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Opis: 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.
Ključne besede: SPIN MODEL, WATER, PROTEIN FOLDING
Objavljeno v RUNG: 04.09.2023; Ogledov: 143; Prenosov: 1
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Opis: Studies of biopolymer conformations essentially rely on theoretical models that are routinely used to process and analyze experimental data. While modern experiments allow study of single molecules in vivo, corresponding theories date back to the early 1950s and require an essential update to include the recent significant progress in the description of water. The Hamiltonian formulation of the Zimm-Bragg model we propose includes a simplified, yet explicit model of water-polypeptide interactions that transforms into the equivalent implicit description after performing the summation of solvent degrees of freedom in the partition function. Here we show that our model fits very well to the circular dichroism experimental data for both heat and cold denaturation and provides the energies of inter- and intra- molecular H-bonds, unavailable with other processing methods. The revealed delicate balance between these energies determines the conditions for the existence of cold dena- turation and thus clarifies its absence in some proteins.
Ključne besede: protein folding, cold denaturation, water, Zimm-Bragg model
Objavljeno v RUNG: 06.05.2021; Ogledov: 1614; Prenosov: 12
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