model and using the solvent effects we derived an expression for heat capacity in proteins and successfuly fit it to experimental data. As we show, our model provides a better fit to experimental data, as compared to the 2-state model. The model we propose takes into account also water effects and we show that it fits better to experimental data giving inter- and intra-molecular H-bonding energies instead of reporting only one total enthalpy.
Keywords: Zimm-Bragg model, water model, helix-coil transition, protein folding, differential scanning calorimetry
Published in RUNG: 18.10.2023; Views: 835; Downloads: 0
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6. Biological applications of synthetic binders isolated from a conceptually new adhiron libraryClaudia D'Ercole, Matteo De March, Gianluca Veggiani, Sandra Oloketuyi, Rossella Svigelj, Ario De Marco, 2023, original scientific article Keywords: synthetic library, adhirons, affimers, C-reactive protein, SpyCatcher
Published in RUNG: 17.10.2023; Views: 836; Downloads: 3
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8. Spin model of water and post-processing of protein folding experimentsArtem 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: 898; Downloads: 4
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9. Affinity maturation of antibody fragments : a review encompassing the development from random approaches to computational rational optimizationJiaqi Liu, Guangbo Kang, Jiewen Wang, Haibin Yuan, Yili Wu, Shuxian Meng, Ping Wang, Miao Zhang, Yuli Wang, Yuanhang Feng, He Huang, Ario De Marco, 2023, review article Keywords: deep learning, protein modeling, random mutagenesis, rational mutagenesis
Published in RUNG: 17.07.2023; Views: 940; Downloads: 4
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10. Potts spins, protein conformations and implicit water modelArtem 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: 1186; Downloads: 6
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