Behavior of Proteins under Pressure from Experimental Pressure-Dependent Structures

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Fernández del Río, Beatriz and Rey Gayo, Antonio (2021) Behavior of Proteins under Pressure from Experimental Pressure-Dependent Structures. Journal Of Physical Chemistry B, 125 . pp. 6179-6191. ISSN 1520-6106

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Official URL: https://doi.org/10.1021/acs.jpcb.1c03313



Abstract

Structure-based models are coarse-grained representations
of the interactions responsible for the protein folding process. In their simplest form, they use only the native contact map of a given protein to predict the main features of its folding process by computer simulation. Given their limitations, these models are frequently complemented with sequence-dependent contributions or additional information. Specifically, to analyze the effect of pressure on the folding/unfolding transition, special forms of these interaction potentials are employed, which may a priori determine the outcome of the simulations. In this work, we have tried to keep the original simplicity of structure-based models. Therefore, we have used folded structures that have been experimentally determined at different pressures to define native contact maps and thus interactions dependent on pressure. Despite the apparently tiny structural differences induced by pressure, our simulation results provide different thermodynamic and kinetic behaviors, which roughly correspond to experimental observations (when there is a possible comparison) of two proteins used as benchmarks, hen egg-white lysozyme and dihydrofolate reductase. Therefore, this work shows the feasibility of using experimental native structures at different pressures to analyze the global effects of this physical property on the protein folding process.


Item Type:Article
Uncontrolled Keywords:Protein structure, Thermodynamics, Peptides and proteins, Kinetics, Nucleic acid structure
Subjects:Sciences > Chemistry > Chemistry, Physical and theoretical
ID Code:68433
Deposited On:02 Nov 2021 08:35
Last Modified:21 Dec 2021 09:55

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