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Simulating protein unfolding under pressure with a coarse-grained model

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Perezzan, Ramiro and Rey, Antonio (2012) Simulating protein unfolding under pressure with a coarse-grained model. The Journal of Chemical Physics, 137 (18). p. 185102. ISSN 0021-9606

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Official URL: http://aip.scitation.org/doi/10.1063/1.4765057



Abstract

We describe and test a coarse-grained molecular model for the simulation of the effects of pressure on the folding/unfolding transition of proteins. The model is a structure-based one, which takes into account the desolvation barrier for the formation of the native contacts. The pressure is taken into account in a qualitative, mean field approach, acting on the parameters describing the native stabilizing interactions. The model has been tested by simulating the thermodynamic and structural behavior of protein GB1 with a parallel tempering Monte Carlo algorithm. At low effective pressures, the model reproduces the standard two-state thermal transition between the native and denatured states. However, at large pressures a new state appears. Its structural characteristics have been analyzed, showing that it corresponds to a swollen version of the native structure. This swollen state is at equilibrium with the native state at low temperatures, but gradually transforms into the thermally denatured state as temperature is increased. Therefore, our model predicts a downhill transition between the swollen and the denatured states. The analysis of the model permits us to obtain a phase diagram for the pressure-temperature behavior of the simulated system, which is compatible with the known elliptical shape of this diagram for real proteins.


Item Type:Article
Subjects:Sciences > Chemistry > Chemistry, Physical and theoretical
ID Code:43830
Deposited On:13 Jul 2017 12:03
Last Modified:21 Jul 2017 10:52

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